Quantum electron-vibrational dynamics at finite temperature: Thermo field dynamics approach

NASA Astrophysics Data System (ADS)

Borrelli, Raffaele; Gelin, Maxim F.

2016-12-01

Quantum electron-vibrational dynamics in molecular systems at finite temperature is described using an approach based on the thermo field dynamics theory. This formulation treats temperature effects in the Hilbert space without introducing the Liouville space. A comparison with the theoretically equivalent density matrix formulation shows the key numerical advantages of the present approach. The solution of thermo field dynamics equations with a novel technique for the propagation of tensor trains (matrix product states) is discussed. Numerical applications to model spin-boson systems show that the present approach is a promising tool for the description of quantum dynamics of complex molecular systems at finite temperature.

Structure and Entanglement Factors on Dynamics of Polymer-Grafted Nanoparticles

DOE PAGES

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

2016-04-15

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

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.

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

NASA Astrophysics Data System (ADS)

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

2011-10-01

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

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

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

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

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

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

DOE PAGES

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

2015-06-26

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

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.

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

Liu, Siqi; Senses, Erkan; Jiao, Yang

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

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.

Confinement of anomalous liquids in nanoporous matrices.

PubMed

Strekalova, Elena G; Luo, Jiayuan; Stanley, H Eugene; Franzese, Giancarlo; Buldyrev, Sergey V

2012-09-07

Using molecular dynamics simulations, we investigate the effects of different nanoconfinements on complex liquids-e.g., colloids or protein solutions-with density anomalies and a liquid-liquid phase transition (LLPT). In all the confinements, we find a strong depletion effect with a large increase in liquid density near the confining surface. If the nanoconfinement is modeled by an ordered matrix of nanoparticles, we find that the anomalies are preserved. On the contrary, if the confinement is modeled by a disordered matrix of nanoparticles, we find a drastically different phase diagram: the LLPT shifts to lower pressures and temperatures, and the anomalies become weaker, as the disorder increases. We find that the density heterogeneities induced by the disordered matrix are responsible for the weakening of the LLPT and the disappearance of the anomalies.

Efficient parallel linear scaling construction of the density matrix for Born-Oppenheimer molecular dynamics.

PubMed

Mniszewski, S M; Cawkwell, M J; Wall, M E; Mohd-Yusof, J; Bock, N; Germann, T C; Niklasson, A M N

2015-10-13

We present an algorithm for the calculation of the density matrix that for insulators scales linearly with system size and parallelizes efficiently on multicore, shared memory platforms with small and controllable numerical errors. The algorithm is based on an implementation of the second-order spectral projection (SP2) algorithm [ Niklasson, A. M. N. Phys. Rev. B 2002 , 66 , 155115 ] in sparse matrix algebra with the ELLPACK-R data format. We illustrate the performance of the algorithm within self-consistent tight binding theory by total energy calculations of gas phase poly(ethylene) molecules and periodic liquid water systems containing up to 15,000 atoms on up to 16 CPU cores. We consider algorithm-specific performance aspects, such as local vs nonlocal memory access and the degree of matrix sparsity. Comparisons to sparse matrix algebra implementations using off-the-shelf libraries on multicore CPUs, graphics processing units (GPUs), and the Intel many integrated core (MIC) architecture are also presented. The accuracy and stability of the algorithm are illustrated with long duration Born-Oppenheimer molecular dynamics simulations of 1000 water molecules and a 303 atom Trp cage protein solvated by 2682 water molecules.

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

PubMed

Chawla, Raj; Sharma, Sumit

2018-03-18

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

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.

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

NASA Astrophysics Data System (ADS)

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

2004-01-01

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

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

Recurrence quantity analysis based on matrix eigenvalues

NASA Astrophysics Data System (ADS)

Yang, Pengbo; Shang, Pengjian

2018-06-01

Recurrence plots is a powerful tool for visualization and analysis of dynamical systems. Recurrence quantification analysis (RQA), based on point density and diagonal and vertical line structures in the recurrence plots, is considered to be alternative measures to quantify the complexity of dynamical systems. In this paper, we present a new measure based on recurrence matrix to quantify the dynamical properties of a given system. Matrix eigenvalues can reflect the basic characteristics of the complex systems, so we show the properties of the system by exploring the eigenvalues of the recurrence matrix. Considering that Shannon entropy has been defined as a complexity measure, we propose the definition of entropy of matrix eigenvalues (EOME) as a new RQA measure. We confirm that EOME can be used as a metric to quantify the behavior changes of the system. As a given dynamical system changes from a non-chaotic to a chaotic regime, the EOME will increase as well. The bigger EOME values imply higher complexity and lower predictability. We also study the effect of some factors on EOME,including data length, recurrence threshold, the embedding dimension, and additional noise. Finally, we demonstrate an application in physiology. The advantage of this measure lies in a high sensitivity and simple computation.

Random density matrices versus random evolution of open system

NASA Astrophysics Data System (ADS)

Pineda, Carlos; Seligman, Thomas H.

2015-10-01

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

The density-matrix renormalization group: a short introduction.

PubMed

Schollwöck, Ulrich

2011-07-13

The density-matrix renormalization group (DMRG) method has established itself over the last decade as the leading method for the simulation of the statics and dynamics of one-dimensional strongly correlated quantum lattice systems. The DMRG is a method that shares features of a renormalization group procedure (which here generates a flow in the space of reduced density operators) and of a variational method that operates on a highly interesting class of quantum states, so-called matrix product states (MPSs). The DMRG method is presented here entirely in the MPS language. While the DMRG generally fails in larger two-dimensional systems, the MPS picture suggests a straightforward generalization to higher dimensions in the framework of tensor network states. The resulting algorithms, however, suffer from difficulties absent in one dimension, apart from a much more unfavourable efficiency, such that their ultimate success remains far from clear at the moment.

Lanczos algorithm with matrix product states for dynamical correlation functions

NASA Astrophysics Data System (ADS)

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

2012-05-01

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

Transport dynamics of a high-power-density matrix-type hydrogen-oxygen fuel cell

NASA Technical Reports Server (NTRS)

Prokopius, P. R.; Hagedorn, N. H.

1974-01-01

Experimental transport dynamics tests were made on a space power fuel cell of current design. Various operating transients were introduced and transport-related response data were recorded with fluidic humidity sensing instruments. Also, sampled data techniques were developed for measuring the cathode-side electrolyte concentration during transient operation.

Muscle-tendon units localization and activation level analysis based on high-density surface EMG array and NMF algorithm

NASA Astrophysics Data System (ADS)

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

2016-12-01

Objective. Some skeletal muscles can be subdivided into smaller segments called muscle-tendon units (MTUs). The purpose of this paper is to propose a framework to locate the active region of the corresponding MTUs within a single skeletal muscle and to analyze the activation level varieties of different MTUs during a dynamic motion task. Approach. Biceps brachii and gastrocnemius were selected as targeted muscles and three dynamic motion tasks were designed and studied. Eight healthy male subjects participated in the data collection experiments, and 128-channel surface electromyographic (sEMG) signals were collected with a high-density sEMG electrode grid (a grid consists of 8 rows and 16 columns). Then the sEMG envelopes matrix was factorized into a matrix of weighting vectors and a matrix of time-varying coefficients by nonnegative matrix factorization algorithm. Main results. The experimental results demonstrated that the weightings vectors, which represent invariant pattern of muscle activity across all channels, could be used to estimate the location of MTUs and the time-varying coefficients could be used to depict the variation of MTUs activation level during dynamic motion task. Significance. The proposed method provides one way to analyze in-depth the functional state of MTUs during dynamic tasks and thus can be employed on multiple noteworthy sEMG-based applications such as muscle force estimation, muscle fatigue research and the control of myoelectric prostheses. This work was supported by the National Nature Science Foundation of China under Grant 61431017 and 61271138.

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.

Density-Gradient Theory: A Macroscopic Approach to Quantum Confinement and Tunneling in Semiconductor Devices

DTIC Science & Technology

2011-01-01

that are attractive as luminescent biolabels, and possibly also for optoelectronic devices and solar cells . The equilibrium nature of such situations...The boundary layers as- sociated with the diffusion and Debye lengths are familiar, while that of LQ defines the layer in which the quantum in...circuits, transmission lines Diffusion -drift, density-gradient Semi-classical electron dynamics, Boltzmann transport Schrödinger, density- matrix, Wigner

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.

Nonlinear optical microscopy reveals invading endothelial cells anisotropically alter three-dimensional collagen matrices

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

Lee, P.-F.; Yeh, Alvin T.; Bayless, Kayla J.

The interactions between endothelial cells (ECs) and the extracellular matrix (ECM) are fundamental in mediating various steps of angiogenesis, including cell adhesion, migration and sprout formation. Here, we used a noninvasive and non-destructive nonlinear optical microscopy (NLOM) technique to optically image endothelial sprouting morphogenesis in three-dimensional (3D) collagen matrices. We simultaneously captured signals from collagen fibers and endothelial cells using second harmonic generation (SHG) and two-photon excited fluorescence (TPF), respectively. Dynamic 3D imaging revealed EC interactions with collagen fibers along with quantifiable alterations in collagen matrix density elicited by EC movement through and morphogenesis within the matrix. Specifically, we observedmore » increased collagen density in the area between bifurcation points of sprouting structures and anisotropic increases in collagen density around the perimeter of lumenal structures, but not advancing sprout tips. Proteinase inhibition studies revealed membrane-associated matrix metalloproteinase were utilized for sprout advancement and lumen expansion. Rho-associated kinase (p160ROCK) inhibition demonstrated that the generation of cell tension increased collagen matrix alterations. This study followed sprouting ECs within a 3D matrix and revealed that the advancing structures recognize and significantly alter their extracellular environment at the periphery of lumens as they progress.« less

Recursive Factorization of the Inverse Overlap Matrix in Linear-Scaling Quantum Molecular Dynamics Simulations.

PubMed

Negre, Christian F A; Mniszewski, Susan M; Cawkwell, Marc J; Bock, Nicolas; Wall, Michael E; Niklasson, Anders M N

2016-07-12

We present a reduced complexity algorithm to compute the inverse overlap factors required to solve the generalized eigenvalue problem in a quantum-based molecular dynamics (MD) simulation. Our method is based on the recursive, iterative refinement of an initial guess of Z (inverse square root of the overlap matrix S). The initial guess of Z is obtained beforehand by using either an approximate divide-and-conquer technique or dynamical methods, propagated within an extended Lagrangian dynamics from previous MD time steps. With this formulation, we achieve long-term stability and energy conservation even under the incomplete, approximate, iterative refinement of Z. Linear-scaling performance is obtained using numerically thresholded sparse matrix algebra based on the ELLPACK-R sparse matrix data format, which also enables efficient shared-memory parallelization. As we show in this article using self-consistent density-functional-based tight-binding MD, our approach is faster than conventional methods based on the diagonalization of overlap matrix S for systems as small as a few hundred atoms, substantially accelerating quantum-based simulations even for molecular structures of intermediate size. For a 4158-atom water-solvated polyalanine system, we find an average speedup factor of 122 for the computation of Z in each MD step.

Recursive Factorization of the Inverse Overlap Matrix in Linear Scaling Quantum Molecular Dynamics Simulations

DOE PAGES

Negre, Christian F. A; Mniszewski, Susan M.; Cawkwell, Marc Jon; ...

2016-06-06

We present a reduced complexity algorithm to compute the inverse overlap factors required to solve the generalized eigenvalue problem in a quantum-based molecular dynamics (MD) simulation. Our method is based on the recursive iterative re nement of an initial guess Z of the inverse overlap matrix S. The initial guess of Z is obtained beforehand either by using an approximate divide and conquer technique or dynamically, propagated within an extended Lagrangian dynamics from previous MD time steps. With this formulation, we achieve long-term stability and energy conservation even under incomplete approximate iterative re nement of Z. Linear scaling performance ismore » obtained using numerically thresholded sparse matrix algebra based on the ELLPACK-R sparse matrix data format, which also enables e cient shared memory parallelization. As we show in this article using selfconsistent density functional based tight-binding MD, our approach is faster than conventional methods based on the direct diagonalization of the overlap matrix S for systems as small as a few hundred atoms, substantially accelerating quantum-based simulations even for molecular structures of intermediate size. For a 4,158 atom water-solvated polyalanine system we nd an average speedup factor of 122 for the computation of Z in each MD step.« less

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.

Effective field theory of dissipative fluids

DOE PAGES

Crossley, Michael; Glorioso, Paolo; Liu, Hong

2017-09-20

We develop an effctive fi eld theory for dissipative fluids which governs the dynamics of long-lived gapless modes associated with conserved quantities. The resulting theory gives a path integral formulation of fluctuating hydrodynamics which systematically incorporates nonlinear interactions of noises. The dynamical variables are mappings between a "fluid spacetime" and the physical spacetime and an essential aspect of our formulation is to identify the appropriate symmetries in the fluid spacetime. The theory applies to nonlinear disturbances around a general density matrix. For a thermal density matrix, we require an additional Z2 symmetry, to which we refer as the local KMSmore » condition. This leads to the standard constraints of hydrodynamics, as well as a nonlinear generalization of the Onsager relations. It also leads to an emergent supersymmetry in the classical statistical regime, and a higher derivative deformation of supersymmetry in the full quantum regime.« less

Effective field theory of dissipative fluids

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

Crossley, Michael; Glorioso, Paolo; Liu, Hong

We develop an effctive fi eld theory for dissipative fluids which governs the dynamics of long-lived gapless modes associated with conserved quantities. The resulting theory gives a path integral formulation of fluctuating hydrodynamics which systematically incorporates nonlinear interactions of noises. The dynamical variables are mappings between a "fluid spacetime" and the physical spacetime and an essential aspect of our formulation is to identify the appropriate symmetries in the fluid spacetime. The theory applies to nonlinear disturbances around a general density matrix. For a thermal density matrix, we require an additional Z2 symmetry, to which we refer as the local KMSmore » condition. This leads to the standard constraints of hydrodynamics, as well as a nonlinear generalization of the Onsager relations. It also leads to an emergent supersymmetry in the classical statistical regime, and a higher derivative deformation of supersymmetry in the full quantum regime.« less

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.

Quadratic canonical transformation theory and higher order density matrices.

PubMed

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

2009-03-28

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

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

PubMed

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

2016-01-01

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

Towards a formal definition of static and dynamic electronic correlations.

PubMed

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

2017-05-24

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

Extending the range of real time density matrix renormalization group simulations

NASA Astrophysics Data System (ADS)

Kennes, D. M.; Karrasch, C.

2016-03-01

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

Watching excitons move: the time-dependent transition density matrix

NASA Astrophysics Data System (ADS)

Ullrich, Carsten

2012-02-01

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

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.

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.

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

PubMed Central

Smith, Lachlan J; Fazzalari, Nicola L

2006-01-01

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

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.

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.

Revisit of Rotational Dynamics of Asteroid 4179 Toutatis from Chang'e-2's flyby

NASA Astrophysics Data System (ADS)

Zhao, Yuhui; Hu, Shoucun; Ji, Jianghui

2015-08-01

In this work we investigate the rotational dynamics of Toutatis based on the derived results from Chang'e-2's close flyby to the asteroid (Huang et al. 2013). Toutatis' non-principal axis rotation (NPA) was revealed by radar observations captured from its Earth approaches in the past two decades. Matrix of inertia calculated from radar derived shape model are inconsistent with observations, which may indicate an uneven density distribution of the asteroid. We perform numerical simulations of rotational evolution of Toutatis and figure out the relative rotational parameters of Euler angles, rotational velocities and matrix of inertia. According to the major morphological feature of the ginger-shaped asteroid, we suggest a density ratio of the two lobes. On the basis of these results, we will evaluate the magnitude of the bias of mass center and figure center, which may have slight effects in the momentum variation calculation. These results are in good agreements with the previous radar observation derived results (Takahashi et al. 2013).

Molecular dynamics modeling of helium bubbles in austenitic steels

NASA Astrophysics Data System (ADS)

Jelea, A.

2018-06-01

The austenitic steel devices from pressurized water reactors are continuously subjected to neutron irradiation that produces crystalline point defects and helium atoms in the steel matrix. These species evolve into large defects such as dislocation loops and helium filled bubbles. This paper analyzes, through molecular dynamics simulations with recently developed interatomic potentials, the impact of the helium/steel interface on the helium behavior in nanosize bubbles trapped in an austenitic steel matrix. It is shown that the repulsive helium-steel interactions induce higher pressures in the bubble compared to bulk helium at the same temperature and average density. A new equation of state for helium is proposed in order to take into account these interface effects.

Bioreactor-based bone tissue engineering: The influence of dynamic flow on osteoblast phenotypic expression and matrix mineralization

PubMed Central

Yu, Xiaojun; Botchwey, Edward A.; Levine, Elliot M.; Pollack, Solomon R.; Laurencin, Cato T.

2004-01-01

An important issue in tissue engineering concerns the possibility of limited tissue ingrowth in tissue-engineered constructs because of insufficient nutrient transport. We report a dynamic flow culture system using high-aspect-ratio vessel rotating bioreactors and 3D scaffolds for culturing rat calvarial osteoblast cells. 3D scaffolds were designed by mixing lighter-than-water (density, <1g/ml) and heavier-than-water (density, >1g/ml) microspheres of 85:15 poly(lactide-co-glycolide). We quantified the rate of 3D flow through the scaffolds by using a particle-tracking system, and the results suggest that motion trajectories and, therefore, the flow velocity around and through scaffolds in rotating bioreactors can be manipulated by varying the ratio of heavier-than-water to lighter-than-water microspheres. When rat primary calvarial cells were cultured on the scaffolds in bioreactors for 7 days, the 3D dynamic flow environment affected bone cell distribution and enhanced cell phenotypic expression and mineralized matrix synthesis within tissue-engineered constructs compared with static conditions. These studies provide a foundation for exploring the effects of dynamic flow on osteoblast function and provide important insight into the design and optimization of 3D scaffolds suitable in bioreactors for in vitro tissue engineering of bone. PMID:15277663

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.

Local Descriptors of Dynamic and Nondynamic Correlation.

PubMed

Ramos-Cordoba, Eloy; Matito, Eduard

2017-06-13

Quantitatively accurate electronic structure calculations rely on the proper description of electron correlation. A judicious choice of the approximate quantum chemistry method depends upon the importance of dynamic and nondynamic correlation, which is usually assesed by scalar measures. Existing measures of electron correlation do not consider separately the regions of the Cartesian space where dynamic or nondynamic correlation are most important. We introduce real-space descriptors of dynamic and nondynamic electron correlation that admit orbital decomposition. Integration of the local descriptors yields global numbers that can be used to quantify dynamic and nondynamic correlation. Illustrative examples over different chemical systems with varying electron correlation regimes are used to demonstrate the capabilities of the local descriptors. Since the expressions only require orbitals and occupation numbers, they can be readily applied in the context of local correlation methods, hybrid methods, density matrix functional theory, and fractional-occupancy density functional theory.

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.

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

PubMed

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

2005-02-08

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

Mapping the Dynamics of Shear Stress—Induced Structural Changes in Endothelial Cells

PubMed Central

Mott, Rosalind E.; Helmke, Brian P.

2009-01-01

Hemodynamic shear stress regulates endothelial cell biochemical processes that govern cytoskeletal contractility, focal adhesion dynamics, and extracellular matrix assembly. Since shear stress causes rapid strain focusing at discrete locations in the cytoskeleton, we hypothesized that shear stress coordinately alters structural dynamics in the cytoskeleton, focal adhesion sites, and extracellular matrix on a time scale of minutes. Using multi-wavelength 4-D fluorescence microscopy, we measured the displacement of rhodamine-fibronectin and of GFP-labeled actin, vimentin, paxillin, and/or vinculin in aortic endothelial cells before and after onset of steady unidirectional shear stress. In the cytoskeleton, the onset of shear stress increased actin polymerization into lamellipodia, altered the angle of lateral displacement of actin stress fibers and vimentin filaments, and decreased centripetal remodeling of actin stress fibers in both subconfluent and confluent cell layers. Shear stress induced the formation of new focal complexes and reduced the centripetal remodeling of focal adhesions in regions of new actin polymerization. The structural dynamics of focal adhesions and the fibronectin matrix varied with cell density. In subconfluent cell layers, shear stress onset decreased the displacement of focal adhesions and fibronectin fibrils. In confluent monolayers, the direction of fibronectin and focal adhesion displacement shifted significantly towards the downstream direction within one minute after onset of shear stress. These spatially coordinated rapid changes in the structural dynamics of cytoskeleton, focal adhesions, and extracellular matrix are consistent with focusing of mechanical stress and/or strain near major sites of shear stress-mediated mechanotransduction. PMID:17855768

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

NASA Astrophysics Data System (ADS)

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

2014-03-01

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

Self-healing multiphase polymers via dynamic metal-ligand interactions.

PubMed

Mozhdehi, Davoud; Ayala, Sergio; Cromwell, Olivia R; Guan, Zhibin

2014-11-19

A new self-healing multiphase polymer is developed in which a pervasive network of dynamic metal-ligand (zinc-imidazole) interactions are programmed in the soft matrix of a hard/soft two-phase brush copolymer system. The mechanical and dynamic properties of the materials can be tuned by varying a number of molecular parameters (e.g., backbone/brush degree of polymerization and brush density) as well as the ligand/metal ratio. Following mechanical damage, these thermoplastic elastomers show excellent self-healing ability under ambient conditions without any intervention.

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.

Coupled Cluster Method with Single and Double Excitations Tailored by Matrix Product State Wave Functions.

PubMed

Veis, Libor; Antalík, Andrej; Brabec, Jiří; Neese, Frank; Legeza, Örs; Pittner, Jiří

2016-10-03

In the past decade, the quantum chemical version of the density matrix renormalization group (DMRG) method has established itself as the method of choice for calculations of strongly correlated molecular systems. Despite its favorable scaling, it is in practice not suitable for computations of dynamic correlation. We present a novel method for accurate "post-DMRG" treatment of dynamic correlation based on the tailored coupled cluster (CC) theory in which the DMRG method is responsible for the proper description of nondynamic correlation, whereas dynamic correlation is incorporated through the framework of the CC theory. We illustrate the potential of this method on prominent multireference systems, in particular, N 2 and Cr 2 molecules and also oxo-Mn(Salen), for which we have performed the first post-DMRG computations in order to shed light on the energy ordering of the lowest spin states.

Lattice Boltzmann simulation of dissolution-induced changes in permeability and porosity in 3D CO2 reactive transport

NASA Astrophysics Data System (ADS)

Tian, Zhiwei; Wang, Junye

2018-02-01

Dissolution and precipitation of rock matrix are one of the most important processes of geological CO2 sequestration in reservoirs. They change connections of pore channels and properties of matrix, such as bulk density, microporosity and hydraulic conductivity. This study builds on a recently developed multi-layer model to account for dynamic changes of microporous matrix that can accurately predict variations in hydraulic properties and reaction rates due to dynamic changes in matrix porosity and pore connectivity. We apply the model to simulate the dissolution and precipitation processes of rock matrix in heterogeneous porous media to quantify (1) the effect of the reaction rate on dissolution and matrix porosity, (2) the effect of microporous matrix diffusion on the overall effective diffusion and (3) the effect of heterogeneity on hydraulic conductivity. The results show the CO2 storage influenced by factors including the matrix porosity change, reaction front movement, velocity and initial properties. We also simulated dissolution-induced permeability enhancement as well as effects of initial porosity heterogeneity. The matrix with very low permeability, which can be unresolved on X-ray CT, do contribute to flow patterns and dispersion. The concentration of reactant H+ increases along the main fracture paths where the flow velocity increases. The product Ca++ shows the inversed distribution pattern against the H+ concentration. This demonstrates the capability of this model to investigate the complex CO2 reactive transport in real 3D heterogeneous porous media.

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

PubMed

Kurashige, Yuki; Yanai, Takeshi

2011-09-07

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

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.

Density-matrix renormalization group method for the conductance of one-dimensional correlated systems using the Kubo formula

NASA Astrophysics Data System (ADS)

Bischoff, Jan-Moritz; Jeckelmann, Eric

2017-11-01

We improve the density-matrix renormalization group (DMRG) evaluation of the Kubo formula for the zero-temperature linear conductance of one-dimensional correlated systems. The dynamical DMRG is used to compute the linear response of a finite system to an applied ac source-drain voltage; then the low-frequency finite-system response is extrapolated to the thermodynamic limit to obtain the dc conductance of an infinite system. The method is demonstrated on the one-dimensional spinless fermion model at half filling. Our method is able to replicate several predictions of the Luttinger liquid theory such as the renormalization of the conductance in a homogeneous conductor, the universal effects of a single barrier, and the resonant tunneling through a double barrier.

EVALUATING EFFECTS OF LOW QUALITY HABITATS ON REGIONAL GROWTH IN PEOMYCUS LEUCOPUS: INSIGHTS FROM FIELD-PARAMETERIZED SPATIAL MATRIX MODELS.

EPA Science Inventory

Due to complex population dynamics and source-sink metapopulation processes, animal fitness sometimes varies across landscapes in ways that cannot be deduced from simple density patterns. In this study, we examine spatial patterns in fitness using a combination of intensive fiel...

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

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.

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.

Semiclassics for matrix Hamiltonians: The Gutzwiller trace formula with applications to graphene-type systems

NASA Astrophysics Data System (ADS)

Vogl, M.; Pankratov, O.; Shallcross, S.

2017-07-01

We present a tractable and physically transparent semiclassical theory of matrix-valued Hamiltonians, i.e., those that describe quantum systems with internal degrees of freedoms, based on a generalization of the Gutzwiller trace formula for a n ×n dimensional Hamiltonian H (p ̂,q ̂) . The classical dynamics is governed by n Hamilton-Jacobi (HJ) equations that act in a phase space endowed with a classical Berry curvature encoding anholonomy in the parallel transport of the eigenvectors of H (p ,q ) ; these vectors describe the internal structure of the semiclassical particles. At the O (ℏ1) level and for nondegenerate HJ systems, this curvature results in an additional semiclassical phase composed of (i) a Berry phase and (ii) a dynamical phase resulting from the classical particles "moving through the Berry curvature". We show that the dynamical part of this semiclassical phase will, generally, be zero only for the case in which the Berry phase is topological (i.e., depends only on the winding number). We illustrate the method by calculating the Landau spectrum for monolayer graphene, the four-band model of AB bilayer graphene, and for a more complicated matrix Hamiltonian describing the silicene band structure. Finally, we apply our method to an inhomogeneous system consisting of a strain engineered one-dimensional moiré in bilayer graphene, finding localized states near the Dirac point that arise from electron trapping in a semiclassical moiré potential. The semiclassical density of states of these localized states we show to be in perfect agreement with an exact quantum mechanical calculation of the density of states.

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.

Ab initio molecular dynamics in a finite homogeneous electric field.

PubMed

Umari, P; Pasquarello, Alfredo

2002-10-07

We treat homogeneous electric fields within density functional calculations with periodic boundary conditions. A nonlocal energy functional depending on the applied field is used within an ab initio molecular dynamics scheme. The reliability of the method is demonstrated in the case of bulk MgO for the Born effective charges, and the high- and low-frequency dielectric constants. We evaluate the static dielectric constant by performing a damped molecular dynamics in an electric field and avoiding the calculation of the dynamical matrix. Application of this method to vitreous silica shows good agreement with experiment and illustrates its potential for systems of large size.

Dynamical quadrupole structure factor of frustrated ferromagnetic chain

NASA Astrophysics Data System (ADS)

Onishi, Hiroaki

2018-05-01

We investigate the dynamical quadrupole structure factor of a spin-1/2 J1-J2 Heisenberg chain with competing ferromagnetic J1 and antiferromagnetic J2 in a magnetic field by exploiting density-matrix renormalization group techniques. In a field-induced spin nematic regime, we observe gapless excitations at q = π according to quasi-long-range antiferro-quadrupole correlations. The gapless excitation mode has a quadratic form at the saturation, while it changes into a linear dispersion as the magnetization decreases.

Multi-Scale Simulation of Interfacial Phenomena and Nano-Particle Placement in Polymer Matrix Composites

DTIC Science & Technology

2012-08-01

Molecular Dynamics Simulations Coarse-Grain Particle Dynamics Simulations Local structure; Force field parameterization Extended structure...K) C8H18 C12H26 C16H34 Adhesive forces can cause local density gradients and defects " Pronounced layering of polymer near interfaces...reactive end groups (CnH2n+1S) on Cu Gap SubPc on C60 Pentacene on a-SiO2 Cyclopentene on Au Crystalline CuPc on Al Polyimide on Si

Superfluidity, Bose-Einstein condensation, and structure in one-dimensional Luttinger liquids

NASA Astrophysics Data System (ADS)

Vranješ Markić, L.; Vrcan, H.; Zuhrianda, Z.; Glyde, H. R.

2018-01-01

We report diffusion Monte Carlo (DMC) and path integral Monte Carlo (PIMC) calculations of the properties of a one-dimensional (1D) Bose quantum fluid. The equation of state, the superfluid fraction ρS/ρ0 , the one-body density matrix n (x ) , the pair distribution function g (x ) , and the static structure factor S (q ) are evaluated. The aim is to test Luttinger liquid (LL) predictions for 1D fluids over a wide range of fluid density and LL parameter K . The 1D Bose fluid examined is a single chain of 4He atoms confined to a line in the center of a narrow nanopore. The atoms cannot exchange positions in the nanopore, the criterion for 1D. The fluid density is varied from the spinodal density where the 1D liquid is unstable to droplet formation to the density of bulk liquid 4He. In this range, K varies from K >2 at low density, where a robust superfluid is predicted, to K <0.5 , where fragile 1D superflow and solidlike peaks in S (q ) are predicted. For uniform pore walls, the ρS/ρ0 scales as predicted by LL theory. The n (x ) and g (x ) show long range oscillations and decay with x as predicted by LL theory. The amplitude of the oscillations is large at high density (small K ) and small at low density (large K ). The K values obtained from different properties agree well verifying the internal structure of LL theory. In the presence of disorder, the ρS/ρ0 does not scale as predicted by LL theory. A single vJ parameter in the LL theory that recovers LL scaling was not found. The one body density matrix (OBDM) in disorder is well predicted by LL theory. The "dynamical" superfluid fraction, ρSD/ρ0 , is determined. The physics of the deviation from LL theory in disorder and the "dynamical" ρSD/ρ0 are discussed.

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

NASA Astrophysics Data System (ADS)

Oberhofer, Harald; Blumberger, Jochen

2010-12-01

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

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.

Particle size effect on strength, failure, and shock behavior in polytetrafluoroethylene-Al-W granular composite materials

NASA Astrophysics Data System (ADS)

Herbold, E. B.; Nesterenko, V. F.; Benson, D. J.; Cai, J.; Vecchio, K. S.; Jiang, F.; Addiss, J. W.; Walley, S. M.; Proud, W. G.

2008-11-01

The variation of metallic particle size and sample porosity significantly alters the dynamic mechanical properties of high density granular composite materials processed using a cold isostatically pressed mixture of polytetrafluoroethylene (PTFE), aluminum (Al), and tungsten (W) powders. Quasistatic and dynamic experiments are performed with identical constituent mass fractions with variations in the size of the W particles and pressing conditions. The relatively weak polymer matrix allows the strength and fracture modes of this material to be governed by the granular type behavior of agglomerated metal particles. A higher ultimate compressive strength was observed in relatively high porosity samples with small W particles compared to those with coarse W particles in all experiments. Mesoscale granular force chains of the metallic particles explain this unusual phenomenon as observed in hydrocode simulations of a drop-weight test. Macrocracks forming below the critical failure strain for the matrix and unusual behavior due to a competition between densification and fracture in dynamic tests of porous samples were also observed. Numerical modeling of shock loading of this granular composite material demonstrated that the internal energy, specifically thermal energy, of the soft PTFE matrix can be tailored by the W particle size distribution.

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

PubMed

Saitow, Masaaki; Kurashige, Yuki; Yanai, Takeshi

2013-07-28

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

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.

A Scalable O(N) Algorithm for Large-Scale Parallel First-Principles Molecular Dynamics Simulations

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

Osei-Kuffuor, Daniel; Fattebert, Jean-Luc

2014-01-01

Traditional algorithms for first-principles molecular dynamics (FPMD) simulations only gain a modest capability increase from current petascale computers, due to their O(N 3) complexity and their heavy use of global communications. To address this issue, we are developing a truly scalable O(N) complexity FPMD algorithm, based on density functional theory (DFT), which avoids global communications. The computational model uses a general nonorthogonal orbital formulation for the DFT energy functional, which requires knowledge of selected elements of the inverse of the associated overlap matrix. We present a scalable algorithm for approximately computing selected entries of the inverse of the overlap matrix,more » based on an approximate inverse technique, by inverting local blocks corresponding to principal submatrices of the global overlap matrix. The new FPMD algorithm exploits sparsity and uses nearest neighbor communication to provide a computational scheme capable of extreme scalability. Accuracy is controlled by the mesh spacing of the finite difference discretization, the size of the localization regions in which the electronic orbitals are confined, and a cutoff beyond which the entries of the overlap matrix can be omitted when computing selected entries of its inverse. We demonstrate the algorithm's excellent parallel scaling for up to O(100K) atoms on O(100K) processors, with a wall-clock time of O(1) minute per molecular dynamics time step.« less

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

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

Localization of soft modes at the depinning transition

NASA Astrophysics Data System (ADS)

Cao, Xiangyu; Bouzat, Sebastian; Kolton, Alejandro B.; Rosso, Alberto

2018-02-01

We characterize the soft modes of the dynamical matrix at the depinning transition, and compare the matrix with the properties of the Anderson model (and long-range generalizations). The density of states at the edge of the spectrum displays a universal linear tail, different from the Lifshitz tails. The eigenvectors are instead very similar in the two matrix ensembles. We focus on the ground state (soft mode), which represents the epicenter of avalanche instabilities. We expect it to be localized in all finite dimensions, and make a clear connection between its localization length and the Larkin length of the depinning model. In the fully connected model, we show that the weak-strong pinning transition coincides with a peculiar localization transition of the ground state.

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.

Structural behavior and dynamics of an anomalous fluid between attractive and repulsive walls: Templating, molding, and superdiffusion

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

Leoni, Fabio; Franzese, Giancarlo

2014-11-07

Confinement can modify the dynamics, the thermodynamics, and the structural properties of liquid water, the prototypical anomalous liquid. By considering a generic model for anomalous liquids, suitable for describing solutions of globular proteins, colloids, or liquid metals, we study by molecular dynamics simulations the effect that an attractive wall with structure and a repulsive wall without structure have on the phases, the crystal nucleation, and the dynamics of the fluid. We find that at low temperatures the large density of the attractive wall induces a high-density, high-energy structure in the first layer (“templating” effect). In turn, the first layer inducesmore » a “molding” effect on the second layer determining a structure with reduced energy and density, closer to the average density of the system. This low-density, low-energy structure propagates further through the layers by templating effect and can involve all the existing layers at the lowest temperatures investigated. Therefore, although the high-density, high-energy structure does not self-reproduce further than the first layer, the structured wall can have a long-range influence thanks to a sequence of templating, molding, and templating effects through the layers. We find that the walls also have an influence on the dynamics of the liquid, with a stronger effect near the attractive wall. In particular, we observe that the dynamics is largely heterogeneous (i) among the layers, as a consequence of the sequence of structures caused by the walls presence, and (ii) within the same layer, due to superdiffusive liquid veins within a frozen matrix of particles near the walls at low temperature and high density. Hence, the partial freezing of the first layer does not correspond necessarily to an effective reduction of the channel's section in terms of transport properties, as suggested by other authors.« less

Structural behavior and dynamics of an anomalous fluid between attractive and repulsive walls: templating, molding, and superdiffusion.

PubMed

Leoni, Fabio; Franzese, Giancarlo

2014-11-07

Confinement can modify the dynamics, the thermodynamics, and the structural properties of liquid water, the prototypical anomalous liquid. By considering a generic model for anomalous liquids, suitable for describing solutions of globular proteins, colloids, or liquid metals, we study by molecular dynamics simulations the effect that an attractive wall with structure and a repulsive wall without structure have on the phases, the crystal nucleation, and the dynamics of the fluid. We find that at low temperatures the large density of the attractive wall induces a high-density, high-energy structure in the first layer ("templating" effect). In turn, the first layer induces a "molding" effect on the second layer determining a structure with reduced energy and density, closer to the average density of the system. This low-density, low-energy structure propagates further through the layers by templating effect and can involve all the existing layers at the lowest temperatures investigated. Therefore, although the high-density, high-energy structure does not self-reproduce further than the first layer, the structured wall can have a long-range influence thanks to a sequence of templating, molding, and templating effects through the layers. We find that the walls also have an influence on the dynamics of the liquid, with a stronger effect near the attractive wall. In particular, we observe that the dynamics is largely heterogeneous (i) among the layers, as a consequence of the sequence of structures caused by the walls presence, and (ii) within the same layer, due to superdiffusive liquid veins within a frozen matrix of particles near the walls at low temperature and high density. Hence, the partial freezing of the first layer does not correspond necessarily to an effective reduction of the channel's section in terms of transport properties, as suggested by other authors.

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.

The open quantum Brownian motions

NASA Astrophysics Data System (ADS)

Bauer, Michel; Bernard, Denis; Tilloy, Antoine

2014-09-01

Using quantum parallelism on random walks as the original seed, we introduce new quantum stochastic processes, the open quantum Brownian motions. They describe the behaviors of quantum walkers—with internal degrees of freedom which serve as random gyroscopes—interacting with a series of probes which serve as quantum coins. These processes may also be viewed as the scaling limit of open quantum random walks and we develop this approach along three different lines: the quantum trajectory, the quantum dynamical map and the quantum stochastic differential equation. We also present a study of the simplest case, with a two level system as an internal gyroscope, illustrating the interplay between the ballistic and diffusive behaviors at work in these processes. Notation H_z : orbital (walker) Hilbert space, {C}^{{Z}} in the discrete, L^2({R}) in the continuum H_c : internal spin (or gyroscope) Hilbert space H_sys=H_z\\otimesH_c : system Hilbert space H_p : probe (or quantum coin) Hilbert space, H_p={C}^2 \\rho^tot_t : density matrix for the total system (walker + internal spin + quantum coins) \\bar \\rho_t : reduced density matrix on H_sys : \\bar\\rho_t=\\int dxdy\\, \\bar\\rho_t(x,y)\\otimes | x \\rangle _z\\langle y | \\hat \\rho_t : system density matrix in a quantum trajectory: \\hat\\rho_t=\\int dxdy\\, \\hat\\rho_t(x,y)\\otimes | x \\rangle _z\\langle y | . If diagonal and localized in position: \\hat \\rho_t=\\rho_t\\otimes| X_t \\rangle _z\\langle X_t | ρt: internal density matrix in a simple quantum trajectory Xt: walker position in a simple quantum trajectory Bt: normalized Brownian motion ξt, \\xi_t^\\dagger : quantum noises

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

Physical aging and its influence on the reliability of network epoxies and epoxy-matrix composites

NASA Technical Reports Server (NTRS)

Heinemann, K.

1983-01-01

The matrix-dominated physical and mechanical properties of a carbon fiber reinforced epoxy composite and a neat epoxy resin were found to be affected by sub-Tg annealing in nitrogen and dark atmosphere. Postcured specimens of Thornel 300 carbon-fiber/Fiberite 934 epoxy as well as Fiberite 934 epoxy resin were quenched from above Tg and given annealing at 140 C, 110 C, or 80 C, for time up to one-hundred thousand minutes. No weight loss was observed during annealing at these temperatures. Significant variations were found in density, modulus, hardness, damping, moisture absorption ability, thermal expansivity. Moisture-epoxy interactious were also studied. The kinetics of aging as well as the molecular aggregation during this densification process were monitored by differential scanning calorimetry, dynamic mechanical analysis, density gradient column, microhardness tester, Instron, and solid-state nuclear magnetic resonance spectroscopy.

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

NASA Astrophysics Data System (ADS)

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

2018-06-01

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

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

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

PubMed

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

2018-05-03

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

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.

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.

Finite-temperature dynamic structure factor of the spin-1 XXZ chain with single-ion anisotropy

NASA Astrophysics Data System (ADS)

Lange, Florian; Ejima, Satoshi; Fehske, Holger

2018-02-01

Improving matrix-product state techniques based on the purification of the density matrix, we are able to accurately calculate the finite-temperature dynamic response of the infinite spin-1 XXZ chain with single-ion anisotropy in the Haldane, large-D , and antiferromagnetic phases. Distinct thermally activated scattering processes make a significant contribution to the spectral weight in all cases. In the Haldane phase, intraband magnon scattering is prominent, and the on-site anisotropy causes the magnon to split into singlet and doublet branches. In the large-D phase response, the intraband signal is separated from an exciton-antiexciton continuum. In the antiferromagnetic phase, holons are the lowest-lying excitations, with a gap that closes at the transition to the Haldane state. At finite temperatures, scattering between domain-wall excitations becomes especially important and strongly enhances the spectral weight for momentum transfer π .

Strongly contracted canonical transformation theory

NASA Astrophysics Data System (ADS)

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

2010-01-01

Canonical transformation (CT) theory describes dynamic correlation in multireference systems with large active spaces. Here we discuss CT theory's intruder state problem and why our previous approach of overlap matrix truncation becomes infeasible for sufficiently large active spaces. We propose the use of strongly and weakly contracted excitation operators as alternatives for dealing with intruder states in CT theory. The performance of these operators is evaluated for the H2O, N2, and NiO molecules, with comparisons made to complete active space second order perturbation theory and Davidson-corrected multireference configuration interaction theory. Finally, using a combination of strongly contracted CT theory and orbital-optimized density matrix renormalization group theory, we evaluate the singlet-triplet gap of free base porphin using an active space containing all 24 out-of-plane 2p orbitals. Modeling dynamic correlation with an active space of this size is currently only possible using CT theory.

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.

Dynamic regime of coherent population trapping and optimization of frequency modulation parameters in atomic clocks.

PubMed

Yudin, V I; Taichenachev, A V; Basalaev, M Yu; Kovalenko, D V

2017-02-06

We theoretically investigate the dynamic regime of coherent population trapping (CPT) in the presence of frequency modulation (FM). We have formulated the criteria for quasi-stationary (adiabatic) and dynamic (non-adiabatic) responses of atomic system driven by this FM. Using the density matrix formalism for Λ system, the error signal is exactly calculated and optimized. It is shown that the optimal FM parameters correspond to the dynamic regime of atomic-field interaction, which significantly differs from conventional description of CPT resonances in the frame of quasi-stationary approach (under small modulation frequency). Obtained theoretical results are in good qualitative agreement with different experiments. Also we have found CPT-analogue of Pound-Driver-Hall regime of frequency stabilization.

