A real-space stochastic density matrix approach for density functional electronic structure.
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.
Reduced density matrix hybrid approach: Application to electronic energy transfer
Berkelbach, Timothy C.; Reichman, David R.; Markland, Thomas E.
2012-02-28
Electronic energy transfer in the condensed phase, such as that occurring in photosynthetic complexes, frequently occurs in regimes where the energy scales of the system and environment are similar. This situation provides a challenge to theoretical investigation since most approaches are accurate only when a certain energetic parameter is small compared to others in the problem. Here we show that in these difficult regimes, the Ehrenfest approach provides a good starting point for a dynamical description of the energy transfer process due to its ability to accurately treat coupling to slow environmental modes. To further improve on the accuracy of the Ehrenfest approach, we use our reduced density matrix hybrid framework to treat the faster environmental modes quantum mechanically, at the level of a perturbative master equation. This combined approach is shown to provide an efficient and quantitative description of electronic energy transfer in a model dimer and the Fenna-Matthews-Olson complex and is used to investigate the effect of environmental preparation on the resulting dynamics.
Density Functional Approach and Random Matrix Theory in Proteogenesis
NASA Astrophysics Data System (ADS)
Yamanaka, Masanori
2017-02-01
We study the energy-level statistics of amino acids by random matrix theory. The molecular orbital and the Kohn-Sham orbital energies are calculated using ab initio and density-functional formalisms for 20 different amino acids. To generate statistical data, we performed a multipoint calculation on 10000 molecular structures produced via a molecular dynamics simulation. For the valence orbitals, the energy-level statistics exhibit repulsion, but the universality in the random matrix cannot be determined. For the unoccupied orbitals, the energy-level statistics indicate an intermediate distribution between the Gaussian orthogonal ensemble and the semi-Poisson statistics for all 20 different amino acids. These amino acids are considered to be in a type of critical state.
Spectral density of the correlation matrix of factor models: a random matrix theory approach.
Lillo, F; Mantegna, R N
2005-07-01
We studied the eigenvalue spectral density of the correlation matrix of factor models of multivariate time series. By making use of the random matrix theory, we analytically quantified the effect of statistical uncertainty on the spectral density due to the finiteness of the sample. We considered a broad range of models, ranging from one-factor models to hierarchical multifactor models.
Sensitivity of the NMR density matrix to pulse sequence parameters: a simplified analytic approach.
Momot, Konstantin I; Takegoshi, K
2012-08-01
We present a formalism for the analysis of sensitivity of nuclear magnetic resonance pulse sequences to variations of pulse sequence parameters, such as radiofrequency pulses, gradient pulses or evolution delays. The formalism enables the calculation of compact, analytic expressions for the derivatives of the density matrix and the observed signal with respect to the parameters varied. The analysis is based on two constructs computed in the course of modified density-matrix simulations: the error interrogation operators and error commutators. The approach presented is consequently named the Error Commutator Formalism (ECF). It is used to evaluate the sensitivity of the density matrix to parameter variation based on the simulations carried out for the ideal parameters, obviating the need for finite-difference calculations of signal errors. The ECF analysis therefore carries a computational cost comparable to a single density-matrix or product-operator simulation. Its application is illustrated using a number of examples from basic NMR spectroscopy. We show that the strength of the ECF is its ability to provide analytic insights into the propagation of errors through pulse sequences and the behaviour of signal errors under phase cycling. Furthermore, the approach is algorithmic and easily amenable to implementation in the form of a programming code. It is envisaged that it could be incorporated into standard NMR product-operator simulation packages.
NASA Astrophysics Data System (ADS)
Nocera, A.; Alvarez, G.
2016-11-01
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. This paper proposes an alternative to calculate the correction vector: to use the Krylov-space approach. This paper then studies the accuracy and performance of the Krylov-space approach, when applied to the Heisenberg, the t-J, and the Hubbard models. The cases studied indicate that the 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.
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
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 the 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.
Nocera, A; Alvarez, G
2016-11-01
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. This paper proposes an alternative to calculate the correction vector: to use the Krylov-space approach. This paper then studies the accuracy and performance of the Krylov-space approach, when applied to the Heisenberg, the t-J, and the Hubbard models. The cases studied indicate that the 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.
Eigenvalue density of linear stochastic dynamical systems: A random matrix approach
NASA Astrophysics Data System (ADS)
Adhikari, S.; Pastur, L.; Lytova, A.; Du Bois, J.
2012-02-01
Eigenvalue problems play an important role in the dynamic analysis of engineering systems modeled using the theory of linear structural mechanics. When uncertainties are considered, the eigenvalue problem becomes a random eigenvalue problem. In this paper the density of the eigenvalues of a discretized continuous system with uncertainty is discussed by considering the model where the system matrices are the Wishart random matrices. An analytical expression involving the Stieltjes transform is derived for the density of the eigenvalues when the dimension of the corresponding random matrix becomes asymptotically large. The mean matrices and the dispersion parameters associated with the mass and stiffness matrices are necessary to obtain the density of the eigenvalues in the frameworks of the proposed approach. The applicability of a simple eigenvalue density function, known as the Marenko-Pastur (MP) density, is investigated. The analytical results are demonstrated by numerical examples involving a plate and the tail boom of a helicopter with uncertain properties. The new results are validated using an experiment on a vibrating plate with randomly attached spring-mass oscillators where 100 nominally identical samples are physically created and individually tested within a laboratory framework.