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.

Renormalized dynamics of the Dean-Kawasaki model

NASA Astrophysics Data System (ADS)

Bidhoodi, Neeta; Das, Shankar P.

2015-07-01

We study the model of a supercooled liquid for which the equation of motion for the coarse-grained density ρ (x ,t ) is the nonlinear diffusion equation originally proposed by Dean and Kawasaki, respectively, for Brownian and Newtonian dynamics of fluid particles. Using a Martin-Siggia-Rose (MSR) field theory we study the renormalization of the dynamics in a self-consistent form in terms of the so-called self-energy matrix Σ . The appropriate model for the renormalized dynamics involves an extended set of field variables {ρ ,θ } , linked through a nonlinear constraint. The latter incorporates, in a nonperturbative manner, the effects of an infinite number of density nonlinearities in the dynamics. We show that the contributing element of Σ which renormalizes the bare diffusion constant D0 to DR is same as that proposed by Kawasaki and Miyazima [Z. Phys. B Condens. Matter 103, 423 (1997), 10.1007/s002570050396]. DR sharply decreases with increasing density. We consider the likelihood of a ergodic-nonergodic (ENE) transition in the model beyond a critical point. The transition is characterized by the long-time limit of the density correlation freezing at a nonzero value. From our analysis we identify an element of Σ which arises from the above-mentioned nonlinear constraint and is key to the viability of the ENE transition. If this self-energy would be zero, then the model supports a sharp ENE transition with DR=0 as predicted by Kawasaki and Miyazima. With the full model having nonzero value for this self-energy, the density autocorrelation function decays to zero in the long-time limit. Hence the ENE transition is not supported in the model.

Decoherence in quantum lossy systems: superoperator and matrix techniques

NASA Astrophysics Data System (ADS)

Yazdanpanah, Navid; Tavassoly, Mohammad Kazem; Moya-Cessa, Hector Manuel

2017-06-01

Due to the unavoidably dissipative interaction between quantum systems with their environments, the decoherence flows inevitably into the systems. Therefore, to achieve a better understanding on how decoherence affects on the damped systems, a fundamental investigation of master equation seems to be required. In this regard, finding out the missed information which has been lost due to irreversibly of the dissipative systems, is also of practical importance in quantum information science. Motivating by these facts, in this work we want to use superoperator and matrix techniques, by which we are able to illustrate two methods to obtain the explicit form of density operators corresponding to damped systems at arbitrary temperature T ≥ 0. To establish the potential abilities of the suggested methods, we apply them to deduce the density operator of some practical well-known quantum systems. Using the superoperator techniques, at first we obtain the density operator of a damped system which includes a qubit interacting with a single-mode quantized field within an optical cavity. As the second system, we study the decoherence of a quantized field within an optical damped cavity. We also use our proposed matrix method to study the decoherence of a system which includes two qubits in the interaction with each other via dipole-dipole interaction and at the same time with a quantized field in a lossy cavity. The influences of dissipation on the decoherence of dynamical properties of these systems are also numerically investigated. At last, the advantages of the proposed superoperator techniques in comparison with matrix method are explained.

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.

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

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

NASA Astrophysics Data System (ADS)

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

2018-06-01

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

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.

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

Quantum Dynamics in Biological Systems

NASA Astrophysics Data System (ADS)

Shim, Sangwoo

In the first part of this dissertation, recent efforts to understand quantum mechanical effects in biological systems are discussed. Especially, long-lived quantum coherences observed during the electronic energy transfer process in the Fenna-Matthews-Olson complex at physiological condition are studied extensively using theories of open quantum systems. In addition to the usual master equation based approaches, the effect of the protein structure is investigated in atomistic detail through the combined application of quantum chemistry and molecular dynamics simulations. To evaluate the thermalized reduced density matrix, a path-integral Monte Carlo method with a novel importance sampling approach is developed for excitons coupled to an arbitrary phonon bath at a finite temperature. In the second part of the thesis, simulations of molecular systems and applications to vibrational spectra are discussed. First, the quantum dynamics of a molecule is simulated by combining semiclassical initial value representation and density funcitonal theory with analytic derivatives. A computationally-tractable approximation to the sum-of-states formalism of Raman spectra is subsequently discussed.

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.

Controllability of flow-conservation networks

NASA Astrophysics Data System (ADS)

Zhao, Chen; Zeng, An; Jiang, Rui; Yuan, Zhengzhong; Wang, Wen-Xu

2017-07-01

The ultimate goal of exploring complex networks is to control them. As such, controllability of complex networks has been intensively investigated. Despite recent advances in studying the impact of a network's topology on its controllability, a comprehensive understanding of the synergistic impact of network topology and dynamics on controllability is still lacking. Here, we explore the controllability of flow-conservation networks, trying to identify the minimal number of driver nodes that can guide the network to any desirable state. We develop a method to analyze the controllability on flow-conservation networks based on exact controllability theory, transforming the original analysis on adjacency matrix to Laplacian matrix. With this framework, we systematically investigate the impact of some key factors of networks, including link density, link directionality, and link polarity, on the controllability of these networks. We also obtain the analytical equations by investigating the network's structural properties approximatively and design the efficient tools. Finally, we consider some real networks with flow dynamics, finding that their controllability is significantly different from that predicted by only considering the topology. These findings deepen our understanding of network controllability with flow-conservation dynamics and provide a general framework to incorporate real dynamics in the analysis of network controllability.

Dynamics of many-body localization in the presence of particle loss

NASA Astrophysics Data System (ADS)

van Nieuwenburg, EPL; Yago Malo, J.; Daley, AJ; Fischer, MH

2018-01-01

At long times, residual couplings to the environment become relevant even in the most isolated experiments, a crucial difficulty for the study of fundamental aspects of many-body dynamics. A particular example is many-body localization in a cold-atom setting, where incoherent photon scattering introduces both dephasing and particle loss. Whereas dephasing has been studied in detail and is known to destroy localization already on the level of non-interacting particles, the effect of particle loss is less well understood. A difficulty arises due to the ‘non-local’ nature of the loss process, complicating standard numerical tools using matrix product decomposition. Utilizing symmetries of the Lindbladian dynamics, we investigate the particle loss on both the dynamics of observables, as well as the structure of the density matrix and the individual states. We find that particle loss in the presence of interactions leads to dissipation and a strong suppression of the (operator space) entanglement entropy. Our approach allows for the study of the interplay of dephasing and loss for pure and mixed initial states to long times, which is important for future experiments using controlled coupling of the environment.

Dynamical Epidemic Suppression Using Stochastic Prediction and Control

DTIC Science & Technology

2004-10-28

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

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.

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.

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

PubMed

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

2016-05-01

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

Polymer-mediated nanorod self-assembly predicted by dissipative particle dynamics simulations.

PubMed

Khani, Shaghayegh; Jamali, Safa; Boromand, Arman; Hore, Michael J A; Maia, Joao

2015-09-14

Self-assembly of nanoparticles in polymer matrices is an interesting and growing subject in the field of nanoscience and technology. We report herein on modelling studies of the self-assembly and phase behavior of nanorods in a homopolymer matrix, with the specific goal of evaluating the role of deterministic entropic and enthalpic factors that control the aggregation/dispersion in such systems. Grafting polymer brushes from the nanorods is one approach to control/impact their self-assembly capabilities within a polymer matrix. From an energetic point of view, miscible interactions between the brush and the matrix are required for achieving a better dispersibility; however, grafting density and brush length are the two important parameters in dictating the morphology. Unlike in previous computational studies, the present Dissipative Particle Dynamics (DPD) simulation framework is able to both predict dispersion or aggregation of nanorods and determine the self-assembled structure, allowing for the determination of a phase diagram, which takes all of these factors into account. Three types of morphologies are predicted: dispersion, aggregation and partial aggregation. Moreover, favorable enthalpic interactions between the brush and the matrix are found to be essential for expanding the window for achieving a well-dispersed morphology. A three-dimensional phase diagram is mapped on which all the afore-mentioned parameters are taken into account. Additionally, in the case of immiscibility between brushes and the matrix, simulations predict the formation of some new and tunable structures.

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.

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

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

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

2005-11-07

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

Solutions of the two-dimensional Hubbard model: Benchmarks and results from a wide range of numerical algorithms

DOE PAGES

LeBlanc, J. P. F.; Antipov, Andrey E.; Becca, Federico; ...

2015-12-14

Numerical results for ground-state and excited-state properties (energies, double occupancies, and Matsubara-axis self-energies) of the single-orbital Hubbard model on a two-dimensional square lattice are presented, in order to provide an assessment of our ability to compute accurate results in the thermodynamic limit. Many methods are employed, including auxiliary-field quantum Monte Carlo, bare and bold-line diagrammatic Monte Carlo, method of dual fermions, density matrix embedding theory, density matrix renormalization group, dynamical cluster approximation, diffusion Monte Carlo within a fixed-node approximation, unrestricted coupled cluster theory, and multireference projected Hartree-Fock methods. Comparison of results obtained by different methods allows for the identification ofmore » uncertainties and systematic errors. The importance of extrapolation to converged thermodynamic-limit values is emphasized. Furthermore, cases where agreement between different methods is obtained establish benchmark results that may be useful in the validation of new approaches and the improvement of existing methods.« less

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.

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.

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.

Energy-free machine learning force field for aluminum.

PubMed

Kruglov, Ivan; Sergeev, Oleg; Yanilkin, Alexey; Oganov, Artem R

2017-08-17

We used the machine learning technique of Li et al. (PRL 114, 2015) for molecular dynamics simulations. Atomic configurations were described by feature matrix based on internal vectors, and linear regression was used as a learning technique. We implemented this approach in the LAMMPS code. The method was applied to crystalline and liquid aluminum and uranium at different temperatures and densities, and showed the highest accuracy among different published potentials. Phonon density of states, entropy and melting temperature of aluminum were calculated using this machine learning potential. The results are in excellent agreement with experimental data and results of full ab initio calculations.

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.

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.

Products of random matrices from fixed trace and induced Ginibre ensembles

NASA Astrophysics Data System (ADS)

Akemann, Gernot; Cikovic, Milan

2018-05-01

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

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.

The role of parasites in the dynamics of a reindeer population.

PubMed Central

Albon, S D; Stien, A; Irvine, R J; Langvatn, R; Ropstad, E; Halvorsen, O

2002-01-01

Even though theoretical models show that parasites may regulate host population densities, few empirical studies have given support to this hypothesis. We present experimental and observational evidence for a host-parasite interaction where the parasite has sufficient impact on host population dynamics for regulation to occur. During a six year study of the Svalbard reindeer and its parasitic gastrointestinal nematode Ostertagia gruehneri we found that anthelminthic treatment in April-May increased the probability of a reindeer having a calf in the next year, compared with untreated controls. However, treatment did not influence the over-winter survival of the reindeer. The annual variation in the degree to which parasites depressed fecundity was positively related to the abundance of O. gruehneri infection the previous October, which in turn was related to host density two years earlier. In addition to the treatment effect, there was a strong negative effect of winter precipitation on the probability of female reindeer having a calf. A simple matrix model was parameterized using estimates from our experimental and observational data. This model shows that the parasite-mediated effect on fecundity was sufficient to regulate reindeer densities around observed host densities. PMID:12184833

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

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.

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.

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.

Content and distribution of noncollagenous matrix proteins in bone and cementum: relationship to speed of formation and collagen packing density.

PubMed

Nanci, A

1999-06-30

The organic matrix of collagen-based calcified tissues consists of a supporting collagen meshwork and various noncollagenous matrix proteins (NCPs). Together, they contribute to determining the structure and biomechanical properties of the tissue. Their respective organization and interrelation can advantageously be examined by immunocytochemistry, an approach which allows correlation of composition with structure. The aim of this article is to review postembedding immuno- and lectin-gold-labeling data on the characterization of the noncollagenous compartment in rat and human bone and cementum, and on its relationship to collagen. The two major NCPs, bone sialoprotein and osteopontin, generally codistribute and accumulate in cement lines and in the spaces among the mineralized collagen fibrils. However, there are variations in their distribution and density of labeling throughout the tissue. Indeed, bone and cementum can form in environments that are either poor or enriched in NCPs. The amount of NCPs generally correlates with bone and cementum types and with speed of formation of the tissue and packing density of collagen fibrils. Taken together, the data suggest that production of both collagenous and noncollagenous constituents can be "modulated" during formation of collagen-based calcified tissues. It is concluded that, in addition to structural and compositional parameters, tissue dynamics must be taken into consideration in order to understand the significance of the apparent accumulation of NCPs at some sites and to determine the mechanisms of normal and pathological calcified tissue formation. Copyright 1999 Academic Press.

Soil-related variations in the population dynamics of six dipterocarp tree species with strong habitat preferences.

PubMed

Yamada, Toshihiro; Yamada, Yuko; Okuda, Toshinori; Fletcher, Christine

2013-07-01

Differences in the density of conspecific tree individuals in response to environmental gradients are well documented for many tree species, but how such density differences are generated and maintained is poorly understood. We examined the segregation of six dipterocarp species among three soil types in the Pasoh tropical forest, Malaysia. We examined how individual performance and population dynamics changed across the soil types using 10-year demographic data to compare tree performance across soil types, and constructed population matrix models to analyze the population dynamics. Species showed only minor changes in mortality and juvenile growth across soil types, although recruitment differed greatly. Clear, interspecific demographic trade-offs between growth and mortality were found in all soil types. The relative trade-offs by a species did not differ substantially among the soil types. Population sizes were projected to remain stable in all soil types for all species with one exception. Our life-table response experiment demonstrated that the population dynamics of a species differed only subtly among soil types. Therefore, species with strong density differences across soil types do not necessarily differ greatly in their population dynamics across the soil types. In contrast, interspecific differences in population dynamics were large. The trade-off between mortality and growth led to a negative correlation between the contributions of mortality and growth to variations in the population growth rate (λ) and thus reduced their net contributions. Recruitment had little impact on the variation in λ. The combination of these factors resulted in little variation in λ among species.

Unusual instability mode of transparent all oxide thin film transistor under dynamic bias condition

NASA Astrophysics Data System (ADS)

Oh, Himchan; Hwang, Chi-Sun; Pi, Jae-Eun; Ki Ryu, Min; Ko Park, Sang-Hee; Yong Chu, Hye

2013-09-01

We report a degradation behavior of fully transparent oxide thin film transistor under dynamic bias stress which is the condition similar to actual pixel switching operation in active matrix display. After the stress test, drain current increased while the threshold voltage was almost unchanged. We found that shortening of effective channel length is leading cause of increase in drain current. Electrons activate the neutral donor defects by colliding with them during short gate-on period. These ionized donors are stabilized during the subsequent gate-off period due to electron depletion. This local increase in doping density reduces the channel length.

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.

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

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.

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.

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.

Super Nonlinear Electrodeposition-Diffusion-Controlled Thin-Film Selector.

PubMed

Ji, Xinglong; Song, Li; He, Wei; Huang, Kejie; Yan, Zhiyuan; Zhong, Shuai; Zhang, Yishu; Zhao, Rong

2018-03-28

Selector elements with high nonlinearity are an indispensable part in constructing high density, large-scale, 3D stackable emerging nonvolatile memory and neuromorphic network. Although significant efforts have been devoted to developing novel thin-film selectors, it remains a great challenge in achieving good switching performance in the selectors to satisfy the stringent electrical criteria of diverse memory elements. In this work, we utilized high-defect-density chalcogenide glass (Ge 2 Sb 2 Te 5 ) in conjunction with high mobility Ag element (Ag-GST) to achieve a super nonlinear selective switching. A novel electrodeposition-diffusion dynamic selector based on Ag-GST exhibits superior selecting performance including excellent nonlinearity (<5 mV/dev), ultra-low leakage (<10 fA), and bidirectional operation. With the solid microstructure evidence and dynamic analyses, we attributed the selective switching to the competition between the electrodeposition and diffusion of Ag atoms in the glassy GST matrix under electric field. A switching model is proposed, and the in-depth understanding of the selective switching mechanism offers an insight of switching dynamics for the electrodeposition-diffusion-controlled thin-film selector. This work opens a new direction of selector designs by combining high mobility elements and high-defect-density chalcogenide glasses, which can be extended to other materials with similar properties.

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.

Estimation of beam material random field properties via sensitivity-based model updating using experimental frequency response functions

NASA Astrophysics Data System (ADS)

Machado, M. R.; Adhikari, S.; Dos Santos, J. M. C.; Arruda, J. R. F.

2018-03-01

Structural parameter estimation is affected not only by measurement noise but also by unknown uncertainties which are present in the system. Deterministic structural model updating methods minimise the difference between experimentally measured data and computational prediction. Sensitivity-based methods are very efficient in solving structural model updating problems. Material and geometrical parameters of the structure such as Poisson's ratio, Young's modulus, mass density, modal damping, etc. are usually considered deterministic and homogeneous. In this paper, the distributed and non-homogeneous characteristics of these parameters are considered in the model updating. The parameters are taken as spatially correlated random fields and are expanded in a spectral Karhunen-Loève (KL) decomposition. Using the KL expansion, the spectral dynamic stiffness matrix of the beam is expanded as a series in terms of discretized parameters, which can be estimated using sensitivity-based model updating techniques. Numerical and experimental tests involving a beam with distributed bending rigidity and mass density are used to verify the proposed method. This extension of standard model updating procedures can enhance the dynamic description of structural dynamic models.

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.

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.

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.

Elastic scattering losses from colliding Bose-Einstein condensates

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

Zin Pawel; Chwedenczuk, Jan; Trippenbach, Marek

2006-03-15

Bragg diffraction divides a Bose-Einstein condensate into two overlapping components, moving with respect to each other with high momentum. Elastic collisions between atoms from distinct wave packets can significantly deplete the condensate. Recently, Zin et al. [Phys. Rev. Lett. 94, 200401 (2005)] introduced a model of two counterpropagating atomic Gaussian wave packets incorporating the dynamics of the incoherent scattering processes. Here we study the properties of this model in detail, including the nature of the transition from spontaneous to stimulated scattering. Within the first-order approximation, we derive analytical expressions for the density matrix and anomalous density that provide excellent insightmore » into correlation properties of scattered atoms.« less

Estimating Allee dynamics before they can be observed: polar bears as a case study.

PubMed

Molnár, Péter K; Lewis, Mark A; Derocher, Andrew E

2014-01-01

Allee effects are an important component in the population dynamics of numerous species. Accounting for these Allee effects in population viability analyses generally requires estimates of low-density population growth rates, but such data are unavailable for most species and particularly difficult to obtain for large mammals. Here, we present a mechanistic modeling framework that allows estimating the expected low-density growth rates under a mate-finding Allee effect before the Allee effect occurs or can be observed. The approach relies on representing the mechanisms causing the Allee effect in a process-based model, which can be parameterized and validated from data on the mechanisms rather than data on population growth. We illustrate the approach using polar bears (Ursus maritimus), and estimate their expected low-density growth by linking a mating dynamics model to a matrix projection model. The Allee threshold, defined as the population density below which growth becomes negative, is shown to depend on age-structure, sex ratio, and the life history parameters determining reproduction and survival. The Allee threshold is thus both density- and frequency-dependent. Sensitivity analyses of the Allee threshold show that different combinations of the parameters determining reproduction and survival can lead to differing Allee thresholds, even if these differing combinations imply the same stable-stage population growth rate. The approach further shows how mate-limitation can induce long transient dynamics, even in populations that eventually grow to carrying capacity. Applying the models to the overharvested low-density polar bear population of Viscount Melville Sound, Canada, shows that a mate-finding Allee effect is a plausible mechanism for slow recovery of this population. Our approach is generalizable to any mating system and life cycle, and could aid proactive management and conservation strategies, for example, by providing a priori estimates of minimum conservation targets for rare species or minimum eradication targets for pests and invasive species.

Estimating Allee Dynamics before They Can Be Observed: Polar Bears as a Case Study

PubMed Central

Molnár, Péter K.; Lewis, Mark A.; Derocher, Andrew E.

2014-01-01

Allee effects are an important component in the population dynamics of numerous species. Accounting for these Allee effects in population viability analyses generally requires estimates of low-density population growth rates, but such data are unavailable for most species and particularly difficult to obtain for large mammals. Here, we present a mechanistic modeling framework that allows estimating the expected low-density growth rates under a mate-finding Allee effect before the Allee effect occurs or can be observed. The approach relies on representing the mechanisms causing the Allee effect in a process-based model, which can be parameterized and validated from data on the mechanisms rather than data on population growth. We illustrate the approach using polar bears (Ursus maritimus), and estimate their expected low-density growth by linking a mating dynamics model to a matrix projection model. The Allee threshold, defined as the population density below which growth becomes negative, is shown to depend on age-structure, sex ratio, and the life history parameters determining reproduction and survival. The Allee threshold is thus both density- and frequency-dependent. Sensitivity analyses of the Allee threshold show that different combinations of the parameters determining reproduction and survival can lead to differing Allee thresholds, even if these differing combinations imply the same stable-stage population growth rate. The approach further shows how mate-limitation can induce long transient dynamics, even in populations that eventually grow to carrying capacity. Applying the models to the overharvested low-density polar bear population of Viscount Melville Sound, Canada, shows that a mate-finding Allee effect is a plausible mechanism for slow recovery of this population. Our approach is generalizable to any mating system and life cycle, and could aid proactive management and conservation strategies, for example, by providing a priori estimates of minimum conservation targets for rare species or minimum eradication targets for pests and invasive species. PMID:24427306

Predictive model to describe water migration in cellular solid foods during storage.

PubMed

Voogt, Juliën A; Hirte, Anita; Meinders, Marcel B J

2011-11-01

Water migration in cellular solid foods during storage causes loss of crispness. To improve crispness retention, physical understanding of this process is needed. Mathematical models are suitable tools to gain this physical knowledge. Water migration in cellular solid foods involves migration through both the air cells and the solid matrix. For systems in which the water migration distance is large compared with the cell wall thickness of the solid matrix, the overall water flux through the system is dominated by the flux through the air. For these systems, water migration can be approximated well by a Fickian diffusion model. The effective diffusion coefficient can be expressed in terms of the material properties of the solid matrix (i.e. the density, sorption isotherm and diffusion coefficient of water in the solid matrix) and the morphological properties of the cellular structure (i.e. water vapour permeability and volume fraction of the solid matrix). The water vapour permeability is estimated from finite element method modelling using a simplified model for the cellular structure. It is shown that experimentally observed dynamical water profiles of bread rolls that differ in crust permeability are predicted well by the Fickian diffusion model. Copyright © 2011 Society of Chemical Industry.

Cracking evolution behaviors of lightweight materials based on in situ synchrotron X-ray tomography: A review

NASA Astrophysics Data System (ADS)

Luo, Y.; Wu, S. C.; Hu, Y. N.; Fu, Y. N.

2018-03-01

Damage accumulation and failure behaviors are crucial concerns during the design and service of a critical component, leading researchers and engineers to thoroughly identifying the crack evolution. Third-generation synchrotron radiation X-ray computed microtomography can be used to detect the inner damage evolution of a large-density material or component. This paper provides a brief review of studying the crack initiation and propagation inside lightweight materials with advanced synchrotron three-dimensional (3D) X-ray imaging, such as aluminum materials. Various damage modes under both static and dynamic loading are elucidated for pure aluminum, aluminum alloy matrix, aluminum alloy metal matrix composite, and aluminum alloy welded joint. For aluminum alloy matrix, metallurgical defects (porosity, void, inclusion, precipitate, etc.) or artificial defects (notch, scratch, pit, etc.) strongly affect the crack initiation and propagation. For aluminum alloy metal matrix composites, the fracture occurs either from the particle debonding or voids at the particle/matrix interface, and the void evolution is closely related with fatigued cycles. For the hybrid laser welded aluminum alloy, fatigue cracks usually initiate from gas pores located at the surface or sub-surface and gradually propagate to a quarter ellipse or a typical semi-ellipse profile.

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.

Performance of low-rank QR approximation of the finite element Biot-Savart law

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

White, D; Fasenfest, B

2006-10-16

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

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.

Excitation energies from range-separated time-dependent density and density matrix functional theory.

PubMed

Pernal, Katarzyna

2012-05-14

Time-dependent density functional theory (TD-DFT) in the adiabatic formulation exhibits known failures when applied to predicting excitation energies. One of them is the lack of the doubly excited configurations. On the other hand, the time-dependent theory based on a one-electron reduced density matrix functional (time-dependent density matrix functional theory, TD-DMFT) has proven accurate in determining single and double excitations of H(2) molecule if the exact functional is employed in the adiabatic approximation. We propose a new approach for computing excited state energies that relies on functionals of electron density and one-electron reduced density matrix, where the latter is applied in the long-range region of electron-electron interactions. A similar approach has been recently successfully employed in predicting ground state potential energy curves of diatomic molecules even in the dissociation limit, where static correlation effects are dominating. In the paper, a time-dependent functional theory based on the range-separation of electronic interaction operator is rigorously formulated. To turn the approach into a practical scheme the adiabatic approximation is proposed for the short- and long-range components of the coupling matrix present in the linear response equations. In the end, the problem of finding excitation energies is turned into an eigenproblem for a symmetric matrix. Assignment of obtained excitations is discussed and it is shown how to identify double excitations from the analysis of approximate transition density matrix elements. The proposed method used with the short-range local density approximation (srLDA) and the long-range Buijse-Baerends density matrix functional (lrBB) is applied to H(2) molecule (at equilibrium geometry and in the dissociation limit) and to Be atom. The method accounts for double excitations in the investigated systems but, unfortunately, the accuracy of some of them is poor. The quality of the other excitations is in general much better than that offered by TD-DFT-LDA or TD-DMFT-BB approximations if the range-separation parameter is properly chosen. The latter remains an open problem.

Emergence of a new pair-coherent phase in many-body quenches of repulsive bosons

NASA Astrophysics Data System (ADS)

Fischer, Uwe R.; Lee, Kang-Soo; Xiong, Bo

2011-07-01

We investigate the dynamical mode population statistics and associated first- and second-order coherence of an interacting bosonic two-mode model when the pair-exchange coupling is quenched from negative to positive values. It is shown that for moderately rapid second-order transitions, a new pair-coherent phase emerges on the positive coupling side in an excited state, which is not fragmented as the ground-state single-particle density matrix would prescribe it to be.

Dynamic signatures of the transition from stacking disordered to hexagonal ice: Dielectric and nuclear magnetic resonance studies

NASA Astrophysics Data System (ADS)

Gainaru, C.; Vynokur, E.; Köster, K. W.; Fuentes-Landete, V.; Spettel, N.; Zollner, J.; Loerting, T.; Böhmer, R.

2018-04-01

Using various temperature-cycling protocols, the dynamics of ice I were studied via dielectric spectroscopy and nuclear magnetic resonance relaxometry on protonated and deuterated samples obtained by heating high-density amorphous ices as well as crystalline ice XII. Previous structural studies of ice I established that at temperatures of about 230 K, the stacking disorder of the cubic/hexagonal oxygen lattice vanishes. The present dielectric and nuclear magnetic resonance investigations of spectral changes disclose that the memory of the existence of a precursor phase is preserved in the hydrogen matrix up to 270 K. This finding of hydrogen mobility lower than that of the undoped hexagonal ice near the melting point highlights the importance of dynamical investigations of the transitions between various ice phases and sheds new light on the dynamics in ice I in general.

Many-body dynamics of driven-dissipative Rydberg cavity polaritons

NASA Astrophysics Data System (ADS)

Pistorius, Tim; Fan, Jingtao; Weimer, Hendrik

2017-04-01

The usage of photons as long-range information carriers has greatly increased the interest in systems with nonlinear optical properties in recent years. The nonlinearity is easily achievable in Rydberg mediums through the strong van der Waals interaction which makes them one of the best candidates for such a system. Here, we propose a way to analyze the steady state solutions of a Rydberg medium in a cavity through the combination of the variational principle for open quantum systems and the P-distribution of the density matrix. To get a better understanding of the many-body-dynamics a transformation into the polariton picture is performed and investigated. Volkswagen Foundation, Deutsche Forschungsgemeinschaft.

Decoherence dynamics of interacting qubits coupled to a bath of local optical phonons

NASA Astrophysics Data System (ADS)

Lone, Muzaffar Qadir; Yarlagadda, S.

2016-04-01

We study decoherence in an interacting qubit system described by infinite range Heisenberg model (IRHM) in a situation where the system is coupled to a bath of local optical phonons. Using perturbation theory in polaron frame of reference, we derive an effective Hamiltonian that is valid in the regime of strong spin-phonon coupling under nonadiabatic conditions. It is shown that the effective Hamiltonian commutes with the IRHM upto leading orders of perturbation and thus has the same eigenstates as the IRHM. Using a quantum master equation with Markovian approximation of dynamical evolution, we show that the off-diagonal elements of the density matrix do not decay in the energy eigen basis of IRHM.

Information loss in effective field theory: Entanglement and thermal entropies

NASA Astrophysics Data System (ADS)

Boyanovsky, Daniel

2018-03-01

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

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

PubMed

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

2013-01-01

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

Density matrix renormalization group study of a three-orbital Hubbard model with spin-orbit coupling in one dimension

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

Kaushal, Nitin; Herbrych, Jacek W.; Nocera, Alberto

Using the density matrix renormalization group technique we study the effect of spin-orbit coupling on a three-orbital Hubbard model in the (t 2g) 4 sector and in one dimension. Fixing the Hund coupling to a robust value compatible with some multiorbital materials, we present the phase diagram varying the Hubbard U and spin-orbit coupling λ, at zero temperature. Our results are shown to be qualitatively similar to those recently reported using the dynamical mean-field theory in higher dimensions, providing a robust basis to approximate many-body techniques. Among many results, we observe an interesting transition from an orbital-selective Mott phase tomore » an excitonic insulator with increasing λ at intermediate U. In the strong U coupling limit, we find a nonmagnetic insulator with an effective angular momentum <(J eff) 2>≠0 near the excitonic phase, smoothly connected to the <(J eff) 2>=0 regime. In conclusion, we also provide a list of quasi-one-dimensional materials where the physics discussed in this paper could be realized.« less

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

NASA Astrophysics Data System (ADS)

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

2018-06-01

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

Density matrix renormalization group study of a three-orbital Hubbard model with spin-orbit coupling in one dimension

NASA Astrophysics Data System (ADS)

Kaushal, Nitin; Herbrych, Jacek; Nocera, Alberto; Alvarez, Gonzalo; Moreo, Adriana; Reboredo, F. A.; Dagotto, Elbio

2017-10-01

Using the density matrix renormalization group technique we study the effect of spin-orbit coupling on a three-orbital Hubbard model in the (t2g) 4 sector and in one dimension. Fixing the Hund coupling to a robust value compatible with some multiorbital materials, we present the phase diagram varying the Hubbard U and spin-orbit coupling λ , at zero temperature. Our results are shown to be qualitatively similar to those recently reported using the dynamical mean-field theory in higher dimensions, providing a robust basis to approximate many-body techniques. Among many results, we observe an interesting transition from an orbital-selective Mott phase to an excitonic insulator with increasing λ at intermediate U . In the strong U coupling limit, we find a nonmagnetic insulator with an effective angular momentum 〈(Jeff)2〉≠0 near the excitonic phase, smoothly connected to the 〈(Jeff)2〉=0 regime. We also provide a list of quasi-one-dimensional materials where the physics discussed in this paper could be realized.

Density matrix renormalization group study of a three-orbital Hubbard model with spin-orbit coupling in one dimension

DOE PAGES

Kaushal, Nitin; Herbrych, Jacek W.; Nocera, Alberto; ...

2017-10-09

Using the density matrix renormalization group technique we study the effect of spin-orbit coupling on a three-orbital Hubbard model in the (t 2g) 4 sector and in one dimension. Fixing the Hund coupling to a robust value compatible with some multiorbital materials, we present the phase diagram varying the Hubbard U and spin-orbit coupling λ, at zero temperature. Our results are shown to be qualitatively similar to those recently reported using the dynamical mean-field theory in higher dimensions, providing a robust basis to approximate many-body techniques. Among many results, we observe an interesting transition from an orbital-selective Mott phase tomore » an excitonic insulator with increasing λ at intermediate U. In the strong U coupling limit, we find a nonmagnetic insulator with an effective angular momentum <(J eff) 2>≠0 near the excitonic phase, smoothly connected to the <(J eff) 2>=0 regime. In conclusion, we also provide a list of quasi-one-dimensional materials where the physics discussed in this paper could be realized.« less

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.

Landscape matrix mediates occupancy dynamics of Neotropical avian insectivores

USGS Publications Warehouse

Kennedy, Christina M.; Campbell Grant, Evan H.; Neel, Maile C.; Fagan, William F.; Marpa, Peter P.

2011-01-01

In addition to patch-level attributes (i.e., area and isolation), the nature of land cover between habitat patches (the matrix) may drive colonization and extinction dynamics in fragmented landscapes. Despite a long-standing recognition of matrix effects in fragmented systems, an understanding of the relative impacts of different types of land cover on patterns and dynamics of species occurrence remains limited. We employed multi-season occupancy models to determine the relative influence of patch area, patch isolation, within-patch vegetation structure, and landscape matrix on occupancy dynamics of nine Neotropical nsectivorous birds in 99 forest patches embedded in four matrix types (agriculture, suburban evelopment, bauxite mining, and forest) in central Jamaica. We found that within-patch vegetation structure and the matrix type between patches were more important than patch area and patch isolation in determining local colonization and local extinction probabilities, and that the effects of patch area, isolation, and vegetation structure on occupancy dynamics tended to be matrix and species dependent. Across the avian community, the landscape matrix influenced local extinction more than local colonization, indicating that extinction processes, rather than movement, likely drive interspecific differences in occupancy dynamics. These findings lend crucial empirical support to the hypothesis that species occupancy dynamics in fragmented systems may depend greatly upon the landscape context.

Mean, covariance, and effective dimension of stochastic distributed delay dynamics

NASA Astrophysics Data System (ADS)

René, Alexandre; Longtin, André

2017-11-01

Dynamical models are often required to incorporate both delays and noise. However, the inherently infinite-dimensional nature of delay equations makes formal solutions to stochastic delay differential equations (SDDEs) challenging. Here, we present an approach, similar in spirit to the analysis of functional differential equations, but based on finite-dimensional matrix operators. This results in a method for obtaining both transient and stationary solutions that is directly amenable to computation, and applicable to first order differential systems with either discrete or distributed delays. With fewer assumptions on the system's parameters than other current solution methods and no need to be near a bifurcation, we decompose the solution to a linear SDDE with arbitrary distributed delays into natural modes, in effect the eigenfunctions of the differential operator, and show that relatively few modes can suffice to approximate the probability density of solutions. Thus, we are led to conclude that noise makes these SDDEs effectively low dimensional, which opens the possibility of practical definitions of probability densities over their solution space.

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

Recursive flexible multibody system dynamics using spatial operators

NASA Technical Reports Server (NTRS)

Jain, A.; Rodriguez, G.

1992-01-01

This paper uses spatial operators to develop new spatially recursive dynamics algorithms for flexible multibody systems. The operator description of the dynamics is identical to that for rigid multibody systems. Assumed-mode models are used for the deformation of each individual body. The algorithms are based on two spatial operator factorizations of the system mass matrix. The first (Newton-Euler) factorization of the mass matrix leads to recursive algorithms for the inverse dynamics, mass matrix evaluation, and composite-body forward dynamics for the systems. The second (innovations) factorization of the mass matrix, leads to an operator expression for the mass matrix inverse and to a recursive articulated-body forward dynamics algorithm. The primary focus is on serial chains, but extensions to general topologies are also described. A comparison of computational costs shows that the articulated-body, forward dynamics algorithm is much more efficient than the composite-body algorithm for most flexible multibody systems.

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.

The dynamical behavior of the s-trioxane radical cation-A low-temperature EPR and theoretical study.

PubMed

Naumov, Sergej S; Knolle, Wolfgang; Naumov, Sergej P; Pöppl, Andreas; Janovský, Igor

2014-10-28

The radical cation of s-trioxane, radiolytically generated in a freon (CF3CCl3) matrix, was studied in the 10-140 K temperature region. Reversible changes of the EPR spectra were observed, arising from both ring puckering and ring inversion through the molecular plane. The ESREXN program based on the Liouville density matrix equation, allowing the treatment of dynamical exchange, has been used to analyze the experimental results. Two limiting conformer structures of the s-trioxane radical cation were taken into account, namely "rigid" half-boat and averaged planar ones, differing strongly in their electron distribution. The spectrum due to the "rigid" half-boat conformer can be observed only at very low (<60 K) temperatures, when the exchange of conformers is very slow. Two transition states for interconversion by puckering and ring-inversion were identified, close in activation energy (2.3 and 3.0 kJ/mol calculated). Since the energy difference is very small, both processes set on at a comparable temperature. In the case of nearly complete equilibration (fast exchange) between six energetically equivalent structures at T > 120 K in CF3CCl3, a septet due to six equivalent protons (hfs splitting constant 5.9 mT) is observed, characteristic of the dynamically averaged planar geometry of the radical cation. DFT quantum chemical calculations and spectral simulation including intramolecular dynamical exchange support the interpretation.

Investigations on the properties of NH4HCO3 filled natural rubber based magnetorheological elastomers (MREs)

NASA Astrophysics Data System (ADS)

Fan, Lili; Wang, Guoping; Wang, Wenju; Shi, Guanxin; Yang, Fufeng; Rui, Xiaoting

2018-04-01

Various anisotropic magnetorheological elastomers (MREs) were synthesized using the rubber mixing technique. Magnetic and temperature distributions of the experimental equipment and test instruments were analyzed by the ANSYS. NH4HCO3 was filled in the natural rubber matrix to modify properties of MREs. Microstructures and compositions of samples were studied by the scanning electron microscope (SEM), the energy dispersive x-ray spectroscopy (EDAX) analysis and x-ray powder diffraction (XRD). Via vibrating sample magnetometer (VSM) and density functional theory (DFT) method, the magnetic property of carbonyl iron (CI) was illuminated. The shear storage modulus and MR effect of MREs were investigated by the dynamic mechanical analyzer (DMA). It indicated that distributions of magnetic and temperature in the experimental and testing devices were uniform. Before vulcanization, CI particles were uniformly distributed in the matrix, while a CI chain structure was formed and embedded in the matrix after the vulcanization process. Moderate addition of NH4HCO3 accelerated the rubber vulcanization and enhanced the MR effect.

Effect of Interfacial Bonding on Interphase Properties in SiO2/Epoxy Nanocomposite: A Molecular Dynamics Simulation Study.

PubMed

Wang, Zhikun; Lv, Qiang; Chen, Shenghui; Li, Chunling; Sun, Shuangqing; Hu, Songqing

2016-03-23

Atomistic molecular dynamics simulations have been performed to explore the effect of interfacial bonding on the interphase properties of a nanocomposite system that consists of a silica nanoparticle and the highly cross-linked epoxy matrix. For the structural properties, results show that interfacial covalent bonding can broaden the interphase region by increasing the radial effect range of fluctuated mass density and oriented chains, as well as strengthen the interphase region by improving the thermal stability of interfacial van der Waals excluded volume and reducing the proportion of cis conformers of epoxy segments. The improved thermal stability of the interphase region in the covalently bonded model results in an increase of ∼21 K in the glass transition temperature (Tg) compared to that of the pure epoxy. It is also found that interfacial covalent bonding mainly restricts the volume thermal expansion of the model at temperatures near or larger than Tg. Furthermore, investigations from mean-square displacement and fraction of immobile atoms point out that interfacial covalent and noncovalent bonding induces lower and higher mobility of interphase atoms than that of the pure epoxy, respectively. The obtained critical interfacial bonding ratio when the interphase and matrix atoms have the same mobility is 5.8%. These results demonstrate that the glass transitions of the interphase and matrix will be asynchronous when the interfacial bonding ratio is not 5.8%. Specifically, the interphase region will trigger the glass transition of the matrix when the ratio is larger than 5.8%, whereas it restrains the glass transition of the matrix when the ratio is smaller than 5.8%.

Quantum theory of open systems based on stochastic differential equations of generalized Langevin (non-Wiener) type

NASA Astrophysics Data System (ADS)

Basharov, A. M.

2012-09-01

It is shown that the effective Hamiltonian representation, as it is formulated in author's papers, serves as a basis for distinguishing, in a broadband environment of an open quantum system, independent noise sources that determine, in terms of the stationary quantum Wiener and Poisson processes in the Markov approximation, the effective Hamiltonian and the equation for the evolution operator of the open system and its environment. General stochastic differential equations of generalized Langevin (non-Wiener) type for the evolution operator and the kinetic equation for the density matrix of an open system are obtained, which allow one to analyze the dynamics of a wide class of localized open systems in the Markov approximation. The main distinctive features of the dynamics of open quantum systems described in this way are the stabilization of excited states with respect to collective processes and an additional frequency shift of the spectrum of the open system. As an illustration of the general approach developed, the photon dynamics in a single-mode cavity without losses on the mirrors is considered, which contains identical intracavity atoms coupled to the external vacuum electromagnetic field. For some atomic densities, the photons of the cavity mode are "locked" inside the cavity, thus exhibiting a new phenomenon of radiation trapping and non-Wiener dynamics.

Strain rate effects on fracture behavior of Austempered Ductile Irons

NASA Astrophysics Data System (ADS)

Ruggiero, Andrew; Bonora, Nicola; Gentile, Domenico; Iannitti, Gianluca; Testa, Gabriel; Hörnqvist Colliander, Magnus; Masaggia, Stefano; Vettore, Federico

2017-06-01

Austempered Ductile Irons (ADIs), combining high strength, good ductility and low density, are candidates to be a suitable alternative to high-strength steels. Nevertheless, the concern about a low ductility under dynamic loads often leads designers to exclude cast irons for structural applications. However, results from dynamic tensile tests contradict this perception showing larger failure strain with respect to quasistatic data. The fracture behaviour of ADIs depends on damage mechanisms occurring in the spheroids of graphite, in the matrix and at their interface, with the matrix (ausferrite) consisting of acicular ferrite in carbon-enriched austenite. Here, a detailed microstructural analysis was performed on the ADI 1050-6 deformed under different conditions of strain rates, temperatures, and states of stress. Beside the smooth specimens used for uniaxial tensile tests, round notched bars to evaluate the ductility reduction with increasing stress triaxiality and tophat geometries to evaluate the propensity to shear localization and the associated microstructural alterations were tested. The aim of the work is to link the mechanical and fracture behavior of ADIs to the load condition through the microstructural modifications that occur for the corresponding deformation path.

Dynamic Hydrostatic Pressure Regulates Nucleus Pulposus Phenotypic Expression and Metabolism in a Cell Density-Dependent Manner.

PubMed

Shah, Bhranti S; Chahine, Nadeen O

2018-02-01

Dynamic hydrostatic pressure (HP) loading can modulate nucleus pulposus (NP) cell metabolism, extracellular matrix (ECM) composition, and induce transformation of notochordal NP cells into mature phenotype. However, the effects of varying cell density and dynamic HP magnitude on NP phenotype and metabolism are unknown. This study examined the effects of physiological magnitudes of HP loading applied to bovine NP cells encapsulated within three-dimensional (3D) alginate beads. Study 1: seeding density (1 M/mL versus 4 M/mL) was evaluated in unloaded and loaded (0.1 MPa, 0.1 Hz) conditions. Study 2: loading magnitude (0, 0.1, and 0.6 MPa) applied at 0.1 Hz to 1 M/mL for 7 days was evaluated. Study 1: 4 M/mL cell density had significantly lower adenosine triphosphate (ATP), glycosaminoglycan (GAG) and collagen content, and increased lactate dehydrogenase (LDH). HP loading significantly increased ATP levels, and expression of aggrecan, collagen I, keratin-19, and N-cadherin in HP loaded versus unloaded groups. Study 2: aggrecan expression increased in a dose dependent manner with HP magnitude, whereas N-cadherin and keratin-19 expression were greatest in low HP loading compared to unloaded. Overall, the findings of the current study indicate that cell seeding density within a 3D construct is a critical variable influencing the mechanobiological response of NP cells to HP loading. NP mechanobiology and phenotypic expression was also found to be dependent on the magnitude of HP loading. These findings suggest that HP loading and culture conditions of NP cells may require complex optimization for engineering an NP replacement tissue.

Study of multiband disordered systems using the typical medium dynamical cluster approximation

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

Zhang, Yi; Terletska, Hanna; Moore, C.

We generalize the typical medium dynamical cluster approximation to multiband disordered systems. Using our extended formalism, we perform a systematic study of the nonlocal correlation effects induced by disorder on the density of states and the mobility edge of the three-dimensional two-band Anderson model. We include interband and intraband hopping and an intraband disorder potential. Our results are consistent with those obtained by the transfer matrix and the kernel polynomial methods. We also apply the method to K xFe 2-ySe 2 with Fe vacancies. Despite the strong vacancy disorder and anisotropy, we find the material is not an Anderson insulator.more » Moreover our results demonstrate the application of the typical medium dynamical cluster approximation method to study Anderson localization in real materials.« less

Study of multiband disordered systems using the typical medium dynamical cluster approximation

DOE PAGES

Zhang, Yi; Terletska, Hanna; Moore, C.; ...

2015-11-06

We generalize the typical medium dynamical cluster approximation to multiband disordered systems. Using our extended formalism, we perform a systematic study of the nonlocal correlation effects induced by disorder on the density of states and the mobility edge of the three-dimensional two-band Anderson model. We include interband and intraband hopping and an intraband disorder potential. Our results are consistent with those obtained by the transfer matrix and the kernel polynomial methods. We also apply the method to K xFe 2-ySe 2 with Fe vacancies. Despite the strong vacancy disorder and anisotropy, we find the material is not an Anderson insulator.more » Moreover our results demonstrate the application of the typical medium dynamical cluster approximation method to study Anderson localization in real materials.« less

The spin-temperature theory of dynamic nuclear polarization and nuclear spin-lattice relaxation

NASA Technical Reports Server (NTRS)

Byvik, C. E.; Wollan, D. S.

1974-01-01

A detailed derivation of the equations governing dynamic nuclear polarization (DNP) and nuclear spin lattice relaxation by use of the spin temperature theory has been carried to second order in a perturbation expansion of the density matrix. Nuclear spin diffusion in the rapid diffusion limit and the effects of the coupling of the electron dipole-dipole reservoir (EDDR) with the nuclear spins are incorporated. The complete expression for the dynamic nuclear polarization has been derived and then examined in detail for the limit of well resolved solid effect transitions. Exactly at the solid effect transition peaks, the conventional solid-effect DNP results are obtained, but with EDDR effects on the nuclear relaxation and DNP leakage factor included. Explicit EDDR contributions to DNP are discussed, and a new DNP effect is predicted.

Dynamics and thermodynamics of linear quantum open systems.

PubMed

Martinez, Esteban A; Paz, Juan Pablo

2013-03-29

We analyze the evolution of the quantum state of networks of quantum oscillators coupled with arbitrary external environments. We show that the reduced density matrix of the network always obeys a local master equation with a simple analytical solution. We use this to study the emergence of thermodynamical laws in the long time regime demonstrating two main results: First, we show that it is impossible to build a quantum absorption refrigerator using linear networks (thus, nonlinearity is an essential resource for such refrigerators recently studied by Levy and Kosloff [Phys. Rev. Lett. 108, 070604 (2012)] and Levy et al. [Phys. Rev. B 85, 061126 (2012)]). Then, we show that the third law imposes constraints on the low frequency behavior of the environmental spectral densities.

Recurrence Density Enhanced Complex Networks for Nonlinear Time Series Analysis

NASA Astrophysics Data System (ADS)

Costa, Diego G. De B.; Reis, Barbara M. Da F.; Zou, Yong; Quiles, Marcos G.; Macau, Elbert E. N.

We introduce a new method, which is entitled Recurrence Density Enhanced Complex Network (RDE-CN), to properly analyze nonlinear time series. Our method first transforms a recurrence plot into a figure of a reduced number of points yet preserving the main and fundamental recurrence properties of the original plot. This resulting figure is then reinterpreted as a complex network, which is further characterized by network statistical measures. We illustrate the computational power of RDE-CN approach by time series by both the logistic map and experimental fluid flows, which show that our method distinguishes different dynamics sufficiently well as the traditional recurrence analysis. Therefore, the proposed methodology characterizes the recurrence matrix adequately, while using a reduced set of points from the original recurrence plots.

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.

Defined Essential 8™ Medium and Vitronectin Efficiently Support Scalable Xeno-Free Expansion of Human Induced Pluripotent Stem Cells in Stirred Microcarrier Culture Systems

PubMed Central

Badenes, Sara M.; Fernandes, Tiago G.; Cordeiro, Cláudia S. M.; Boucher, Shayne; Kuninger, David; Vemuri, Mohan C.; Diogo, Maria Margarida; Cabral, Joaquim M. S.

2016-01-01

Human induced pluripotent stem (hiPS) cell culture using Essential 8™ xeno-free medium and the defined xeno-free matrix vitronectin was successfully implemented under adherent conditions. This matrix was able to support hiPS cell expansion either in coated plates or on polystyrene-coated microcarriers, while maintaining hiPS cell functionality and pluripotency. Importantly, scale-up of the microcarrier-based system was accomplished using a 50 mL spinner flask, under dynamic conditions. A three-level factorial design experiment was performed to identify optimal conditions in terms of a) initial cell density b) agitation speed, and c) to maximize cell yield in spinner flask cultures. A maximum cell yield of 3.5 is achieved by inoculating 55,000 cells/cm2 of microcarrier surface area and using 44 rpm, which generates a cell density of 1.4x106 cells/mL after 10 days of culture. After dynamic culture, hiPS cells maintained their typical morphology upon re-plating, exhibited pluripotency-associated marker expression as well as tri-lineage differentiation capability, which was verified by inducing their spontaneous differentiation through embryoid body formation, and subsequent downstream differentiation to specific lineages such as neural and cardiac fates was successfully accomplished. In conclusion, a scalable, robust and cost-effective xeno-free culture system was successfully developed and implemented for the scale-up production of hiPS cells. PMID:26999816

The non-human primate striatum undergoes marked prolonged remodeling during postnatal development

PubMed Central

Martin, Lee J.; Cork, Linda C.

2014-01-01

We examined the postnatal ontogeny of the striatum in rhesus monkeys (Macaca mulatta) to identify temporal and spatial patterns of histological and chemical maturation. Our goal was to determine whether this forebrain structure is developmentally static or dynamic in postnatal life. Brains from monkeys at 1 day, 1, 4, 6, 9, and 12 months of age (N = 12) and adult monkeys (N = 4) were analyzed. Nissl staining was used to assess striatal volume, cytoarchitecture, and apoptosis. Immunohistochemistry was used to localize and measure substance P (SP), leucine-enkephalin (LENK), tyrosine hydroxylase (TH), and calbindin D28 (CAL) immunoreactivities. Mature brain to body weight ratio was achieved at 4 months of age, and striatal volume increased from ∼1.2 to ∼1.4 cm3 during the first postnatal year. Nissl staining identified, prominently in the caudate nucleus, developmentally persistent discrete cell islands with neuronal densities greater than the surrounding striatal parenchyma (matrix). Losses in neuronal density were observed in island and matrix regions during maturation, and differential developmental programmed cell death was observed in islands and matrix regions. Immunohistochemistry revealed striking changes occurring postnatally in striatal chemical neuroanatomy. At birth, the immature dopaminergic nigrostriatal innervation was characterized by islands enriched in TH-immunoreactive puncta (putative terminals) in the neuropil; TH-enriched islands aligned completely with areas enriched in SP immunoreactivity but low in LENK immunoreactivity. These areas enriched in SP immunoreactivity but low in LENK immunoreactivity were identified as striosome and matrix areas, respectively, because CAL immunoreactivity clearly delineated these territories. SP, LENK, and CAL immunoreactivities appeared as positive neuronal cell bodies, processes, and puncta. The matrix compartment at birth contained relatively low TH-immunoreactive processes and few SP-positive neurons but was densely populated with LENK-immunoreactive neurons. The nucleus accumbens part of the ventral striatum also showed prominent differences in SP, LENK, and CAL immunoreactivities in shell and core territories. During 12 months of postnatal maturation salient changes occurred in neurotransmitter marker localization: TH-positive afferents densely innervated the matrix to exceed levels of immunoreactivity in the striosomes; SP immunoreactivity levels increased in the matrix; and LENK-immunoreactivity levels decreased in the matrix and increased in the striosomes. At 12 months of age, striatal chemoarchitecture was similar qualitatively to adult patterns, but quantitatively different in LENK and SP in caudate, putamen, and nucleus accumbens. This study shows for the first time that the rhesus monkey striatum requires more than 12 months after birth to develop an adult-like pattern of chemical neuroanatomy and that principal neurons within striosomes and matrix have different developmental programs for neuropeptide expression. We conclude that postnatal maturation of the striatal mosaic in primates is not static but, rather, is a protracted and dynamic process that requires many synchronous and compartment-selective changes in afferent innervation and in the expression of genes that regulate neuronal phenotypes. PMID:25294985

The Principle of Energetic Consistency

NASA Technical Reports Server (NTRS)

Cohn, Stephen E.

2009-01-01

A basic result in estimation theory is that the minimum variance estimate of the dynamical state, given the observations, is the conditional mean estimate. This result holds independently of the specifics of any dynamical or observation nonlinearity or stochasticity, requiring only that the probability density function of the state, conditioned on the observations, has two moments. For nonlinear dynamics that conserve a total energy, this general result implies the principle of energetic consistency: if the dynamical variables are taken to be the natural energy variables, then the sum of the total energy of the conditional mean and the trace of the conditional covariance matrix (the total variance) is constant between observations. Ensemble Kalman filtering methods are designed to approximate the evolution of the conditional mean and covariance matrix. For them the principle of energetic consistency holds independently of ensemble size, even with covariance localization. However, full Kalman filter experiments with advection dynamics have shown that a small amount of numerical dissipation can cause a large, state-dependent loss of total variance, to the detriment of filter performance. The principle of energetic consistency offers a simple way to test whether this spurious loss of variance limits ensemble filter performance in full-blown applications. The classical second-moment closure (third-moment discard) equations also satisfy the principle of energetic consistency, independently of the rank of the conditional covariance matrix. Low-rank approximation of these equations offers an energetically consistent, computationally viable alternative to ensemble filtering. Current formulations of long-window, weak-constraint, four-dimensional variational methods are designed to approximate the conditional mode rather than the conditional mean. Thus they neglect the nonlinear bias term in the second-moment closure equation for the conditional mean. The principle of energetic consistency implies that, to precisely the extent that growing modes are important in data assimilation, this term is also important.

Properties of networks with partially structured and partially random connectivity

NASA Astrophysics Data System (ADS)

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

2015-01-01

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

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.

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.

Temperature effect on mechanical and tribological characterization of Mg-SiC nanocomposite fabricated by high rate compaction

NASA Astrophysics Data System (ADS)

Majzoobi, G. H.; Rahmani, K.; Atrian, A.

2018-01-01

In this paper, dynamic compaction is employed to produce Mg-SiC nanocomposite samples using a mechanical drop hammer. Different volume fractions of SiC nano reinforcement and magnesium (Mg) micron-size powder as the matrix are mechanically milled and consolidated at different temperatures. It is found that with the increase of temperature the sintering requirements is satisfied and higher quality samples are fabricated. The density, hardness, compressive strength and the wear resistance of the compacted specimens are characterized in this work. It was found that by increasing the content of nano reinforcement, the relative density of the compacted samples decreases, whereas, the micro-hardness and the strength of the samples enhance. Furthermore, higher densification temperatures lead to density increase and hardness reduction. Additionally, it is found that the wear rate of the nanocomposite is increased remarkably by increasing the SiC nano reinforcement.

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...

Controlling Interfacial Dynamics: Covalent Bonding versus Physical Adsorption in Polymer Nanocomposites

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

Holt, Adam P.; Bocharova, Vera; Cheng, Shiwang

It is generally believed that the strength of the polymer nanoparticle interaction controls the modification of near-interface segmental mobility in polymer nanocomposites (PNCs). However, little is known about the effect of covalent bonding on the segmental dynamics and glass transition of matrix-free polymer-grafted nanoparticles (PGNs), especially when compared to PNCs. In this article, we directly compare the static and dynamic properties of poly(2-vinylpyridine)/silica-based nanocomposites with polymer chains either physically adsorbed (PNCs) or covalently bonded (PGNs) to identical silica nanoparticles (RNP = 12.5 nm) for three different molecular weight (MW) systems. Interestingly, when the MW of the matrix is as lowmore » as 6 kg/mol (RNP/Rg = 5.4) or as high as 140 kg/mol (RNP/Rg= 1.13), both small-angle X-ray scattering and broadband dielectric spectroscopy show similar static and dynamic properties for PNCs and PGNs. However, for the intermediate MW of 18 kg/mol (RNP/Rg = 3.16), the difference between physical adsorption and covalent bonding can be clearly identified in the static and dynamic properties of the interfacial layer. We ascribe the differences in the interfacial properties of PNCs and PGNs to changes in chain stretching, as quantified by self-consistent field theory calculations. These results demonstrate that the dynamic suppression at the interface is affected by the chain stretching; that is, it depends on the anisotropy of the segmental conformations, more so than the strength of the interaction, which suggests that the interfacial dynamics can be effectively tuned by the degree of stretching a parameter accessible from the MW or grafting density.« less

Controlling Interfacial Dynamics: Covalent Bonding versus Physical Adsorption in Polymer Nanocomposites

DOE PAGES

Holt, Adam P.; Bocharova, Vera; Cheng, Shiwang; ...

2016-06-23

It is generally believed that the strength of the polymer nanoparticle interaction controls the modification of near-interface segmental mobility in polymer nanocomposites (PNCs). However, little is known about the effect of covalent bonding on the segmental dynamics and glass transition of matrix-free polymer-grafted nanoparticles (PGNs), especially when compared to PNCs. In this article, we directly compare the static and dynamic properties of poly(2-vinylpyridine)/silica-based nanocomposites with polymer chains either physically adsorbed (PNCs) or covalently bonded (PGNs) to identical silica nanoparticles (RNP = 12.5 nm) for three different molecular weight (MW) systems. Interestingly, when the MW of the matrix is as lowmore » as 6 kg/mol (RNP/Rg = 5.4) or as high as 140 kg/mol (RNP/Rg= 1.13), both small-angle X-ray scattering and broadband dielectric spectroscopy show similar static and dynamic properties for PNCs and PGNs. However, for the intermediate MW of 18 kg/mol (RNP/Rg = 3.16), the difference between physical adsorption and covalent bonding can be clearly identified in the static and dynamic properties of the interfacial layer. We ascribe the differences in the interfacial properties of PNCs and PGNs to changes in chain stretching, as quantified by self-consistent field theory calculations. These results demonstrate that the dynamic suppression at the interface is affected by the chain stretching; that is, it depends on the anisotropy of the segmental conformations, more so than the strength of the interaction, which suggests that the interfacial dynamics can be effectively tuned by the degree of stretching a parameter accessible from the MW or grafting density.« less

Parallel scalability of Hartree-Fock calculations

NASA Astrophysics Data System (ADS)

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

2015-03-01

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

Effect of atomic spontaneous decay on entanglement in the generalized Jaynes-Cummings model

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

Hessian, H.A.; Obada, A.-S.F.; Mohamed, A.-B.A.

2010-03-15

Some aspects of the irreversible dynamics of a generalized Jaynes-Cummings model are addressed. By working in the dressed-state representation, it is possible to split the dynamics of the entanglement and coherence. The exact solution of the master equation in the case of a high-Q cavity with atomic decay is found. Effects of the atomic spontaneous decay on the temporal evolution of partial entropies of the atom or the field and the total entropy as a quantitative measure entanglement are elucidated. The degree of entanglement, through the sum of the negative eigenvalues of the partially transposed density matrix and the negativemore » mutual information has been studied and compared with other measures.« less

Vibrational and vibronic coherences in the dynamics of the FMO complex

NASA Astrophysics Data System (ADS)

Liu, Xiaomeng; Kühn, Oliver

2016-12-01

The coupled exciton-vibrational dynamics of a seven site Frenkel exciton model of the Fenna-Matthews-Olson (FMO) complex is investigated using a Quantum Master Equation approach. Thereby, one vibrational mode per monomer is treated explicitly as being part of the relevant system. Emphasis is put on the comparison of this model with that of a purely excitonic relevant system. Further, the effects of two different approximations to the exciton-vibrational basis are investigated, namely the one- and two-particle description. Analysis of the vibronic and vibrational density matrix in the site basis points to the importance of on- and inter-site coherences for the exciton transfer. Here, one- and two-particle approximations give rise to qualitatively different results.

Effects of lattice morphology upon reaction dynamics in matrix-isolated systems

NASA Astrophysics Data System (ADS)

Raff, Lionel M.

1992-11-01

The dynamics of the cis-d2-ethylene+F2 addition reaction and the subsequent reaction dynamics of the products isolated in vapor-deposited Ar matrices at 12 K are investigated using trajectory methods that incorporate nonstatistical sampling to enhance the reaction probabilities. The matrix-isolated cis-d2-ethylene+F2 system is generated using a combination of Monte Carlo, damped trajectory, and volume contraction methods. Transport effects of the bulk are simulated using the velocity reset procedure developed by Riley et al. [J. Chem. Phys. 88, 5934 (1988)]. The potential-energy hypersurface is the same as that employed in our previous investigations of the matrix-isolated, decomposition dynamics of 1,2-difluoroethane-d4 and the bimolecular cis-d2-ethylene+F2 system in face-centered-cubic (fcc) matrices [J. Chem. Phys. 93, 3160 (1990); 95, 8901 (1991)]. It is found that matrices generated by these methods are amorphous with numerous vacancies and other imperfections. On the average, there are approximately three vacancies about each lattice atom compared to the fcc crystal. The calculated lattice density is about 82% that for a bulk fcc Ar solid. Computed radial distribution functions resemble those expected for a liquid which exhibits some short-range order. The imperfections of the lattice remain even after substantial annealing at 50 K. The calculated energy relaxation rate to the lattice phonon modes in these amorphous matrices is about a factor of 4 less than that for a close-packed fcc lattice. The 1,2-difluoroethane product is formed primarily via an αβ-addition process, as is the case for fcc matrices. However, the prominence of this pathway is greatly reduced. The major process leading to a fluoroethylene elimination product in amorphous matrices involves an atomic addition mechanism. Such a reaction path accounts for 94% of the elimination reactions. The probability of internal rotation about the C■C double bond in the fluoroethylene product is increased fivefold over that for fcc lattices. The calculated stabilization/elimination product ratio, the cis/trans ratios of fluoroethylene products, and the HF/DF elimination ratio are all found to be in fair to good accord with the reported experimental data. It is concluded that accurate simulation of matrix-isolation experiments requires a matrix model that properly represents the lattice structure present in the experiments.

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.

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.

Density-based cluster algorithms for the identification of core sets

NASA Astrophysics Data System (ADS)

Lemke, Oliver; Keller, Bettina G.

2016-10-01

The core-set approach is a discretization method for Markov state models of complex molecular dynamics. Core sets are disjoint metastable regions in the conformational space, which need to be known prior to the construction of the core-set model. We propose to use density-based cluster algorithms to identify the cores. We compare three different density-based cluster algorithms: the CNN, the DBSCAN, and the Jarvis-Patrick algorithm. While the core-set models based on the CNN and DBSCAN clustering are well-converged, constructing core-set models based on the Jarvis-Patrick clustering cannot be recommended. In a well-converged core-set model, the number of core sets is up to an order of magnitude smaller than the number of states in a conventional Markov state model with comparable approximation error. Moreover, using the density-based clustering one can extend the core-set method to systems which are not strongly metastable. This is important for the practical application of the core-set method because most biologically interesting systems are only marginally metastable. The key point is to perform a hierarchical density-based clustering while monitoring the structure of the metric matrix which appears in the core-set method. We test this approach on a molecular-dynamics simulation of a highly flexible 14-residue peptide. The resulting core-set models have a high spatial resolution and can distinguish between conformationally similar yet chemically different structures, such as register-shifted hairpin structures.

Matrix viscoplasticity and its shielding by active mechanics in microtissue models: experiments and mathematical modeling

NASA Astrophysics Data System (ADS)

Liu, Alan S.; Wang, Hailong; Copeland, Craig R.; Chen, Christopher S.; Shenoy, Vivek B.; Reich, Daniel H.

2016-09-01

The biomechanical behavior of tissues under mechanical stimulation is critically important to physiological function. We report a combined experimental and modeling study of bioengineered 3D smooth muscle microtissues that reveals a previously unappreciated interaction between active cell mechanics and the viscoplastic properties of the extracellular matrix. The microtissues’ response to stretch/unstretch actuations, as probed by microcantilever force sensors, was dominated by cellular actomyosin dynamics. However, cell lysis revealed a viscoplastic response of the underlying model collagen/fibrin matrix. A model coupling Hill-type actomyosin dynamics with a plastic perfectly viscoplastic description of the matrix quantitatively accounts for the microtissue dynamics, including notably the cells’ shielding of the matrix plasticity. Stretch measurements of single cells confirmed the active cell dynamics, and were well described by a single-cell version of our model. These results reveal the need for new focus on matrix plasticity and its interactions with active cell mechanics in describing tissue dynamics.

Matrix viscoplasticity and its shielding by active mechanics in microtissue models: experiments and mathematical modeling

PubMed Central

Liu, Alan S.; Wang, Hailong; Copeland, Craig R.; Chen, Christopher S.; Shenoy, Vivek B.; Reich, Daniel H.

2016-01-01

The biomechanical behavior of tissues under mechanical stimulation is critically important to physiological function. We report a combined experimental and modeling study of bioengineered 3D smooth muscle microtissues that reveals a previously unappreciated interaction between active cell mechanics and the viscoplastic properties of the extracellular matrix. The microtissues’ response to stretch/unstretch actuations, as probed by microcantilever force sensors, was dominated by cellular actomyosin dynamics. However, cell lysis revealed a viscoplastic response of the underlying model collagen/fibrin matrix. A model coupling Hill-type actomyosin dynamics with a plastic perfectly viscoplastic description of the matrix quantitatively accounts for the microtissue dynamics, including notably the cells’ shielding of the matrix plasticity. Stretch measurements of single cells confirmed the active cell dynamics, and were well described by a single-cell version of our model. These results reveal the need for new focus on matrix plasticity and its interactions with active cell mechanics in describing tissue dynamics. PMID:27671239

Statistical inference for noisy nonlinear ecological dynamic systems.

PubMed

Wood, Simon N

2010-08-26

Chaotic ecological dynamic systems defy conventional statistical analysis. Systems with near-chaotic dynamics are little better. Such systems are almost invariably driven by endogenous dynamic processes plus demographic and environmental process noise, and are only observable with error. Their sensitivity to history means that minute changes in the driving noise realization, or the system parameters, will cause drastic changes in the system trajectory. This sensitivity is inherited and amplified by the joint probability density of the observable data and the process noise, rendering it useless as the basis for obtaining measures of statistical fit. Because the joint density is the basis for the fit measures used by all conventional statistical methods, this is a major theoretical shortcoming. The inability to make well-founded statistical inferences about biological dynamic models in the chaotic and near-chaotic regimes, other than on an ad hoc basis, leaves dynamic theory without the methods of quantitative validation that are essential tools in the rest of biological science. Here I show that this impasse can be resolved in a simple and general manner, using a method that requires only the ability to simulate the observed data on a system from the dynamic model about which inferences are required. The raw data series are reduced to phase-insensitive summary statistics, quantifying local dynamic structure and the distribution of observations. Simulation is used to obtain the mean and the covariance matrix of the statistics, given model parameters, allowing the construction of a 'synthetic likelihood' that assesses model fit. This likelihood can be explored using a straightforward Markov chain Monte Carlo sampler, but one further post-processing step returns pure likelihood-based inference. I apply the method to establish the dynamic nature of the fluctuations in Nicholson's classic blowfly experiments.

Fibonacci family of dynamical universality classes.

PubMed

Popkov, Vladislav; Schadschneider, Andreas; Schmidt, Johannes; Schütz, Gunter M

2015-10-13

Universality is a well-established central concept of equilibrium physics. However, in systems far away from equilibrium, a deeper understanding of its underlying principles is still lacking. Up to now, a few classes have been identified. Besides the diffusive universality class with dynamical exponent [Formula: see text], another prominent example is the superdiffusive Kardar-Parisi-Zhang (KPZ) class with [Formula: see text]. It appears, e.g., in low-dimensional dynamical phenomena far from thermal equilibrium that exhibit some conservation law. Here we show that both classes are only part of an infinite discrete family of nonequilibrium universality classes. Remarkably, their dynamical exponents [Formula: see text] are given by ratios of neighboring Fibonacci numbers, starting with either [Formula: see text] (if a KPZ mode exist) or [Formula: see text] (if a diffusive mode is present). If neither a diffusive nor a KPZ mode is present, all dynamical modes have the Golden Mean [Formula: see text] as dynamical exponent. The universal scaling functions of these Fibonacci modes are asymmetric Lévy distributions that are completely fixed by the macroscopic current density relation and compressibility matrix of the system and hence accessible to experimental measurement.

Practical implementation of tetrahedral mesh reconstruction in emission tomography

PubMed Central

Boutchko, R.; Sitek, A.; Gullberg, G. T.

2014-01-01

This paper presents a practical implementation of image reconstruction on tetrahedral meshes optimized for emission computed tomography with parallel beam geometry. Tetrahedral mesh built on a point cloud is a convenient image representation method, intrinsically three-dimensional and with a multi-level resolution property. Image intensities are defined at the mesh nodes and linearly interpolated inside each tetrahedron. For the given mesh geometry, the intensities can be computed directly from tomographic projections using iterative reconstruction algorithms with a system matrix calculated using an exact analytical formula. The mesh geometry is optimized for a specific patient using a two stage process. First, a noisy image is reconstructed on a finely-spaced uniform cloud. Then, the geometry of the representation is adaptively transformed through boundary-preserving node motion and elimination. Nodes are removed in constant intensity regions, merged along the boundaries, and moved in the direction of the mean local intensity gradient in order to provide higher node density in the boundary regions. Attenuation correction and detector geometric response are included in the system matrix. Once the mesh geometry is optimized, it is used to generate the final system matrix for ML-EM reconstruction of node intensities and for visualization of the reconstructed images. In dynamic PET or SPECT imaging, the system matrix generation procedure is performed using a quasi-static sinogram, generated by summing projection data from multiple time frames. This system matrix is then used to reconstruct the individual time frame projections. Performance of the new method is evaluated by reconstructing simulated projections of the NCAT phantom and the method is then applied to dynamic SPECT phantom and patient studies and to a dynamic microPET rat study. Tetrahedral mesh-based images are compared to the standard voxel-based reconstruction for both high and low signal-to-noise ratio projection datasets. The results demonstrate that the reconstructed images represented as tetrahedral meshes based on point clouds offer image quality comparable to that achievable using a standard voxel grid while allowing substantial reduction in the number of unknown intensities to be reconstructed and reducing the noise. PMID:23588373

Practical implementation of tetrahedral mesh reconstruction in emission tomography

NASA Astrophysics Data System (ADS)

Boutchko, R.; Sitek, A.; Gullberg, G. T.

2013-05-01

This paper presents a practical implementation of image reconstruction on tetrahedral meshes optimized for emission computed tomography with parallel beam geometry. Tetrahedral mesh built on a point cloud is a convenient image representation method, intrinsically three-dimensional and with a multi-level resolution property. Image intensities are defined at the mesh nodes and linearly interpolated inside each tetrahedron. For the given mesh geometry, the intensities can be computed directly from tomographic projections using iterative reconstruction algorithms with a system matrix calculated using an exact analytical formula. The mesh geometry is optimized for a specific patient using a two stage process. First, a noisy image is reconstructed on a finely-spaced uniform cloud. Then, the geometry of the representation is adaptively transformed through boundary-preserving node motion and elimination. Nodes are removed in constant intensity regions, merged along the boundaries, and moved in the direction of the mean local intensity gradient in order to provide higher node density in the boundary regions. Attenuation correction and detector geometric response are included in the system matrix. Once the mesh geometry is optimized, it is used to generate the final system matrix for ML-EM reconstruction of node intensities and for visualization of the reconstructed images. In dynamic PET or SPECT imaging, the system matrix generation procedure is performed using a quasi-static sinogram, generated by summing projection data from multiple time frames. This system matrix is then used to reconstruct the individual time frame projections. Performance of the new method is evaluated by reconstructing simulated projections of the NCAT phantom and the method is then applied to dynamic SPECT phantom and patient studies and to a dynamic microPET rat study. Tetrahedral mesh-based images are compared to the standard voxel-based reconstruction for both high and low signal-to-noise ratio projection datasets. The results demonstrate that the reconstructed images represented as tetrahedral meshes based on point clouds offer image quality comparable to that achievable using a standard voxel grid while allowing substantial reduction in the number of unknown intensities to be reconstructed and reducing the noise.

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.

Rheological principles of development hetero-modulus and hetero-viscous complex materials with extreme dynamic strength

NASA Astrophysics Data System (ADS)

Gömze, L. A.; Gömze, L. N.

2017-02-01

Materials with different crystalline and morphological compositions have different chemical, physical, mechanical and rheological properties, including wear protection, melting temperature, module of elasticity and viscosity. Examining the material structures and behaviors of differentceramic bodies and CMCs under high speed collisions in several years the authors have understood the advantages of hetero-modulus and hetero-viscous complex material systems to absorb and dissipate the kinetic energy of objects during high speed collisions. Applying the rheo-mechanical principles the authors successfully developed a new family of hetero-modulus and hetero-viscous alumina matrix composite materials with extreme mechanical properties including dynamic strength. These new corundum-matrix composite materials reinforced with Si2ON 2, Si3N4 , SiAlON and AlN submicron and nanoparticles have excellent dynamic strength during collisions with high density metallic bodies with speeds about 1000 m/sec or more. At the same time in the alumina matrix composites can be observed a phase transformation of submicron and nanoparticles of alpha and beta silicone-nitride crystals into cubicc-Si3N4 diamond-like particles can be observed, when the high speed collision processes are taken place in vacuum or oxygen-free atmosphere. Using the rheological principles and the energy engorgement by fractures, heating and melting of components the authors successfully developed several new hetero-modulus, hetero-viscous and hetero-plastic complex materials. These materials generally are based on ceramic matrixes and components having different melting temperatures and modules of elasticity from low values like carbon and light metals (Mg, Al, Ti, Si) up to very high values like boride, nitride and carbide ceramics. Analytical methods applied in this research were scanning electron microscopy, X-ray diffractions and energy dispersive spectrometry. Digital image analysis was applied to microscopy results to enhance the results of transformations.

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.

Preparation and Dynamic Mechanical Properties at Elevated Temperatures of a Tungsten/Glass Composite

NASA Astrophysics Data System (ADS)

Gao, Chong; Wang, Yingchun; Ma, Xueya; Liu, Keyi; Wang, Yubing; Li, Shukui; Cheng, Xingwang

2018-03-01

Experiments were conducted to prepare a borosilicate glass matrix composite containing 50 vol.% tungsten and examine its dynamic compressive behavior at elevated temperatures in the range of 450-775 °C. The results show that the homogenous microstructure of the tungsten/glass composite with relative density of 97% can be obtained by hot-pressing sintering at 800 °C for 1 h under pressure of 30 MPa. Dynamic compressive testing was carried out by a separate Hopkinson pressure bar system with a synchronous device. The results show that the peak stress decreases and the composite transforms from brittle to ductile in nature with testing temperature increasing from 450 to 750 °C. The brittle-ductile transition temperature is about 500 °C. Over 775 °C, the composite loses load-bearing capacity totally because of the excessive softening of the glass phase. In addition, the deformation and failure mechanism were analyzed.

High temperature phonon dispersion in graphene using classical molecular dynamics

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

Anees, P., E-mail: anees@igcar.gov.in; Panigrahi, B. K.; Valsakumar, M. C., E-mail: anees@igcar.gov.in

2014-04-24

Phonon dispersion and phonon density of states of graphene are calculated using classical molecular dynamics simulations. In this method, the dynamical matrix is constructed based on linear response theory by computing the displacement of atoms during the simulations. The computed phonon dispersions show excellent agreement with experiments. The simulations are done in both NVT and NPT ensembles at 300 K and found that the LO/TO modes are getting hardened at the Γ point. The NPT ensemble simulations capture the anharmonicity of the crystal accurately and the hardening of LO/TO modes is more pronounced. We also found that at 300 Kmore » the C-C bond length reduces below the equilibrium value and the ZA bending mode frequency becomes imaginary close to Γ along K-Γ direction, which indicates instability of the flat 2D graphene sheets.« less

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.

In vitro cartilage construct generation from silk fibroin- chitosan porous scaffold and umbilical cord blood derived human mesenchymal stem cells in dynamic culture condition.

PubMed

Agrawal, Parinita; Pramanik, Krishna; Biswas, Amit; Ku Patra, Ranjan

2018-02-01

Cartilage construct generation includes a scaffold with appropriate composition to mimic matrix of the damaged tissue on which the stem cells grow and differentiate. In this study, umbilical cord blood (UCB) derived human mesenchymal stem cells (hMSCs) were seeded on freeze dried porous silk-fibroin (SF)/chitosan (CS) scaffolds. Influence of static and dynamic (spinner flask bioreactor) culture conditions on the developing cartilage construct were studied by in-vitro characterization for viability, proliferation, distribution, and chondrogenic differentiation of hMSCs over the scaffold. Constructs developed in spinner flask consisted of 62% live cells, and exhibited 543% more cell density at the core than constructs cultured in static system. Quantification of DNA and glycosaminoglycans accumulation after 21 days showed the progression of chondrogenic differentiation of hMSCs was higher in dynamic culture compared to static one. In constructs generated under dynamic condition, histology staining for proteoglycan matrix, and fluorescence staining for collagen-II and aggrecan showed positive correlation between early and late stage chondrogenic markers, which was further confirmed by quantitative PCR analysis, showing low collagen-I expression and highly expressed Sox9, collagen-II and aggrecan. The present study demonstrated that construct generated by combining 3D SF/CS scaffold with UCB-hMSCs under dynamic condition using spinner flask bioreactor can be used for cartilage tissue regeneration for future medical treatments. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 106A: 397-407, 2018. © 2017 Wiley Periodicals, Inc.

A propagator matrix method for the Rayleigh-Taylor instability of multiple layers: a case study on crustal delamination in the early Earth

NASA Astrophysics Data System (ADS)

Mondal, Puskar; Korenaga, Jun

2018-03-01

The dispersion relation of the Rayleigh-Taylor instability, a gravitational instability associated with unstable density stratification, is of profound importance in various geophysical contexts. When more than two layers are involved, a semi-analytical technique based on the biharmonic formulation of Stokes flow has been extensively used to obtain such dispersion relation. However, this technique may become cumbersome when applied to lithospheric dynamics, where a number of layers are necessary to represent the continuous variation of viscosity over many orders of magnitude. Here, we present an alternative and more efficient method based on the propagator matrix formulation of Stokes flow. With this approach, the original instability problem is reduced to a compact eigenvalue equation whose size is solely determined by the number of primary density contrasts. We apply this new technique to the stability of the early crust, and combined with the Monte Carlo sensitivity analysis, we derive an empirical formula to compute the growth rate of the Rayleigh-Taylor instability for this particular geophysical setting. Our analysis indicates that the likelihood of crustal delamination hinges critically on the effective viscosity of eclogite.

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.

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)].

Surface-hopping dynamics and decoherence with quantum equilibrium structure.

PubMed

Grunwald, Robbie; Kim, Hyojoon; Kapral, Raymond

2008-04-28

In open quantum systems, decoherence occurs through interaction of a quantum subsystem with its environment. The computation of expectation values requires a knowledge of the quantum dynamics of operators and sampling from initial states of the density matrix describing the subsystem and bath. We consider situations where the quantum evolution can be approximated by quantum-classical Liouville dynamics and examine the circumstances under which the evolution can be reduced to surface-hopping dynamics, where the evolution consists of trajectory segments exclusively evolving on single adiabatic surfaces, with probabilistic hops between these surfaces. The justification for the reduction depends on the validity of a Markovian approximation on a bath averaged memory kernel that accounts for quantum coherence in the system. We show that such a reduction is often possible when initial sampling is from either the quantum or classical bath initial distributions. If the average is taken only over the quantum dispersion that broadens the classical distribution, then such a reduction is not always possible.

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).

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

Sechin, Ivan, E-mail: shnbuz@gmail.com, E-mail: zotov@mi.ras.ru; ITEP, B. Cheremushkinskaya Str. 25, Moscow 117218; Zotov, Andrei, E-mail: shnbuz@gmail.com, E-mail: zotov@mi.ras.ru

In this paper we propose versions of the associative Yang-Baxter equation and higher order R-matrix identities which can be applied to quantum dynamical R-matrices. As is known quantum non-dynamical R-matrices of Baxter-Belavin type satisfy this equation. Together with unitarity condition and skew-symmetry it provides the quantum Yang-Baxter equation and a set of identities useful for different applications in integrable systems. The dynamical R-matrices satisfy the Gervais-Neveu-Felder (or dynamical Yang-Baxter) equation. Relation between the dynamical and non-dynamical cases is described by the IRF (interaction-round-a-face)-Vertex transformation. An alternative approach to quantum (semi-)dynamical R-matrices and related quantum algebras was suggested by Arutyunov, Chekhov,more » and Frolov (ACF) in their study of the quantum Ruijsenaars-Schneider model. The purpose of this paper is twofold. First, we prove that the ACF elliptic R-matrix satisfies the associative Yang-Baxter equation with shifted spectral parameters. Second, we directly prove a simple relation of the IRF-Vertex type between the Baxter-Belavin and the ACF elliptic R-matrices predicted previously by Avan and Rollet. It provides the higher order R-matrix identities and an explanation of the obtained equations through those for non-dynamical R-matrices. As a by-product we also get an interpretation of the intertwining transformation as matrix extension of scalar theta function likewise R-matrix is interpreted as matrix extension of the Kronecker function. Relations to the Gervais-Neveu-Felder equation and identities for the Felder’s elliptic R-matrix are also discussed.« less

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

PubMed

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

2010-06-01

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

Analysis of Nonlinear Dynamics by Square Matrix Method

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

Yu, Li Hua

The nonlinear dynamics of a system with periodic structure can be analyzed using a square matrix. In this paper, we show that because the special property of the square matrix constructed for nonlinear dynamics, we can reduce the dimension of the matrix from the original large number for high order calculation to low dimension in the first step of the analysis. Then a stable Jordan decomposition is obtained with much lower dimension. The transformation to Jordan form provides an excellent action-angle approximation to the solution of the nonlinear dynamics, in good agreement with trajectories and tune obtained from tracking. Andmore » more importantly, the deviation from constancy of the new action-angle variable provides a measure of the stability of the phase space trajectories and their tunes. Thus the square matrix provides a novel method to optimize the nonlinear dynamic system. The method is illustrated by many examples of comparison between theory and numerical simulation. Finally, in particular, we show that the square matrix method can be used for optimization to reduce the nonlinearity of a system.« less

An updated Lagrangian discontinuous Galerkin hydrodynamic method for gas dynamics

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

Wu, Tong; Shashkov, Mikhail Jurievich; Morgan, Nathaniel Ray

Here, we present a new Lagrangian discontinuous Galerkin (DG) hydrodynamic method for gas dynamics. The new method evolves conserved unknowns in the current configuration, which obviates the Jacobi matrix that maps the element in a reference coordinate system or the initial coordinate system to the current configuration. The density, momentum, and total energy (ρ, ρu, E) are approximated with conservative higher-order Taylor expansions over the element and are limited toward a piecewise constant field near discontinuities using a limiter. Two new limiting methods are presented for enforcing the bounds on the primitive variables of density, velocity, and specific internal energymore » (ρ, u, e). The nodal velocity, and the corresponding forces, are calculated by solving an approximate Riemann problem at the element nodes. An explicit second-order method is used to temporally advance the solution. This new Lagrangian DG hydrodynamic method conserves mass, momentum, and total energy. 1D Cartesian coordinates test problem results are presented to demonstrate the accuracy and convergence order of the new DG method with the new limiters.« less

Current reversals and metastable states in the infinite Bose-Hubbard chain with local particle loss

NASA Astrophysics Data System (ADS)

Kiefer-Emmanouilidis, M.; Sirker, J.