Density matrix renormalization group approach to two-fluid open many-fermion systems
NASA Astrophysics Data System (ADS)
Rotureau, J.; Michel, N.; Nazarewicz, W.; Płoszajczak, M.; Dukelsky, J.
2009-01-01
We have extended the density matrix renormalization group (DMRG) approach to two-fluid open many-fermion systems governed by complex-symmetric Hamiltonians. The applications are carried out for three- and four-nucleon (proton-neutron) systems within the Gamow shell model (GSM) in the complex-energy plane. We study necessary and sufficient conditions for the GSM+DMRG method to yield the correct ground-state eigenvalue and discuss different truncation schemes within the DMRG. The proposed approach will enable configuration interaction studies of weakly bound and unbound strongly interacting complex systems, which, because of a prohibitively large size of Fock space, cannot be treated by means of the direct diagonalization.
NASA Astrophysics Data System (ADS)
Pan, Andrew; Burnett, Benjamin A.; Chui, Chi On; Williams, Benjamin S.
2017-08-01
We derive a density matrix (DM) theory for quantum cascade lasers (QCLs) that describes the influence of scattering on coherences through a generalized scattering superoperator. The theory enables quantitative modeling of QCLs, including localization and tunneling effects, using the well-defined energy eigenstates rather than the ad hoc localized basis states required by most previous DM models. Our microscopic approach to scattering also eliminates the need for phenomenological transition or dephasing rates. We discuss the physical interpretation and numerical implementation of the theory, presenting sets of both energy-resolved and thermally averaged equations, which can be used for detailed or compact device modeling. We illustrate the theory's applications by simulating a high performance resonant-phonon terahertz (THz) QCL design, which cannot be easily or accurately modeled using conventional DM methods. We show that the theory's inclusion of coherences is crucial for describing localization and tunneling effects consistent with experiment.
Electrically tunable spin polarization in silicene: A multi-terminal spin density matrix approach
NASA Astrophysics Data System (ADS)
Chen, Son-Hsien
2016-05-01
Recent realized silicene field-effect transistor yields promising electronic applications. Using a multi-terminal spin density matrix approach, this paper presents an analysis of the spin polarizations in a silicene structure of the spin field-effect transistor by considering the intertwined intrinsic and Rashba spin-orbit couplings, gate voltage, Zeeman splitting, as well as disorder. Coexistence of the stagger potential and intrinsic spin-orbit coupling results in spin precession, making any in-plane polarization directions reachable by the gate voltage; specifically, the intrinsic coupling allows one to electrically adjust the in-plane components of the polarizations, while the Rashba coupling to adjust the out-of-plan polarizations. Larger electrically tunable ranges of in-plan polarizations are found in oppositely gated silicene than in the uniformly gated silicene. Polarizations in different phases behave distinguishably in weak disorder regime, while independent of the phases, stronger disorder leads to a saturation value.
Density matrix perturbation theory.
Niklasson, Anders M N; Challacombe, Matt
2004-05-14
An orbital-free quantum perturbation theory is proposed. It gives the response of the density matrix upon variation of the Hamiltonian by quadratically convergent recursions based on perturbed projections. The technique allows treatment of embedded quantum subsystems with a computational cost scaling linearly with the size of the perturbed region, O(N(pert.)), and as O(1) with the total system size. The method allows efficient high order perturbation expansions, as demonstrated with an example involving a 10th order expansion. Density matrix analogs of Wigner's 2n+1 rule are also presented.
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
NASA Astrophysics Data System (ADS)
Chen, GuanHua; Su, ZhongMin; Shen, ZhenWen; Yan, YiJing
1998-08-01
A new variation method is proposed to determine the effective Hamiltonians for conjugated π-electron systems. This method is based on the minimization of the difference between the ground state reduced single electron density matrix calculated from the effective Hamiltonian and its ab initio counterpart under a set of well-defined constraints. Applications are made to various oligomers of polymethineimine (PMI), polyazine (PAZ) and polyazoethene (PAE) at the Hartree-Fock level. Calculated are also the optical gaps of these oligomers. The effective Hamiltonians contain electron-electron Coulomb interactions and are suitable for the study of excited state dynamic processes such as nonlinear optical properties in π-conjugated systems.
Vibrational Density Matrix Renormalization Group.
Baiardi, Alberto; Stein, Christopher J; Barone, Vincenzo; Reiher, Markus
2017-08-08
Variational approaches for the calculation of vibrational wave functions and energies are a natural route to obtain highly accurate results with controllable errors. Here, we demonstrate how the density matrix renormalization group (DMRG) can be exploited to optimize vibrational wave functions (vDMRG) expressed as matrix product states. We study the convergence of these calculations with respect to the size of the local basis of each mode, the number of renormalized block states, and the number of DMRG sweeps required. We demonstrate the high accuracy achieved by vDMRG for small molecules that were intensively studied in the literature. We then proceed to show that the complete fingerprint region of the sarcosyn-glycin dipeptide can be calculated with vDMRG.
Nuclear motion effects on the density matrix of crystals: An ab initio Monte Carlo harmonic approach
NASA Astrophysics Data System (ADS)
Pisani, Cesare; Erba, Alessandro; Ferrabone, Matteo; Dovesi, Roberto
2012-07-01
In the frame of the Born-Oppenheimer approximation, nuclear motions in crystals can be simulated rather accurately using a harmonic model. In turn, the electronic first-order density matrix (DM) can be expressed as the statistically weighted average over all its determinations each resulting from an instantaneous nuclear configuration. This model has been implemented in a computational scheme which adopts an ab initio one-electron (Hartree-Fock or Kohn-Sham) Hamiltonian in the CRYSTAL program. After selecting a supercell of reasonable size and solving the corresponding vibrational problem in the harmonic approximation, a Metropolis algorithm is adopted for generating a sample of nuclear configurations which reflects their probability distribution at a given temperature. For each configuration in the sample the "instantaneous" DM is calculated, and its contribution to the observables of interest is extracted. Translational and point symmetry of the crystal as reflected in its average DM are fully exploited. The influence of zero-point and thermal motion of nuclei on such important first-order observables as x-ray structure factors and Compton profiles can thus be estimated.
Pisani, Cesare; Erba, Alessandro; Ferrabone, Matteo; Dovesi, Roberto
2012-07-28
In the frame of the Born-Oppenheimer approximation, nuclear motions in crystals can be simulated rather accurately using a harmonic model. In turn, the electronic first-order density matrix (DM) can be expressed as the statistically weighted average over all its determinations each resulting from an instantaneous nuclear configuration. This model has been implemented in a computational scheme which adopts an ab initio one-electron (Hartree-Fock or Kohn-Sham) Hamiltonian in the CRYSTAL program. After selecting a supercell of reasonable size and solving the corresponding vibrational problem in the harmonic approximation, a Metropolis algorithm is adopted for generating a sample of nuclear configurations which reflects their probability distribution at a given temperature. For each configuration in the sample the "instantaneous" DM is calculated, and its contribution to the observables of interest is extracted. Translational and point symmetry of the crystal as reflected in its average DM are fully exploited. The influence of zero-point and thermal motion of nuclei on such important first-order observables as x-ray structure factors and Compton profiles can thus be estimated.
1983-12-15
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Biplab Dey, Michael E. McCracken, David G. Ireland, Curtis A. Meyer
2011-05-01
The complete expression for the intensity in pseudo-scalar meson photoproduction with a polarized beam, target, and recoil baryon is derived using a density matrix approach that offers great economy of notation. A Cartesian basis with spins for all particles quantized along a single direction, the longitudinal beam direction, is used for consistency and clarity in interpretation. A single spin-quantization axis for all particles enables the amplitudes to be written in a manifestly covariant fashion with simple relations to those of the well-known CGLN formalism. Possible sign discrepancies between theoretical amplitude-level expressions and experimentally measurable intensity profiles are dealt with carefully. Our motivation is to provide a coherent framework for coupled-channel partial-wave analysis of several meson photoproduction reactions, incorporating recently published and forthcoming polarization data from Jefferson Lab.
Dey, Biplab; Meyer, Curtis A.; McCracken, Michael E.; Ireland, David G.
2011-05-15
The complete expression for the intensity in pseudo-scalar meson photoproduction with a polarized beam, target, and recoil baryon is derived using a density matrix approach that offers great economy of notation. A Cartesian basis with spins for all particles quantized along a single direction, the longitudinal beam direction, is used for consistency and clarity in interpretation. A single spin-quantization axis for all particles enables the amplitudes to be written in a manifestly covariant fashion with simple relations to those of the well-known Chew-Goldberger-Low-Nambu formalism. Possible sign discrepancies between theoretical amplitude-level expressions and experimentally measurable intensity profiles are dealt with carefully. Our motivation is to provide a coherent framework for coupled-channel partial-wave analysis of several meson photoproduction reactions, incorporating recently published and forthcoming polarization data from Jefferson Lab.
NASA Astrophysics Data System (ADS)
Dey, Biplab; McCracken, Michael E.; Ireland, David G.; Meyer, Curtis A.
2011-05-01
The complete expression for the intensity in pseudo-scalar meson photoproduction with a polarized beam, target, and recoil baryon is derived using a density matrix approach that offers great economy of notation. A Cartesian basis with spins for all particles quantized along a single direction, the longitudinal beam direction, is used for consistency and clarity in interpretation. A single spin-quantization axis for all particles enables the amplitudes to be written in a manifestly covariant fashion with simple relations to those of the well-known Chew-Goldberger-Low-Nambu formalism. Possible sign discrepancies between theoretical amplitude-level expressions and experimentally measurable intensity profiles are dealt with carefully. Our motivation is to provide a coherent framework for coupled-channel partial-wave analysis of several meson photoproduction reactions, incorporating recently published and forthcoming polarization data from Jefferson Lab.