2017-12-01

We present an algorithm which combines the quantum trajectory approach to open quantum systems with a density-matrix renormalization-group scheme for infinite one-dimensional lattice systems. We apply this method to investigate the long-time dynamics in the Bose-Hubbard model with local particle loss starting from a Mott-insulating initial state with one boson per site. While the short-time dynamics can be described even quantitatively by an equation of motion (EOM) approach at the mean-field level, many-body interactions lead to unexpected effects at intermediate and long times: local particle currents far away from the dissipative site start to reverse direction ultimately leading to a metastable state with a total particle current pointing away from the lossy site. An alternative EOM approach based on an effective fermion model shows that the reversal of currents can be understood qualitatively by the creation of holon-doublon pairs at the edge of the region of reduced particle density. The doublons are then able to escape while the holes move towards the dissipative site, a process reminiscent—in a loose sense—of Hawking radiation.

Pairing from dynamically screened Coulomb repulsion in bismuth

NASA Astrophysics Data System (ADS)

Ruhman, Jonathan; Lee, Patrick A.

2017-12-01

Recently, Prakash et al. have discovered bulk superconductivity in single crystals of bismuth, which is a semimetal with extremely low carrier density. At such low density, we argue that conventional electron-phonon coupling is too weak to be responsible for the binding of electrons into Cooper pairs. We study a dynamically screened Coulomb interaction with effective attraction generated on the scale of the collective plasma modes. We model the electronic states in bismuth to include three Dirac pockets with high velocity and one hole pocket with a significantly smaller velocity. We find a weak-coupling instability, which is greatly enhanced by the presence of the hole pocket. Therefore we argue that bismuth is the first material to exhibit superconductivity driven by retardation effects of Coulomb repulsion alone. By using realistic parameters for bismuth we find that the acoustic plasma mode does not play the central role in pairing. We also discuss a matrix element effect, resulting from the Dirac nature of the conduction band, which may affect Tc in the s -wave channel without breaking time-reversal symmetry.

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.).

An updated Lagrangian discontinuous Galerkin hydrodynamic method for gas dynamics

DOE PAGES

Wu, Tong; Shashkov, Mikhail Jurievich; Morgan, Nathaniel Ray; ...

2018-04-09

Here, we present a new Lagrangian discontinuous Galerkin (DG) hydrodynamic method for gas dynamics. The new method evolves conserved unknowns in the current configuration, which obviates the Jacobi matrix that maps the element in a reference coordinate system or the initial coordinate system to the current configuration. The density, momentum, and total energy (ρ, ρu, E) are approximated with conservative higher-order Taylor expansions over the element and are limited toward a piecewise constant field near discontinuities using a limiter. Two new limiting methods are presented for enforcing the bounds on the primitive variables of density, velocity, and specific internal energymore » (ρ, u, e). The nodal velocity, and the corresponding forces, are calculated by solving an approximate Riemann problem at the element nodes. An explicit second-order method is used to temporally advance the solution. This new Lagrangian DG hydrodynamic method conserves mass, momentum, and total energy. 1D Cartesian coordinates test problem results are presented to demonstrate the accuracy and convergence order of the new DG method with the new limiters.« less

Detecting Damage in Ceramic Matrix Composites Using Electrical Resistance

NASA Technical Reports Server (NTRS)

Smith, Craig E.; Gyekenyesi, Andrew

2011-01-01

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

Detecting Cracks in Ceramic Matrix Composites by Electrical Resistance

NASA Technical Reports Server (NTRS)

Smith, Craig; Gyekenyesi, Andrew

2011-01-01

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

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

NASA Astrophysics Data System (ADS)

Roehl, Jan Hendrik; Oberrath, Jens

2016-09-01

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

Stability analysis of BWR nuclear-coupled thermal-hyraulics using a simple model

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

Karve, A.A.; Rizwan-uddin; Dorning, J.J.

1995-09-01

A simple mathematical model is developed to describe the dynamics of the nuclear-coupled thermal-hydraulics in a boiling water reactor (BWR) core. The model, which incorporates the essential features of neutron kinetics, and single-phase and two-phase thermal-hydraulics, leads to simple dynamical system comprised of a set of nonlinear ordinary differential equations (ODEs). The stability boundary is determined and plotted in the inlet-subcooling-number (enthalpy)/external-reactivity operating parameter plane. The eigenvalues of the Jacobian matrix of the dynamical system also are calculated at various steady-states (fixed points); the results are consistent with those of the direct stability analysis and indicate that a Hopf bifurcationmore » occurs as the stability boundary in the operating parameter plane is crossed. Numerical simulations of the time-dependent, nonlinear ODEs are carried out for selected points in the operating parameter plane to obtain the actual damped and growing oscillations in the neutron number density, the channel inlet flow velocity, and the other phase variables. These indicate that the Hopf bifurcation is subcritical, hence, density wave oscillations with growing amplitude could result from a finite perturbation of the system even where the steady-state is stable. The power-flow map, frequently used by reactor operators during start-up and shut-down operation of a BWR, is mapped to the inlet-subcooling-number/neutron-density (operating-parameter/phase-variable) plane, and then related to the stability boundaries for different fixed inlet velocities corresponding to selected points on the flow-control line. The stability boundaries for different fixed inlet subcooling numbers corresponding to those selected points, are plotted in the neutron-density/inlet-velocity phase variable plane and then the points on the flow-control line are related to their respective stability boundaries in this plane.« less

K* vector meson resonance dynamics in heavy-ion collisions

NASA Astrophysics Data System (ADS)

Ilner, Andrej; Cabrera, Daniel; Markert, Christina; Bratkovskaya, Elena

2017-01-01

We study the strange vector meson (K*,K¯* ) dynamics in relativistic heavy-ion collisions based on the microscopic parton-hadron-string dynamics (PHSD) transport approach which incorporates partonic and hadronic degrees of freedom, a phase transition from hadronic to partonic matter—quark-gluon-plasma (QGP)—and a dynamical hadronization of quarks and antiquarks as well as final hadronic interactions. We investigate the role of in-medium effects on the K*,K¯* meson dynamics by employing Breit-Wigner spectral functions for the K* with self-energies obtained from a self-consistent coupled-channel G -matrix approach. Furthermore, we confront the PHSD calculations with experimental data for p +p , Cu+Cu , and Au+Au collisions at energies up to √{sN N}=200 GeV. Our analysis shows that, at relativistic energies, most of the final K* (observed experimentally) are produced during the late hadronic phase, dominantly by the K +π →K* channel, such that the fraction of the K* from the QGP is small and can hardly be reconstructed from the final observables. The influence of the in-medium effects on the K* dynamics at energies typical of the BNL Relativistic Heavy Ion Collider is rather modest due to their dominant production at low baryon densities (but high meson densities); however, it increases with decreasing beam energy. Moreover, we find that the additional cut on the invariant-mass region of the K* further influences the shape and the height of the final spectra. This imposes severe constraints on the interpretation of the experimental results.

Dynamic Manipulation of Hydrogels to Control Cell Behavior: A Review

PubMed Central

Vats, Kanika

2013-01-01

For many tissue engineering applications and studies to understand how materials fundamentally affect cellular functions, it is important to have the ability to synthesize biomaterials that can mimic elements of native cell–extracellular matrix interactions. Hydrogels possess many properties that are desirable for studying cell behavior. For example, hydrogels are biocompatible and can be biochemically and mechanically altered by exploiting the presentation of cell adhesive epitopes or by changing hydrogel crosslinking density. To establish physical and biochemical tunability, hydrogels can be engineered to alter their properties upon interaction with external driving forces such as pH, temperature, electric current, as well as exposure to cytocompatible irradiation. Additionally, hydrogels can be engineered to respond to enzymes secreted by cells, such as matrix metalloproteinases and hyaluronidases. This review details different strategies and mechanisms by which biomaterials, specifically hydrogels, can be manipulated dynamically to affect cell behavior. By employing the appropriate combination of stimuli and hydrogel composition and architecture, cell behavior such as adhesion, migration, proliferation, and differentiation can be controlled in real time. This three-dimensional control in cell behavior can help create programmable cell niches that can be useful for fundamental cell studies and in a variety of tissue engineering applications. PMID:23541134

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

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.

Dynamics of open quantum systems by interpolation of von Neumann and classical master equations, and its application to quantum annealing

NASA Astrophysics Data System (ADS)

Kadowaki, Tadashi

2018-02-01

We propose a method to interpolate dynamics of von Neumann and classical master equations with an arbitrary mixing parameter to investigate the thermal effects in quantum dynamics. The two dynamics are mixed by intervening to continuously modify their solutions, thus coupling them indirectly instead of directly introducing a coupling term. This maintains the quantum system in a pure state even after the introduction of thermal effects and obtains not only a density matrix but also a state vector representation. Further, we demonstrate that the dynamics of a two-level system can be rewritten as a set of standard differential equations, resulting in quantum dynamics that includes thermal relaxation. These equations are equivalent to the optical Bloch equations at the weak coupling and asymptotic limits, implying that the dynamics cause thermal effects naturally. Numerical simulations of ferromagnetic and frustrated systems support this idea. Finally, we use this method to study thermal effects in quantum annealing, revealing nontrivial performance improvements for a spin glass model over a certain range of annealing time. This result may enable us to optimize the annealing time of real annealing machines.

Exploring the nonequilibrium dynamics of ultracold quantum gases by using numerical tools

NASA Astrophysics Data System (ADS)

Heidrich-Meisner, Fabian

Numerical tools such as exact diagonalization or the density matrix renormalization group method have been vital for the study of the nonequilibrium dynamics of strongly correlated many-body systems. Moreover, they provided unique insight for the interpretation of quantum gas experiments, whenever a direct comparison with theory is possible. By considering the example of the experiment by Ronzheimer et al., in which both an interaction quench and the release of bosons from a trap into an empty optical lattice (sudden expansion) was realized, I discuss several nonequilibrium effects of strongly interacting quantum gases. These include the thermalization of a closed quantum system and its connection to the eigenstate thermalization hypothesis, nonequilibrium mass transport, dynamical fermionization, and transient phenomena such as quantum distillation or dynamical quasicondensation. I highlight the role of integrability in giving rise to ballistic transport in strongly interacting 1D systems and in determining the asymptotic state after a quantum quench. The talk concludes with a perspective on open questions concerning 2D systems and the numerical simulation of their nonequilibrium dynamics. Supported by Deutsche Forschungsgemeinschaft (DFG) via FOR 801.

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.

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.

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

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.

Off-stoichiometric defect clustering in irradiated oxides

NASA Astrophysics Data System (ADS)

Khalil, Sarah; Allen, Todd; EL-Azab, Anter

2017-04-01

A cluster dynamics model describing the formation of vacancy and interstitial clusters in irradiated oxides has been developed. The model, which tracks the composition of the oxide matrix and the defect clusters, was applied to the early stage formation of voids and dislocation loops in UO2, and the effects of irradiation temperature and dose rate on the evolution of their densities and composition was investigated. The results show that Frenkel defects dominate the nucleation process in irradiated UO2. The results also show that oxygen vacancies drive vacancy clustering while the migration energy of uranium vacancies is a rate-limiting factor for the nucleation and growth of voids. In a stoichiometric UO2 under irradiation, off-stoichiometric vacancy clusters exist with a higher concentration of hyper-stoichiometric clusters. Similarly, off-stoichiometric interstitial clusters form with a higher concentration of hyper-stoichiometric clusters. The UO2 matrix was found to be hyper-stoichiometric due to the accumulation of uranium vacancies.

Correlated matrix-fluctuation-mediated activated transport of dilute penetrants in glass-forming liquids and suspensions

NASA Astrophysics Data System (ADS)

Zhang, Rui; Schweizer, Kenneth S.

2017-05-01

We formulate a microscopic, force-level statistical mechanical theory for the activated diffusion of dilute penetrants in dense liquids, colloidal suspensions, and glasses. The approach explicitly and self-consistently accounts for coupling between penetrant hopping and matrix dynamic displacements that actively facilitate the hopping event. The key new ideas involve two mechanistically (at a stochastic trajectory level) coupled dynamic free energy functions for the matrix and spherical penetrant particles. A single dynamic coupling parameter quantifies how much the matrix displaces relative to the penetrant when the latter reaches its transition state which is determined via the enforcement of a temporal causality or coincidence condition. The theory is implemented for dilute penetrants smaller than the matrix particles, with or without penetrant-matrix attractive forces. Model calculations reveal a rich dependence of the penetrant diffusion constant and degree of dynamic coupling on size ratio, volume fraction, and attraction strength. In the absence of attractions, a near exponential decrease of penetrant diffusivity with size ratio over an intermediate range is predicted, in contrast to the much steeper, non-exponential variation if one assumes local matrix dynamical fluctuations are not correlated with penetrant motion. For sticky penetrants, the relative and absolute influence of caging versus physical bond formation is studied. The conditions for a dynamic crossover from the case where a time scale separation between penetrant and matrix activated hopping exists to a "slaved" or "constraint release" fully coupled regime are determined. The particle mixture model is mapped to treat experimental thermal systems and applied to make predictions for the diffusivity of water, toluene, methanol, and oxygen in polyvinylacetate liquids and glasses. The theory agrees well with experiment with values of the penetrant-matrix size ratio close to their chemically intuitive values.

Correlated matrix-fluctuation-mediated activated transport of dilute penetrants in glass-forming liquids and suspensions

PubMed Central

Schweizer, Kenneth S.

2017-01-01

We formulate a microscopic, force-level statistical mechanical theory for the activated diffusion of dilute penetrants in dense liquids, colloidal suspensions, and glasses. The approach explicitly and self-consistently accounts for coupling between penetrant hopping and matrix dynamic displacements that actively facilitate the hopping event. The key new ideas involve two mechanistically (at a stochastic trajectory level) coupled dynamic free energy functions for the matrix and spherical penetrant particles. A single dynamic coupling parameter quantifies how much the matrix displaces relative to the penetrant when the latter reaches its transition state which is determined via the enforcement of a temporal causality or coincidence condition. The theory is implemented for dilute penetrants smaller than the matrix particles, with or without penetrant-matrix attractive forces. Model calculations reveal a rich dependence of the penetrant diffusion constant and degree of dynamic coupling on size ratio, volume fraction, and attraction strength. In the absence of attractions, a near exponential decrease of penetrant diffusivity with size ratio over an intermediate range is predicted, in contrast to the much steeper, non-exponential variation if one assumes local matrix dynamical fluctuations are not correlated with penetrant motion. For sticky penetrants, the relative and absolute influence of caging versus physical bond formation is studied. The conditions for a dynamic crossover from the case where a time scale separation between penetrant and matrix activated hopping exists to a “slaved” or “constraint release” fully coupled regime are determined. The particle mixture model is mapped to treat experimental thermal systems and applied to make predictions for the diffusivity of water, toluene, methanol, and oxygen in polyvinylacetate liquids and glasses. The theory agrees well with experiment with values of the penetrant-matrix size ratio close to their chemically intuitive values. PMID:28527449

Dynamic heterogeneities and non-Gaussian behavior in two-dimensional randomly confined colloidal fluids

NASA Astrophysics Data System (ADS)

Schnyder, Simon K.; Skinner, Thomas O. E.; Thorneywork, Alice L.; Aarts, Dirk G. A. L.; Horbach, Jürgen; Dullens, Roel P. A.

2017-03-01

A binary mixture of superparamagnetic colloidal particles is confined between glass plates such that the large particles become fixed and provide a two-dimensional disordered matrix for the still mobile small particles, which form a fluid. By varying fluid and matrix area fractions and tuning the interactions between the superparamagnetic particles via an external magnetic field, different regions of the state diagram are explored. The mobile particles exhibit delocalized dynamics at small matrix area fractions and localized motion at high matrix area fractions, and the localization transition is rounded by the soft interactions [T. O. E. Skinner et al., Phys. Rev. Lett. 111, 128301 (2013), 10.1103/PhysRevLett.111.128301]. Expanding on previous work, we find the dynamics of the tracers to be strongly heterogeneous and show that molecular dynamics simulations of an ideal gas confined in a fixed matrix exhibit similar behavior. The simulations show how these soft interactions make the dynamics more heterogeneous compared to the disordered Lorentz gas and lead to strong non-Gaussian fluctuations.

Extracellular matrix-associated proteins form an integral and dynamic system during Pseudomonas aeruginosa biofilm development.

PubMed

Zhang, Weipeng; Sun, Jin; Ding, Wei; Lin, Jinshui; Tian, Renmao; Lu, Liang; Liu, Xiaofen; Shen, Xihui; Qian, Pei-Yuan

2015-01-01

Though the essential role of extracellular matrix in biofilm development has been extensively documented, the function of matrix-associated proteins is elusive. Determining the dynamics of matrix-associated proteins would be a useful way to reveal their functions in biofilm development. Therefore, we applied iTRAQ-based quantitative proteomics to evaluate matrix-associated proteins isolated from different phases of Pseudomonas aeruginosa ATCC27853 biofilms. Among the identified 389 proteins, 54 changed their abundance significantly. The increased abundance of stress resistance and nutrient metabolism-related proteins over the period of biofilm development was consistent with the hypothesis that biofilm matrix forms micro-environments in which cells are optimally organized to resist stress and use available nutrients. Secreted proteins, including novel putative effectors of the type III secretion system were identified, suggesting that the dynamics of pathogenesis-related proteins in the matrix are associated with biofilm development. Interestingly, there was a good correlation between the abundance changes of matrix-associated proteins and their expression. Further analysis revealed complex interactions among these modulated proteins, and the mutation of selected proteins attenuated biofilm development. Collectively, this work presents the first dynamic picture of matrix-associated proteins during biofilm development, and provides evidences that the matrix-associated proteins may form an integral and well regulated system that contributes to stress resistance, nutrient acquisition, pathogenesis and the stability of the biofilm.

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

NASA Technical Reports Server (NTRS)

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

1997-01-01

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

Active tissue stiffness modulation controls valve interstitial cell phenotype and osteogenic potential in 3D culture.

PubMed

Duan, Bin; Yin, Ziying; Hockaday Kang, Laura; Magin, Richard L; Butcher, Jonathan T

2016-05-01

Calcific aortic valve disease (CAVD) progression is a highly dynamic process whereby normally fibroblastic valve interstitial cells (VIC) undergo osteogenic differentiation, maladaptive extracellular matrix (ECM) composition, structural remodeling, and tissue matrix stiffening. However, how VIC with different phenotypes dynamically affect matrix properties and how the altered matrix further affects VIC phenotypes in response to physiological and pathological conditions have not yet been determined. In this study, we develop 3D hydrogels with tunable matrix stiffness to investigate the dynamic interplay between VIC phenotypes and matrix biomechanics. We find that VIC populated within hydrogels with valve leaflet like stiffness differentiate towards myofibroblasts in osteogenic media, but surprisingly undergo osteogenic differentiation when cultured within lower initial stiffness hydrogels. VIC differentiation progressively stiffens the hydrogel microenvironment, which further upregulates both early and late osteogenic markers. These findings identify a dynamic positive feedback loop that governs acceleration of VIC calcification. Temporal stiffening of pathologically lower stiffness matrix back to normal level, or blocking the mechanosensitive RhoA/ROCK signaling pathway, delays the osteogenic differentiation process. Therefore, direct ECM biomechanical modulation can affect VIC phenotypes towards and against osteogenic differentiation in 3D culture. These findings highlight the importance of the homeostatic maintenance of matrix stiffness to restrict pathological VIC differentiation. We implement 3D hydrogels with tunable matrix stiffness to investigate the dynamic interaction between valve interstitial cells (VIC, major cell population in heart valve) and matrix biomechanics. This work focuses on how human VIC responses to changing 3D culture environments. Our findings identify a dynamic positive feedback loop that governs acceleration of VIC calcification, which is the hallmark of calcific aortic valve disease. Temporal stiffening of pathologically lower stiffness matrix back to normal level, or blocking the mechanosensitive signaling pathway, delays VIC osteogenic differentiation. Our findings provide an improved understanding of VIC-matrix interactions to aid in interpretation of VIC calcification studies in vitro and suggest that ECM disruption resulting in local tissue stiffness decreases may promote calcific aortic valve disease. Copyright © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

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.

Ultrahigh-density sub-10 nm nanowire array formation via surface-controlled phase separation.

PubMed

Tian, Yuan; Mukherjee, Pinaki; Jayaraman, Tanjore V; Xu, Zhanping; Yu, Yongsheng; Tan, Li; Sellmyer, David J; Shield, Jeffrey E

2014-08-13

We present simple, self-assembled, and robust fabrication of ultrahigh density cobalt nanowire arrays. The binary Co-Al and Co-Si systems phase-separate during physical vapor deposition, resulting in Co nanowire arrays with average diameter as small as 4.9 nm and nanowire density on the order of 10(16)/m(2). The nanowire diameters were controlled by moderating the surface diffusivity, which affected the lateral diffusion lengths. High resolution transmission electron microscopy reveals that the Co nanowires formed in the face-centered cubic structure. Elemental mapping showed that in both systems the nanowires consisted of Co with undetectable Al or Si and that the matrix consisted of Al with no distinguishable Co in the Co-Al system and a mixture of Si and Co in the Co-Si system. Magnetic measurements clearly indicate anisotropic behavior consistent with shape anisotropy. The dynamics of nanowire growth, simulated using an Ising model, is consistent with the experimental phase and geometry of the nanowires.

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.

Charge and Spin Dynamics of the Hubbard Chains

NASA Technical Reports Server (NTRS)

Park, Youngho; Liang, Shoudan

1999-01-01

We calculate the local correlation functions of charge and spin for the one-chain and two-chain Hubbard model using density matrix renormalization group method and the recursion technique. Keeping only finite number of states we get good accuracy for the low energy excitations. We study the charge and spin gaps, bandwidths and weights of the spectra for various values of the on-site Coulomb interaction U and the electron filling. In the low energy part, the local correlation functions are different for the charge and spin. The bandwidths are proportional to t for the charge and J for the spin respectively.

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.

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

PubMed

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

2018-04-28

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

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

PubMed

Nair, Nitish; Wentzel, Nathaniel; Jayaraman, Arthi

2011-05-21

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

Progress on Complex Langevin simulations of a finite density matrix model for QCD

NASA Astrophysics Data System (ADS)

Bloch, Jacques; Glesaaen, Jonas; Verbaarschot, Jacobus; Zafeiropoulos, Savvas

2018-03-01

We study the Stephanov model, which is an RMT model for QCD at finite density, using the Complex Langevin algorithm. Naive implementation of the algorithm shows convergence towards the phase quenched or quenched theory rather than to intended theory with dynamical quarks. A detailed analysis of this issue and a potential resolution of the failure of this algorithm are discussed. We study the effect of gauge cooling on the Dirac eigenvalue distribution and time evolution of the norm for various cooling norms, which were specifically designed to remove the pathologies of the complex Langevin evolution. The cooling is further supplemented with a shifted representation for the random matrices. Unfortunately, none of these modifications generate a substantial improvement on the complex Langevin evolution and the final results still do not agree with the analytical predictions.

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

Nicholas Metropolis Award for Outstanding Doctoral Thesis Work in Computational Physics: Quantum many-body physics of ultracold molecules in optical lattices: models and simulation methods

NASA Astrophysics Data System (ADS)

Wall, Michael

2014-03-01

Experimental progress in generating and manipulating synthetic quantum systems, such as ultracold atoms and molecules in optical lattices, has revolutionized our understanding of quantum many-body phenomena and posed new challenges for modern numerical techniques. Ultracold molecules, in particular, feature long-range dipole-dipole interactions and a complex and selectively accessible internal structure of rotational and hyperfine states, leading to many-body models with long range interactions and many internal degrees of freedom. Additionally, the many-body physics of ultracold molecules is often probed far from equilibrium, and so algorithms which simulate quantum many-body dynamics are essential. Numerical methods which are to have significant impact in the design and understanding of such synthetic quantum materials must be able to adapt to a variety of different interactions, physical degrees of freedom, and out-of-equilibrium dynamical protocols. Matrix product state (MPS)-based methods, such as the density-matrix renormalization group (DMRG), have become the de facto standard for strongly interacting low-dimensional systems. Moreover, the flexibility of MPS-based methods makes them ideally suited both to generic, open source implementation as well as to studies of the quantum many-body dynamics of ultracold molecules. After introducing MPSs and variational algorithms using MPSs generally, I will discuss my own research using MPSs for many-body dynamics of long-range interacting systems. In addition, I will describe two open source implementations of MPS-based algorithms in which I was involved, as well as educational materials designed to help undergraduates and graduates perform research in computational quantum many-body physics using a variety of numerical methods including exact diagonalization and static and dynamic variational MPS methods. Finally, I will mention present research on ultracold molecules in optical lattices, such as the exploration of many-body physics with polyatomic molecules, and the next generation of open source matrix product state codes. This work was performed in the research group of Prof. Lincoln D. Carr.

The matrix exponential in transient structural analysis

NASA Technical Reports Server (NTRS)

Minnetyan, Levon

1987-01-01

The primary usefulness of the presented theory is in the ability to represent the effects of high frequency linear response with accuracy, without requiring very small time steps in the analysis of dynamic response. The matrix exponential contains a series approximation to the dynamic model. However, unlike the usual analysis procedure which truncates the high frequency response, the approximation in the exponential matrix solution is in the time domain. By truncating the series solution to the matrix exponential short, the solution is made inaccurate after a certain time. Yet, up to that time the solution is extremely accurate, including all high frequency effects. By taking finite time increments, the exponential matrix solution can compute the response very accurately. Use of the exponential matrix in structural dynamics is demonstrated by simulating the free vibration response of multi degree of freedom models of cantilever beams.

Long-range corrected density functional through the density matrix expansion based semilocal exchange hole.

PubMed

Patra, Bikash; Jana, Subrata; Samal, Prasanjit

2018-03-28

The exchange hole, which is one of the principal constituents of the density functional formalism, can be used to design accurate range-separated hybrid functionals in association with appropriate correlation. In this regard, the exchange hole derived from the density matrix expansion has gained attention due to its fulfillment of some of the desired exact constraints. Thus, the new long-range corrected density functional proposed here combines the meta generalized gradient approximation level exchange functional designed from the density matrix expansion based exchange hole coupled with the ab initio Hartree-Fock exchange through the range separation of the Coulomb interaction operator using the standard error function technique. Then, in association with the Lee-Yang-Parr correlation functional, the assessment and benchmarking of the above newly constructed range-separated functional with various well-known test sets shows its reasonable performance for a broad range of molecular properties, such as thermochemistry, non-covalent interaction and barrier heights of the chemical reactions.

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

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

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

Quantum spin chains with multiple dynamics

NASA Astrophysics Data System (ADS)

Chen, Xiao; Fradkin, Eduardo; Witczak-Krempa, William

2017-11-01

Many-body systems with multiple emergent time scales arise in various contexts, including classical critical systems, correlated quantum materials, and ultracold atoms. We investigate such nontrivial quantum dynamics in a different setting: a spin-1 bilinear-biquadratic chain. It has a solvable entangled ground state, but a gapless excitation spectrum that is poorly understood. By using large-scale density matrix renormalization group simulations, we find that the lowest excitations have a dynamical exponent z that varies from 2 to 3.2 as we vary a coupling in the Hamiltonian. We find an additional gapless mode with a continuously varying exponent 2 ≤z <2.7 , which establishes the presence of multiple dynamics. In order to explain these striking properties, we construct a continuum wave function for the ground state, which correctly describes the correlations and entanglement properties. We also give a continuum parent Hamiltonian, but show that additional ingredients are needed to capture the excitations of the chain. By using an exact mapping to the nonequilibrium dynamics of a classical spin chain, we find that the large dynamical exponent is due to subdiffusive spin motion. Finally, we discuss the connections to other spin chains and to a family of quantum critical models in two dimensions.

Fibonacci family of dynamical universality classes

PubMed Central

Popkov, Vladislav; Schadschneider, Andreas; Schmidt, Johannes; Schütz, Gunter M.

2015-01-01

Universality is a well-established central concept of equilibrium physics. However, in systems far away from equilibrium, a deeper understanding of its underlying principles is still lacking. Up to now, a few classes have been identified. Besides the diffusive universality class with dynamical exponent z=2, another prominent example is the superdiffusive Kardar−Parisi−Zhang (KPZ) class with z=3/2. It appears, e.g., in low-dimensional dynamical phenomena far from thermal equilibrium that exhibit some conservation law. Here we show that both classes are only part of an infinite discrete family of nonequilibrium universality classes. Remarkably, their dynamical exponents zα are given by ratios of neighboring Fibonacci numbers, starting with either z1=3/2 (if a KPZ mode exist) or z1=2 (if a diffusive mode is present). If neither a diffusive nor a KPZ mode is present, all dynamical modes have the Golden Mean z=(1+5)/2 as dynamical exponent. The universal scaling functions of these Fibonacci modes are asymmetric Lévy distributions that are completely fixed by the macroscopic current density relation and compressibility matrix of the system and hence accessible to experimental measurement. PMID:26424449

Simple expression for the quantum Fisher information matrix

NASA Astrophysics Data System (ADS)

Šafránek, Dominik

2018-04-01

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

Tensile strength of Fe-Ni and Mg-Al nanocomposites: Molecular dynamic simulations

NASA Astrophysics Data System (ADS)

Pogorelko, V. V.; Mayer, A. E.

2018-01-01

In this work, molecular dynamic simulations of the tensile strength of Fe-Ni and Mg-Al nanocomposites in the conditions of high-rate uniaxial tension were carried out. Two different mechanisms of fracture were identified. In the case of nickel inclusion in iron matrix, the fracture begins on the interface between the inclusion and the matrix, a formed void penetrates both into the inclusion and into the matrix; presence of inclusion reduces the tensile strength. In the case of aluminum inclusion in magnesium matrix, fracture takes place into magnesium matrix and does not touch the inclusion; presence of inclusion has practically no effect on the tensile strength. Molecular dynamic simulations were carried out in a wide range of strain rates and temperatures.

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

Demographic variation across successional stages and their effects on the population dynamics of the neotropical palm Euterpe precatoria.

PubMed

Otárola, Mauricio Fernández; Avalos, Gerardo

2014-06-01

• Premise of the study: Environmental heterogeneity is a strong selective force shaping adaptation and population dynamics across temporal and spatial scales. Natural and anthropogenic gradients influence the variation of environmental and biotic factors, which determine population demography and dynamics. Successional gradients are expected to influence demographic parameters, but the relationship between these gradients and the species life history, habitat requirements, and degree of variation in demographic traits remains elusive.• Methods: We used the palm Euterpe precatoria to test the effect of successional stage on plant demography within a continuous population. We calculated demographic parameters for size stages and performed matrix analyses to investigate the demographic variation within primary and secondary forests of La Selva, Costa Rica.• Key results: We observed differences in mortality and recruitment of small juveniles between primary and secondary forests. Matrix models described satisfactorily the chronosequence of population changes, which were characterized by high population growth rate in disturbed areas, and decreased growth rate in old successional forests until reaching stability.• Conclusions: Different demographic parameters can be expressed in contiguous subpopulations along a gradient of successional stages with important consequences for population dynamics. Demographic variation superimposed on these gradients contributes to generate subpopulations with different demographic composition, density, and ecological properties. Therefore, the effects of spatial variation must be reconsidered in the design of demographic analyses of tropical palms, which are prime examples of subtle local adaptation. These considerations are crucial in the implementation of management plans for palm species within spatially complex and heterogeneous tropical landscapes. © 2014 Botanical Society of America, Inc.

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

PubMed Central

Wen, Xiaotong; Rangarajan, Govindan; Ding, Mingzhou

2013-01-01

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

Simple Derivation of the Lindblad Equation

ERIC Educational Resources Information Center

Pearle, Philip

2012-01-01

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

Modeling the population dynamics of Culex quinquefasciatus (Diptera: Culcidae), along an elevational gradient in Hawaii

USGS Publications Warehouse

Ahumada, Jorge A.; LaPointe, Dennis; Samuel, Michael D.

2004-01-01

We present a population model to understand the effects of temperature and rainfall on the population dynamics of the southern house mosquito, Culex quinquefasciatus Say, along an elevational gradient in Hawaii. We use a novel approach to model the effects of temperature on population growth by dynamically incorporating developmental rate into the transition matrix, by using physiological ages of immatures instead of chronological age or stages. We also model the effects of rainfall on survival of immatures as the cumulative number of days below a certain rain threshold. Finally, we incorporate density dependence into the model as competition between immatures within breeding sites. Our model predicts the upper altitudinal distributions of Cx. quinquefasciatus on the Big Island of Hawaii for self-sustaining mosquito and migrating summer sink populations at 1,475 and 1,715 m above sea level, respectively. Our model predicts that mosquitoes at lower elevations can grow under a broader range of rainfall parameters than middle and high elevation populations. Density dependence in conjunction with the seasonal forcing imposed by temperature and rain creates cycles in the dynamics of the population that peak in the summer and early fall. The model provides a reasonable fit to the available data on mosquito abundance for the east side of Mauna Loa, Hawaii. The predictions of our model indicate the importance of abiotic conditions on mosquito dynamics and have important implications for the management of diseases transmitted by Cx. quinquefasciatus in Hawaii and elsewhere.

Gas sorption and barrier properties of polymeric membranes from molecular dynamics and Monte Carlo simulations.

PubMed

Cozmuta, Ioana; Blanco, Mario; Goddard, William A

2007-03-29

It is important for many industrial processes to design new materials with improved selective permeability properties. Besides diffusion, the molecule's solubility contributes largely to the overall permeation process. This study presents a method to calculate solubility coefficients of gases such as O2, H2O (vapor), N2, and CO2 in polymeric matrices from simulation methods (Molecular Dynamics and Monte Carlo) using first principle predictions. The generation and equilibration (annealing) of five polymer models (polypropylene, polyvinyl alcohol, polyvinyl dichloride, polyvinyl chloride-trifluoroethylene, and polyethylene terephtalate) are extensively described. For each polymer, the average density and Hansen solubilities over a set of ten samples compare well with experimental data. For polyethylene terephtalate, the average properties between a small (n = 10) and a large (n = 100) set are compared. Boltzmann averages and probability density distributions of binding and strain energies indicate that the smaller set is biased in sampling configurations with higher energies. However, the sample with the lowest cohesive energy density from the smaller set is representative of the average of the larger set. Density-wise, low molecular weight polymers tend to have on average lower densities. Infinite molecular weight samples do however provide a very good representation of the experimental density. Solubility constants calculated with two ensembles (grand canonical and Henry's constant) are equivalent within 20%. For each polymer sample, the solubility constant is then calculated using the faster (10x) Henry's constant ensemble (HCE) from 150 ps of NPT dynamics of the polymer matrix. The influence of various factors (bad contact fraction, number of iterations) on the accuracy of Henry's constant is discussed. To validate the calculations against experimental results, the solubilities of nitrogen and carbon dioxide in polypropylene are examined over a range of temperatures between 250 and 650 K. The magnitudes of the calculated solubilities agree well with experimental results, and the trends with temperature are predicted correctly. The HCE method is used to predict the solubility constants at 298 K of water vapor and oxygen. The water vapor solubilities follow more closely the experimental trend of permeabilities, both ranging over 4 orders of magnitude. For oxygen, the calculated values do not follow entirely the experimental trend of permeabilities, most probably because at this temperature some of the polymers are in the glassy regime and thus are diffusion dominated. Our study also concludes large confidence limits are associated with the calculated Henry's constants. By investigating several factors (terminal ends of the polymer chains, void distribution, etc.), we conclude that the large confidence limits are intimately related to the polymer's conformational changes caused by thermal fluctuations and have to be regarded--at least at microscale--as a characteristic of each polymer and the nature of its interaction with the solute. Reducing the mobility of the polymer matrix as well as controlling the distribution of the free (occupiable) volume would act as mechanisms toward lowering both the gas solubility and the diffusion coefficients.

Dynamic Mechanical Properties of Bio-Polymer Graphite Thin Films

NASA Astrophysics Data System (ADS)

Saddam Kamarudin, M.; Rus, Anika Zafiah M.; Munirah Abdullah, Nur; Abdullah, M. F. L.

2017-08-01

Waste cooking oil is used as the main substances in producing graphite biopolymer thin films. Biopolymer is produce from the reaction of bio-monomer and cross linker with the ratio of 2:1 and addition of graphite with an increment of 2% through a slip casting method. The morphological surface properties of the samples are observed by using Scanning Electron Microscope (SEM). It is shown that the graphite particle is well mixed and homogenously dispersed in biopolymer matrix. Meanwhile, the mechanical response of materials by monitoring the change in the material properties in terms of frequency and temperature of the samples were determined using Dynamic Mechanical Analysis (DMA). The calculated cross-linked density of biopolymer composites revealed the increment of graphite particle loading at 8% gives highest results with 260.012 x 103 M/m3.

Multi-objective control of nonlinear boiler-turbine dynamics with actuator magnitude and rate constraints.

PubMed

Chen, Pang-Chia

2013-01-01

This paper investigates multi-objective controller design approaches for nonlinear boiler-turbine dynamics subject to actuator magnitude and rate constraints. System nonlinearity is handled by a suitable linear parameter varying system representation with drum pressure as the system varying parameter. Variation of the drum pressure is represented by suitable norm-bounded uncertainty and affine dependence on system matrices. Based on linear matrix inequality algorithms, the magnitude and rate constraints on the actuator and the deviations of fluid density and water level are formulated while the tracking abilities on the drum pressure and power output are optimized. Variation ranges of drum pressure and magnitude tracking commands are used as controller design parameters, determined according to the boiler-turbine's operation range. Copyright © 2012 ISA. Published by Elsevier Ltd. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

2016-07-01

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

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

PubMed

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

2016-07-07

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

One-dimensional continuum electronic structure with the density-matrix renormalization group and its implications for density-functional theory.

PubMed

Stoudenmire, E M; Wagner, Lucas O; White, Steven R; Burke, Kieron

2012-08-03

We extend the density matrix renormalization group to compute exact ground states of continuum many-electron systems in one dimension with long-range interactions. We find the exact ground state of a chain of 100 strongly correlated artificial hydrogen atoms. The method can be used to simulate 1D cold atom systems and to study density-functional theory in an exact setting. To illustrate, we find an interacting, extended system which is an insulator but whose Kohn-Sham system is metallic.

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

Dynamic interactions between cells and their extracellular matrix mediate embryonic development.

PubMed

Goody, Michelle F; Henry, Clarissa A

2010-06-01

Cells and their surrounding extracellular matrix microenvironment interact throughout all stages of life. Understanding the continuously changing scope of cell-matrix interactions in vivo is crucial to garner insights into both congenital birth defects and disease progression. A current challenge in the field of developmental biology is to adapt in vitro tools and rapidly evolving imaging technology to study cell-matrix interactions in a complex 4-D environment. In this review, we highlight the dynamic modulation of cell-matrix interactions during development. We propose that individual cell-matrix adhesion proteins are best considered as complex proteins that can play multiple, often seemingly contradictory roles, depending upon the context of the microenvironment. In addition, cell-matrix proteins can also exert different short versus long term effects. It is thus important to consider cell behavior in light of the microenvironment because of the constant and dynamic reciprocal interactions occurring between them. Finally, we suggest that analysis of cell-matrix interactions at multiple levels (molecules, cells, tissues) in vivo is critical for an integrated understanding because different information can be acquired from all size scales. Copyright 2010 Wiley-Liss, Inc.

Entanglement dynamics in a non-Markovian environment: An exactly solvable model

NASA Astrophysics Data System (ADS)

Wilson, Justin H.; Fregoso, Benjamin M.; Galitski, Victor M.

2012-05-01

We study the non-Markovian effects on the dynamics of entanglement in an exactly solvable model that involves two independent oscillators, each coupled to its own stochastic noise source. First, we develop Lie algebraic and functional integral methods to find an exact solution to the single-oscillator problem which includes an analytic expression for the density matrix and the complete statistics, i.e., the probability distribution functions for observables. For long bath time correlations, we see nonmonotonic evolution of the uncertainties in observables. Further, we extend this exact solution to the two-particle problem and find the dynamics of entanglement in a subspace. We find the phenomena of “sudden death” and “rebirth” of entanglement. Interestingly, all memory effects enter via the functional form of the energy and hence the time of death and rebirth is controlled by the amount of noisy energy added into each oscillator. If this energy increases above (decreases below) a threshold, we obtain sudden death (rebirth) of entanglement.

Free-time and fixed end-point optimal control theory in dissipative media: application to entanglement generation and maintenance.

PubMed

Mishima, K; Yamashita, K

2009-07-07

We develop monotonically convergent free-time and fixed end-point optimal control theory (OCT) in the density-matrix representation to deal with quantum systems showing dissipation. Our theory is more general and flexible for tailoring optimal laser pulses in order to control quantum dynamics with dissipation than the conventional fixed-time and fixed end-point OCT in that the optimal temporal duration of laser pulses can also be optimized exactly. To show the usefulness of our theory, it is applied to the generation and maintenance of the vibrational entanglement of carbon monoxide adsorbed on the copper (100) surface, CO/Cu(100). We demonstrate the numerical results and clarify how to combat vibrational decoherence as much as possible by the tailored shapes of the optimal laser pulses. It is expected that our theory will be general enough to be applied to a variety of dissipative quantum dynamics systems because the decoherence is one of the quantum phenomena sensitive to the temporal duration of the quantum dynamics.

Neural network based feed-forward high density associative memory

NASA Technical Reports Server (NTRS)

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

1987-01-01

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

Dynamical Jahn-Teller effect of fullerene anions

NASA Astrophysics Data System (ADS)

Liu, Dan; Iwahara, Naoya; Chibotaru, Liviu F.

2018-03-01

The dynamical Jahn-Teller effect of C60n - anions (n =1 -5) is studied using the numerical diagonalization of the linear pn⊗8 d Jahn-Teller Hamiltonian with the currently established coupling parameters. It is found that in all anions the Jahn-Teller effect stabilizes the low-spin states, resulting in the violation of Hund's rule. The energy gain due to the Jahn-Teller dynamics is found to be comparable to the static Jahn-Teller stabilization. The Jahn-Teller dynamics influences the thermodynamic properties via strong variation of the density of vibronic states with energy. Thus the large vibronic entropy in the low-spin states enhances the effective spin gap of C603 - quenching the spin crossover. From the calculations of the effective spin gap as a function of the Hund's rule coupling, we found that the latter should amount 40 ±5 meV in order to cope with the violation of Hund's rule and to reproduce the large spin gap. With the obtained numerical solutions, the matrix elements of electronic operators for the low-lying vibronic levels and the vibronic reduction factors are calculated for all anions.

Entanglement between atomic thermal states and coherent or squeezed photons in a damping cavity

NASA Astrophysics Data System (ADS)

Yadollahi, F.; Safaiee, R.; Golshan, M. M.

2018-02-01

In the present study, the standard Jaynes-Cummings model, in a lossy cavity, is employed to characterize the entanglement between atoms and photons when the former is initially in a thermal state (mixed ensemble) while the latter is described by either coherent or squeezed distributions. The whole system is thus assumed to be in equilibrium with a heat reservoir at a finite temperature T, and the measure of negativity is used to determine the time evolution of atom-photon entanglement. To this end, the master equation for the density matrix, in the secular approximation, is solved and a partial transposition of the result is made. The degree of atom-photon entanglement is then numerically computed, through the negativity, as a function of time and temperature. To justify the behavior of atom-photon entanglement, moreover, we employ the so obtained total density matrix to compute and analyze the time evolution of the initial photonic coherent or squeezed probability distributions and the squeezing parameters. On more practical points, our results demonstrate that as the initial photon mean number increases, the atom-photon entanglement decays at a faster pace for the coherent distribution compared to the squeezed one. Moreover, it is shown that the degree of atom-photon entanglement is much higher and more stable for the squeezed distribution than that for the coherent one. Consequently, we conclude that the time intervals during which the atom-photon entanglement is distillable is longer for the squeezed distribution. It is also illustrated that as the temperature increases the rate of approaching separability is faster for the coherent initial distribution. The novel point of the present report is the calculation of dynamical density matrix (containing all physical information) for the combined system of atom-photon in a lossy cavity, as well as the corresponding negativity, at a finite temperature.

Cell motility and ECM proteolysis regulate tumor growth and tumor relapse by altering the fraction of cancer stem cells and their spatial scattering

NASA Astrophysics Data System (ADS)

Kumar, Sandeep; Kulkarni, Rahul; Sen, Shamik

2016-06-01

Tumors consist of multiple cell sub-populations including cancer stem cells (CSCs), transiently amplifying cells and terminally differentiated cells (TDCs), with the CSC fraction dictating the aggressiveness of the tumor and drug sensitivity. In epithelial cancers, tumor growth is influenced greatly by properties of the extracellular matrix (ECM), with cancer progression associated with an increase in ECM density. However, the extent to which increased ECM confinement induced by an increase in ECM density influences tumor growth and post treatment relapse dynamics remains incompletely understood. In this study, we use a cellular automata-based discrete modeling approach to study the collective influence of ECM density, cell motility and ECM proteolysis on tumor growth, tumor heterogeneity, and tumor relapse after drug treatment. We show that while increased confinement suppresses tumor growth and the spatial scattering of CSCs, this effect can be reversed when cells become more motile and proteolytically active. Our results further suggest that, in addition to the absolute number of CSCs, their spatial positioning also plays an important role in driving tumor growth. In a nutshell, our study suggests that, in confined environments, cell motility and ECM proteolysis are two key factors that regulate tumor growth and tumor relapse dynamics by altering the number and spatial distribution of CSCs.

Study of Polyurethane Foaming Dynamics Using a Heat Flow Meter

NASA Astrophysics Data System (ADS)

Koniorczyk, P.; Trzyna, M.; Zmywaczyk, J.; Zygmunt, B.; Preiskorn, M.

2017-05-01

This work presents the results of the study concerning the effects of fillers addition on the heat flux density \\dot{q}( t ) of foaming of polyurethane-polystyrene porous composite (PSUR) and describes the dynamics of this process during the first 600 s. This foaming process resulted in obtaining porous materials that were based on HFC 365/225 blown rigid polyurethane foam (PUR) matrix, which contained thermoplastic expandable polystyrene (EPS) beads as the filler. In PSUR composites, the EPS beads were expanded after being heated to a temperature above the glass transition temperature of EPS and vaporing gas incorporated inside, by using the heat of exothermic reaction of polyol with isocyanate. From the start (t=0) to the end of the PSUR composite foaming process (t=tk), \\dot{q}( t ) was measured with the use of the heat flow meter. For the purpose of the study two PUR systems were selected: one with high and one with low heat density of foaming process q. EPS beads were selected from the same manufacturer with large and small diameter. The mass fraction of EPS in PSUR foam varied during the measurements. Additionally, a study of volume fractions of expanded EPS phase in PSUR foams as a function of mass fractions of EPS was conducted. In order to verify effects of the EPS addition on the heat flux density during PSUR foaming process, the thermal conductivity measurements were taken.

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.

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.

Optimization of matrix tablets controlled drug release using Elman dynamic neural networks and decision trees.

PubMed

Petrović, Jelena; Ibrić, Svetlana; Betz, Gabriele; Đurić, Zorica

2012-05-30

The main objective of the study was to develop artificial intelligence methods for optimization of drug release from matrix tablets regardless of the matrix type. Static and dynamic artificial neural networks of the same topology were developed to model dissolution profiles of different matrix tablets types (hydrophilic/lipid) using formulation composition, compression force used for tableting and tablets porosity and tensile strength as input data. Potential application of decision trees in discovering knowledge from experimental data was also investigated. Polyethylene oxide polymer and glyceryl palmitostearate were used as matrix forming materials for hydrophilic and lipid matrix tablets, respectively whereas selected model drugs were diclofenac sodium and caffeine. Matrix tablets were prepared by direct compression method and tested for in vitro dissolution profiles. Optimization of static and dynamic neural networks used for modeling of drug release was performed using Monte Carlo simulations or genetic algorithms optimizer. Decision trees were constructed following discretization of data. Calculated difference (f(1)) and similarity (f(2)) factors for predicted and experimentally obtained dissolution profiles of test matrix tablets formulations indicate that Elman dynamic neural networks as well as decision trees are capable of accurate predictions of both hydrophilic and lipid matrix tablets dissolution profiles. Elman neural networks were compared to most frequently used static network, Multi-layered perceptron, and superiority of Elman networks have been demonstrated. Developed methods allow simple, yet very precise way of drug release predictions for both hydrophilic and lipid matrix tablets having controlled drug release. Copyright © 2012 Elsevier B.V. All rights reserved.

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

PubMed

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

2016-11-01

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

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.

Dynamical vanishing of the order parameter in a confined Bardeen-Cooper-Schrieffer Fermi gas after an interaction quench

NASA Astrophysics Data System (ADS)

Hannibal, S.; Kettmann, P.; Croitoru, M. D.; Axt, V. M.; Kuhn, T.

2018-01-01

We present a numerical study of the Higgs mode in an ultracold confined Fermi gas after an interaction quench and find a dynamical vanishing of the superfluid order parameter. Our calculations are done within a microscopic density-matrix approach in the Bogoliubov-de Gennes framework which takes the three-dimensional cigar-shaped confinement explicitly into account. In this framework, we study the amplitude mode of the order parameter after interaction quenches starting on the BCS side of the BEC-BCS crossover close to the transition and ending in the BCS regime. We demonstrate the emergence of a dynamically vanishing superfluid order parameter in the spatiotemporal dynamics in a three-dimensional trap. Further, we show that the signal averaged over the whole trap mirrors the spatiotemporal behavior and allows us to systematically study the effects of the system size and aspect ratio on the observed dynamics. Our analysis enables us to connect the confinement-induced modifications of the dynamics to the pairing properties of the system. Finally, we demonstrate that the signature of the Higgs mode is contained in the dynamical signal of the condensate fraction, which, therefore, might provide a new experimental access to the nonadiabatic regime of the Higgs mode.

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.

Matrix density effects on the mechanical properties of SiC fiber-reinforced silicon nitride matrix properties

NASA Technical Reports Server (NTRS)

Bhatt, Ramakrishna T.; Kiser, Lames D.

1990-01-01

The room temperature mechanical properties were measured for SiC fiber reinforced reaction-bonded silicon nitride composites (SiC/RBSN) of different densities. The composites consisted of approx. 30 vol percent uniaxially aligned 142 micron diameter SiC fibers (Textron SCS-6) in a reaction-bonded Si3N4 matrix. The composite density was varied by changing the consolidation pressure during RBSN processing and by hot isostatically pressing the SiC/RBSN composites. Results indicate that as the consolidation pressure was increased from 27 to 138 MPa, the average pore size of the nitrided composites decreased from 0.04 to 0.02 microns and the composite density increased from 2.07 to 2.45 gm/cc. Nonetheless, these improvements resulted in only small increases in the first matrix cracking stress, primary elastic modulus, and ultimate tensile strength values of the composites. In contrast, HIP consolidation of SiC/RBSN resulted in a fully dense material whose first matrix cracking stress and elastic modulus were approx. 15 and 50 percent higher, respectively, and ultimate tensile strength values were approx. 40 percent lower than those for unHIPed SiC/RBSN composites. The modulus behavior for all specimens can be explained by simple rule-of-mixture theory. Also, the loss in ultimate strength for the HIPed composites appears to be related to a degradation in fiber strength at the HIP temperature. However, the density effect on matrix fracture strength was much less than would be expected based on typical monolithic Si3N4 behavior, suggesting that composite theory is indeed operating. Possible practical implications of these observations are discussed.

Suspensions of polymer-grafted nanoparticles with added polymers-Structure and effective pair-interactions.

PubMed

Chandran, Sivasurender; Saw, Shibu; Kandar, A K; Dasgupta, C; Sprung, M; Basu, J K

2015-08-28

We present the results of combined experimental and theoretical (molecular dynamics simulations and integral equation theory) studies of the structure and effective interactions of suspensions of polymer grafted nanoparticles (PGNPs) in the presence of linear polymers. Due to the absence of systematic experimental and theoretical studies of PGNPs, it is widely believed that the structure and effective interactions in such binary mixtures would be very similar to those of an analogous soft colloidal material-star polymers. In our study, polystyrene-grafted gold nanoparticles with functionality f = 70 were mixed with linear polystyrene (PS) of two different molecular weights for obtaining two PGNP:PS size ratios, ξ = 0.14 and 2.76 (where, ξ = Mg/Mm, Mg and Mm being the molecular weights of grafting and matrix polymers, respectively). The experimental structure factor of PGNPs could be modeled with an effective potential (Model-X), which has been found to be widely applicable for star polymers. Similarly, the structure factor of the blends with ξ = 0.14 could be modeled reasonably well, while the structure of blends with ξ = 2.76 could not be captured, especially for high density of added polymers. A model (Model-Y) for effective interactions between PGNPs in a melt of matrix polymers also failed to provide good agreement with the experimental data for samples with ξ = 2.76 and high density of added polymers. We tentatively attribute this anomaly in modeling the structure factor of blends with ξ = 2.76 to the questionable assumption of Model-X in describing the added polymers as star polymers with functionality 2, which gets manifested in both polymer-polymer and polymer-PGNP interactions especially at higher fractions of added polymers. The failure of Model-Y may be due to the neglect of possible many-body interactions among PGNPs mediated by matrix polymers when the fraction of added polymers is high. These observations point to the need for a new framework to understand not only the structural behavior of PGNPs but also possibly their dynamics and thermo-mechanical properties as well.

Monitoring the Cure State of Thermosetting Resins by Ultrasound.

PubMed

Lionetto, Francesca; Maffezzoli, Alfonso

2013-09-05

The propagation of low intensity ultrasound in a curing resin, acting as a high frequency oscillatory excitation, has been recently proposed as an ultrasonic dynamic mechanical analysis (UDMA) for cure monitoring. The technique measures sound velocity and attenuation, which are very sensitive to changes in the viscoelastic characteristics of the curing resin, since the velocity is related to the resin storage modulus and density, while the attenuation is related to the energy dissipation and scattering in the curing resin. The paper reviews the results obtained by the authors' research group in the last decade by means of in-house made ultrasonic set-ups for both contact and air-coupled ultrasonic experiments. The basics of the ultrasonic wave propagation in polymers and examples of measurements of the time-evolution of ultrasonic longitudinal modulus and chemical conversion of different thermosetting resins are presented. The effect of temperature on the cure kinetics, the comparison with rheological, low frequency dynamic mechanical and calorimetric results, and the correlation between ultrasonic modulus and crosslinking density will be also discussed. The paper highlights the reliability of ultrasonic wave propagation for monitoring the physical changes taking place during curing and the potential for online monitoring during polymer and polymer matrix composite processing.

Monitoring the Cure State of Thermosetting Resins by Ultrasound

PubMed Central

Lionetto, Francesca; Maffezzoli, Alfonso

2013-01-01

The propagation of low intensity ultrasound in a curing resin, acting as a high frequency oscillatory excitation, has been recently proposed as an ultrasonic dynamic mechanical analysis (UDMA) for cure monitoring. The technique measures sound velocity and attenuation, which are very sensitive to changes in the viscoelastic characteristics of the curing resin, since the velocity is related to the resin storage modulus and density, while the attenuation is related to the energy dissipation and scattering in the curing resin. The paper reviews the results obtained by the authors’ research group in the last decade by means of in-house made ultrasonic set-ups for both contact and air-coupled ultrasonic experiments. The basics of the ultrasonic wave propagation in polymers and examples of measurements of the time-evolution of ultrasonic longitudinal modulus and chemical conversion of different thermosetting resins are presented. The effect of temperature on the cure kinetics, the comparison with rheological, low frequency dynamic mechanical and calorimetric results, and the correlation between ultrasonic modulus and crosslinking density will be also discussed. The paper highlights the reliability of ultrasonic wave propagation for monitoring the physical changes taking place during curing and the potential for online monitoring during polymer and polymer matrix composite processing. PMID:28788306

Magnetic switching in granular FePt layers promoted by near-field laser enhancement

DOE PAGES

Granitzka, Patrick W.; Jal, Emmanuelle; Le Guyader, Loic; ...

2017-03-08

Light-matter interaction at the nanoscale in magnetic materials is a topic of intense research in view of potential applications in next-generation high-density magnetic recording. Laser-assisted switching provides a pathway for overcoming the material constraints of high-anisotropy and high-packing density media, though much about the dynamics of the switching process remains unexplored. We use ultrafast small-angle X-ray scattering at an X-ray free-electron laser to probe the magnetic switching dynamics of FePt nanoparticles embedded in a carbon matrix following excitation by an optical femtosecond laser pulse. We observe that the combination of laser excitation and applied static magnetic field, 1 order ofmore » magnitude smaller than the coercive field, can overcome the magnetic anisotropy barrier between “up” and “down” magnetization, enabling magnetization switching. This magnetic switching is found to be inhomogeneous throughout the material with some individual FePt nanoparticles neither switching nor demagnetizing. The origin of this behavior is identified as the near-field modification of the incident laser radiation around FePt nanoparticles. Furthermore, the fraction of not-switching nanoparticles is influenced by the heat flow between FePt and a heat-sink layer.« less

Progress on Complex Langevin simulations of a finite density matrix model for QCD

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

Bloch, Jacques; Glesaan, Jonas; Verbaarschot, Jacobus

We study the Stephanov model, which is an RMT model for QCD at finite density, using the Complex Langevin algorithm. Naive implementation of the algorithm shows convergence towards the phase quenched or quenched theory rather than to intended theory with dynamical quarks. A detailed analysis of this issue and a potential resolution of the failure of this algorithm are discussed. We study the effect of gauge cooling on the Dirac eigenvalue distribution and time evolution of the norm for various cooling norms, which were specifically designed to remove the pathologies of the complex Langevin evolution. The cooling is further supplementedmore » with a shifted representation for the random matrices. Unfortunately, none of these modifications generate a substantial improvement on the complex Langevin evolution and the final results still do not agree with the analytical predictions.« less

Normal modes and frequencies from covariances in molecular dynamics or Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Strachan, Alejandro

2004-01-01

We propose a simple method to obtain normal modes (NMs) and their characteristic frequencies from molecular dynamics or Monte Carlo simulations at any temperature. The resulting NM are consistent with the vibrational density of states (DOS) (every feature of the DOS can be attributed to one or few NMs). At low temperatures they coincide with the ones obtained from the Hessian matrix. We define the NMs (ρi) by imposing the condition that their velocities be uncorrelated to each other: <ρ˙i(t)ρ˙j(t)>∝δij, where < > denotes time average and δij is Kronecker's delta. With this definition the modes are the eigenvectors of the matrix Kijv=1/2<√mimj vivj> [i, j=1,…,3N (N being the number of atoms); m are masses and v atomic velocities]. The eigenvalues of Kijv, λiv, represent the kinetic energy in each NM. The ratio between the eigenvalues (λiv) and those obtained using positions (λir), accelerations (λia) in Kijv instead of velocities are a very good approximation to the mode frequencies: 2πνi˜(λiv/λix)(1/2)˜(λia/λix)(1/4). We demonstrate the new method using with two cases: an isolated water molecule and a crystalline polymer.

Eigenvalue Attraction

NASA Astrophysics Data System (ADS)

Movassagh, Ramis

2016-02-01

We prove that the complex conjugate (c.c.) eigenvalues of a smoothly varying real matrix attract (Eq. 15). We offer a dynamical perspective on the motion and interaction of the eigenvalues in the complex plane, derive their governing equations and discuss applications. C.c. pairs closest to the real axis, or those that are ill-conditioned, attract most strongly and can collide to become exactly real. As an application we consider random perturbations of a fixed matrix M. If M is Normal, the total expected force on any eigenvalue is shown to be only the attraction of its c.c. (Eq. 24) and when M is circulant the strength of interaction can be related to the power spectrum of white noise. We extend this by calculating the expected force (Eq. 41) for real stochastic processes with zero-mean and independent intervals. To quantify the dominance of the c.c. attraction, we calculate the variance of other forces. We apply the results to the Hatano-Nelson model and provide other numerical illustrations. It is our hope that the simple dynamical perspective herein might help better understanding of the aggregation and low density of the eigenvalues of real random matrices on and near the real line respectively. In the appendix we provide a Matlab code for plotting the trajectories of the eigenvalues.

Approaching the alloy limit of thermal conductivity in single-crystalline Si-based thermoelectric nanocomposites: A molecular dynamics investigation

PubMed Central

Guo, Ruiqiang; Huang, Baoling

2015-01-01

Single-crystalline Si-based nanocomposites have become promising candidates for thermoelectric applications due to their prominent merits. Reducing the thermal conductivity κ without deteriorating the electrical properties is the key to improve their performance. Through non-equilibrium molecular dynamics simulations, we show that κ of single-crystalline Si-based nanocomposites can be reduced to the alloy limit by embedding various nanoinclusions of similar lattice constants but different lattice orientations or space symmetries with respect to the matrix. The surprisingly low κ is mainly due to the large acoustic phonon density of states mismatch caused by the destruction of lattice periodicity at the interfaces between the nanoinclusions and matrix, which leads to the substantial reduction of phonon group velocity and relaxation time, as well as the enhancement of phonon localization. The resulting κ is also temperature-insensitive due to the dominance of boundary scattering. The increase in thermal resistance induced by lattice structure mismatch mainly comes from the nanoinclusions and the channels between them and is caused by the enhanced boundary scattering at the interfaces parallel to the heat flux. Approaching the alloy limit of κ with potentially improved electrical properties by fillers will remarkably improve ZT of single-crystalline Si-based nanocomposites and extend their application. PMID:25851401

Molecular dynamics simulation of diffusion of gases in a carbon-nanotube-polymer composite

NASA Astrophysics Data System (ADS)

Lim, Seong Y.; Sahimi, Muhammad; Tsotsis, Theodore T.; Kim, Nayong

2007-07-01

Extensive molecular dynamics (MD) simulations were carried out to compute the solubilities and self-diffusivities of CO2 and CH4 in amorphous polyetherimide (PEI) and mixed-matrix PEI generated by inserting single-walled carbon nanotubes into the polymer. Atomistic models of PEI and its composites were generated using energy minimizations, MD simulations, and the polymer-consistent force field. Two types of polymer composite were generated by inserting (7,0) and (12,0) zigzag carbon nanotubes into the PEI structure. The morphologies of PEI and its composites were characterized by their densities, radial distribution functions, and the accessible free volumes, which were computed with probe molecules of different sizes. The distributions of the cavity volumes were computed using the Voronoi tessellation method. The computed self-diffusivities of the gases in the polymer composites are much larger than those in pure PEI. We find, however, that the increase is not due to diffusion of the gases through the nanotubes which have smooth energy surfaces and, therefore, provide fast transport paths. Instead, the MD simulations indicate a squeezing effect of the nanotubes on the polymer matrix that changes the composite polymers’ free-volume distributions and makes them more sharply peaked. The presence of nanotubes also creates several cavities with large volumes that give rise to larger diffusivities in the polymer composites. This effect is due to the repulsive interactions between the polymer and the nanotubes. The solubilities of the gases in the polymer composites are also larger than those in pure PEI, hence indicating larger gas permeabilities for mixed-matrix PEI than PEI itself.

Dynamic graph system for a semantic database

DOEpatents

Mizell, David

2016-04-12

A method and system in a computer system for dynamically providing a graphical representation of a data store of entries via a matrix interface is disclosed. A dynamic graph system provides a matrix interface that exposes to an application program a graphical representation of data stored in a data store such as a semantic database storing triples. To the application program, the matrix interface represents the graph as a sparse adjacency matrix that is stored in compressed form. Each entry of the data store is considered to represent a link between nodes of the graph. Each entry has a first field and a second field identifying the nodes connected by the link and a third field with a value for the link that connects the identified nodes. The first, second, and third fields represent the rows, column, and elements of the adjacency matrix.

Dynamic graph system for a semantic database

DOEpatents

Mizell, David

2015-01-27

A method and system in a computer system for dynamically providing a graphical representation of a data store of entries via a matrix interface is disclosed. A dynamic graph system provides a matrix interface that exposes to an application program a graphical representation of data stored in a data store such as a semantic database storing triples. To the application program, the matrix interface represents the graph as a sparse adjacency matrix that is stored in compressed form. Each entry of the data store is considered to represent a link between nodes of the graph. Each entry has a first field and a second field identifying the nodes connected by the link and a third field with a value for the link that connects the identified nodes. The first, second, and third fields represent the rows, column, and elements of the adjacency matrix.

Lithium-coated polymeric matrix as a minimum volume-change and dendrite-free lithium metal anode

PubMed Central

Liu, Yayuan; Lin, Dingchang; Liang, Zheng; Zhao, Jie; Yan, Kai; Cui, Yi

2016-01-01

Lithium metal is the ideal anode for the next generation of high-energy-density batteries. Nevertheless, dendrite growth, side reactions and infinite relative volume change have prevented it from practical applications. Here, we demonstrate a promising metallic lithium anode design by infusing molten lithium into a polymeric matrix. The electrospun polyimide employed is stable against highly reactive molten lithium and, via a conformal layer of zinc oxide coating to render the surface lithiophilic, molten lithium can be drawn into the matrix, affording a nano-porous lithium electrode. Importantly, the polymeric backbone enables uniform lithium stripping/plating, which successfully confines lithium within the matrix, realizing minimum volume change and effective dendrite suppression. The porous electrode reduces the effective current density; thus, flat voltage profiles and stable cycling of more than 100 cycles is achieved even at a high current density of 5 mA cm−2 in both carbonate and ether electrolyte. The advantages of the porous, polymeric matrix provide important insights into the design principles of lithium metal anodes. PMID:26987481

Lithium-coated polymeric matrix as a minimum volume-change and dendrite-free lithium metal anode

DOE PAGES

Liu, Yayuan; Lin, Dingchang; Liang, Zheng; ...

2016-03-18

Lithium metal is the ideal anode for the next generation of high-energy-density batteries. Nevertheless, dendrite growth, side reactions and infinite relative volume change have prevented it from practical applications. Here, we demonstrate a promising metallic lithium anode design by infusing molten lithium into a polymeric matrix. The electrospun polyimide employed is stable against highly reactive molten lithium and, via a conformal layer of zinc oxide coating to render the surface lithiophilic, molten lithium can be drawn into the matrix, affording a nano-porous lithium electrode. Importantly, the polymeric backbone enables uniform lithium stripping/plating, which successfully confines lithium within the matrix, realizingmore » minimum volume change and effective dendrite suppression. The porous electrode reduces the effective current density; thus, flat voltage profiles and stable cycling of more than 100 cycles is achieved even at a high current density of 5 mA cm -2 in both carbonate and ether electrolyte. Furthermore, the advantages of the porous, polymeric matrix provide important insights into the design principles of lithium metal anodes.« less

Lithium-coated polymeric matrix as a minimum volume-change and dendrite-free lithium metal anode

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

Liu, Yayuan; Lin, Dingchang; Liang, Zheng

Lithium metal is the ideal anode for the next generation of high-energy-density batteries. Nevertheless, dendrite growth, side reactions and infinite relative volume change have prevented it from practical applications. Here, we demonstrate a promising metallic lithium anode design by infusing molten lithium into a polymeric matrix. The electrospun polyimide employed is stable against highly reactive molten lithium and, via a conformal layer of zinc oxide coating to render the surface lithiophilic, molten lithium can be drawn into the matrix, affording a nano-porous lithium electrode. Importantly, the polymeric backbone enables uniform lithium stripping/plating, which successfully confines lithium within the matrix, realizingmore » minimum volume change and effective dendrite suppression. The porous electrode reduces the effective current density; thus, flat voltage profiles and stable cycling of more than 100 cycles is achieved even at a high current density of 5 mA cm -2 in both carbonate and ether electrolyte. Furthermore, the advantages of the porous, polymeric matrix provide important insights into the design principles of lithium metal anodes.« less

STABCAR: A program for finding characteristic root systems having transcendental stability matrices

NASA Technical Reports Server (NTRS)

Adams, W. M., Jr.; Tiffany, S. H.; Newsom, J. R.; Peele, E. L.

1984-01-01

STABCAR can be used to determine the characteristic roots of flexible, actively controlled aircraft, including the effects of unsteady aerodynamics. A modal formulation and a transfer-matrix representation of the control system are employed. Operable in either a batch or an interactive mode, STABCAR can provide graphical or tabular output of the variation of the roots with velocity, density, altitude, dynamic pressure or feedback gains. Herein the mathematical model, program structure, input requirements, output capabilities, and a series of sample cases are detailed. STABCAR was written for use on CDC CYBER 175 equipment; modification would be required for operation on other machines.

Improving the efficiency of the Finite Temperature Density Matrix Renormalization Group method

NASA Astrophysics Data System (ADS)

Nocera, Alberto; Alvarez, Gonzalo

I review the basics of the finite temperature DMRG method, and then show how its efficiency can be improved by working on reduced Hilbert spaces and by using canonical approaches. My talk explains the applicability of the ancilla DMRG method beyond spins systems to t-J and Hubbard models, and addresses the computation of static and dynamical observables at finite temperature. Finally, I discuss the features of and roadmap for our DMRG + + codebase. Work done at CNMS, sponsored by the SUF Division, BES, U.S. DOE under contract with UT-Battelle. Support by the early career research program, DSUF, BES, DOE.

Stockholder projector analysis: A Hilbert-space partitioning of the molecular one-electron density matrix with orthogonal projectors

NASA Astrophysics Data System (ADS)

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

2012-01-01

A previously introduced partitioning of the molecular one-electron density matrix over atoms and bonds [D. Vanfleteren et al., J. Chem. Phys. 133, 231103 (2010)] is investigated in detail. Orthogonal projection operators are used to define atomic subspaces, as in Natural Population Analysis. The orthogonal projection operators are constructed with a recursive scheme. These operators are chemically relevant and obey a stockholder principle, familiar from the Hirshfeld-I partitioning of the electron density. The stockholder principle is extended to density matrices, where the orthogonal projectors are considered to be atomic fractions of the summed contributions. All calculations are performed as matrix manipulations in one-electron Hilbert space. Mathematical proofs and numerical evidence concerning this recursive scheme are provided in the present paper. The advantages associated with the use of these stockholder projection operators are examined with respect to covalent bond orders, bond polarization, and transferability.

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

PubMed

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

2016-04-07

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

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

NASA Astrophysics Data System (ADS)

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

2016-04-01

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

Prediction of changes in important physical parameters during composting of separated animal slurry solid fractions.

PubMed

Chowdhury, Md Albarune; de Neergaard, Andreas; Jensen, Lars Stoumann

2014-01-01

Solid-liquid separation of animal slurry, with solid fractions used for composting, has gained interest recently. However, efficient composting of separated animal slurry solid fractions (SSFs) requires a better understanding of the process dynamics in terms of important physical parameters and their interacting physical relationships in the composting matrix. Here we monitored moisture content, bulk density, particle density and air-filled porosity (AFP) during composting of SSF collected from four commercially available solid-liquid separators. Composting was performed in laboratory-scale reactors for 30 days (d) under forced aeration and measurements were conducted on the solid samples at the beginning of composting and at 10-d intervals during composting. The results suggest that differences in initial physical properties of SSF influence the development of compost maximum temperatures (40-70 degreeC). Depending on SSF, total wet mass and volume losses (expressed as % of initial value) were up to 37% and 34%, respectively. After 30 d of composting, relative losses of total solids varied from 17.9% to 21.7% and of volatile solids (VS) from 21.3% to 27.5%, depending on SSF. VS losses in all composts showed different dynamics as described by the first-order kinetic equation. The estimated component particle density of 1441 kg m-3 for VS and 2625 kg m-3 for fixed solids can be used to improve estimates of AFP for SSF within the range tested. The linear relationship between wet bulk density and AFP reported by previous researchers held true for SSF.

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.

Matrix Perturbation Techniques in Structural Dynamics

NASA Technical Reports Server (NTRS)

Caughey, T. K.

1973-01-01

Matrix perturbation are developed techniques which can be used in the dynamical analysis of structures where the range of numerical values in the matrices extreme or where the nature of the damping matrix requires that complex valued eigenvalues and eigenvectors be used. The techniques can be advantageously used in a variety of fields such as earthquake engineering, ocean engineering, aerospace engineering and other fields concerned with the dynamical analysis of large complex structures or systems of second order differential equations. A number of simple examples are included to illustrate the techniques.

Integrable Floquet dynamics, generalized exclusion processes and "fused" matrix ansatz

NASA Astrophysics Data System (ADS)

Vanicat, Matthieu

2018-04-01

We present a general method for constructing integrable stochastic processes, with two-step discrete time Floquet dynamics, from the transfer matrix formalism. The models can be interpreted as a discrete time parallel update. The method can be applied for both periodic and open boundary conditions. We also show how the stationary distribution can be built as a matrix product state. As an illustration we construct parallel discrete time dynamics associated with the R-matrix of the SSEP and of the ASEP, and provide the associated stationary distributions in a matrix product form. We use this general framework to introduce new integrable generalized exclusion processes, where a fixed number of particles is allowed on each lattice site in opposition to the (single particle) exclusion process models. They are constructed using the fusion procedure of R-matrices (and K-matrices for open boundary conditions) for the SSEP and ASEP. We develop a new method, that we named "fused" matrix ansatz, to build explicitly the stationary distribution in a matrix product form. We use this algebraic structure to compute physical observables such as the correlation functions and the mean particle current.

Single-Sided Noinvasive Inspection of Multielement Sample Using Fan-Beam Multiplexed Compton Scatter Tomography

DTIC Science & Technology

2000-05-01

a vector , ρ "# represents the set of voxel densities sorted into a vector , and ( )A ρ $# "# represents a 8 mapping of the voxel densities to...density vector in equation (4) suggests that solving for ρ "# by direct inversion is not possible, calling for an iterative technique beginning with...the vector of measured spectra, and D is the diagonal matrix of the inverse of the variances. The diagonal matrix provides weighting terms, which

Dynamic bed reactor

DOEpatents

Stormo, Keith E.

1996-07-02

A dynamic bed reactor is disclosed in which a compressible open cell foam matrix is periodically compressed and expanded to move a liquid or fluid through the matrix. In preferred embodiments, the matrix contains an active material such as an enzyme, biological cell, chelating agent, oligonucleotide, adsorbent or other material that acts upon the liquid or fluid passing through the matrix. The active material may be physically immobilized in the matrix, or attached by covalent or ionic bonds. Microbeads, substantially all of which have diameters less than 50 microns, can be used to immobilize the active material in the matrix and further improve reactor efficiency. A particularly preferred matrix is made of open cell polyurethane foam, which adsorbs pollutants such as polychlorophenol or o-nitrophenol. The reactors of the present invention allow unidirectional non-laminar flow through the matrix, and promote intimate exposure of liquid reactants to active agents such as microorganisms immobilized in the matrix.

Deconstruction of a Metastatic Tumor Microenvironment Reveals a Common Matrix Response in Human Cancers.

PubMed

Pearce, Oliver M T; Delaine-Smith, Robin M; Maniati, Eleni; Nichols, Sam; Wang, Jun; Böhm, Steffen; Rajeeve, Vinothini; Ullah, Dayem; Chakravarty, Probir; Jones, Roanne R; Montfort, Anne; Dowe, Tom; Gribben, John; Jones, J Louise; Kocher, Hemant M; Serody, Jonathan S; Vincent, Benjamin G; Connelly, John; Brenton, James D; Chelala, Claude; Cutillas, Pedro R; Lockley, Michelle; Bessant, Conrad; Knight, Martin M; Balkwill, Frances R

2018-03-01

We have profiled, for the first time, an evolving human metastatic microenvironment by measuring gene expression, matrisome proteomics, cytokine and chemokine levels, cellularity, extracellular matrix organization, and biomechanical properties, all on the same sample. Using biopsies of high-grade serous ovarian cancer metastases that ranged from minimal to extensive disease, we show how nonmalignant cell densities and cytokine networks evolve with disease progression. Multivariate integration of the different components allowed us to define, for the first time, gene and protein profiles that predict extent of disease and tissue stiffness, while also revealing the complexity and dynamic nature of matrisome remodeling during development of metastases. Although we studied a single metastatic site from one human malignancy, a pattern of expression of 22 matrisome genes distinguished patients with a shorter overall survival in ovarian and 12 other primary solid cancers, suggesting that there may be a common matrix response to human cancer. Significance: Conducting multilevel analysis with data integration on biopsies with a range of disease involvement identifies important features of the evolving tumor microenvironment. The data suggest that despite the large spectrum of genomic alterations, some human malignancies may have a common and potentially targetable matrix response that influences the course of disease. Cancer Discov; 8(3); 304-19. ©2017 AACR. This article is highlighted in the In This Issue feature, p. 253 . ©2017 American Association for Cancer Research.

Quantum dissipation theory and applications to quantum transport and quantum measurement in mesoscopic systems

NASA Astrophysics Data System (ADS)

Cui, Ping

The thesis comprises two major themes of quantum statistical dynamics. One is the development of quantum dissipation theory (QDT). It covers the establishment of some basic relations of quantum statistical dynamics, the construction of several nonequivalent complete second-order formulations, and the development of exact QDT. Another is related to the applications of quantum statistical dynamics to a variety of research fields. In particular, unconventional but novel theories of the electron transfer in Debye solvents, quantum transport, and quantum measurement are developed on the basis of QDT formulations. The thesis is organized as follows. In Chapter 1, we present some background knowledge in relation to the aforementioned two themes of this thesis. The key quantity in QDT is the reduced density operator rho(t) ≡ trBrho T(t); i.e., the partial trace of the total system and bath composite rhoT(t) over the bath degrees of freedom. QDT governs the evolution of reduced density operator, where the effects of bath are treated in a quantum statistical manner. In principle, the reduced density operator contains all dynamics information of interest. However, the conventional quantum transport theory is formulated in terms of nonequilibrium Green's function. The newly emerging field of quantum measurement in relation to quantum information and quantum computing does exploit a sort of QDT formalism. Besides the background of the relevant theoretical development, some representative experiments on molecular nanojunctions are also briefly discussed. In chapter 2, we outline some basic (including new) relations that highlight several important issues on QDT. The content includes the background of nonequilibrium quantum statistical mechanics, the general description of the total composite Hamiltonian with stochastic system-bath interaction, a novel parameterization scheme for bath correlation functions, a newly developed exact theory of driven Brownian oscillator (DBO) systems, and its closely related solvation mode transformation of system-bath coupling Hamiltonian in general. The exact QDT of DBO systems is also used to clarify the validity of conventional QDT formulations that involve Markovian approximation. In Chapter 3, we develop three nonequivalent but all complete second-order QDT (CS-QDT) formulations. Two of them are of the conventional prescriptions in terms of time-local dissipation and memory kernel, respectively. The third one is called the correlated driving-dissipation equations of motion (CODDE). This novel CS-QDT combines the merits of the former two for its advantages in both the application and numerical implementation aspects. Also highlighted is the importance of correlated driving-dissipation effects on the dynamics of the reduced system. In Chapter 4, we construct an exact QDT formalism via the calculus on path integrals. The new theory aims at the efficient evaluation of non-Markovian dissipation beyond the weak system-bath interaction regime in the presence of time-dependent external field. By adopting exponential-like expansions for bath correlation function, hierarchical equations of motion formalism and continued fraction Liouville-space Green's function formalism are established. The latter will soon be used together with the Dyson equation technique for an efficient evaluation of non-perturbative reduced density matrix dynamics. The interplay between system-bath interaction strength, non-Markovian property, and the required level of hierarchy is also studied with the aid of simple spin-boson systems, together with the three proposed schemes to truncate the infinite hierarchy. In Chapter 5, we develop a nonperturbative theory of electron transfer (ET) in Debye solvents. The resulting exact and analytical rate expression is constructed on the basis of the aforementioned continued fraction Liouville-space Green's function formalism, together with the Dyson equation technique. Not only does it recover the celebrated Marcus' inversion and Kramers' turnover behaviors, the new theory also shows some distinct quantum solvation effects that can alter the ET mechanism. Moreover, the present theory predicts further for the ET reaction thermodynamics, such as equilibrium Gibbs free-energy and entropy, some interesting solvent-dependent features that are calling for experimental verification. In Chapter 6, we discuss the constructed QDTs, in terms of their unified mathematical structure that supports a linear dynamics space, and thus facilitates their applications to various physical problems. The involving details are exemplified with the CODDE form of QDT. As the linear space is concerned, we identify the Schrodinger versus Heisenberg picture and the forward versus backward propagation of the reduced, dissipative Liouville dynamics. For applications we discuss the reduced linear response theory and the optimal control problems, in which the correlated effects of non-Markovian dissipation and field driving are shown to be important. In Chapter 7, we turn to quantum transport, i.e., electric current through molecular or mesoscopic systems under finite applied voltage. By viewing the nonequilibrium transport setup as a quantum open system, we develop a reduced-density-matrix approach to quantum transport. The resulting current is explicitly expressed in terms of the molecular reduced density matrix by tracing out the degrees of freedom of the electrodes at finite bias and temperature. We propose a conditional quantum master equation theory, which is an extension of the conventional (or unconditional) QDT by tracing out the well-defined bath subsets individually, instead of the entire bath degrees of freedom. Both the current and the noise spectrum can be conveniently analyzed in terms of the conditional reduced density matrix dynamics. By far, the QDT (including the conditional one) has only been exploited in second-order form. A self-consistent Born approximation for the system-electrode coupling is further proposed to recover all existing nonlinear current-voltage behaviors including the nonequilibrium Kondo effect. Transport theory based on the exact QDT formalism will be developed in future. In Chapter 8, we study the quantum measurement of a qubit with a quantum-point-contact detector. On the basis of a unified quantum master equation (a form of QDT), we study the measurement-induced relaxation and dephasing of the qubit. Our treatment pays particular attention on the detailed-balance relation, which is a consequence of properly accounting for the energy exchange between the qubit and detector during the measurement process. We also derive a conditional quantum master equation for quantum measurement in general, and study the readout characteristics of the qubit measurement. Our theory is applicable to the quantum measurement at arbitrary voltage and temperature. A number of remarkable new features are found and highlighted in concern with their possible relevance to future experiments. In Chapter 9, we discuss the further development of QDT, aiming at an efficient evaluation of many-electron systems. This will be carried out by reducing the many-particle (Fermion or Boson) QDT to a single-particle one by exploring, e.g. the Wick's contraction theorem. It also results in a time-dependent density functional theory (TDDFT) for transport through complex large-scale (e.g. molecules) systems. Primary results of the TDDFT-QDT are reported. In Chapter 10, we summary the thesis, and comment and remark on the future work on both the theoretical and application aspects of QDT.

Quantum spin liquid signatures in Kitaev-like frustrated magnets

NASA Astrophysics Data System (ADS)

Gohlke, Matthias; Wachtel, Gideon; Yamaji, Youhei; Pollmann, Frank; Kim, Yong Baek

2018-02-01

Motivated by recent experiments on α -RuCl3 , we investigate a possible quantum spin liquid ground state of the honeycomb-lattice spin model with bond-dependent interactions. We consider the K -Γ model, where K and Γ represent the Kitaev and symmetric-anisotropic interactions between spin-1/2 moments on the honeycomb lattice. Using the infinite density matrix renormalization group, we provide compelling evidence for the existence of quantum spin liquid phases in an extended region of the phase diagram. In particular, we use transfer-matrix spectra to show the evolution of two-particle excitations with well-defined two-dimensional dispersion, which is a strong signature of a quantum spin liquid. These results are compared with predictions from Majorana mean-field theory and used to infer the quasiparticle excitation spectra. Further, we compute the dynamical structure factor using finite-size cluster computations and show that the results resemble the scattering continuum seen in neutron-scattering experiments on α -RuCl3 . We discuss these results in light of recent and future experiments.

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

PubMed

Abbey, Colette A; Bayless, Kayla J

2014-09-01

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

Spin-adapted matrix product states and operators

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

Keller, Sebastian, E-mail: sebastian.keller@phys.chem.ethz.ch; Reiher, Markus, E-mail: markus.reiher@phys.chem.ethz.ch

Matrix product states (MPSs) and matrix product operators (MPOs) allow an alternative formulation of the density matrix renormalization group algorithm introduced by White. Here, we describe how non-abelian spin symmetry can be exploited in MPSs and MPOs by virtue of the Wigner–Eckart theorem at the example of the spin-adapted quantum chemical Hamiltonian operator.

Entanglement complexity in quantum many-body dynamics, thermalization, and localization

NASA Astrophysics Data System (ADS)

Yang, Zhi-Cheng; Hamma, Alioscia; Giampaolo, Salvatore M.; Mucciolo, Eduardo R.; Chamon, Claudio

2017-07-01

Entanglement is usually quantified by von Neumann entropy, but its properties are much more complex than what can be expressed with a single number. We show that the three distinct dynamical phases known as thermalization, Anderson localization, and many-body localization are marked by different patterns of the spectrum of the reduced density matrix for a state evolved after a quantum quench. While the entanglement spectrum displays Poisson statistics for the case of Anderson localization, it displays universal Wigner-Dyson statistics for both the cases of many-body localization and thermalization, albeit the universal distribution is asymptotically reached within very different time scales in these two cases. We further show that the complexity of entanglement, revealed by the possibility of disentangling the state through a Metropolis-like algorithm, is signaled by whether the entanglement spectrum level spacing is Poisson or Wigner-Dyson distributed.