Richter, Marten Knorr, Andreas
2010-04-15
Time convolution less density matrix theory (TCL) is a powerful and well established tool to investigate strong system-bath coupling for linear optical spectra. We show that TCL equations can be generalised to the nonlinear optical response up to a chosen order in the optical field. This goal is achieved via an time convolution less perturbation scheme for the reduced density matrices of the electronic system. In our approach, the most important results are the inclusion of a electron-phonon coupling non-diagonal in the electronic states and memory effects of the bath: First, the considered model system is introduced. Second, the time evolution of the statistical operator is expanded with respect to the external optical field. This expansion is the starting point to explain how a TCL theory can treat the response up to in a certain order in the external field. Third, new TCL equations, including bath memory effects, are derived and the problem of information loss in the reduced density matrix is analysed. For this purpose, new dimensions are added to the reduced statistical operator to compensate lack of information in comparison with the full statistical operator. The theory is benchmarked with a two level system and applied to a three level system including non-diagonal phonon coupling. In our analysis of pump-probe experiments, the bath memory is influenced by the system state occupied between pump and probe pulse. In particular, the memory of the bath influences the dephasing process of electronic coherences developing during the time interval between pump and probe pulses.
Hammond, Jeff R.; Mazziotti, David A.
2006-01-15
An alternative approach to open-shell molecular calculations using the variational two-electron reduced-density-matrix (2-RDM) theory [Mazziotti, Phys. Rev. Lett. 93, 213001 (2004)] is presented. The energy and 2-RDM of the open-shell molecule (or radical) are computed from the limit of dissociating one or more hydrogen atoms from a molecule in a singlet state. Because the ground-state energy of an 'infinitely' separated hydrogen atom in a given finite basis is known, we can determine the energy of the radical by subtracting the energy of one or more hydrogen atoms from the energy of the total dissociated system. The 2-RDM is constrained to have singlet symmetry in all calculations. Two sets of N-representability conditions are employed: (i) two-positivity conditions, and (ii) two-positivity conditions plus the T{sub 2} condition, which is a subset of the three-positivity conditions. Optimization of the energy with respect to the 2-RDM is performed with a first-order algorithm for solving the semidefinite program within the variational 2-RDM method. We present calculations of several radicals near equilibrium as well as the dissociation curves of the diatomic radicals CH and OH.
NASA Astrophysics Data System (ADS)
Khemani, Vedika; Pollmann, Frank; Sondhi, S. L.
2016-06-01
The eigenstates of many-body localized (MBL) Hamiltonians exhibit low entanglement. We adapt the highly successful density-matrix renormalization group method, which is usually used to find modestly entangled ground states of local Hamiltonians, to find individual highly excited eigenstates of MBL Hamiltonians. The adaptation builds on the distinctive spatial structure of such eigenstates. We benchmark our method against the well-studied random field Heisenberg model in one dimension. At moderate to large disorder, the method successfully obtains excited eigenstates with high accuracy, thereby enabling a study of MBL systems at much larger system sizes than those accessible to exact-diagonalization methods.
Ness, H
2013-08-01
In this paper, we formally demonstrate that the nonequilibrium density matrix developed by Hershfield for the steady state has the form of a McLennan-Zubarev nonequilibrium ensemble. The correction term in this pseudoequilibrium Gibbs-like ensemble is directly related to the entropy production in the quantum open system. The fact that both methods state that a nonequilibrium steady state can be mapped onto a pseudoequilibrium, permits us to develop nonequilibrium quantities from formal expressions equivalent to the equilibrium case. We provide an example: the derivation of a nonequilibrium distribution function for the electron population in a scattering region in the context of quantum transport.
Khemani, Vedika; Pollmann, Frank; Sondhi, S L
2016-06-17
The eigenstates of many-body localized (MBL) Hamiltonians exhibit low entanglement. We adapt the highly successful density-matrix renormalization group method, which is usually used to find modestly entangled ground states of local Hamiltonians, to find individual highly excited eigenstates of MBL Hamiltonians. The adaptation builds on the distinctive spatial structure of such eigenstates. We benchmark our method against the well-studied random field Heisenberg model in one dimension. At moderate to large disorder, the method successfully obtains excited eigenstates with high accuracy, thereby enabling a study of MBL systems at much larger system sizes than those accessible to exact-diagonalization methods.
NASA Astrophysics Data System (ADS)
Afzali, R.; Ebrahimian, N.; Eghbalifar, B.
2016-10-01
By approximating the energy gap, entering nano-size effect via gap fluctuation and calculating the Green's functions and the space-spin density matrix, the dependence of quantum correlation (entanglement, discord and tripartite entanglement) on the relative distance of two electron spins forming Cooper pairs, the energy gap and the length of bulk and nano interacting Fermi system (a nodal d-wave superconductor) is determined. In contrast to a s-wave superconductor, quantum correlation of the system is sensitive to the change of the gap magnitude and strongly depends on the length of the grain. Also, quantum discord oscillates. Furthermore, the entanglement length and the correlation length are investigated. Discord becomes zero at a characteristic length of the d-wave superconductor.
Yan, YiJing
2014-02-07
This work establishes a strongly correlated system-and-bath dynamics theory, the many-dissipaton density operators formalism. It puts forward a quasi-particle picture for environmental influences. This picture unifies the physical descriptions and algebraic treatments on three distinct classes of quantum environments, electron bath, phonon bath, and two-level spin or exciton bath, as their participating in quantum dissipation processes. Dynamical variables for theoretical description are no longer just the reduced density matrix for system, but remarkably also those for quasi-particles of bath. The present theoretical formalism offers efficient and accurate means for the study of steady-state (nonequilibrium and equilibrium) and real-time dynamical properties of both systems and hybridizing environments. It further provides universal evaluations, exact in principle, on various correlation functions, including even those of environmental degrees of freedom in coupling with systems. Induced environmental dynamics could be reflected directly in experimentally measurable quantities, such as Fano resonances and quantum transport current shot noise statistics.
Parameterized local hybrid functionals from density-matrix similarity metrics.
Janesko, Benjamin G; Scuseria, Gustavo E
2008-02-28
We recently proposed a real-space similarity metric comparing the Kohn-Sham one-particle density matrix to the local spin-density approximation model density matrix [Janesko and Scuseria, J. Chem. Phys. 127, 164117 (2007)]. This metric provides a useful ingredient for constructing local hybrid density functionals that locally mix exact exchange and semilocal density functional theory exchange. Here we present two lines of inquiry: An approximate similarity metric comparing exact versus generalized gradient approximation (GGA), exchange and parameterized mixing functions using these similarity metrics. This approach yields significantly improved thermochemistry, including GGA local hybrids whose thermochemical performance approaches GGA global hybrids.
Polarizable Embedding Density Matrix Renormalization Group.
Hedegård, Erik D; Reiher, Markus
2016-09-13
The polarizable embedding (PE) approach is a flexible embedding model where a preselected region out of a larger system is described quantum mechanically, while the interaction with the surrounding environment is modeled through an effective operator. This effective operator represents the environment by atom-centered multipoles and polarizabilities derived from quantum mechanical calculations on (fragments of) the environment. Thereby, the polarization of the environment is explicitly accounted for. Here, we present the coupling of the PE approach with the density matrix renormalization group (DMRG). This PE-DMRG method is particularly suitable for embedded subsystems that feature a dense manifold of frontier orbitals which requires large active spaces. Recovering such static electron-correlation effects in multiconfigurational electronic structure problems, while accounting for both electrostatics and polarization of a surrounding environment, allows us to describe strongly correlated electronic structures in complex molecular environments. We investigate various embedding potentials for the well-studied first excited state of water with active spaces that correspond to a full configuration-interaction treatment. Moreover, we study the environment effect on the first excited state of a retinylidene Schiff base within a channelrhodopsin protein. For this system, we also investigate the effect of dynamical correlation included through short-range density functional theory.
Beau, Mathieu; Savoie, Baptiste
2014-05-15
In this paper, we rigorously investigate the reduced density matrix (RDM) associated to the ideal Bose gas in harmonic traps. We present a method based on a sum-decomposition of the RDM allowing to treat not only the isotropic trap, but also general anisotropic traps. When focusing on the isotropic trap, the method is analogous to the loop-gas approach developed by Mullin [“The loop-gas approach to Bose-Einstein condensation for trapped particles,” Am. J. Phys. 68(2), 120 (2000)]. Turning to the case of anisotropic traps, we examine the RDM for some anisotropic trap models corresponding to some quasi-1D and quasi-2D regimes. For such models, we bring out an additional contribution in the local density of particles which arises from the mesoscopic loops. The close connection with the occurrence of generalized-Bose-Einstein condensation is discussed. Our loop-gas-like approach provides relevant information which can help guide numerical investigations on highly anisotropic systems based on the Path Integral Monte Carlo method.
NASA Astrophysics Data System (ADS)
Finger, Karin; Saalfrank, Peter
1997-04-01
The experimentally observed vibrational excitation of NO molecules photodesorbing from a Pt(111) surface is investigated numerically with the help of open-system density matrix theory. We extend Gadzuk's jumping wave packet model to treat DIET processes (desorption induced by electronic transitions, single-excitation limit) which is equivalent to a one-channel open system Liouville-von Neumann equation with coordinate-independent quenching, to cases when the electronic relaxation becomes coordinate-dependent. This allows for a more realistic but still economic and, hence, systematic study of DIET within a two-state, two-degrees of freedom model. Adopting "reasonable" Antoniewicz-type model potentials, we find that the experimental observations can semi-quantitatively be rationalized if an electronic quenching rate decreasing with increasing NO separation, is assumed. Preliminary two-mode DIMET simulations (desorption induced by multiple electronic transitions, multiple-excitation limit) within a stochastic wave packet approach are also presented.
NASA Astrophysics Data System (ADS)
Jacobs, Verne
2015-05-01
The frequency-dependent transition rates for multi-photon processes in quantized many-electron systems are evaluated using a reduced-density-matrix approach. A fundamental foundation, based on quantum electrodynamics, is provided for systematic spectral simulations for electromagnetic interactions in quantized many-electron systems, including atomic, molecular, and solid-state systems. A perturbation expansion of the frequency-domain Liouville-space self-energy operator is employed in detailed evaluations of the spectral-line shapes. The self-energy contributions associated with environmental electron-photon and electron-phonon interactions are systematically taken into account. Detailed evaluations have been carried out for the spectral-line widths and shifts in the diagonal-resolvent, lowest order (Born), and short-memory-time (Markov) approximations. Work supported by the Office of Naval Research through the Basic Research Program at The Naval Research Laboratory.