The dynamics of the optically driven Lambda transition of the 15N-V- center in diamond.

PubMed

González, Gabriel; Leuenberger, Michael N

2010-07-09

Recent experimental results demonstrate the possibility of writing quantum information in the ground state triplet of the (15)N-V(-) center in diamond by means of an optically driven spin non-conserving two-photon Lambda transition in the presence of a strong applied electric field. Our calculations show that the hyperfine interaction in the (15)N-V(-) center is capable of mediating such a transition. We use a density matrix approach to describe the exact dynamics for the allowed optical spin non-conserving transitions between two sublevels of the ground state triplet. This approach allows us to calculate the Rabi oscillations, by means of which we obtain a Rabi frequency with an upper bound determined by the hyperfine interaction. This result is crucial for the success of implementing optically driven quantum information processing with the N-V center in diamond.

Attosecond sublevel beating and nonlinear dressing on the 3d-to-5p and 3p-to-5s core-transitions at 91.3 eV and 210.4 eV in krypton.

PubMed

Seres, Enikoe; Seres, Jozsef; Namba, Shinichi; Afa, John; Serrat, Carles

2017-12-11

Applying extreme ultraviolet (XUV) transient absorption spectroscopy, the dynamics of the two laser dressed transitions 3d 5/2 -to-5p 3/2 and 3p 3/2 -to-5s 1/2 at photon energies of 91.3 eV and 210.4 eV were examined with attosecond temporal resolution. The dressing process was modeled with density matrix equations which are found to describe very accurately both the experimentally observed transmission dynamics and the linear and nonlinear dressing oscillations at 0.75 PHz and 1.5 PHz frequencies. Furthermore, using Fourier transform XUV spectroscopy, quantum beats from the 3d 5/2 -3d 3/2 and 3p 3/2 -3p 1/2 sublevels at 0.3 PHz and 2.0 PHz were experimentally identified and resolved.

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.

Modification of transparent materials with ultrashort laser pulses: What is energetically and mechanically meaningful?

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

Bulgakova, Nadezhda M., E-mail: nadezhda.bulgakova@hilase.cz; Institute of Thermophysics SB RAS, 1 Lavrentyev Ave., 630090 Novosibirsk; Zhukov, Vladimir P.

A comprehensive analysis of laser-induced modification of bulk glass by single ultrashort laser pulses is presented which is based on combination of optical Maxwell-based modeling with thermoelastoplastic simulations of post-irradiation behavior of matter. A controversial question on free electron density generated inside bulk glass by ultrashort laser pulses in modification regimes is addressed on energy balance grounds. Spatiotemporal dynamics of laser beam propagation in fused silica have been elucidated for the regimes used for direct laser writing in bulk glass. 3D thermoelastoplastic modeling of material relocation dynamics under laser-induced stresses has been performed up to the microsecond timescale when allmore » motions in the material decay. The final modification structure is found to be imprinted into material matrix already at sub-nanosecond timescale. Modeling results agree well with available experimental data on laser light transmission through the sample and the final modification structure.« less

Ultrafast fragmentation dynamics of triply charged carbon dioxide: Vibrational-mode-dependent molecular bond breakage

NASA Astrophysics Data System (ADS)

Yang, HongJiang; Wang, Enliang; Dong, WenXiu; Gong, Maomao; Shen, Zhenjie; Tang, Yaguo; Shan, Xu; Chen, Xiangjun

2018-05-01

The a b i n i t i o molecular dynamics (MD) simulations using an atom-centered density matrix propagation method have been carried out to investigate the fragmentation of the ground-state triply charged carbon dioxide, CO23 +→C+ + Oa+ + Ob+ . Ten thousands of trajectories have been simulated. By analyzing the momentum correlation of the final fragments, it is demonstrated that the sequential fragmentation dominates in the three-body dissociation, consistent with our experimental observations which were performed by electron collision at impact energy of 1500 eV. Furthermore, the MD simulations allow us to have detailed insight into the ultrafast evolution of the molecular bond breakage at a very early stage, within several tens of femtoseconds, and the result shows that the initial nuclear vibrational mode plays a decisive role in switching the dissociation pathways.

Transient dynamics of a nonlinear magneto-optical rotation

NASA Astrophysics Data System (ADS)

Grewal, Raghwinder Singh; Pustelny, S.; Rybak, A.; Florkowski, M.

2018-04-01

We analyze nonlinear magneto-optical rotation (NMOR) in rubidium vapor subjected to a continuously scanned magnetic field. By varying the magnetic-field sweep rate, a transition from traditionally observed dispersivelike NMOR signals (low sweep rate) to oscillating signals (higher sweep rates) is demonstrated. The transient oscillatory behavior is studied versus light and magnetic-field parameters, revealing a strong dependence of the signals on magnetic sweep rate and light intensity. The experimental results are supported with density-matrix calculations, which enable quantitative analysis of the effect. Fitting of the signals simulated versus different parameters with a theoretically motivated curve reveals the presence of oscillatory and static components in the signals. The components depend differently on the system parameters, which suggests their distinct nature. The investigations provide insight into the dynamics of ground-state coherence generation and enable application of NMOR in detection of transient spin couplings.

Quantum ergodicity in the SYK model

NASA Astrophysics Data System (ADS)

Altland, Alexander; Bagrets, Dmitry

2018-05-01

We present a replica path integral approach describing the quantum chaotic dynamics of the SYK model at large time scales. The theory leads to the identification of non-ergodic collective modes which relax and eventually give way to an ergodic long time regime (describable by random matrix theory). These modes, which play a role conceptually similar to the diffusion modes of dirty metals, carry quantum numbers which we identify as the generators of the Clifford algebra: each of the 2N different products that can be formed from N Majorana operators defines one effective mode. The competition between a decay rate quickly growing in the order of the product and a density of modes exponentially growing in the same parameter explains the characteristics of the system's approach to the ergodic long time regime. We probe this dynamics through various spectral correlation functions and obtain favorable agreement with existing numerical data.

Exact stochastic unraveling of an optical coherence dynamics by cumulant expansion

NASA Astrophysics Data System (ADS)

Olšina, Jan; Kramer, Tobias; Kreisbeck, Christoph; Mančal, Tomáš

2014-10-01

A numerically exact Monte Carlo scheme for calculation of open quantum system dynamics is proposed and implemented. The method consists of a Monte Carlo summation of a perturbation expansion in terms of trajectories in Liouville phase-space with respect to the coupling between the excited states of the molecule. The trajectories are weighted by a complex decoherence factor based on the second-order cumulant expansion of the environmental evolution. The method can be used with an arbitrary environment characterized by a general correlation function and arbitrary coupling strength. It is formally exact for harmonic environments, and it can be used with arbitrary temperature. Time evolution of an optically excited Frenkel exciton dimer representing a molecular exciton interacting with a charge transfer state is calculated by the proposed method. We calculate the evolution of the optical coherence elements of the density matrix and linear absorption spectrum, and compare them with the predictions of standard simulation methods.

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.

Dynamic Compression Promotes the Matrix Synthesis of Nucleus Pulposus Cells Through Up-Regulating N-CDH Expression in a Perfusion Bioreactor Culture.

PubMed

Xu, Yichun; Yao, Hui; Li, Pei; Xu, Wenbin; Zhang, Junbin; Lv, Lulu; Teng, Haijun; Guo, Zhiliang; Zhao, Huiqing; Hou, Gang

2018-01-01

An adequate matrix production of nucleus pulposus (NP) cells is an important tissue engineering-based strategy to regenerate degenerative discs. Here, we mainly aimed to investigate the effects and mechanism of mechanical compression (i.e., static compression vs. dynamic compression) on the matrix synthesis of three-dimensional (3D) cultured NP cells in vitro. Rat NP cells seeded on small intestinal submucosa (SIS) cryogel scaffolds were cultured in the chambers of a self-developed, mechanically active bioreactor for 10 days. Meanwhile, the NP cells were subjected to compression (static compression or dynamic compression at a 10% scaffold deformation) for 6 hours once per day. Unloaded NP cells were used as controls. The cellular phenotype and matrix biosynthesis of NP cells were investigated by real-time PCR and Western blotting assays. Lentivirus-mediated N-cadherin (N-CDH) knockdown and an inhibitor, LY294002, were used to further investigate the role of N-CDH and the PI3K/Akt pathway in this process. Dynamic compression better maintained the expression of cell-specific markers (keratin-19, FOXF1 and PAX1) and matrix macromolecules (aggrecan and collagen II), as well as N-CDH expression and the activity of the PI3K/Akt pathway, in the 3D-cultured NP cells compared with those expression levels and activity in the cells grown under static compression. Further analysis showed that the N-CDH knockdown significantly down-regulated the expression of NP cell-specific markers and matrix macromolecules and inhibited the activation of the PI3K/Akt pathway under dynamic compression. However, inhibition of the PI3K/Akt pathway had no effects on N-CDH expression but down-regulated the expression of NP cell-specific markers and matrix macromolecules under dynamic compression. Dynamic compression increases the matrix synthesis of 3D-cultured NP cells compared with that of the cells under static compression, and the N-CDH-PI3K/Akt pathway is involved in this regulatory process. This study provides a promising strategy to promote the matrix deposition of tissue-engineered NP tissue in vitro prior to clinical transplantation. © 2018 The Author(s). Published by S. Karger AG, Basel.

Polymer Chain Conformation and Dynamical Confinement in a Model One-Component Nanocomposite

NASA Astrophysics Data System (ADS)

Mark, C.; Holderer, O.; Allgaier, J.; Hübner, E.; Pyckhout-Hintzen, W.; Zamponi, M.; Radulescu, A.; Feoktystov, A.; Monkenbusch, M.; Jalarvo, N.; Richter, D.

2017-07-01

We report a neutron-scattering investigation on the structure and dynamics of a single-component nanocomposite based on SiO2 particles that were grafted with polyisoprene chains at the entanglement limit. By skillful labeling, we access both the monomer density in the corona as well as the conformation of the grafted chains. While the corona profile follows a r-1 power law, the conformation of a grafted chain is identical to that of a chain in a reference melt, implying a high mutual penetration of the coronas from different particles. The brush crowding leads to topological confinement of the chain dynamics: (i) At local scales, the segmental dynamics is unchanged compared to the reference melt, while (ii) at the scale of the chain, the dynamics appears to be slowed down; (iii) by performing a mode analysis in terms of end-fixed Rouse chains, the slower dynamics is tracked to topological confinement within the cone spanned by the adjacent grafts; (iv) by adding 50% matrix chains, the topological confinement sensed by the grafted chain is lifted partially and the apparent chain motion is accelerated. We observe a crossover from pure Rouse motion at short times to topological confined motion beyond the time when the segmental mean squared displacement has reached the distance to the next graft.

Floating matrix tablets based on low density foam powder: effects of formulation and processing parameters on drug release.

PubMed

Streubel, A; Siepmann, J; Bodmeier, R

2003-01-01

The aim of this study was to develop and physicochemically characterize single unit, floating controlled drug delivery systems consisting of (i). polypropylene foam powder, (ii). matrix-forming polymer(s), (iii). drug, and (iv). filler (optional). The highly porous foam powder provided low density and, thus, excellent in vitro floating behavior of the tablets. All foam powder-containing tablets remained floating for at least 8 h in 0.1 N HCl at 37 degrees C. Different types of matrix-forming polymers were studied: hydroxypropyl methylcellulose (HPMC), polyacrylates, sodium alginate, corn starch, carrageenan, gum guar and gum arabic. The tablets eroded upon contact with the release medium, and the relative importance of drug diffusion, polymer swelling and tablet erosion for the resulting release patterns varied significantly with the type of matrix former. The release rate could effectively be modified by varying the "matrix-forming polymer/foam powder" ratio, the initial drug loading, the tablet geometry (radius and height), the type of matrix-forming polymer, the use of polymer blends and the addition of water-soluble or water-insoluble fillers (such as lactose or microcrystalline cellulose). The floating behavior of the low density drug delivery systems could successfully be combined with accurate control of the drug release patterns.

Improved Dielectric Properties and Energy Storage Density of Poly(vinylidene fluoride-co-hexafluoropropylene) Nanocomposite with Hydantoin Epoxy Resin Coated BaTiO3.

PubMed

Luo, Hang; Zhang, Dou; Jiang, Chao; Yuan, Xi; Chen, Chao; Zhou, Kechao

2015-04-22

Energy storage materials are urgently demanded in modern electric power supply and renewable energy systems. The introduction of inorganic fillers to polymer matrix represents a promising avenue for the development of high energy density storage materials, which combines the high dielectric constant of inorganic fillers with supernal dielectric strength of polymer matrix. However, agglomeration and phase separation of inorganic fillers in the polymer matrix remain the key barriers to promoting the practical applications of the composites for energy storage. Here, we developed a low-cost and environmentally friendly route to modifying BaTiO3 (BT) nanoparticles by a kind of water-soluble hydantoin epoxy resin. The modified BT nanoparticles exhibited homogeneous dispersion in the ferroelectric polymer poly(vinylidene fluoride-co-hexafluoropropylene) (P(VDF-HFP)) matrix and strong interfacial adhesion with the polymer matrix. The dielectric constants of the nanocomposites increased significantly with the increase of the coated BT loading, while the dielectric loss of the nanocomposites was still as low as that of the pure P(VDF-HFP). The energy storage density of the nanocomposites was largely enhanced with the coated BT loading at the same electric field. The nanocomposite with 20 vol % BT exhibited an estimated maximum energy density of 8.13 J cm(-3), which was much higher than that of pure P(VDF-HFP) and other dielectric polymers. The findings of this research could provide a feasible approach to produce high energy density materials for practical application in energy storage.

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.

Modeling and parameter identification of impulse response matrix of mechanical systems

NASA Astrophysics Data System (ADS)

Bordatchev, Evgueni V.

1998-12-01

A method for studying the problem of modeling, identification and analysis of mechanical system dynamic characteristic in view of the impulse response matrix for the purpose of adaptive control is developed here. Two types of the impulse response matrices are considered: (i) on displacement, which describes the space-coupled relationship between vectors of the force and simulated displacement, which describes the space-coupled relationship between vectors of the force and simulated displacement and (ii) on acceleration, which also describes the space-coupled relationship between the vectors of the force and measured acceleration. The idea of identification consists of: (a) the practical obtaining of the impulse response matrix on acceleration by 'impact-response' technique; (b) the modeling and parameter estimation of the each impulse response function on acceleration through the fundamental representation of the impulse response function on displacement as a sum of the damped sine curves applying linear and non-linear least square methods; (c) simulating the impulse provides the additional possibility to calculate masses, damper and spring constants. The damped natural frequencies are used as a priori information and are found through the standard FFT analysis. The problem of double numerical integration is avoided by taking two derivations of the fundamental dynamic model of a mechanical system as linear combination of the mass-damper-spring subsystems. The identified impulse response matrix on displacement represents the dynamic properties of the mechanical system. From the engineering point of view, this matrix can be also understood as a 'dynamic passport' of the mechanical system and can be used for dynamic certification and analysis of the dynamic quality. In addition, the suggested approach mathematically reproduces amplitude-frequency response matrix in a low-frequency band and on zero frequency. This allows the possibility of determining the matrix of the static stiffness due to dynamic testing over the time of 10- 15 minutes. As a practical example, the dynamic properties in view of the impulse and frequency response matrices of the lathe spindle are obtained, identified and investigated. The developed approach for modeling and parameter identification appears promising for a wide range o industrial applications; for example, rotary systems.

Making molecular balloons in laser-induced explosive boiling of polymer solutions.

PubMed

Leveugle, Elodie; Sellinger, Aaron; Fitz-Gerald, James M; Zhigilei, Leonid V

2007-05-25

The effect of the dynamic molecular rearrangements leading to compositional segregation is revealed in coarse-grained molecular dynamics simulations of short pulse laser interaction with a polymer solution in a volatile matrix. An internal release of matrix vapor at the onset of the explosive boiling of the overheated liquid is capable of pushing polymer molecules to the outskirts of a transient bubble, forming a polymer-rich surface layer enclosing the volatile matrix material. The results explain unexpected "deflated balloon" structures observed in films deposited by the matrix-assisted pulsed laser evaporation technique.

Tuning three-dimensional collagen matrix stiffness independently of collagen concentration modulates endothelial cell behavior.

PubMed

Mason, Brooke N; Starchenko, Alina; Williams, Rebecca M; Bonassar, Lawrence J; Reinhart-King, Cynthia A

2013-01-01

Numerous studies have described the effects of matrix stiffening on cell behavior using two-dimensional synthetic surfaces; however, less is known about the effects of matrix stiffening on cells embedded in three-dimensional in vivo-like matrices. A primary limitation in investigating the effects of matrix stiffness in three dimensions is the lack of materials that can be tuned to control stiffness independently of matrix density. Here, we use collagen-based scaffolds where the mechanical properties are tuned using non-enzymatic glycation of the collagen in solution, prior to polymerization. Collagen solutions glycated prior to polymerization result in collagen gels with a threefold increase in compressive modulus without significant changes to the collagen architecture. Using these scaffolds, we show that endothelial cell spreading increases with matrix stiffness, as does the number and length of angiogenic sprouts and the overall spheroid outgrowth. Differences in sprout length are maintained even when the receptor for advanced glycation end products is inhibited. Our results demonstrate the ability to de-couple matrix stiffness from matrix density and structure in collagen gels, and that increased matrix stiffness results in increased sprouting and outgrowth. Copyright © 2012 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Microstructure characterization of Al matrix composite reinforced with Ti-6Al-4V meshes after compression by scanning electron microscope and transmission electron microscope.

PubMed

Guo, Q; Sun, D L; Han, X L; Cheng, S R; Chen, G Q; Jiang, L T; Wu, G H

2012-02-01

Compressive properties of Al matrix composite reinforced with Ti-6Al-4V meshes (TC4(m)/5A06 Al composite) under the strain rates of 10(-3)S(-1) and 1S(-1) at different temperature were measured and microstructure of composites after compression was characterized by scanning electron microscope (SEM) and transmission electron microscope (TEM). Compressive strength decreased with the test temperature increased and the strain-rate sensitivity (R) of composite increased with the increasing temperature. SEM observations showed that grains of Al matrix were elongated severely along 45° direction (angle between axis direction and fracture surface) and TC4 fibres were sheared into several parts in composite compressed under the strain rate of 10(-3)S(-1) at 25°C and 250°C. Besides, amounts of cracks were produced at the interfacial layer between TC4 fibre and Al matrix and in (Fe, Mn)Al(6) phases. With the compressive temperature increasing to 400°C, there was no damage at the interfacial layer between TC4 fibre and Al matrix and in (Fe, Mn)Al(6) phases, while equiaxed recrystal grains with sizes about 10 μm at the original grain boundaries of Al matrix were observed. However, interface separation of TC4 fibres and Al matrix occurred in composite compressed under the strain rate of 1S(-1) at 250°C and 400°C. With the compressive temperature increasing from 25°C to 100°C under the strain rate of 10(-3) S(-1), TEM microstructure in Al matrix exhibited high density dislocations and slipping bands (25°C), polygonized dislocations and dynamic recovery (100°C), equiaxed recrystals with sizes below 500 μm (250°C) and growth of equiaxed recrystals (400°C), respectively. Copyright © 2011 Elsevier Ltd. All rights reserved.

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.

Endocytosis of collagen by hepatic stellate cells regulates extracellular matrix dynamics

PubMed Central

Bi, Yan; Mukhopadhyay, Dhriti; Drinane, Mary; Ji, Baoan; Li, Xing; Cao, Sheng

2014-01-01

Hepatic stellate cells (HSCs) generate matrix, which in turn may also regulate HSCs function during liver fibrosis. We hypothesized that HSCs may endocytose matrix proteins to sense and respond to changes in microenvironment. Primary human HSCs, LX2, or mouse embryonic fibroblasts (MEFs) [wild-type; c-abl−/−; or Yes, Src, and Fyn knockout mice (YSF−/−)] were incubated with fluorescent-labeled collagen or gelatin. Fluorescence-activated cell sorting analysis and confocal microscopy were used for measuring cellular internalization of matrix proteins. Targeted PCR array and quantitative real-time PCR were used to evaluate gene expression changes. HSCs and LX2 cells endocytose collagens in a concentration- and time-dependent manner. Endocytosed collagen colocalized with Dextran 10K, a marker of macropinocytosis, and 5-ethylisopropyl amiloride, an inhibitor of macropinocytosis, reduced collagen internalization by 46%. Cytochalasin D and ML7 blocked collagen internalization by 47% and 45%, respectively, indicating that actin and myosin are critical for collagen endocytosis. Wortmannin and AKT inhibitor blocked collagen internalization by 70% and 89%, respectively, indicating that matrix macropinocytosis requires phosphoinositide-3-kinase (PI3K)/AKT signaling. Overexpression of dominant-negative dynamin-2 K44A blocked matrix internalization by 77%, indicating a role for dynamin-2 in matrix macropinocytosis. Whereas c-abl−/− MEF showed impaired matrix endocytosis, YSF−/− MEF surprisingly showed increased matrix endocytosis. It was also associated with complex gene regulations that related with matrix dynamics, including increased matrix metalloproteinase 9 (MMP-9) mRNA levels and zymographic activity. HSCs endocytose matrix proteins through macropinocytosis that requires a signaling network composed of PI3K/AKT, dynamin-2, and c-abl. Interaction with extracellular matrix regulates matrix dynamics through modulating multiple gene expressions including MMP-9. PMID:25080486

Endocytosis of collagen by hepatic stellate cells regulates extracellular matrix dynamics.

PubMed

Bi, Yan; Mukhopadhyay, Dhriti; Drinane, Mary; Ji, Baoan; Li, Xing; Cao, Sheng; Shah, Vijay H

2014-10-01

Hepatic stellate cells (HSCs) generate matrix, which in turn may also regulate HSCs function during liver fibrosis. We hypothesized that HSCs may endocytose matrix proteins to sense and respond to changes in microenvironment. Primary human HSCs, LX2, or mouse embryonic fibroblasts (MEFs) [wild-type; c-abl(-/-); or Yes, Src, and Fyn knockout mice (YSF(-/-))] were incubated with fluorescent-labeled collagen or gelatin. Fluorescence-activated cell sorting analysis and confocal microscopy were used for measuring cellular internalization of matrix proteins. Targeted PCR array and quantitative real-time PCR were used to evaluate gene expression changes. HSCs and LX2 cells endocytose collagens in a concentration- and time-dependent manner. Endocytosed collagen colocalized with Dextran 10K, a marker of macropinocytosis, and 5-ethylisopropyl amiloride, an inhibitor of macropinocytosis, reduced collagen internalization by 46%. Cytochalasin D and ML7 blocked collagen internalization by 47% and 45%, respectively, indicating that actin and myosin are critical for collagen endocytosis. Wortmannin and AKT inhibitor blocked collagen internalization by 70% and 89%, respectively, indicating that matrix macropinocytosis requires phosphoinositide-3-kinase (PI3K)/AKT signaling. Overexpression of dominant-negative dynamin-2 K44A blocked matrix internalization by 77%, indicating a role for dynamin-2 in matrix macropinocytosis. Whereas c-abl(-/-) MEF showed impaired matrix endocytosis, YSF(-/-) MEF surprisingly showed increased matrix endocytosis. It was also associated with complex gene regulations that related with matrix dynamics, including increased matrix metalloproteinase 9 (MMP-9) mRNA levels and zymographic activity. HSCs endocytose matrix proteins through macropinocytosis that requires a signaling network composed of PI3K/AKT, dynamin-2, and c-abl. Interaction with extracellular matrix regulates matrix dynamics through modulating multiple gene expressions including MMP-9. Copyright © 2014 the American Physiological Society.

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.

Quantum Effects at a Proton Relaxation at Low Temperatures

NASA Astrophysics Data System (ADS)

Kalytka, V. A.; Korovkin, M. V.

2016-11-01

Quantum effects during migratory polarization in multi-well crystals (including multi-well silicates and crystalline hydrates) are investigated in a variable electric field at low temperatures by direct quantum-mechanical calculations. Based on analytical solution of the quantum Liouville kinetic equation in the linear approximation for the polarizing field, the non-stationary density matrix is calculated for an ensemble of non-interacting protons moving in the field of one-dimensional multi-well crystal potential relief of rectangular shape. An expression for the complex dielectric constant convenient for a comparison with experiment and calculation of relaxer parameters is derived using the nonequilibrium polarization density matrix. The density matrix apparatus can be used for analytical investigation of the quantum mechanism of spontaneous polarization of a ferroelectric material (KDP and DKDP).

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Quantum non-Abelian hydrodynamics: Anyonic or spin-orbital entangled liquids, nonunitarity of scattering matrix and charge fractionalization

NASA Astrophysics Data System (ADS)

Pareek, Tribhuvan Prasad

2015-09-01

In this article, we develop an exact (nonadiabatic, nonperturbative) density matrix scattering theory for a two component quantum liquid which interacts or scatters off from a generic spin-dependent quantum potential. The generic spin dependent quantum potential [Eq. (1)] is a matrix potential, hence, adiabaticity criterion is ill-defined. Therefore the full matrix potential should be treated nonadiabatically. We succeed in doing so using the notion of vectorial matrices which allows us to obtain an exact analytical expression for the scattered density matrix (SDM), ϱsc [Eq. (30)]. We find that the number or charge density in scattered fluid, Tr(ϱsc), expressions in Eqs. (32) depends on nontrivial quantum interference coefficients, Qα β 0ijk, which arises due to quantum interference between spin-independent and spin-dependent scattering amplitudes and among spin-dependent scattering amplitudes. Further it is shown that Tr(ϱsc) can be expressed in a compact form [Eq. (39)] where the effect of quantum interference coefficients can be included using a vector Qαβ, which allows us to define a vector order parameterQ. Since the number density is obtained using an exact scattered density matrix, therefore, we do not need to prove that Q is non-zero. However, for sake of completeness, we make detailed mathematical analysis for the conditions under which the vector order parameterQ would be zero or nonzero. We find that in presence of spin-dependent interaction the vector order parameterQ is necessarily nonzero and is related to the commutator and anti-commutator of scattering matrix S with its dagger S† [Eq. (78)]. It is further shown that Q≠0, implies four physically equivalent conditions,i.e., spin-orbital entanglement is nonzero, non-Abelian scattering phase, i.e., matrices, scattering matrix is nonunitary and the broken time reversal symmetry for SDM. This also implies that quasi particle excitation are anyonic in nature, hence, charge fractionalization is a natural consequence. This aspect has also been discussed from the perspective of number or charge density conservation, which implies i.e., Tr(ϱ} sc) = Tr(ϱin). On the other hand Q = 0 turns out to be a mathematically forced unphysical solution in presence of spin-dependent potential or scattering which is equivalent to Abelian hydrodynamics, unitary scattering matrix, absence of spin-space entanglement and preserved time reversal symmetry. We have formulated the theory using mesoscopic language, specifically, we have considered two terminal systems connected to spin-dependent scattering region, which is equivalent to having two potential wells separated by a generic spin-dependent potential barrier. The formulation using mesoscopic language is practically useful because it leads directly to the measured quantities such as conductance and spin-polarization density in the leads, however, the presented formulation is not limited to the mesoscopic system only, its generality has been stressed at various places in this article.

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

Glycerol in micellar confinement with tunable rigidity

NASA Astrophysics Data System (ADS)

Lannert, Michael; Müller, Allyn; Gouirand, Emmanuel; Talluto, Vincenzo; Rosenstihl, Markus; Walther, Thomas; Stühn, Bernd; Blochowicz, Thomas; Vogel, Michael

2016-12-01

We investigate the glassy dynamics of glycerol in the confinement of a microemulsion system, which is stable on cooling down to the glass transition of its components. By changing the composition, we vary the viscosity of the matrix, while keeping the confining geometry intact, as is demonstrated by small angle X-ray scattering. By means of 2H NMR, differential scanning calorimetry, and triplet solvation dynamics we, thus, probe the dynamics of glycerol in confinements of varying rigidity. 2H NMR results show that, at higher temperatures, the dynamics of confined glycerol is unchanged compared to bulk behavior, while the reorientation of glycerol molecules becomes significantly faster than in the bulk in the deeply supercooled regime. However, comparison of different 2H NMR findings with data from calorimetry and solvation dynamics reveals that this acceleration is not due to the changed structural relaxation of glycerol, but rather due to the rotational motion of essentially rigid glycerol droplets or of aggregates of such droplets in a more fluid matrix. Thus, independent of the matrix mobility, the glycerol dynamics remains unchanged except for the smallest droplets, where an increase of Tg and, thus, a slowdown of the structural relaxation is observed even in a fluid matrix.

Terrestrial population models for ecological risk assessment: A state-of-the-art review

USGS Publications Warehouse

Emlen, J.M.

1989-01-01

Few attempts have been made to formulate models for predicting impacts of xenobiotic chemicals on wildlife populations. However, considerable effort has been invested in wildlife optimal exploitation models. Because death from intoxication has a similar effect on population dynamics as death by harvesting, these management models are applicable to ecological risk assessment. An underlying Leslie-matrix bookkeeping formulation is widely applicable to vertebrate wildlife populations. Unfortunately, however, the various submodels that track birth, death, and dispersal rates as functions of the physical, chemical, and biotic environment are by their nature almost inevitably highly species- and locale-specific. Short-term prediction of one-time chemical applications requires only information on mortality before and after contamination. In such cases a simple matrix formulation may be adequate for risk assessment. But generally, risk must be projected over periods of a generation or more. This precludes generic protocols for risk assessment and also the ready and inexpensive predictions of a chemical's influence on a given population. When designing and applying models for ecological risk assessment at the population level, the endpoints (output) of concern must be carefully and rigorously defined. The most easily accessible and appropriate endpoints are (1) pseudoextinction (the frequency or probability of a population falling below a prespecified density), and (2) temporal mean population density. Spatial and temporal extent of predicted changes must be clearly specified a priori to avoid apparent contradictions and confusion.

Multiscale simulations of PS-SiO2 nanocomposites: from melt to glassy state.

PubMed

Mathioudakis, I G; Vogiatzis, G G; Tzoumanekas, C; Theodorou, D N

2016-09-28

The interaction energetics, molecular packing, entanglement network properties, segmental dynamics, and elastic constants of atactic polystyrene-amorphous silica nanocomposites in the molten and the glassy state are studied via molecular simulations using two interconnected levels of representation: (a) a coarse-grained one, wherein each polystyrene repeat unit is mapped onto a single "superatom" and the silica nanoparticle is viewed as a solid sphere. Equilibration at all length scales at this level is achieved via connectivity-altering Monte Carlo simulations. (b) A united-atom (UA) level, wherein the polymer chains are represented in terms of a united-atom forcefield and the silica nanoparticle is represented in terms of a simplified, fully atomistic model. Initial configurations for UA molecular dynamics (MD) simulations are obtained by reverse mapping well-equilibrated coarse-grained configurations. By analysing microcanonical UA MD trajectories, the polymer density profile is studied and the polymer is found to exhibit layering in the vicinity of the nanoparticle surface. An estimate of the enthalpy of mixing between polymer and nanoparticles, derived from the UA simulations, compares favourably against available experimental values. The dynamical behaviour of polystyrene (in neat and filled melt systems) is characterized in terms of bond orientation and dihedral angle time autocorrelation functions. At low concentration in the molten polymer matrix, silica nanoparticles are found to cause a slight deceleration of the segmental dynamics close to their surface compared to the bulk polymer. Well-equilibrated coarse-grained long-chain configurations are reduced to entanglement networks via topological analysis with the CReTA algorithm, yielding a slightly lower density of entanglements in the filled than in the neat systems. UA melt configurations are glassified by MD cooling. The elastic moduli of the resulting glassy nanocomposites are computed through an analysis of strain fluctuations in the undeformed state and through explicit mechanical deformation by MD, showing a stiffening of the polymer in the presence of nanoparticles. UA simulation results for the elastic constants are compared to continuum micromechanical calculations invoked in homogenization models of the overall mechanical behaviour of heterogeneous materials. They can be interpreted in terms of the presence of an "interphase" of approximate thickness 2 nm around the nanoparticles, with elastic constants intermediate between those of the filler and the matrix.

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.

Self-amplified CMOS image sensor using a current-mode readout circuit

NASA Astrophysics Data System (ADS)

Santos, Patrick M.; de Lima Monteiro, Davies W.; Pittet, Patrick

2014-05-01

The feature size of the CMOS processes decreased during the past few years and problems such as reduced dynamic range have become more significant in voltage-mode pixels, even though the integration of more functionality inside the pixel has become easier. This work makes a contribution on both sides: the possibility of a high signal excursion range using current-mode circuits together with functionality addition by making signal amplification inside the pixel. The classic 3T pixel architecture was rebuild with small modifications to integrate a transconductance amplifier providing a current as an output. The matrix with these new pixels will operate as a whole large transistor outsourcing an amplified current that will be used for signal processing. This current is controlled by the intensity of the light received by the matrix, modulated pixel by pixel. The output current can be controlled by the biasing circuits to achieve a very large range of output signal levels. It can also be controlled with the matrix size and this permits a very high degree of freedom on the signal level, observing the current densities inside the integrated circuit. In addition, the matrix can operate at very small integration times. Its applications would be those in which fast imaging processing, high signal amplification are required and low resolution is not a major problem, such as UV image sensors. Simulation results will be presented to support: operation, control, design, signal excursion levels and linearity for a matrix of pixels that was conceived using this new concept of sensor.

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.

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.

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

NASA Technical Reports Server (NTRS)

Gupta, K. K.

1975-01-01

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

The tissue-type plasminogen activator–plasminogen activator inhibitor 1 complex promotes neurovascular injury in brain trauma: evidence from mice and humans

PubMed Central

Sashindranath, Maithili; Sales, Eunice; Daglas, Maria; Freeman, Roxann; Samson, Andre L.; Cops, Elisa J.; Beckham, Simone; Galle, Adam; McLean, Catriona; Morganti-Kossmann, Cristina; Rosenfeld, Jeffrey V.; Madani, Rime; Vassalli, Jean-Dominique; Su, Enming J.; Lawrence, Daniel A.

2012-01-01

The neurovascular unit provides a dynamic interface between the circulation and central nervous system. Disruption of neurovascular integrity occurs in numerous brain pathologies including neurotrauma and ischaemic stroke. Tissue plasminogen activator is a serine protease that converts plasminogen to plasmin, a protease that dissolves blood clots. Besides its role in fibrinolysis, tissue plasminogen activator is abundantly expressed in the brain where it mediates extracellular proteolysis. However, proteolytically active tissue plasminogen activator also promotes neurovascular disruption after ischaemic stroke; the molecular mechanisms of this process are still unclear. Tissue plasminogen activator is naturally inhibited by serine protease inhibitors (serpins): plasminogen activator inhibitor-1, neuroserpin or protease nexin-1 that results in the formation of serpin:protease complexes. Proteases and serpin:protease complexes are cleared through high-affinity binding to low-density lipoprotein receptors, but their binding to these receptors can also transmit extracellular signals across the plasma membrane. The matrix metalloproteinases are the second major proteolytic system in the mammalian brain, and like tissue plasminogen activators are pivotal to neurological function but can also degrade structures of the neurovascular unit after injury. Herein, we show that tissue plasminogen activator potentiates neurovascular damage in a dose-dependent manner in a mouse model of neurotrauma. Surprisingly, inhibition of activity following administration of plasminogen activator inhibitor-1 significantly increased cerebrovascular permeability. This led to our finding that formation of complexes between tissue plasminogen activator and plasminogen activator inhibitor-1 in the brain parenchyma facilitates post-traumatic cerebrovascular damage. We demonstrate that following trauma, the complex binds to low-density lipoprotein receptors, triggering the induction of matrix metalloproteinase-3. Accordingly, pharmacological inhibition of matrix metalloproteinase-3 attenuates neurovascular permeability and improves neurological function in injured mice. Our results are clinically relevant, because concentrations of tissue plasminogen activator: plasminogen activator inhibitor-1 complex and matrix metalloproteinase-3 are significantly elevated in cerebrospinal fluid of trauma patients and correlate with neurological outcome. In a separate study, we found that matrix metalloproteinase-3 and albumin, a marker of cerebrovascular damage, were significantly increased in brain tissue of patients with neurotrauma. Perturbation of neurovascular homeostasis causing oedema, inflammation and cell death is an important cause of acute and long-term neurological dysfunction after trauma. A role for the tissue plasminogen activator–matrix metalloproteinase axis in promoting neurovascular disruption after neurotrauma has not been described thus far. Targeting tissue plasminogen activator: plasminogen activator inhibitor-1 complex signalling or downstream matrix metalloproteinase-3 induction may provide viable therapeutic strategies to reduce cerebrovascular permeability after neurotrauma. PMID:22822039

Simple derivation of the Lindblad equation

NASA Astrophysics Data System (ADS)

Pearle, Philip

2012-07-01

The Lindblad equation is an evolution equation for the density matrix in quantum theory. It is the general linear, Markovian, form which ensures that the density matrix is Hermitian, trace 1, positive and completely positive. Some elementary examples of the Lindblad equation are given. The derivation of the Lindblad equation presented here is ‘simple’ in that all it uses is the expression of a Hermitian matrix in terms of its orthonormal eigenvectors and real eigenvalues. Thus, it is appropriate for students who have learned the algebra of quantum theory. Where helpful, arguments are first given in a two-dimensional Hilbert space.

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.

Low-dimensional Representation of Error Covariance

NASA Technical Reports Server (NTRS)

Tippett, Michael K.; Cohn, Stephen E.; Todling, Ricardo; Marchesin, Dan

2000-01-01

Ensemble and reduced-rank approaches to prediction and assimilation rely on low-dimensional approximations of the estimation error covariances. Here stability properties of the forecast/analysis cycle for linear, time-independent systems are used to identify factors that cause the steady-state analysis error covariance to admit a low-dimensional representation. A useful measure of forecast/analysis cycle stability is the bound matrix, a function of the dynamics, observation operator and assimilation method. Upper and lower estimates for the steady-state analysis error covariance matrix eigenvalues are derived from the bound matrix. The estimates generalize to time-dependent systems. If much of the steady-state analysis error variance is due to a few dominant modes, the leading eigenvectors of the bound matrix approximate those of the steady-state analysis error covariance matrix. The analytical results are illustrated in two numerical examples where the Kalman filter is carried to steady state. The first example uses the dynamics of a generalized advection equation exhibiting nonmodal transient growth. Failure to observe growing modes leads to increased steady-state analysis error variances. Leading eigenvectors of the steady-state analysis error covariance matrix are well approximated by leading eigenvectors of the bound matrix. The second example uses the dynamics of a damped baroclinic wave model. The leading eigenvectors of a lowest-order approximation of the bound matrix are shown to approximate well the leading eigenvectors of the steady-state analysis error covariance matrix.

Detection of density dependence requires density manipulations and calculation of lambda.

PubMed

Fowler, N L; Overath, R Deborah; Pease, Craig M

2006-03-01

To investigate density-dependent population regulation in the perennial bunchgrass Bouteloua rigidiseta, we experimentally manipulated density by removing adults or adding seeds to replicate quadrats in a natural population for three annual intervals. We monitored the adjacent control quadrats for 14 annual intervals. We constructed a population projection matrix for each quadrat in each interval, calculated lambda, and did a life table response experiment (LTRE) analysis. We tested the effects of density upon lambda by comparing experimental and control quadrats, and by an analysis of the 15-year observational data set. As measured by effects on lambda and on N(t+1/Nt in the experimental treatments, negative density dependence was strong: the population was being effectively regulated. The relative contributions of different matrix elements to treatment effect on lambda differed among years and treatments; overall the pattern was one of small contributions by many different life cycle stages. In contrast, density dependence could not be detected using only the observational (control quadrats) data, even though this data set covered a much longer time span. Nor did experimental effects on separate matrix elements reach statistical significance. These results suggest that ecologists may fail to detect density dependence when it is present if they have only descriptive, not experimental, data, do not have data for the entire life cycle, or analyze life cycle components separately.

Modal identification of dynamic mechanical systems

NASA Astrophysics Data System (ADS)

Srivastava, R. K.; Kundra, T. K.

1992-07-01

This paper reviews modal identification techniques which are now helping designers all over the world to improve the dynamic behavior of vibrating engineering systems. In this context the need to develop more accurate and faster parameter identification is ever increasing. A new dynamic stiffness matrix based identification method which is highly accurate, fast and system-dynamic-modification compatible is presented. The technique is applicable to all those multidegree-of-freedom systems where full receptance matrix can be experimentally measured.

Slush-like polar structures in single-crystal relaxors

NASA Astrophysics Data System (ADS)

Takenaka, Hiroyuki; Grinberg, Ilya; Liu, Shi; Rappe, Andrew M.

2017-06-01

Despite more than 50 years of investigation, it is still unclear how the underlying structure of relaxor ferroelectrics gives rise to their defining properties, such as ultrahigh piezoelectric coefficients, high permittivity over a broad temperature range, diffuse phase transitions, strong frequency dependence in dielectric response, and phonon anomalies. The model of polar nanoregions inside a non-polar matrix has been widely used to describe the structure of relaxor ferroelectrics. However, the lack of precise knowledge about the shapes, growth and dipole patterns of polar nanoregions has led to the characterization of relaxors as “hopeless messes”, and no predictive model for relaxor behaviour is currently available. Here we use molecular dynamics simulations of the prototypical Pb(Mg1/3,Nb2/3)O3-PbTiO3 relaxor material to examine its structure and the spatial and temporal polarization correlations. Our simulations show that the unusual properties of relaxors stem from the presence of a multi-domain state with extremely small domain sizes (2-10 nanometres), and no non-polar matrix, owing to the local dynamics. We find that polar structures in the multi-domain state in relaxors are analogous to those of the slush state of water. The multi-domain structure of relaxors that is revealed by our molecular dynamics simulations is consistent with recent experimental diffuse scattering results and indicates that relaxors have a high density of low-angle domain walls. This insight explains the recently discovered classes of relaxors that cannot be described by the polar nanoregion model, and provides guidance for the design and synthesis of new relaxor materials.

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.

Matrix-Product-State Algorithm for Finite Fractional Quantum Hall Systems

NASA Astrophysics Data System (ADS)

Liu, Zhao; Bhatt, R. N.

2015-09-01

Exact diagonalization is a powerful tool to study fractional quantum Hall (FQH) systems. However, its capability is limited by the exponentially increasing computational cost. In order to overcome this difficulty, density-matrix-renormalization-group (DMRG) algorithms were developed for much larger system sizes. Very recently, it was realized that some model FQH states have exact matrix-product-state (MPS) representation. Motivated by this, here we report a MPS code, which is closely related to, but different from traditional DMRG language, for finite FQH systems on the cylinder geometry. By representing the many-body Hamiltonian as a matrix-product-operator (MPO) and using single-site update and density matrix correction, we show that our code can efficiently search the ground state of various FQH systems. We also compare the performance of our code with traditional DMRG. The possible generalization of our code to infinite FQH systems and other physical systems is also discussed.

Thermodynamic properties of water in confined environments: a Monte Carlo study

NASA Astrophysics Data System (ADS)

Gladovic, Martin; Bren, Urban; Urbic, Tomaž

2018-05-01

Monte Carlo simulations of Mercedes-Benz water in a crowded environment were performed. The simulated systems are representative of both composite, porous or sintered materials and living cells with typical matrix packings. We studied the influence of overall temperature as well as the density and size of matrix particles on water density, particle distributions, hydrogen bond formation and thermodynamic quantities. Interestingly, temperature and space occupancy of matrix exhibit a similar effect on water properties following the competition between the kinetic and the potential energy of the system, whereby temperature increases the kinetic and matrix packing decreases the potential contribution. A novel thermodynamic decomposition approach was applied to gain insight into individual contributions of different types of inter-particle interactions. This decomposition proved to be useful and in good agreement with the total thermodynamic quantities especially at higher temperatures and matrix packings, where higher-order potential-energy mixing terms lose their importance.

Hierarchical spatiotemporal matrix models for characterizing invasions

USGS Publications Warehouse

Hooten, M.B.; Wikle, C.K.; Dorazio, R.M.; Royle, J. Andrew

2007-01-01

The growth and dispersal of biotic organisms is an important subject in ecology. Ecologists are able to accurately describe survival and fecundity in plant and animal populations and have developed quantitative approaches to study the dynamics of dispersal and population size. Of particular interest are the dynamics of invasive species. Such nonindigenous animals and plants can levy significant impacts on native biotic communities. Effective models for relative abundance have been developed; however, a better understanding of the dynamics of actual population size (as opposed to relative abundance) in an invasion would be beneficial to all branches of ecology. In this article, we adopt a hierarchical Bayesian framework for modeling the invasion of such species while addressing the discrete nature of the data and uncertainty associated with the probability of detection. The nonlinear dynamics between discrete time points are intuitively modeled through an embedded deterministic population model with density-dependent growth and dispersal components. Additionally, we illustrate the importance of accommodating spatially varying dispersal rates. The method is applied to the specific case of the Eurasian Collared-Dove, an invasive species at mid-invasion in the United States at the time of this writing.

Hierarchical spatiotemporal matrix models for characterizing invasions

USGS Publications Warehouse

Hooten, M.B.; Wikle, C.K.; Dorazio, R.M.; Royle, J. Andrew

2007-01-01

The growth and dispersal of biotic organisms is an important subject in ecology. Ecologists are able to accurately describe survival and fecundity in plant and animal populations and have developed quantitative approaches to study the dynamics of dispersal and population size. Of particular interest are the dynamics of invasive species. Such nonindigenous animals and plants can levy significant impacts on native biotic communities. Effective models for relative abundance have been developed; however, a better understanding of the dynamics of actual population size (as opposed to relative abundance) in an invasion would be beneficial to all branches of ecology. In this article, we adopt a hierarchical Bayesian framework for modeling the invasion of such species while addressing the discrete nature of the data and uncertainty associated with the probability of detection. The nonlinear dynamics between discrete time points are intuitively modeled through an embedded deterministic population model with density-dependent growth and dispersal components. Additionally, we illustrate the importance of accommodating spatially varying dispersal rates. The method is applied to the specific case of the Eurasian Collared-Dove, an invasive species at mid-invasion in the United States at the time of this writing. ?? 2006, The International Biometric Society.

Matrix density effects on the mechanical properties of SiC/RBSN composites

NASA Technical Reports Server (NTRS)

Bhatt, Ramakrishna T.; Kiser, James D.

1990-01-01

The room temperature mechanical properties were measured for SiC fiber reinforced reaction-bonded silicon nitride composites (SiC/RBSN) of different densities. The composites consisted of approx. 30 vol percent uniaxially aligned 142 micron diameter SiC fibers (Textron SCS-6) in a reaction-bonded Si3N4 matrix. The composite density was varied by changing the consolidation pressure during RBSN processing and by hot isostatically pressing the SiC/RBSN composites. Results indicate that as the consolidation pressure was increased from 27 to 138 MPa, the average pore size of the nitrided composites decreased from 0.04 to 0.02 microns and the composite density increased from 2.07 to 2.45 gm/cc. Nonetheless, these improvements resulted in only small increases in the first matrix cracking stress, primary elastic modulus, and ultimate tensile strength values of the composites. In contrast, HIP consolidation of SiC/RBSN resulted in a fully dense material whose first matrix cracking stress and elastic modulus were approx. 15 and 50 percent higher, respectively, and ultimate tensile strength values were approx. 40 percent lower than those for unHIPed SiC/RBSN composites. The modulus behavior for all specimens can be explained by simple rule-of-mixture theory. Also, the loss in ultimate strength for the HIPed composites appears to be related to a degradation in fiber strength at the HIP temperature. However, the density effect on matrix fracture strength was much less than would be expected based on typical monolithic Si3N4 behavior, suggesting that composite theory is indeed operating. Possible practical implications of these observations are discussed.

Matrix product algorithm for stochastic dynamics on networks applied to nonequilibrium Glauber dynamics

NASA Astrophysics Data System (ADS)

Barthel, Thomas; De Bacco, Caterina; Franz, Silvio

2018-01-01

We introduce and apply an efficient method for the precise simulation of stochastic dynamical processes on locally treelike graphs. Networks with cycles are treated in the framework of the cavity method. Such models correspond, for example, to spin-glass systems, Boolean networks, neural networks, or other technological, biological, and social networks. Building upon ideas from quantum many-body theory, our approach is based on a matrix product approximation of the so-called edge messages—conditional probabilities of vertex variable trajectories. Computation costs and accuracy can be tuned by controlling the matrix dimensions of the matrix product edge messages (MPEM) in truncations. In contrast to Monte Carlo simulations, the algorithm has a better error scaling and works for both single instances as well as the thermodynamic limit. We employ it to examine prototypical nonequilibrium Glauber dynamics in the kinetic Ising model. Because of the absence of cancellation effects, observables with small expectation values can be evaluated accurately, allowing for the study of decay processes and temporal correlations.

The free and forced vibrations of structures using the finite dynamic element method. Ph.D. Thesis, Aug. 1991 Final Report

NASA Technical Reports Server (NTRS)

Fergusson, Neil J.

1992-01-01

In addition to an extensive review of the literature on exact and corrective displacement based methods of vibration analysis, a few theorems are proven concerning the various structural matrices involved in such analyses. In particular, the consistent mass matrix and the quasi-static mass matrix are shown to be equivalent, in the sense that the terms in their respective Taylor expansions are proportional to one another, and that they both lead to the same dynamic stiffness matrix when used with the appropriate stiffness matrix.

Molecular dynamics insight to phase transition in n-alkanes with carbon nanofillers

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

Rastogi, Monisha; Vaish, Rahul, E-mail: rahul@iitmandi.ac.in; Materials Research Centre, Indian Institute of Science, Bangalore 560 012

2015-05-15

The present work aims to investigate the phase transition, dispersion and diffusion behavior of nanocomposites of carbon nanotube (CNT) and straight chain alkanes. These materials are potential candidates for organic phase change materials(PCMs) and have attracted flurry of research recently. Accurate experimental evaluation of the mass, thermal and transport properties of such composites is both difficult as well as economically taxing. Additionally it is crucial to understand the factors that results in modification or enhancement of their characteristic at atomic or molecular level. Classical molecular dynamics approach has been extended to elucidate the same. Bulk atomistic models have been generatedmore » and subjected to rigorous multistage equilibration. To reaffirm the approach, both canonical and constant-temperature, constant- pressure ensembles were employed to simulate the models under consideration. Explicit determination of kinetic, potential, non-bond and total energy assisted in understanding the enhanced thermal and transport property of the nanocomposites from molecular point of view. Crucial parameters including mean square displacement and simulated self diffusion coefficient precisely define the balance of the thermodynamic and hydrodynamic interactions. Radial distribution function also reflected the density variation, strength and mobility of the nanocomposites. It is expected that CNT functionalization could improve the dispersion within n-alkane matrix. This would further ameliorate the mass and thermal properties of the composite. Additionally, the determined density was in good agreement with experimental data. Thus, molecular dynamics can be utilized as a high throughput technique for theoretical investigation of nanocomposites PCMs.« less

Ultrafast Electronic Relaxation through a Conical Intersection: Nonadiabatic Dynamics Disentangled through an Oscillator Strength-Based Diabatization Framework

DOE PAGES

Medders, Gregory R.; Alguire, Ethan C.; Jain, Amber; ...

2017-01-18

Here, we employ surface hopping trajectories to model the short-time dynamics of gas-phase and partially solvated 4-(N,N-dimethylamino)benzonitrile (DMABN), a dual fluorescent molecule that is known to undergo a nonadiabatic transition through a conical intersection. To compare theory vs time-resolved fluorescence measurements, we calculate the mixed quantum–classical density matrix and the ensemble averaged transition dipole moment. We introduce a diabatization scheme based on the oscillator strength to convert the TDDFT adiabatic states into diabatic states of L a and L b character. Somewhat surprisingly, we find that the rate of relaxation reported by emission to the ground state is almost 50%more » slower than the adiabatic population relaxation. Although our calculated adiabatic rates are largely consistent with previous theoretical calculations and no obvious effects of decoherence are seen, the diabatization procedure introduced here enables an explicit picture of dynamics in the branching plane, raising tantalizing questions about geometric phase effects in systems with dozens of atoms.« less

Effect of impurity molecules on the low-temperature vibrational dynamics of polyisobutylene: Investigation by single-molecule spectroscopy

NASA Astrophysics Data System (ADS)

Eremchev, I. Yu.; Naumov, A. V.; Vainer, Yu. G.; Kador, L.

2009-05-01

The influence of impurity chromophore molecules—tetra-tert-butylterrylene (TBT) and dibenzo-anthanthrene (DBATT)—on the vibrational dynamics of the amorphous polymer polyisobutylene (PIB) has been studied via single-molecule spectroscopy. The measurements were performed in the temperature region of 7-30 K, where the interaction of the chromophores with quasilocalized low-frequency vibrational modes (LFMs) determines the observed spectral line broadening. The analysis of the individual temperature dependences of the linewidths for a large number of single probe molecules yielded effective frequency values of those LFMs which are located near the respective chromophores. In this way the distributions of the LFM frequencies were measured for the two systems, and they were found to be similar. Moreover, they are in good agreement with the vibrational density of states as measured in pure PIB by inelastic neutron scattering. This allows us to conclude that, at least in the case of PIB, doping with low concentrations of the nonpolar and neutral molecules TBT and DBATT does not affect the vibrational dynamics of the matrix markedly.

Effective field theory of dissipative fluids (II): classical limit, dynamical KMS symmetry and entropy current

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

Glorioso, Paolo; Crossley, Michael; Liu, Hong

2017-09-20

Here in this paper we further develop the fluctuating hydrodynamics proposed in a number of ways. We first work out in detail the classical limit of the hydrodynamical action, which exhibits many simplifications. In particular, this enables a transparent formulation of the action in physical spacetime in the presence of arbitrary external fields. It also helps to clarify issues related to field redefinitions and frame choices. We then propose that the action is invariant under a Z2 symmetry to which we refer as the dynamical KMS symmetry. The dynamical KMS symmetry is physically equivalent to the previously proposed local KMSmore » condition in the classical limit, but is more convenient to implement and more general. It is applicable to any states in local equilibrium rather than just thermal density matrix perturbed by external background fields. Finally we elaborate the formulation for a conformal fluid, which contains some new features, and work out the explicit form of the entropy current to second order in derivatives for a neutral conformal fluid.« less

Dynamical Localization for Discrete Anderson Dirac Operators

NASA Astrophysics Data System (ADS)

Prado, Roberto A.; de Oliveira, César R.; Carvalho, Silas L.

2017-04-01

We establish dynamical localization for random Dirac operators on the d-dimensional lattice, with d\\in { 1, 2, 3} , in the three usual regimes: large disorder, band edge and 1D. These operators are discrete versions of the continuous Dirac operators and consist in the sum of a discrete free Dirac operator with a random potential. The potential is a diagonal matrix formed by different scalar potentials, which are sequences of independent and identically distributed random variables according to an absolutely continuous probability measure with bounded density and of compact support. We prove the exponential decay of fractional moments of the Green function for such models in each of the above regimes, i.e., (j) throughout the spectrum at larger disorder, (jj) for energies near the band edges at arbitrary disorder and (jjj) in dimension one, for all energies in the spectrum and arbitrary disorder. Dynamical localization in theses regimes follows from the fractional moments method. The result in the one-dimensional regime contrast with one that was previously obtained for 1D Dirac model with Bernoulli potential.

Limitation of Cell Adhesion by the Elasticity of the Extracellular Matrix

PubMed Central

Nicolas, Alice; Safran, Samuel. A.

2006-01-01

Cell/matrix adhesions are modulated by cytoskeletal or external stresses and adapt to the mechanical properties of the extracellular matrix. We propose that this mechanosensitivity arises from the activation of a mechanosensor located within the adhesion itself. We show that this mechanism accounts for the observed directional growth of focal adhesions and the reduction or even cessation of their growth when cells adhere to a soft extracellular matrix. We predict quantitatively that both the elasticity and the thickness of the matrix play a key role in the dynamics of focal adhesions. Two different types of dynamics are expected depending on whether the thickness of the matrix is of order of or much larger than the adhesion size. In the latter situation, we predict that the adhesion region reaches a saturation size that can be tuned by the mechanical properties of the matrix. PMID:16581840

Density-matrix description of heteronuclear decoupling in A mX n systems

NASA Astrophysics Data System (ADS)

McClung, R. E. D.; John, Boban K.

A detailed investigation of the effects of ordinary noise decoupling and spherical randomization decoupling on the elements of the density matrix for A mX n spin systems is presented. The elements are shown to reach steady-state values in the rotating frame of the decoupled nuclei when the decoupling field is strong and is applied for a sufficient time interval. The steady-state values are found to be linear combinations of the density-matrix elements at the beginning of the decoupling period, and often involve mixing of populations with multiple-quantum coherences, and mixing of the perpendicular components of the magnetization with higher coherences. This description of decoupling is shown to account for the "illusions" of spin decoupling in 2D gated-decoupler 13C J-resolved spectra reported by Levitt et al.

Optimization of metabolite detection by quantum mechanics simulations in magnetic resonance spectroscopy.

PubMed

Gambarota, Giulio

2017-07-15

Magnetic resonance spectroscopy (MRS) is a well established modality for investigating tissue metabolism in vivo. In recent years, many efforts by the scientific community have been directed towards the improvement of metabolite detection and quantitation. Quantum mechanics simulations allow for investigations of the MR signal behaviour of metabolites; thus, they provide an essential tool in the optimization of metabolite detection. In this review, we will examine quantum mechanics simulations based on the density matrix formalism. The density matrix was introduced by von Neumann in 1927 to take into account statistical effects within the theory of quantum mechanics. We will discuss the main steps of the density matrix simulation of an arbitrary spin system and show some examples for the strongly coupled two spin system. Copyright © 2016 Elsevier Inc. All rights reserved.

Multiconfiguration Pair-Density Functional Theory.

PubMed

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

2014-09-09

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

Generalized Gibbs ensembles for quantum field theories

NASA Astrophysics Data System (ADS)

Essler, F. H. L.; Mussardo, G.; Panfil, M.

2015-05-01

We consider the nonequilibrium dynamics in quantum field theories (QFTs). After being prepared in a density matrix that is not an eigenstate of the Hamiltonian, such systems are expected to relax locally to a stationary state. In the presence of local conservation laws, these stationary states are believed to be described by appropriate generalized Gibbs ensembles. Here we demonstrate that in order to obtain a correct description of the stationary state, it is necessary to take into account conservation laws that are not (ultra)local in the usual sense of QFTs, but fulfill a significantly weaker form of locality. We discuss the implications of our results for integrable QFTs in one spatial dimension.

An update on the BQCD Hybrid Monte Carlo program

NASA Astrophysics Data System (ADS)

Haar, Taylor Ryan; Nakamura, Yoshifumi; Stüben, Hinnerk

2018-03-01

We present an update of BQCD, our Hybrid Monte Carlo program for simulating lattice QCD. BQCD is one of the main production codes of the QCDSF collaboration and is used by CSSM and in some Japanese finite temperature and finite density projects. Since the first publication of the code at Lattice 2010 the program has been extended in various ways. New features of the code include: dynamical QED, action modification in order to compute matrix elements by using Feynman-Hellman theory, more trace measurements (like Tr(D-n) for K, cSW and chemical potential reweighting), a more flexible integration scheme, polynomial filtering, term-splitting for RHMC, and a portable implementation of performance critical parts employing SIMD.

NMR lineshape equations for hindered methyl group: a comparison of the semi-classical and quantum mechanical models

NASA Astrophysics Data System (ADS)

Bernatowicz, P.; Szymański, S.

2003-09-01

The semiclassical and quantum mechanical NMR lineshape equations for a hindered methyl group are compared. In both the approaches, the stochastic dynamics can be interpreted in terms of a progressive symmetrization of the spin density matrix. However, the respective ways of achieving the same limiting symmetry can be remarkably different. From numerical lineshape simulations it is inferred that in the regime of intermediate exchange, where the conventional theory predicts occurrence of a single Lorentzian, the actual spectrum can have nontrivial features. This observation may open new perspectives in the search for nonclassical effects in the stochastic behavior of methyl groups in liquid-phase NMR.

Ionic effect investigation of a potentiometric sensor for urea and surface morphology observation of entrapped urease/polypyrrole matrix.

PubMed

Syu, Mei-Jywan; Chang, Yu-Sung

2009-04-15

Potentio-dynamic polymerization of buffered urease and pyrrole monomer onto carbon papers was conducted to fabricate an immobilized urease electrode for measuring the urea concentration. To use carbon paper as the substrate for the electro-growth of polypyrrole matrix not only created sufficient adhesion of the conducting polymer layer but also provided superior entrapment of urease enzymes. The potentiometric response corresponding to ammonia, the product formed from the urease catalyzed urea reaction, was employed for the urea concentration measurement. Scanning electron microscopic photographs showed that the polypyrrole matrix deposited on the carbon papers appeared to be of a cylindrical nanotube shape. The charge density applied in the polymerization was found to affect the potentiometric response while the potential-scanning rate showed minor influence. The composite electrodes had high sensitivity in urea detection, showing a response linear to the logarithm of the urea concentration in the range of 10(-3) to 10 mM. The detection of urea solution prepared in water and buffer was also compared. Ionic effect on the sensing of urea solution was investigated. By comparing the data reported in literature, the urease/polypyrrole/carbon paper electrode developed in this work showed superior long-term stability and reusability. The detection of urea in serum was also well performed.

Porosity and Permeability of Chondritic Materials

NASA Technical Reports Server (NTRS)

Zolensky, Michael E.; Corrigan, Catherine M.; Dahl, Jason; Long, Michael

1996-01-01

We have investigated the porosity of a large number of chondritic interplanetary dust particles and meteorites by three techniques: standard liquid/gas flow techniques, a new, non-invasive ultrasonic technique, and image processing of backscattered images . The latter technique is obviously best suited to sub-kg sized samples. We have also measured the gas and liquid permeabilities of some chondrites by two techniques: standard liquid/gas flow techniques, and a new, non-destructive pressure release technique. We find that chondritic IDP's have a somewhat bimodal porosity distribution. Peaks are present at 0 and 4% porosity; a tail then extends to 53%. These values suggest IDP bulk densities of 1.1 to 3.3 g/cc. Type 1-3 chondrite matrix porosities range up to 30%, with a peak at 2%. The bulk porosities for type 1-3 chondrites have the same approximate range as exhibited by matrix, indicating that other components of the bulk meteorites (including chondrules and aggregates) have the same average porosity as matrix. These results reveal that the porosity of primitive materials at scales ranging from nanogram to kilogram are similar, implying similar accretion dynamics operated through 12 orders of size magnitude. Permeabilities of the investigated chondrites vary by several orders of magnitude, and there appears to be no simple dependence of permeability with degree of aqueous alteration, or chondrite type.

Numerically Exact Long Time Magnetization Dynamics Near the Nonequilibrium Kondo Regime

NASA Astrophysics Data System (ADS)

Cohen, Guy; Gull, Emanuel; Reichman, David; Millis, Andrew; Rabani, Eran

2013-03-01

The dynamical and steady-state spin response of the nonequilibrium Anderson impurity model to magnetic fields, bias voltages, and temperature is investigated by a numerically exact method which allows access to unprecedentedly long times. The method is based on using real, continuous time bold Monte Carlo techniques--quantum Monte Carlo sampling of diagrammatic corrections to a partial re-summation--in order to compute the kernel of a memory function, which is then used to determine the reduced density matrix. The method owes its effectiveness to the fact that the memory kernel is dominated by relatively short-time properties even when the system's dynamics are long-ranged. We make predictions regarding the non-monotonic temperature dependence of the system at high bias voltage and the oscillatory quench dynamics at high magnetic fields. We also discuss extensions of the method to the computation of transport properties and correlation functions, and its suitability as an impurity solver free from the need for analytical continuation in the context of dynamical mean field theory. This work is supported by the US Department of Energy under grant DE-SC0006613, by NSF-DMR-1006282 and by the US-Israel Binational Science Foundation. GC is grateful to the Yad Hanadiv-Rothschild Foundation for the award of a Rothschild Fellowship.

Magnetic field dependent dynamics and field-driven metal-to-insulator transition of the half-filled Hubbard model: A DMFT+DMRG study

DOE PAGES

Zhu, Wei; Sheng, D. N.; Zhu, Jian -Xin

2017-08-14

Here, we study the magnetic field-driven metal-to-insulator transition in half-filled Hubbard model on the Bethe lattice, using the dynamical mean-field theory by solving the quantum impurity problem with density-matrix renormalization group algorithm. The method enables us to obtain a high-resolution spectral densities in the presence of a magnetic field. It is found that the Kondo resonance at the Fermi level splits at relatively high magnetic field: the spin-up and -down components move away from the Fermi level and finally form a spin-polarized band insulator. By calculating the magnetization and spin susceptibility, we clarify that an applied magnetic field drives amore » transition from a paramagnetic metallic phase to a band insulating phase. In the weak interaction regime, the nature of the transition is continuous and captured by the Stoner's description, while in the strong interaction regime the transition is very likely to be metamagnetic, evidenced by the hysteresis curve. Furthermore, we determine the phase boundary by tracking the kink in the magnetic susceptibility, and the steplike change of the entanglement entropy and the entanglement gap closing. Interestingly, the phase boundaries determined from these two different ways are largely consistent with each other.« less

Magnetic field dependent dynamics and field-driven metal-to-insulator transition of the half-filled Hubbard model: A DMFT+DMRG study

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

Zhu, Wei; Sheng, D. N.; Zhu, Jian -Xin

Here, we study the magnetic field-driven metal-to-insulator transition in half-filled Hubbard model on the Bethe lattice, using the dynamical mean-field theory by solving the quantum impurity problem with density-matrix renormalization group algorithm. The method enables us to obtain a high-resolution spectral densities in the presence of a magnetic field. It is found that the Kondo resonance at the Fermi level splits at relatively high magnetic field: the spin-up and -down components move away from the Fermi level and finally form a spin-polarized band insulator. By calculating the magnetization and spin susceptibility, we clarify that an applied magnetic field drives amore » transition from a paramagnetic metallic phase to a band insulating phase. In the weak interaction regime, the nature of the transition is continuous and captured by the Stoner's description, while in the strong interaction regime the transition is very likely to be metamagnetic, evidenced by the hysteresis curve. Furthermore, we determine the phase boundary by tracking the kink in the magnetic susceptibility, and the steplike change of the entanglement entropy and the entanglement gap closing. Interestingly, the phase boundaries determined from these two different ways are largely consistent with each other.« less

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

NASA Technical Reports Server (NTRS)

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

1993-01-01

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

Microscopic and histochemical manifestations of hyaline cartilage dynamics.

PubMed

Malinin, G I; Malinin, T I

1999-01-01

Structure and function of hyaline cartilages has been the focus of many correlative studies for over a hundred years. Much of what is known regarding dynamics and function of cartilage constituents has been derived or inferred from biochemical and electron microscopic investigations. Here we show that in conjunction with ultrastructural, and high-magnification transmission light and polarization microscopy, the well-developed histochemical methods are indispensable for the analysis of cartilage dynamics. Microscopically demonstrable aspects of cartilage dynamics include, but are not limited to, formation of the intracellular liquid crystals, phase transitions of the extracellular matrix and tubular connections between chondrocytes. The role of the interchondrocytic liquid crystals is considered in terms of the tensegrity hypothesis and non-apoptotic cell death. Phase transitions of the extracellular matrix are discussed in terms of self-alignment of chondrons, matrix guidance pathways and cartilage growth in the absence of mitosis. The possible role of nonenzymatic glycation reactions in cartilage dynamics is also reviewed.

Microscopic Chain Motion in Polymer Nanocomposites with Dynamically Asymmetric Interphases

PubMed Central

Senses, Erkan; Faraone, Antonio; Akcora, Pinar

2016-01-01

Dynamics of the interphase region between matrix and bound polymers on nanoparticles is important to understand the macroscopic rheological properties of nanocomposites. Here, we present neutron scattering investigations on nanocomposites with dynamically asymmetric interphases formed by a high-glass transition temperature polymer, poly(methyl methacrylate), adsorbed on nanoparticles and a low-glass transition temperature miscible matrix, poly(ethylene oxide). By taking advantage of selective isotope labeling of the chains, we studied the role of interfacial polymer on segmental and collective dynamics of the matrix chains from subnanoseconds to 100 nanoseconds. Our results show that the Rouse relaxation remains unchanged in a weakly attractive composite system while the dynamics significantly slows down in a strongly attractive composite. More importantly, the chains disentangle with a remarkable increase of the reptation tube size when the bound polymer is vitreous. The glassy and rubbery states of the bound polymer as temperature changes underpin the macroscopic stiffening of nanocomposites. PMID:27457056

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

NASA Astrophysics Data System (ADS)

Li, Yonghui; Ullrich, Carsten

2013-03-01

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

Comparison of collagen matrix treatment impregnated with platelet rich plasma vs bone marrow.

PubMed

Minamimura, Ai; Ichioka, Shigeru; Sano, Hitomi; Sekiya, Naomi

2014-02-01

This study has reported the efficacy of an autologous bone marrow-impregnated collagen matrix experimentally and clinically. Then, it reflected that platelet rich plasma (PRP) was as good a source of growth factors as bone marrow and available in a less invasive procedure. This study aimed to compare the efficacy of a PRP-impregnated collagen matrix with that of a bone marrow-impregnated collagen matrix by quantifying wound size and capillary density using genetically diabetic db/db mice. Bone marrow cells were obtained from femurs of ddy mice. Then, a small amount of collagen matrix was immersed in bone marrow suspension. This is called a bone marrow-impregnated collagen matrix. PRP was obtained from healthy human blood and a small amount of collagen matrix was immersed in PRP. This is called a PRP-impregnated collagen matrix. A bone marrow-impregnated collagen matrix and PRP-impregnated collagen matrix were applied to excisional skin wounds on a genetically healing-impaired mouse (n = 6) and wounds were evaluated 6 days after the procedure. Wounds were divided into two groups: PRP (n = 6), in which a PRP-impregnated collagen matrix was applied; and bone marrow (n = 6), in which collagen immersed in a bone marrow suspension was applied. There was no significant difference between the PRP and bone-marrow groups in the rate of vascular density increase or wound size decrease. The present study suggested that the PRP-impregnated collagen matrix promotes repair processes at least as strongly as the bone marrow-impregnated collagen matrix. Given lower invasiveness, the PRP-impregnated collagen matrix would have advantages in clinical use.

Effect of process parameters on the density and porosity of laser melted AlSi10Mg/SiC metal matrix composite

NASA Astrophysics Data System (ADS)

Famodimu, Omotoyosi H.; Stanford, Mark; Oduoza, Chike F.; Zhang, Lijuan

2018-06-01

Laser melting of aluminium alloy—AlSi10Mg has increasingly been used to create specialised products in various industrial applications, however, research on utilising laser melting of aluminium matrix composites in replacing specialised parts have been slow on the uptake. This has been attributed to the complexity of the laser melting process, metal/ceramic feedstock for the process and the reaction of the feedstock material to the laser. Thus, an understanding of the process, material microstructure and mechanical properties is important for its adoption as a manufacturing route of aluminium metal matrix composites. The effects of several parameters of the laser melting process on the mechanical blended composite were thus investigated in this research. This included single track formations of the matrix alloy and the composite alloyed with 5% and 10% respectively for their reaction to laser melting and the fabrication of density blocks to investigate the relative density and porosity over different scan speeds. The results from these experiments were utilised in determining a process window in fabricating near-fully dense parts.

Collective neutrino oscillations and neutrino wave packets

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

Akhmedov, Evgeny; Lindner, Manfred; Kopp, Joachim, E-mail: akhmedov@mpi-hd.mpg.de, E-mail: jkopp@uni-mainz.de, E-mail: lindner@mpi-hd.mpg.de

Effects of decoherence by wave packet separation on collective neutrino oscillations in dense neutrino gases are considered. We estimate the length of the wave packets of neutrinos produced in core collapse supernovae and the expected neutrino coherence length, and then proceed to consider the decoherence effects within the density matrix formalism of neutrino flavour transitions. First, we demonstrate that for neutrino oscillations in vacuum the decoherence effects are described by a damping term in the equation of motion of the density matrix of a neutrino as a whole (as contrasted to that of the fixed-momentum components of the neutrino densitymore » matrix). Next, we consider neutrino oscillations in ordinary matter and dense neutrino backgrounds, both in the adiabatic and non-adiabatic regimes. In the latter case we study two specific models of adiabaticity violation—one with short-term and another with extended non-adiabaticity. It is demonstrated that, while in the adiabatic case a damping term is present in the equation of motion of the neutrino density matrix (just like in the vacuum oscillation case), no such term in general appears in the non-adiabatic regime.« less

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.

Frustration-induced internal stresses are responsible for quasilocalized modes in structural glasses

NASA Astrophysics Data System (ADS)

Lerner, Edan; Bouchbinder, Eran

2018-03-01

It has been recently shown [E. Lerner, G. Düring, and E. Bouchbinder, Phys. Rev. Lett. 117, 035501 (2016), 10.1103/PhysRevLett.117.035501] that the nonphononic vibrational modes of structural glasses at low frequencies ω are quasilocalized and follow a universal density of states D (ω ) ˜ω4 . Here we show that the gapless nature of the observed density of states depends on the existence of internal stresses that generically emerge in glasses due to frustration, thus elucidating a basic element underlying this universal behavior. Similarly to jammed particulate packings, low-frequency modes in structural glasses emerge from a balance between a local elasticity term and an internal stress term in the dynamical matrix, where the difference between them is orders of magnitude smaller than their typical magnitude. By artificially reducing the magnitude of internal stresses in a computer glass former in three dimensions, we show that a gap is formed in the density of states below which no vibrational modes exist, thus demonstrating the crucial importance of internal stresses. Finally, we show that while better annealing the glass upon cooling from the liquid state significantly reduces its internal stresses, the self-organizational processes during cooling render the gapless D (ω ) ˜ω4 density of state unaffected.

Rooting strategies in a subtropical savanna: a landscape-scale three-dimensional assessment.

PubMed

Zhou, Yong; Boutton, Thomas W; Wu, X Ben; Wright, Cynthia L; Dion, Anais L

2018-04-01

In resource-limited savannas, the distribution and abundance of fine roots play an important role in acquiring essential resources and structuring vegetation patterns and dynamics. However, little is known regarding the three-dimensional distribution of fine roots in savanna ecosystems at the landscape scale. We quantified spatial patterns of fine root density to a depth of 1.2 m in a subtropical savanna landscape using spatially specific sampling. Kriged maps revealed that fine root density was highest at the centers of woody patches, decreased towards the canopy edges, and reached lowest values within the grassland matrix throughout the entire soil profile. Lacunarity analyses indicated that spatial heterogeneities of fine root density decreased continuously to a depth of 50 cm and then increased in deeper portions of the soil profile across this landscape. This vertical pattern might be related to inherent differences in root distribution between trees/shrubs and herbaceous species, and the presence/absence of an argillic horizon across this landscape. The greater density of fine roots beneath woody patches in both upper and lower portions of the soil profile suggests an ability to acquire disproportionately more resources than herbaceous species, which may facilitate the development and persistence of woody patches across this landscape.

Proteolytic and non-proteolytic regulation of collective cell invasion: tuning by ECM density and organization

PubMed Central

Kumar, Sandeep; Kapoor, Aastha; Desai, Sejal; Inamdar, Mandar M.; Sen, Shamik

2016-01-01

Cancer cells manoeuvre through extracellular matrices (ECMs) using different invasion modes, including single cell and collective cell invasion. These modes rely on MMP-driven ECM proteolysis to make space for cells to move. How cancer-associated alterations in ECM influence the mode of invasion remains unclear. Further, the sensitivity of the two invasion modes to MMP dynamics remains unexplored. In this paper, we address these open questions using a multiscale hybrid computational model combining ECM density-dependent MMP secretion, MMP diffusion, ECM degradation by MMP and active cell motility. Our results demonstrate that in randomly aligned matrices, collective cell invasion is more efficient than single cell invasion. Although increase in MMP secretion rate enhances invasiveness independent of cell–cell adhesion, sustenance of collective invasion in dense matrices requires high MMP secretion rates. However, matrix alignment can sustain both single cell and collective cell invasion even without ECM proteolysis. Similar to our in-silico observations, increase in ECM density and MMP inhibition reduced migration of MCF-7 cells embedded in sandwich gels. Together, our results indicate that apart from cell intrinsic factors (i.e., high cell–cell adhesion and MMP secretion rates), ECM density and organization represent two important extrinsic parameters that govern collective cell invasion and invasion plasticity. PMID:26832069

X-ray tomography of powder injection moulded micro parts using synchrotron radiation

NASA Astrophysics Data System (ADS)

Heldele, R.; Rath, S.; Merz, L.; Butzbach, R.; Hagelstein, M.; Haußelt, J.

2006-05-01

Powder injection moulding is one of the most promising replication methods for the mass production of metal and ceramic micro parts. The material for injection moulding, a so-called feedstock, consists of thermoplastic binder components and inorganic filler with approximately equal volume fractions. Injection moulding of the feedstock leads to a green part that can be processed to a dense metal or ceramic micro part by debinding and sintering. During the injection moulding process extremely high shear rates are applied. This promotes the separation of powder and binder leading to a particle density variation in the green part causing anisotropic shrinkage during post-processing. The knowledge of introducing density gradients and defects would consequently allow the optimization of the feedstock, the moulding parameters and the validation of a simulation tool based on the Dissipative Particle Dynamics which is currently under development, as well. To determine the particle density and defect distribution in micro parts synchrotron radiation tomography in absorption mode was used. Due to its parallel and monochromatic character a quantitative reconstruction, free of beam hardening artifacts, is possible. For the measurement, bending bars consisting of dispersed fused silica particles in a polymeric matrix were used. The presented results using this set-up show that crucial defects and density variations can be detected.

Theory of activated penetrant diffusion in viscous fluids and colloidal suspensions

NASA Astrophysics Data System (ADS)

Zhang, Rui; Schweizer, Kenneth S.

2015-10-01

We heuristically formulate a microscopic, force level, self-consistent nonlinear Langevin equation theory for activated barrier hopping and non-hydrodynamic diffusion of a hard sphere penetrant in very dense hard sphere fluid matrices. Penetrant dynamics is controlled by a rich competition between force relaxation due to penetrant self-motion and collective matrix structural (alpha) relaxation. In the absence of penetrant-matrix attraction, three activated dynamical regimes are predicted as a function of penetrant-matrix size ratio which are physically distinguished by penetrant jump distance and the nature of matrix motion required to facilitate its hopping. The penetrant diffusion constant decreases the fastest with size ratio for relatively small penetrants where the matrix effectively acts as a vibrating amorphous solid. Increasing penetrant-matrix attraction strength reduces penetrant diffusivity due to physical bonding. For size ratios approaching unity, a distinct dynamical regime emerges associated with strong slaving of penetrant hopping to matrix structural relaxation. A crossover regime at intermediate penetrant-matrix size ratio connects the two limiting behaviors for hard penetrants, but essentially disappears if there are strong attractions with the matrix. Activated penetrant diffusivity decreases strongly with matrix volume fraction in a manner that intensifies as the size ratio increases. We propose and implement a quasi-universal approach for activated diffusion of a rigid atomic/molecular penetrant in a supercooled liquid based on a mapping between the hard sphere system and thermal liquids. Calculations for specific systems agree reasonably well with experiments over a wide range of temperature, covering more than 10 orders of magnitude of variation of the penetrant diffusion constant.

Theory of activated penetrant diffusion in viscous fluids and colloidal suspensions

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

Zhang, Rui; Schweizer, Kenneth S., E-mail: kschweiz@illinois.edu

2015-10-14

We heuristically formulate a microscopic, force level, self-consistent nonlinear Langevin equation theory for activated barrier hopping and non-hydrodynamic diffusion of a hard sphere penetrant in very dense hard sphere fluid matrices. Penetrant dynamics is controlled by a rich competition between force relaxation due to penetrant self-motion and collective matrix structural (alpha) relaxation. In the absence of penetrant-matrix attraction, three activated dynamical regimes are predicted as a function of penetrant-matrix size ratio which are physically distinguished by penetrant jump distance and the nature of matrix motion required to facilitate its hopping. The penetrant diffusion constant decreases the fastest with size ratiomore » for relatively small penetrants where the matrix effectively acts as a vibrating amorphous solid. Increasing penetrant-matrix attraction strength reduces penetrant diffusivity due to physical bonding. For size ratios approaching unity, a distinct dynamical regime emerges associated with strong slaving of penetrant hopping to matrix structural relaxation. A crossover regime at intermediate penetrant-matrix size ratio connects the two limiting behaviors for hard penetrants, but essentially disappears if there are strong attractions with the matrix. Activated penetrant diffusivity decreases strongly with matrix volume fraction in a manner that intensifies as the size ratio increases. We propose and implement a quasi-universal approach for activated diffusion of a rigid atomic/molecular penetrant in a supercooled liquid based on a mapping between the hard sphere system and thermal liquids. Calculations for specific systems agree reasonably well with experiments over a wide range of temperature, covering more than 10 orders of magnitude of variation of the penetrant diffusion constant.« less

The Multi-Domain Fibroblast/Myocyte Coupling in the Cardiac Tissue: A Theoretical Study.

PubMed

Greisas, Ariel; Zlochiver, Sharon

2016-09-01

Cardiac fibroblast proliferation and concomitant collagenous matrix accumulation (fibrosis) develop during multiple cardiac pathologies. Recent studies have demonstrated direct electrical coupling between myocytes and fibroblasts in vitro, and assessed the electrophysiological implications of such coupling. However, in the living tissues, such coupling has not been demonstrated, and only indirect coupling via the extracellular space is likely to exist. In this study we employed a multi-domain model to assess the modulation of the cardiac electrophysiological properties by neighboring fibroblasts assuming only indirect coupling. Numerical simulations in 1D and 2D human atrial models showed that extracellular coupling sustains a significant impact on conduction velocity (CV) and a less significant effect on the action potential duration. Both CV and the slope of the CV restitution increased with increasing fibroblast density. This effect was more substantial for lower extracellular conductance. In 2D, spiral waves exhibited reduced frequency with increasing fibroblast density, and the propensity of wavebreaks and complex dynamics at high pacing rates significantly increased.

Spatial operator factorization and inversion of the manipulator mass matrix

NASA Technical Reports Server (NTRS)

Rodriguez, Guillermo; Kreutz-Delgado, Kenneth

1992-01-01

This paper advances two linear operator factorizations of the manipulator mass matrix. Embedded in the factorizations are many of the techniques that are regarded as very efficient computational solutions to inverse and forward dynamics problems. The operator factorizations provide a high-level architectural understanding of the mass matrix and its inverse, which is not visible in the detailed algorithms. They also lead to a new approach to the development of computer programs or organize complexity in robot dynamics.

Modelling of Rigid-Body and Elastic Aircraft Dynamics for Flight Control Development.

DTIC Science & Technology

1986-06-01

AMAT MATSAV AUGMENT MI NV BMAT MMULT EVAL RLPLOT FASTCHG STABDER The subroutines are fairly well commented so that a person familiar with the theory...performed as in a typical flutter solution. C C Subroutine BMAT computes the B matrix from the forcing function C matrix Q. B is a function of dynamic...and BMAT multiplies matrices. C This is used to form the A and B matrices. C C Subroutine EVAL computes the eigenvalues of the A matrix C The

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

PubMed Central

2017-01-01

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

Applications of Perron-Frobenius theory to population dynamics.

PubMed

Li, Chi-Kwong; Schneider, Hans

2002-05-01

By the use of Perron-Frobenius theory, simple proofs are given of the Fundamental Theorem of Demography and of a theorem of Cushing and Yicang on the net reproductive rate occurring in matrix models of population dynamics. The latter result, which is closely related to the Stein-Rosenberg theorem in numerical linear algebra, is further refined with some additional nonnegative matrix theory. When the fertility matrix is scaled by the net reproductive rate, the growth rate of the model is $1$. More generally, we show how to achieve a given growth rate for the model by scaling the fertility matrix. Demographic interpretations of the results are given.

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

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

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

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

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

A state interaction spin-orbit coupling density matrix renormalization group method

NASA Astrophysics Data System (ADS)

Sayfutyarova, Elvira R.; Chan, Garnet Kin-Lic

2016-06-01

We describe a state interaction spin-orbit (SISO) coupling method using density matrix renormalization group (DMRG) wavefunctions and the spin-orbit mean-field (SOMF) operator. We implement our DMRG-SISO scheme using a spin-adapted algorithm that computes transition density matrices between arbitrary matrix product states. To demonstrate the potential of the DMRG-SISO scheme we present accurate benchmark calculations for the zero-field splitting of the copper and gold atoms, comparing to earlier complete active space self-consistent-field and second-order complete active space perturbation theory results in the same basis. We also compute the effects of spin-orbit coupling on the spin-ladder of the iron-sulfur dimer complex [Fe2S2(SCH3)4]3-, determining the splitting of the lowest quartet and sextet states. We find that the magnitude of the zero-field splitting for the higher quartet and sextet states approaches a significant fraction of the Heisenberg exchange parameter.