Interaction picture density matrix quantum Monte Carlo
Malone, Fionn D. Lee, D. K. K.; Foulkes, W. M. C.; Blunt, N. S.; Shepherd, James J.; Spencer, J. S.
2015-07-28
The recently developed density matrix quantum Monte Carlo (DMQMC) algorithm stochastically samples the N-body thermal density matrix and hence provides access to exact properties of many-particle quantum systems at arbitrary temperatures. We demonstrate that moving to the interaction picture provides substantial benefits when applying DMQMC to interacting fermions. In this first study, we focus on a system of much recent interest: the uniform electron gas in the warm dense regime. The basis set incompleteness error at finite temperature is investigated and extrapolated via a simple Monte Carlo sampling procedure. Finally, we provide benchmark calculations for a four-electron system, comparing our results to previous work where possible.
Diaz-Torres, Alexis
2010-11-15
The coupled-channels density-matrix technique for nuclear reaction dynamics, which is based on the Liouville-von Neumann equation with Lindblad dissipative terms, is developed with the inclusion of full angular momentum couplings. It allows a quantitative study of the role and importance of quantum decoherence in nuclear scattering. Formulas of asymptotic observables that can reveal effects of quantum decoherence are given. A method for extracting energy-resolved scattering information from the time-dependent density matrix is introduced. As an example, model calculations are carried out for the low-energy collision of the {sup 16}O projectile on the {sup 154}Sm target.
Measuring Entanglement Spectrum via Density Matrix Exponentiation
NASA Astrophysics Data System (ADS)
Zhu, Guanyu; Seif, Alireza; Pichler, Hannes; Zoller, Peter; Hafezi, Mohammad
Entanglement spectrum (ES), the eigenvalues of the reduced density matrix of a subsystem, serves as a powerful theoretical tool to study many-body systems. For example, the gap and degeneracies of the entanglement spectrum have been used to identify various topological phases. However, the usefulness of such a concept in real experiments has been debated, since it is believed that obtaining the ES requires full state tomography, at a cost which exponentially grows with the systems size. Inspired by a recent density matrix exponentiation technique, we propose a scheme to measure ES by evolving the system with a Hamiltonian that is the subsystem's own reduced density matrix. Such a time evolution can be induced by an ancilla photon that is coupled to multiple qubits at the same time. The phase associated with the time evolution can be detected and converted into ES through either a digital or an analogue scheme. The digital scheme involves a modified quantum phase estimation algorithm based on random time evolution, while the analogue scheme is in the spirit of Ramsey interferometry. Both schemes are not limited by the size of the system, and are especially sensitive to the gap and degeneracies. We also discuss the implementation in cavity/circuit-QED and ion trap systems.
Density: A Discovery Approach.
ERIC Educational Resources Information Center
Rieck, William
1994-01-01
Describes an activity that allows students to discover the concept of density and that density is a determining physical property of a pure substance. Makes suggestions to further enhance students' understanding of density. (ZWH)
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.
A density functional approach to ferrogels.
Cremer, P; Heinen, M; Menzel, A M; Löwen, H
2017-07-12
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.
Localized density matrix minimization and linear-scaling algorithms
NASA Astrophysics Data System (ADS)
Lai, Rongjie; Lu, Jianfeng
2016-06-01
We propose a convex variational approach to compute localized density matrices for both zero temperature and finite temperature cases, by adding an entry-wise ℓ1 regularization to the free energy of the quantum system. Based on the fact that the density matrix decays exponentially away from the diagonal for insulating systems or systems at finite temperature, the proposed ℓ1 regularized variational method provides an effective way to approximate the original quantum system. We provide theoretical analysis of the approximation behavior and also design convergence guaranteed numerical algorithms based on Bregman iteration. More importantly, the ℓ1 regularized system naturally leads to localized density matrices with banded structure, which enables us to develop approximating algorithms to find the localized density matrices with computation cost linearly dependent on the problem size.
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.
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.
Reduced density-matrix functionals from many-particle theory
NASA Astrophysics Data System (ADS)
Schade, Robert; Kamil, Ebad; Blöchl, Peter
2017-07-01
In materials with strong electron correlation the proper treatment of local atomic physics described by orbital occupations is crucial. Reduced density-matrix functional theory is a natural extension of density functional theory for systems that are dominated by orbital physics. We review the current state of reduced density-matrix functional theory (RDMFT). For atomic structure relaxations or ab-initio molecular dynamics the combination of density functional theory (DFT) and dynamical mean-field theory (DMFT) possesses a number of disadvantages, like the cumbersome evaluation of forces. We therefore describe a method, DFT+RDMFT, that combines many-particle effects based on reduced density-matrix functional theory with a density functional-like framework. A recent development is the construction of density-matrix functionals directly from many-particle theory such as methods from quantum chemistry or many-particle Green's functions. We present the underlying exact theorems and describe current progress towards quantitative functionals.
Sliced Basis Density Matrix Renormalization Group for Electronic Structure
NASA Astrophysics Data System (ADS)
Stoudenmire, E. Miles; White, Steven R.
2017-07-01
We introduce a hybrid approach to applying the density matrix renormalization group to continuous systems, combining a grid approximation along one direction with a finite Gaussian basis set for the remaining two directions. This approach is especially useful for chainlike molecules, where the grid is used in the long direction. For hydrogen chain systems, the computational time scales approximately linearly with the number of atoms, as we show with near-exact minimal basis set calculations with up to 1000 atoms. The linear scaling comes from both the localization of the basis and a compression method for the long-ranged two-electron interaction. For shorter hydrogen chains, we show results with up to triple-ζ bases.
Matrix model approach to cosmology
NASA Astrophysics Data System (ADS)
Chaney, A.; Lu, Lei; Stern, A.
2016-03-01
We perform a systematic search for rotationally invariant cosmological solutions to toy matrix models. These models correspond to the bosonic sector of Lorentzian Ishibashi, Kawai, Kitazawa and Tsuchiya (IKKT)-type matrix models in dimensions d less than ten, specifically d =3 and d =5 . After taking a continuum (or commutative) limit they yield d -1 dimensional Poisson manifolds. The manifolds have a Lorentzian induced metric which can be associated with closed, open, or static space-times. For d =3 , we obtain recursion relations from which it is possible to generate rotationally invariant matrix solutions which yield open universes in the continuum limit. Specific examples of matrix solutions have also been found which are associated with closed and static two-dimensional space-times in the continuum limit. The solutions provide for a resolution of cosmological singularities, at least within the context of the toy matrix models. The commutative limit reveals other desirable features, such as a solution describing a smooth transition from an initial inflation to a noninflationary era. Many of the d =3 solutions have analogues in higher dimensions. The case of d =5 , in particular, has the potential for yielding realistic four-dimensional cosmologies in the continuum limit. We find four-dimensional de Sitter d S4 or anti-de Sitter AdS4 solutions when a totally antisymmetric term is included in the matrix action. A nontrivial Poisson structure is attached to these manifolds which represents the lowest order effect of noncommutativity. For the case of AdS4 , we find one particular limit where the lowest order noncommutativity vanishes at the boundary, but not in the interior.
Information Theory Density Matrix for a Simple Quantum System.
ERIC Educational Resources Information Center
Titus, William J.
1979-01-01
Derives the density matrix that best describes, according to information theory, a one-dimensional single particle quantum system when the only information available is the values for the linear and quadratic position-momentum moments. (Author/GA)
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.
Information Theory Density Matrix for a Simple Quantum System.
ERIC Educational Resources Information Center
Titus, William J.
1979-01-01
Derives the density matrix that best describes, according to information theory, a one-dimensional single particle quantum system when the only information available is the values for the linear and quadratic position-momentum moments. (Author/GA)
Deconstructing Wigner's density matrix concerning the mind-body question
NASA Astrophysics Data System (ADS)
Brandt, Howard E.
2002-06-01
In honor of the centennial of Eugene Wigner’s birth, a possible interpretation is given of the density matrix appearing in his classic paper, “Remarks on the mind-body question.” It is argued that nearinstantaneous vanishing of the quantum coherences of the reduced density matrix of the measured object would occur either in the case of Wigner’s friend, or in the case of any complex measuring automaton (conscious or not) making the measurement.
Stationary density matrix of a pumped polariton system.
Vera, Carlos Andrés; Cabo, Alejandro; González, Augusto
2009-03-27
The density matrix rho of a model polariton system is obtained numerically from a master equation which takes account of pumping and losses. In the stationary limit, the coherences between eigenstates of the Hamiltonian are 3 orders of magnitude smaller than the occupations, meaning that the stationary density matrix is approximately diagonal in the energy representation. A weakly distorted grand canonical Gibbs distribution fits well the occupations.
NASA Astrophysics Data System (ADS)
Miller, William H.; Cotton, Stephen J.
2016-08-01
It is pointed out that the classical phase space distribution in action-angle (a-a) variables obtained from a Wigner function depends on how the calculation is carried out: if one computes the standard Wigner function in Cartesian variables (p, x), and then replaces p and x by their expressions in terms of a-a variables, one obtains a different result than if the Wigner function is computed directly in terms of the a-a variables. Furthermore, the latter procedure gives a result more consistent with classical and semiclassical theory—e.g., by incorporating the Bohr-Sommerfeld quantization condition (quantum states defined by integer values of the action variable) as well as the Heisenberg correspondence principle for matrix elements of an operator between such states—and has also been shown to be more accurate when applied to electronically non-adiabatic applications as implemented within the recently developed symmetrical quasi-classical (SQC) Meyer-Miller (MM) approach. Moreover, use of the Wigner function (obtained directly) in a-a variables shows how our standard SQC/MM approach can be used to obtain off-diagonal elements of the electronic density matrix by processing in a different way the same set of trajectories already used (in the SQC/MM methodology) to obtain the diagonal elements.
Miller, William H.; Cotton, Stephen J.