Generalized Pauli constraints in reduced density matrix functional theory.

PubMed

Theophilou, Iris; Lathiotakis, Nektarios N; Marques, Miguel A L; Helbig, Nicole

2015-04-21

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

GeV-scale hot sterile neutrino oscillations: a numerical solution

NASA Astrophysics Data System (ADS)

Ghiglieri, J.; Laine, M.

2018-02-01

The scenario of baryogenesis through GeV-scale sterile neutrino oscillations is governed by non-linear differential equations for the time evolution of a sterile neutrino density matrix and Standard Model lepton and baryon asymmetries. By employing up-to-date rate coefficients and a non-perturbatively estimated Chern-Simons diffusion rate, we present a numerical solution of this system, incorporating the full momentum and helicity dependences of the density matrix. The density matrix deviates significantly from kinetic equilibrium, with the IR modes equilibrating much faster than the UV modes. For equivalent input parameters, our final results differ moderately (˜50%) from recent benchmarks in the literature. The possibility of producing an observable baryon asymmetry is nevertheless confirmed. We illustrate the dependence of the baryon asymmetry on the sterile neutrino mass splitting and on the CP-violating phase measurable in active neutrino oscillation experiments.

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.

Method and system to estimate variables in an integrated gasification combined cycle (IGCC) plant

DOEpatents

Kumar, Aditya; Shi, Ruijie; Dokucu, Mustafa

2013-09-17

System and method to estimate variables in an integrated gasification combined cycle (IGCC) plant are provided. The system includes a sensor suite to measure respective plant input and output variables. An extended Kalman filter (EKF) receives sensed plant input variables and includes a dynamic model to generate a plurality of plant state estimates and a covariance matrix for the state estimates. A preemptive-constraining processor is configured to preemptively constrain the state estimates and covariance matrix to be free of constraint violations. A measurement-correction processor may be configured to correct constrained state estimates and a constrained covariance matrix based on processing of sensed plant output variables. The measurement-correction processor is coupled to update the dynamic model with corrected state estimates and a corrected covariance matrix. The updated dynamic model may be configured to estimate values for at least one plant variable not originally sensed by the sensor suite.

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

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.

Development of 10×10 Matrix-anode MCP-PMT

NASA Astrophysics Data System (ADS)

Yang, Jie; Li, Yongbin; Xu, Pengxiao; Zhao, Wenjin

2018-02-01

10×10 matrix-anode is developed by high-temperature co-fired ceramics (HTCC) technology. Based on the new matrix-anode, a new kind of photon counting imaging detector - 10×10 matrix-anode MCP-PMT is developed, and its performance parameters are tested. HTCC technology is suitable for the MCP-PMT's air impermeability and its baking process. Its response uniformity is better than the metal-ceramic or metal-glass sealing anode, and it is also a promising method to realize a higher density matrix-anode.

Oil-free hyaluronic acid matrix for serial femtosecond crystallography

NASA Astrophysics Data System (ADS)

Sugahara, Michihiro; Song, Changyong; Suzuki, Mamoru; Masuda, Tetsuya; Inoue, Shigeyuki; Nakane, Takanori; Yumoto, Fumiaki; Nango, Eriko; Tanaka, Rie; Tono, Kensuke; Joti, Yasumasa; Kameshima, Takashi; Hatsui, Takaki; Yabashi, Makina; Nureki, Osamu; Numata, Keiji; Iwata, So

2016-04-01

The grease matrix was originally introduced as a microcrystal-carrier for serial femtosecond crystallography and has been expanded to applications for various types of proteins, including membrane proteins. However, the grease-based matrix has limited application for oil-sensitive proteins. Here we introduce a grease-free, water-based hyaluronic acid matrix. Applications for proteinase K and lysozyme proteins were able to produce electron density maps at 2.3-Å resolution.

A spatial operator algebra for manipulator modeling and control

NASA Technical Reports Server (NTRS)

Rodriguez, G.; Kreutz, K.; Milman, M.

1988-01-01

A powerful new spatial operator algebra for modeling, control, and trajectory design of manipulators is discussed along with its implementation in the Ada programming language. Applications of this algebra to robotics include an operator representation of the manipulator Jacobian matrix; the robot dynamical equations formulated in terms of the spatial algebra, showing the complete equivalence between the recursive Newton-Euler formulations to robot dynamics; the operator factorization and inversion of the manipulator mass matrix which immediately results in O(N) recursive forward dynamics algorithms; the joint accelerations of a manipulator due to a tip contact force; the recursive computation of the equivalent mass matrix as seen at the tip of a manipulator; and recursive forward dynamics of a closed chain system. Finally, additional applications and current research involving the use of the spatial operator algebra are discussed in general terms.

The accuracy of matrix population model projections for coniferous trees in the Sierra Nevada, California

USGS Publications Warehouse

van Mantgem, P.J.; Stephenson, N.L.

2005-01-01

1 We assess the use of simple, size-based matrix population models for projecting population trends for six coniferous tree species in the Sierra Nevada, California. We used demographic data from 16 673 trees in 15 permanent plots to create 17 separate time-invariant, density-independent population projection models, and determined differences between trends projected from initial surveys with a 5-year interval and observed data during two subsequent 5-year time steps. 2 We detected departures from the assumptions of the matrix modelling approach in terms of strong growth autocorrelations. We also found evidence of observation errors for measurements of tree growth and, to a more limited degree, recruitment. Loglinear analysis provided evidence of significant temporal variation in demographic rates for only two of the 17 populations. 3 Total population sizes were strongly predicted by model projections, although population dynamics were dominated by carryover from the previous 5-year time step (i.e. there were few cases of recruitment or death). Fractional changes to overall population sizes were less well predicted. Compared with a null model and a simple demographic model lacking size structure, matrix model projections were better able to predict total population sizes, although the differences were not statistically significant. Matrix model projections were also able to predict short-term rates of survival, growth and recruitment. Mortality frequencies were not well predicted. 4 Our results suggest that simple size-structured models can accurately project future short-term changes for some tree populations. However, not all populations were well predicted and these simple models would probably become more inaccurate over longer projection intervals. The predictive ability of these models would also be limited by disturbance or other events that destabilize demographic rates. ?? 2005 British Ecological Society.

Heuristic Implementation of Dynamic Programming for Matrix Permutation Problems in Combinatorial Data Analysis

ERIC Educational Resources Information Center

Brusco, Michael J.; Kohn, Hans-Friedrich; Stahl, Stephanie

2008-01-01

Dynamic programming methods for matrix permutation problems in combinatorial data analysis can produce globally-optimal solutions for matrices up to size 30x30, but are computationally infeasible for larger matrices because of enormous computer memory requirements. Branch-and-bound methods also guarantee globally-optimal solutions, but computation…

Damping mathematical modelling and dynamic responses for FRP laminated composite plates with polymer matrix

NASA Astrophysics Data System (ADS)

Liu, Qimao

2018-02-01

This paper proposes an assumption that the fibre is elastic material and polymer matrix is viscoelastic material so that the energy dissipation depends only on the polymer matrix in dynamic response process. The damping force vectors in frequency and time domains, of FRP (Fibre-Reinforced Polymer matrix) laminated composite plates, are derived based on this assumption. The governing equations of FRP laminated composite plates are formulated in both frequency and time domains. The direct inversion method and direct time integration method for nonviscously damped systems are employed to solve the governing equations and achieve the dynamic responses in frequency and time domains, respectively. The computational procedure is given in detail. Finally, dynamic responses (frequency responses with nonzero and zero initial conditions, free vibration, forced vibrations with nonzero and zero initial conditions) of a FRP laminated composite plate are computed using the proposed methodology. The proposed methodology in this paper is easy to be inserted into the commercial finite element analysis software. The proposed assumption, based on the theory of material mechanics, needs to be further proved by experiment technique in the future.

Behavior of grafted polymers on nanofillers and their influence on polymer nanocomposite properties

NASA Astrophysics Data System (ADS)

Dukes, Douglas Michael

Polymer nanocomposites continue to receive wide-spread acclaim for their potential to improve composite materials beyond conventional macroscale fillers. The improvement lies both in the altered properties of the particle itself and in the interaction region surrounding the filler. As the surface area of the filler increases, a greater volume fraction of this interphase region is present in the composite. However, simply minimizing the particle size to maximize surface area introduces additional problems; the larger specific surface area promotes aggregation to reduce the surface energy. Since the composite's properties are largely tied to the morphology, aggregation prevents control over the dispersion state of the filler, and thus the properties. Therefore, disaggregation and morphology control are vital to achieving designable nanocomposites. To accomplish both tasks, this thesis focuses on the behavior of grafted polymer coatings on nanoparticles and their in uence on the macroscopic properties. Grafted chains play an integral role in both morphology control and reinforcement. To investigate the behavior of polymer brushes on nanoparticles, polystyrene was grafted on 15 nm silica particles at varying graft densities and molecular weights. Dynamic light scattering studies in dilute solution were performed to obtain the brush height as a function of both graft density and molecular weight. Three distinct regimes of behavior exist, the "mushroom", the semi-dilute polymer brush (SDPB), and the concentrated polymer brush (CPB) regimes. In the CPB regime, which is an extraordinary configuration of highly-stretched chains on densely grafted surfaces, the brush height h was found to scale as h ∝ N4/5, where N is the degree of polymerization. This result is contrary to the observed scaling of the CPB in flat interface systems, where h ∝ N1. To explore the behavior of grafted chains in the melt, molecular dynamics simulations were performed on grafted nanoparticles grafted with varying amounts of polymer chains at different curvatures. Particles as small as 15 monomers in size were found to already be in the large particle limit, a result that has many implications regarding the dispersibility of grafted fillers in composites. At low graft densities, melt chains were found to form entanglements with the brush all the way to the particle surface, implying the particle is not effectively screened by the grafted chains. The mechanical properties of these grafted silica composites were studied as a function of matrix polymer fraction. As more matrix polymer is introduced, the dominant contribution to the behavior shifts from the grafted chains to the matrix chains. This elucidates the role of grafted chains on the mechanical properties of grafted nanoparticle composites. As the graft density is increased, the wettability of grafted chains was shown to decrease, causing fewer entanglements between grafted chains and matrix chains, resulting in poorer reinforcement. Interesting behavior was observed at low graft densities; a pronounced shape memory effect occurred at high particle concentrations. It is proposed that the grafted chains entangle with adjacent grafted chains, forming a three-dimensional network of entangled brushes attached to silica cores. This structure effectively forms "cross-links" as in elastomeric systems, giving an entropic restorative force to stretched chains. Thus, above Tg, when chains have a higher degree of mobility, the composites can be stretched to over 800%. When cooled to below Tg, they retain the deformed geometry. Upon reheating above Tg, the composite is restored to its original dimensions. This work has identified means of improving theoretical models to better guide future experiments and lead to predictability in polymer composite design. Grafted chains have the demonstrated ability to control the morphology and reinforcement in polymer composites. The behavior of grafted chains were shown to demonstrate drastically different properties from their bulk polymer counterparts.

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.

Raney Distributions and Random Matrix Theory

NASA Astrophysics Data System (ADS)

Forrester, Peter J.; Liu, Dang-Zheng

2015-03-01

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

Matrix remodeling between cells and cellular interactions with collagen bundle

NASA Astrophysics Data System (ADS)

Kim, Jihan; Sun, Bo

When cells are surrounded by complex environment, they continuously probe and interact with it by applying cellular traction forces. As cells apply traction forces, they can sense rigidity of their local environment and remodel the matrix microstructure simultaneously. Previous study shows that single human carcinoma cell (MDA-MB-231) remodeled its surrounding extracellular matrix (ECM) and the matrix remodeling was reversible. In this study we examined the matrix microstructure between cells and cellular interaction between them using quantitative confocal microscopy. The result shows that the matrix microstructure is the most significantly remodeled between cells consisting of aligned, and densified collagen fibers (collagen bundle)., the result shows that collagen bundle is irreversible and significantly change micromechanics of ECM around the bundle. We further examined cellular interaction with collagen bundle by analyzing dynamics of actin and talin formation along with the direction of bundle. Lastly, we analyzed dynamics of cellular protrusion and migrating direction of cells along the bundle.

Dynamic Density: An Air Traffic Management Metric

NASA Technical Reports Server (NTRS)

Laudeman, I. V.; Shelden, S. G.; Branstrom, R.; Brasil, C. L.

1998-01-01

The definition of a metric of air traffic controller workload based on air traffic characteristics is essential to the development of both air traffic management automation and air traffic procedures. Dynamic density is a proposed concept for a metric that includes both traffic density (a count of aircraft in a volume of airspace) and traffic complexity (a measure of the complexity of the air traffic in a volume of airspace). It was hypothesized that a metric that includes terms that capture air traffic complexity will be a better measure of air traffic controller workload than current measures based only on traffic density. A weighted linear dynamic density function was developed and validated operationally. The proposed dynamic density function includes a traffic density term and eight traffic complexity terms. A unit-weighted dynamic density function was able to account for an average of 22% of the variance in observed controller activity not accounted for by traffic density alone. A comparative analysis of unit weights, subjective weights, and regression weights for the terms in the dynamic density equation was conducted. The best predictor of controller activity was the dynamic density equation with regression-weighted complexity terms.

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

NASA Technical Reports Server (NTRS)

Clancy, Thomas C.; Gates, Thomas S.

2006-01-01

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

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.

Using Dynamic Multi-Task Non-Negative Matrix Factorization to Detect the Evolution of User Preferences in Collaborative Filtering

PubMed Central

Ju, Bin; Qian, Yuntao; Ye, Minchao; Ni, Rong; Zhu, Chenxi

2015-01-01

Predicting what items will be selected by a target user in the future is an important function for recommendation systems. Matrix factorization techniques have been shown to achieve good performance on temporal rating-type data, but little is known about temporal item selection data. In this paper, we developed a unified model that combines Multi-task Non-negative Matrix Factorization and Linear Dynamical Systems to capture the evolution of user preferences. Specifically, user and item features are projected into latent factor space by factoring co-occurrence matrices into a common basis item-factor matrix and multiple factor-user matrices. Moreover, we represented both within and between relationships of multiple factor-user matrices using a state transition matrix to capture the changes in user preferences over time. The experiments show that our proposed algorithm outperforms the other algorithms on two real datasets, which were extracted from Netflix movies and Last.fm music. Furthermore, our model provides a novel dynamic topic model for tracking the evolution of the behavior of a user over time. PMID:26270539

Using Dynamic Multi-Task Non-Negative Matrix Factorization to Detect the Evolution of User Preferences in Collaborative Filtering.

PubMed

Ju, Bin; Qian, Yuntao; Ye, Minchao; Ni, Rong; Zhu, Chenxi

2015-01-01

Predicting what items will be selected by a target user in the future is an important function for recommendation systems. Matrix factorization techniques have been shown to achieve good performance on temporal rating-type data, but little is known about temporal item selection data. In this paper, we developed a unified model that combines Multi-task Non-negative Matrix Factorization and Linear Dynamical Systems to capture the evolution of user preferences. Specifically, user and item features are projected into latent factor space by factoring co-occurrence matrices into a common basis item-factor matrix and multiple factor-user matrices. Moreover, we represented both within and between relationships of multiple factor-user matrices using a state transition matrix to capture the changes in user preferences over time. The experiments show that our proposed algorithm outperforms the other algorithms on two real datasets, which were extracted from Netflix movies and Last.fm music. Furthermore, our model provides a novel dynamic topic model for tracking the evolution of the behavior of a user over time.

Dynamics of VEGF matrix-retention in vascular network patterning

NASA Astrophysics Data System (ADS)

Köhn-Luque, A.; de Back, W.; Yamaguchi, Y.; Yoshimura, K.; Herrero, M. A.; Miura, T.

2013-12-01

Vascular endothelial growth factor (VEGF) is a central regulator of blood vessel morphogenesis, although its role in patterning of endothelial cells into vascular networks is not fully understood. It has been suggested that binding of soluble VEGF to extracellular matrix components causes spatially restricted cues that guide endothelial cells into network patterns. Yet, current evidence for such a mechanism remains indirect. In this study, we quantitatively analyse the dynamics of VEGF retention in a controlled in vitro situation of human umbilical vascular endothelial cells (HUVECs) in Matrigel. We show that fluorescent VEGF accumulates in pericellular areas and colocalizes with VEGF binding molecules. Analysis of fluorescence recovery after photobleaching reveals that binding/unbinding to matrix molecules dominates VEGF dynamics in the pericellular region. Computational simulations using our experimental measurements of kinetic parameters show that matrix retention of chemotactic signals can lead to the formation of reticular cellular networks on a realistic timescale. Taken together, these results show that VEGF binds to matrix molecules in proximity of HUVECs in Matrigel, and suggest that bound VEGF drives vascular network patterning.

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.

Magnesium Matrix Composite Foams-Density, Mechanical Properties, and Applications

DTIC Science & Technology

2012-07-24

to syntactic foam densities in the range 1–1.5 g/cc, which directly compete with polymer matrix composites. Their inherently high modulus, ductility ...nomenclature of these alloys A, Z, and C refer to aluminum, zinc and copper, respectively. The two letters are followed by two numbers, which correspond to...respectively [27]. Usually, the increased strength of Mg alloys due to the addition of Al or Cu comes at the expense of ductility . Addition of Zn along

SEM and TEM characterization of the microstructure of post-compressed TiB2/2024Al composite.

PubMed

Guo, Q; Jiang, L T; Chen, G Q; Feng, D; Sun, D L; Wu, G H

2012-02-01

In the present work, 55 vol.% TiB(2)/2024Al composites were obtained by pressure infiltration method. Compressive properties of 55 vol.% TiB(2)/2024Al composite under the strain rates of 10(-3) and 1S(-1) at different temperature were measured and microstructure of post-compressed TiB(2)/2024Al composite was characterized by scanning electron microscope (SEM) and transmission electron microscope (TEM). No trace of Al(3)Ti compound flake was found. TiB(2)-Al interface was smooth without significant reaction products, and orientation relationships ( [Formula: see text] and [Formula: see text] ) were revealed by HRTEM. Compressive strength of TiB(2)/2024Al composites decreased with temperature regardless of strain rates. The strain-rate-sensitivity of TiB(2)/2024Al composites increased with the increasing temperature. Fracture surface of specimens compressed at 25 and 250°C under 10(-3)S(-1) were characterized by furrow. Under 10(-3)S(-1), high density dislocations were formed in Al matrix when compressed at 25°C and dynamic recrystallization occurred at 250°C. Segregation of Mg and Cu on the subgrain boundary was also revealed at 550°C. Dislocations, whose density increased with temperature, were formed in TiB(2) particles under 1S(-1). Deformation of composites is affected by matrix, reinforcement and strain rate. Copyright © 2011 Elsevier Ltd. All rights reserved.

High density, uniformly distributed W/UO2 for use in Nuclear Thermal Propulsion

NASA Astrophysics Data System (ADS)

Tucker, Dennis S.; Barnes, Marvin W.; Hone, Lance; Cook, Steven

2017-04-01

An inexpensive, quick method has been developed to obtain uniform distributions of UO2 particles in a tungsten matrix utilizing 0.5 wt percent low density polyethylene. Powders were sintered in a Spark Plasma Sintering (SPS) furnace at 1600 °C, 1700 °C, 1750 °C, 1800 °C and 1850 °C using a modified sintering profile. This resulted in a uniform distribution of UO2 particles in a tungsten matrix with high densities, reaching 99.46% of theoretical for the sample sintered at 1850 °C. The powder process is described and the results of this study are given below.

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

Comparison of Phase Field Crystal and Molecular Dynamics Simulations for a Shrinking Grain

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

Radhakrishnan, Balasubramaniam; Gorti, Sarma B; Nicholson, Don M

2012-01-01

The Phase-Field Crystal (PFC) model represents the atomic density as a continuous function, whose spatial distribution evolves at diffusional, rather than vibrational time scales. PFC provides a tool to study defect interactions at the atomistic level but over longer time scales than in molecular dynamics (MD). We examine the behavior of the PFC model with the goal of relating the PFC parameters to physical parameters of real systems, derived from MD simulations. For this purpose we model the phenomenon of the shrinking of a spherical grain situated in a matrix. By comparing the rate of shrinking of the central grainmore » using MD and PFC we obtain a relationship between PFC and MD time scales for processes driven by grain boundary diffusion. The morphological changes in the central grain including grain shape and grain rotation are also examined in order to assess the accuracy of the PFC in capturing the evolution path predicted by MD.« less

Wave chaos in the elastic disk.

PubMed

Sondergaard, Niels; Tanner, Gregor

2002-12-01

The relation between the elastic wave equation for plane, isotropic bodies and an underlying classical ray dynamics is investigated. We study, in particular, the eigenfrequencies of an elastic disk with free boundaries and their connection to periodic rays inside the circular domain. Even though the problem is separable, wave mixing between the shear and pressure component of the wave field at the boundary leads to an effective stochastic part in the ray dynamics. This introduces phenomena typically associated with classical chaos as, for example, an exponential increase in the number of periodic orbits. Classically, the problem can be decomposed into an integrable part and a simple binary Markov process. Similarly, the wave equation can, in the high-frequency limit, be mapped onto a quantum graph. Implications of this result for the level statistics are discussed. Furthermore, a periodic trace formula is derived from the scattering matrix based on the inside-outside duality between eigenmodes and scattering solutions and periodic orbits are identified by Fourier transforming the spectral density.

Theory of interaction-induced renormalization of Drude weight and plasmon frequency in chiral multilayer graphene

NASA Astrophysics Data System (ADS)

Li, Xiao; Tse, Wang-Kong

2017-02-01

We develop a theory for the optical conductivity of doped ABC-stacked multilayer graphene including the effects of electron-electron interactions. Applying the quantum kinetic formalism, we formulate a set of pseudospin Bloch equations that govern the dynamics of the nonequilibrium density matrix driven by an external ac electric field under the influence of Coulomb interactions. These equations reveal a dynamical mechanism that couples the Drude and interband responses arising from the chirality of pseudospin textures in multilayer graphene systems. We demonstrate that this results in an interaction-induced enhancement of the Drude weight and plasmon frequency strongly dependent on the pseudospin winding number. Using bilayer graphene as an example, we also study the influence of higher-energy bands and find that they contribute considerable renormalization effects not captured by a low-energy two-band description. We argue that this enhancement of Drude weight and plasmon frequency occurs generally in materials characterized by electronic chirality.

Molecular modeling studies of structural properties of polyvinyl alcohol: a comparative study using INTERFACE force field.

PubMed

Radosinski, Lukasz; Labus, Karolina

2017-10-05

Polyvinyl alcohol (PVA) is a material with a variety of applications in separation, biotechnology, and biomedicine. Using combined Monte Carlo and molecular dynamics techniques, we present an extensive comparative study of second- and third-generation force fields Universal, COMPASS, COMPASS II, PCFF, and the newly developed INTERFACE, as applied to this system. In particular, we show that an INTERFACE force field provides a possibility of composing a reliable atomistic model to reproduce density change of PVA matrix in a narrow temperature range (298-348 K) and calculate a thermal expansion coefficient with reasonable accuracy. Thus, the INTERFACE force field may be used to predict mechanical properties of the PVA system, being a scaffold for hydrogels, with much greater accuracy than latter approaches. Graphical abstract Molecular Dynamics and Monte Carlo studies indicate that it is possible to predict properties of the PVA in narrow temperature range by using the INTERFACE force field.

Simultaneous measurement of two noncommuting quantum variables: Solution of a dynamical model

NASA Astrophysics Data System (ADS)

Perarnau-Llobet, Martí; Nieuwenhuizen, Theodorus Maria

2017-05-01

The possibility of performing simultaneous measurements in quantum mechanics is investigated in the context of the Curie-Weiss model for a projective measurement. Concretely, we consider a spin-1/2 system simultaneously interacting with two magnets, which act as measuring apparatuses of two different spin components. We work out the dynamics of this process and determine the final state of the measuring apparatuses, from which we can find the probabilities of the four possible outcomes of the measurements. The measurement is found to be nonideal, as (i) the joint statistics do not coincide with the one obtained by separately measuring each spin component, and (ii) the density matrix of the spin does not collapse in either of the measured observables. However, we give an operational interpretation of the process as a generalized quantum measurement, and show that it is fully informative: The expected value of the measured spin components can be found with arbitrary precision for sufficiently many runs of the experiment.

Smoothed quantum-classical states in time-irreversible hybrid dynamics

NASA Astrophysics Data System (ADS)

Budini, Adrián A.

2017-09-01

We consider a quantum system continuously monitored in time which in turn is coupled to an arbitrary dissipative classical system (diagonal reduced density matrix). The quantum and classical dynamics can modify each other, being described by an arbitrary time-irreversible hybrid Lindblad equation. Given a measurement trajectory, a conditional bipartite stochastic state can be inferred by taking into account all previous recording information (filtering). Here, we demonstrate that the joint quantum-classical state can also be inferred by taking into account both past and future measurement results (smoothing). The smoothed hybrid state is estimated without involving information from unobserved measurement channels. Its average over recording realizations recovers the joint time-irreversible behavior. As an application we consider a fluorescent system monitored by an inefficient photon detector. This feature is taken into account through a fictitious classical two-level system. The average purity of the smoothed quantum state increases over that of the (mixed) state obtained from the standard quantum jump approach.

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

Magnetic excitation spectra of strongly correlated quasi-one-dimensional systems: Heisenberg versus Hubbard-like behavior

NASA Astrophysics Data System (ADS)

Nocera, A.; Patel, N. D.; Fernandez-Baca, J.; Dagotto, E.; Alvarez, G.

2016-11-01

We study the effects of charge degrees of freedom on the spin excitation dynamics in quasi-one-dimensional magnetic materials. Using the density matrix renormalization group method, we calculate the dynamical spin structure factor of the Hubbard model at half electronic filling on a chain and on a ladder geometry, and compare the results with those obtained using the Heisenberg model, where charge degrees of freedom are considered frozen. For both chains and two-leg ladders, we find that the Hubbard model spectrum qualitatively resembles the Heisenberg spectrum—with low-energy peaks resembling spinonic excitations—already at intermediate on-site repulsion as small as U /t ˜2 -3 , although ratios of peak intensities at different momenta continue evolving with increasing U /t converging only slowly to the Heisenberg limit. We discuss the implications of these results for neutron scattering experiments and we propose criteria to establish the values of U /t of quasi-one-dimensional systems described by one-orbital Hubbard models from experimental information.

Linear-response time-dependent density-functional theory with pairing fields.

PubMed

Peng, Degao; van Aggelen, Helen; Yang, Yang; Yang, Weitao

2014-05-14

Recent development in particle-particle random phase approximation (pp-RPA) broadens the perspective on ground state correlation energies [H. van Aggelen, Y. Yang, and W. Yang, Phys. Rev. A 88, 030501 (2013), Y. Yang, H. van Aggelen, S. N. Steinmann, D. Peng, and W. Yang, J. Chem. Phys. 139, 174110 (2013); D. Peng, S. N. Steinmann, H. van Aggelen, and W. Yang, J. Chem. Phys. 139, 104112 (2013)] and N ± 2 excitation energies [Y. Yang, H. van Aggelen, and W. Yang, J. Chem. Phys. 139, 224105 (2013)]. So far Hartree-Fock and approximated density-functional orbitals have been utilized to evaluate the pp-RPA equation. In this paper, to further explore the fundamentals and the potential use of pairing matrix dependent functionals, we present the linear-response time-dependent density-functional theory with pairing fields with both adiabatic and frequency-dependent kernels. This theory is related to the density-functional theory and time-dependent density-functional theory for superconductors, but is applied to normal non-superconducting systems for our purpose. Due to the lack of the proof of the one-to-one mapping between the pairing matrix and the pairing field for time-dependent systems, the linear-response theory is established based on the representability assumption of the pairing matrix. The linear response theory justifies the use of approximated density-functionals in the pp-RPA equation. This work sets the fundamentals for future density-functional development to enhance the description of ground state correlation energies and N ± 2 excitation energies.

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.

Quasi-normal modes from non-commutative matrix dynamics

NASA Astrophysics Data System (ADS)

Aprile, Francesco; Sanfilippo, Francesco

2017-09-01

We explore similarities between the process of relaxation in the BMN matrix model and the physics of black holes in AdS/CFT. Focusing on Dyson-fluid solutions of the matrix model, we perform numerical simulations of the real time dynamics of the system. By quenching the equilibrium distribution we study quasi-normal oscillations of scalar single trace observables, we isolate the lowest quasi-normal mode, and we determine its frequencies as function of the energy. Considering the BMN matrix model as a truncation of N=4 SYM, we also compute the frequencies of the quasi-normal modes of the dual scalar fields in the AdS5-Schwarzschild background. We compare the results, and we finda surprising similarity.

Dynamics of water in strawberry and red onion as studied by dielectric spectroscopy

NASA Astrophysics Data System (ADS)

Jansson, H.; Huldt, C.; Bergman, R.; Swenson, J.

2005-01-01

We have investigated the microscopic dynamics of strawberry and red onion by means of broadband dielectric spectroscopy. In contrast to most of the previous experiments on carbohydrate-rich biological materials, which have mainly considered the more global dynamics of the “biological matrix,” we are here focusing on the microscopic dynamics of mainly the associated water. The results for both strawberry and red onion show that the imaginary part of the permittivity contains one conductivity term and a clear dielectric loss peak, which was found to be similar to the strongest relaxation process of water in carbohydrate solutions. The temperature dependence of the relaxation process was analyzed for different water content. The relaxation process slows down, and its temperature dependence becomes more non-Arrhenius, with decreasing water content. The reason for this is most likely that, on average, the water molecules interact more strongly with carbohydrates and other biological materials at low water content, and the dynamical properties of this biological matrix changes substantially with increasing temperature (from an almost rigid matrix where the water is basically unable to perform long-range diffusion due to confinement effects, to a dynamic matrix with no static confinement effects), which also changes (i.e., reduces) the activation energy of the relaxation process with increasing temperature (i.e., causes a non-Arrhenius temperature dependence). This further changes the conductivity from mainly polarization effects at low temperatures, due to hindered ionic motions, to long-range diffusivity at T>250K . Thus, around this temperature ions in the carbohydrate solution no longer get stuck in confined cavities, since the motion of the biological matrix “opens up” the cavities and the ions are then able to perform long-range migration.

Ultra-lightweight optics for laser communications

NASA Astrophysics Data System (ADS)

Vukobratovich, Daniel

1990-07-01

Recent applications of the very light Al/SiC metal-matrix composite SXA in the construction of telescopes for use as receiver antennas in optical intersatellite communication systems are reviewed and illustrated with drawings and diagrams. Data on the mechanical properties (specific stiffness, fundamental frequency, dynamic response, and fracture toughness) and the thermal expansion, distortion, and diffusivity of SXA are compared with those for Al 6016-T6, Be I-70A, SiC, and Zerodur in tables, and the advantages of SXA structural foams of density 250-500 kg/cu m are indicated. The criteria evaluated for optimization of the mirror shape and the overall telescope design are discussed, and four prototype Cassegrain telescopes (with Meinel or Dall truss structures) are described in detail.

Theoretical analysis for the specific heat and thermal parameters of solid C60

NASA Astrophysics Data System (ADS)

Soto, J. R.; Calles, A.; Castro, J. J.

1997-08-01

We present the results of a theoretical analysis for the thermal parameters and phonon contribution to the specific heat in solid C60. The phonon contribution to the specific heat is calculated through the solution of the corresponding dynamical matrix, for different points in the Brillouin zone, and the construccion of the partial and generalized phonon density of states. The force constants are obtained from a first principle calculation, using a SCF Hartree-Fock wave function from the Gaussian 92 program. The thermal parameters reported are the effective temperatures and vibrational amplitudes as a function of temperature. Using this model we present a parametization scheme in order to reproduce the general behaviour of the experimental specific heat for these materials.

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.

Demonstration of entanglement of electrostatically coupled singlet-triplet qubits.

PubMed

Shulman, M D; Dial, O E; Harvey, S P; Bluhm, H; Umansky, V; Yacoby, A

2012-04-13

Quantum computers have the potential to solve certain problems faster than classical computers. To exploit their power, it is necessary to perform interqubit operations and generate entangled states. Spin qubits are a promising candidate for implementing a quantum processor because of their potential for scalability and miniaturization. However, their weak interactions with the environment, which lead to their long coherence times, make interqubit operations challenging. We performed a controlled two-qubit operation between singlet-triplet qubits using a dynamically decoupled sequence that maintains the two-qubit coupling while decoupling each qubit from its fluctuating environment. Using state tomography, we measured the full density matrix of the system and determined the concurrence and the fidelity of the generated state, providing proof of entanglement.

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.

Dynamic SPECT reconstruction from few projections: a sparsity enforced matrix factorization approach

NASA Astrophysics Data System (ADS)

Ding, Qiaoqiao; Zan, Yunlong; Huang, Qiu; Zhang, Xiaoqun

2015-02-01

The reconstruction of dynamic images from few projection data is a challenging problem, especially when noise is present and when the dynamic images are vary fast. In this paper, we propose a variational model, sparsity enforced matrix factorization (SEMF), based on low rank matrix factorization of unknown images and enforced sparsity constraints for representing both coefficients and bases. The proposed model is solved via an alternating iterative scheme for which each subproblem is convex and involves the efficient alternating direction method of multipliers (ADMM). The convergence of the overall alternating scheme for the nonconvex problem relies upon the Kurdyka-Łojasiewicz property, recently studied by Attouch et al (2010 Math. Oper. Res. 35 438) and Attouch et al (2013 Math. Program. 137 91). Finally our proof-of-concept simulation on 2D dynamic images shows the advantage of the proposed method compared to conventional methods.

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).

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

PubMed

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

2018-05-04

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

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

PubMed

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

2015-11-10

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

Microstructure and Mechanical Behaviors of Titanium Matrix Composites Containing In Situ Whiskers Synthesized via Plasma Activated Sintering.

PubMed

Sun, Yi; Zhang, Jian; Luo, Guoqiang; Shen, Qiang; Zhang, Lianmeng

2018-04-02

In this paper, titanium matrix composites with in situ TiB whiskers were synthesized by the plasma activated sintering technique; crystalline boron and amorphous boron were used as reactants for in situ reactions, respectively. The influence of the sintering process and the crystallography type of boron on the microstructure and mechanical properties of composites were studied and compared. The densities were evaluated using Archimedes' principle. The microstructure and mechanical properties were characterized by SEM, XRD, EBSD, TEM, a universal testing machine, and a Vickers hardness tester. The prepared composite material showed a high density and excellent comprehensive performance under the PAS condition of 20 MPa at 1000 °C for 3 min. Amorphous boron had a higher reaction efficiency than crystalline boron, and it completely reacted with the titanium matrix to generate TiB whiskers, while there was still a certain amount of residual crystalline boron combining well with the titanium matrix at 1100 °C. The composite samples with a relative density of 98.33%, Vickers hardness of 389.75 HV, compression yield strength of up to 1190 MPa, and an ultimate compressive strength of up to 1710 MPa were obtained. Compared with the matrix material, the compressive strength of TC4 titanium alloy containing crystalline boron and amorphous boron was increased by 7.64% and 15.50%, respectively.

Microstructure and Mechanical Behaviors of Titanium Matrix Composites Containing In Situ Whiskers Synthesized via Plasma Activated Sintering

PubMed Central

Luo, Guoqiang; Shen, Qiang; Zhang, Lianmeng

2018-01-01

In this paper, titanium matrix composites with in situ TiB whiskers were synthesized by the plasma activated sintering technique; crystalline boron and amorphous boron were used as reactants for in situ reactions, respectively. The influence of the sintering process and the crystallography type of boron on the microstructure and mechanical properties of composites were studied and compared. The densities were evaluated using Archimedes’ principle. The microstructure and mechanical properties were characterized by SEM, XRD, EBSD, TEM, a universal testing machine, and a Vickers hardness tester. The prepared composite material showed a high density and excellent comprehensive performance under the PAS condition of 20 MPa at 1000 °C for 3 min. Amorphous boron had a higher reaction efficiency than crystalline boron, and it completely reacted with the titanium matrix to generate TiB whiskers, while there was still a certain amount of residual crystalline boron combining well with the titanium matrix at 1100 °C. The composite samples with a relative density of 98.33%, Vickers hardness of 389.75 HV, compression yield strength of up to 1190 MPa, and an ultimate compressive strength of up to 1710 MPa were obtained. Compared with the matrix material, the compressive strength of TC4 titanium alloy containing crystalline boron and amorphous boron was increased by 7.64% and 15.50%, respectively. PMID:29614842

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

PubMed

Ragot, Sébastien; Ruiz, María Belén

2008-09-28

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

Application of texture analysis method for mammogram density classification

NASA Astrophysics Data System (ADS)

Nithya, R.; Santhi, B.

2017-07-01

Mammographic density is considered a major risk factor for developing breast cancer. This paper proposes an automated approach to classify breast tissue types in digital mammogram. The main objective of the proposed Computer-Aided Diagnosis (CAD) system is to investigate various feature extraction methods and classifiers to improve the diagnostic accuracy in mammogram density classification. Texture analysis methods are used to extract the features from the mammogram. Texture features are extracted by using histogram, Gray Level Co-Occurrence Matrix (GLCM), Gray Level Run Length Matrix (GLRLM), Gray Level Difference Matrix (GLDM), Local Binary Pattern (LBP), Entropy, Discrete Wavelet Transform (DWT), Wavelet Packet Transform (WPT), Gabor transform and trace transform. These extracted features are selected using Analysis of Variance (ANOVA). The features selected by ANOVA are fed into the classifiers to characterize the mammogram into two-class (fatty/dense) and three-class (fatty/glandular/dense) breast density classification. This work has been carried out by using the mini-Mammographic Image Analysis Society (MIAS) database. Five classifiers are employed namely, Artificial Neural Network (ANN), Linear Discriminant Analysis (LDA), Naive Bayes (NB), K-Nearest Neighbor (KNN), and Support Vector Machine (SVM). Experimental results show that ANN provides better performance than LDA, NB, KNN and SVM classifiers. The proposed methodology has achieved 97.5% accuracy for three-class and 99.37% for two-class density classification.

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

Two-dimensional enzyme diffusion in laterally confined DNA monolayers.

PubMed

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

2011-01-01

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

Unified theory of quantized electrons, phonons, and photons out of equilibrium: A simplified ab initio approach based on the generalized Baym-Kadanoff ansatz

NASA Astrophysics Data System (ADS)

de Melo, Pedro Miguel M. C.; Marini, Andrea

2016-04-01

We present a full ab initio description of the coupled out-of-equilibrium dynamics of photons, phonons, and electrons. In the present approach, the quantized nature of the electromagnetic field as well as of the nuclear oscillations is fully taken into account. The result is a set of integrodifferential equations, written on the Keldysh contour, for the Green's functions of electrons, phonons, and photons where the different kinds of interactions are merged together. We then concentrate on the electronic dynamics in order to reduce the problem to a computationally feasible approach. By using the generalized Baym-Kadanoff ansatz and the completed collision approximation, we introduce a series of efficient but controllable approximations. In this way, we reduce all equations to a set of decoupled equations for the density matrix that describe all kinds of static and dynamical correlations. The final result is a coherent, general, and inclusive scheme to calculate several physical quantities: carrier dynamics, transient photoabsorption, and light emission, all of which include, at the same time, electron-electron, electron-phonon, and electron-photon interactions. We further discuss how all these observables can be easily calculated within the present scheme using a fully atomistic ab initio approach.

Non-Markovian dynamics in chiral quantum networks with spins and photons

NASA Astrophysics Data System (ADS)

Ramos, Tomás; Vermersch, Benoît; Hauke, Philipp; Pichler, Hannes; Zoller, Peter

2016-06-01

We study the dynamics of chiral quantum networks consisting of nodes coupled by unidirectional or asymmetric bidirectional quantum channels. In contrast to familiar photonic networks where driven two-level atoms exchange photons via 1D photonic nanostructures, we propose and study a setup where interactions between the atoms are mediated by spin excitations (magnons) in 1D X X spin chains representing spin waveguides. While Markovian quantum network theory eliminates quantum channels as structureless reservoirs in a Born-Markov approximation to obtain a master equation for the nodes, we are interested in non-Markovian dynamics. This arises from the nonlinear character of the dispersion with band-edge effects, and from finite spin propagation velocities leading to time delays in interactions. To account for the non-Markovian dynamics we treat the quantum degrees of freedom of the nodes and connecting channel as a composite spin system with the surrounding of the quantum network as a Markovian bath, allowing for an efficient solution with time-dependent density matrix renormalization-group techniques. We illustrate our approach showing non-Markovian effects in the driven-dissipative formation of quantum dimers, and we present examples for quantum information protocols involving quantum state transfer with engineered elements as basic building blocks of quantum spintronic circuits.

Multiple Quantum Coherences (MQ) NMR and Entanglement Dynamics in the Mixed-Three-Spin XXX Heisenberg Model with Single-Ion Anisotropy

NASA Astrophysics Data System (ADS)

Hamid, Arian Zad

2016-12-01

We analytically investigate Multiple Quantum (MQ) NMR dynamics in a mixed-three-spin (1/2,1,1/2) system with XXX Heisenberg model at the front of an external homogeneous magnetic field B. A single-ion anisotropy property ζ is considered for the spin-1. The intensities dependence of MQ NMR coherences on their orders (zeroth and second orders) for two pairs of spins (1,1/2) and (1/2,1/2) of the favorite tripartite system are obtained. It is also investigated dynamics of the pairwise quantum entanglement for the bipartite (sub)systems (1,1/2) and (1/2,1/2) permanently coupled by, respectively, coupling constants J}1 and J}2, by means of concurrence and fidelity. Then, some straightforward comparisons are done between these quantities and the intensities of MQ NMR coherences and ultimately some interesting results are reported. We also show that the time evolution of MQ coherences based on the reduced density matrix of the pair spins (1,1/2) is closely connected with the dynamics of the pairwise entanglement. Finally, we prove that one can introduce MQ coherence of the zeroth order corresponds to the pair spins (1,1/2) as an entanglement witness at some special time intervals.