2016-08-28
It is pointed out that the classical phase space distribution in action-angle (a-a) variables obtained from a Wigner function depends on how the calculation is carried out: if one computes the standard Wigner function in Cartesian variables (p, x), and then replaces p and x by their expressions in terms of a-a variables, one obtains a different result than if the Wigner function is computed directly in terms of the a-a variables. Furthermore, the latter procedure gives a result more consistent with classical and semiclassical theory - e.g., by incorporating the Bohr-Sommerfeld quantization condition (quantum states defined by integer values of the action variable) as well as the Heisenberg correspondence principle for matrix elements of an operator between such states - and has also been shown to be more accurate when applied to electronically non-adiabatic applications as implemented within the recently developed symmetrical quasi-classical (SQC) Meyer-Miller (MM) approach. Moreover, use of the Wigner function (obtained directly) in a-a variables shows how our standard SQC/MM approach can be used to obtain off-diagonal elements of the electronic density matrix by processing in a different way the same set of trajectories already used (in the SQC/MM methodology) to obtain the diagonal elements.
Miller, William H.; Cotton, Stephen J.
2016-08-28
It is pointed out that the classical phase space distribution in action-angle (a-a) variables obtained from a Wigner function depends on how the calculation is carried out: if one computes the standard Wigner function in Cartesian variables (p, x), and then replaces p and x by their expressions in terms of a-a variables, one obtains a different result than if the Wigner function is computed directly in terms of the a-a variables. Furthermore, the latter procedure gives a result more consistent with classical and semiclassical theory - e.g., by incorporating the Bohr-Sommerfeld quantization condition (quantum states defined by integer valuesmore » of the action variable) as well as the Heisenberg correspondence principle for matrix elements of an operator between such states - and has also been shown to be more accurate when applied to electronically non-adiabatic applications as implemented within the recently developed symmetrical quasi-classical (SQC) Meyer-Miller (MM) approach. Moreover, use of the Wigner function (obtained directly) in a-a variables shows how our standard SQC/MM approach can be used to obtain off-diagonal elements of the electronic density matrix by processing in a different way the same set of trajectories already used (in the SQC/MM methodology) to obtain the diagonal elements.« less
Hedegård, Erik Donovan Knecht, Stefan; Reiher, Markus; Kielberg, Jesper Skau; Jensen, Hans Jørgen Aagaard
2015-06-14
We present a new hybrid multiconfigurational method based on the concept of range-separation that combines the density matrix renormalization group approach with density functional theory. This new method is designed for the simultaneous description of dynamical and static electron-correlation effects in multiconfigurational electronic structure problems.
The ab-initio density matrix renormalization group in practice
Olivares-Amaya, Roberto; Hu, Weifeng; Sharma, Sandeep; Yang, Jun; Chan, Garnet Kin-Lic; Nakatani, Naoki
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.
The ab-initio density matrix renormalization group in practice.
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.
Revisting the Density Matrix Expansion with Regulated Chiral Interactions
NASA Astrophysics Data System (ADS)
Dyhdalo, Alexander; Furnstahl, Richard; Bogner, Scott; Schunck, Nicolas; Navarro Perez, Rodrigo
2016-09-01
The density matrix expansion provides a general way to map microscopic interactions to a local functional. Previous density matrix expansion formulations added unregulated chiral long-range potentials to a Skyrme-type functional, which accounted for the short-range contributions. We implement the expansion with new coordinate space regulators using the regulator cutoff as a tool to adiabatically turn on finite-range pion interactions. We discuss `smoking guns' for correct inclusion of 3-body forces, which are implemented in a normal-ordering prescription, and compare to ab initio calculations.
Spectral Density Matrix of a Single Photon Measured
NASA Astrophysics Data System (ADS)
Wasilewski, Wojciech; Kolenderski, Piotr; Frankowski, Robert
2007-09-01
We propose and demonstrate a method for measuring the spectral density matrix of a single photon pulse. The method is based on registering Hong-Ou-Mandel interference between a photon to be measured and a pair of attenuated and suitably delayed laser pulses described by a known spectral amplitude. The density matrix is retrieved from a two-dimensional interferogram of coincidence counts. The method has been implemented for a type-I down-conversion source, pumped by ultrashort laser pulses. The experimental results agree well with a theoretical model which takes into account the temporal as well as spatial effects in the source.
Spectral density matrix of a single photon measured.
Wasilewski, Wojciech; Kolenderski, Piotr; Frankowski, Robert
2007-09-21
We propose and demonstrate a method for measuring the spectral density matrix of a single photon pulse. The method is based on registering Hong-Ou-Mandel interference between a photon to be measured and a pair of attenuated and suitably delayed laser pulses described by a known spectral amplitude. The density matrix is retrieved from a two-dimensional interferogram of coincidence counts. The method has been implemented for a type-I down-conversion source, pumped by ultrashort laser pulses. The experimental results agree well with a theoretical model which takes into account the temporal as well as spatial effects in the source.
Auxiliary Density Matrix Methods for Hartree-Fock Exchange Calculations.
Guidon, Manuel; Hutter, Jürg; VandeVondele, Joost
2010-08-10
The calculation of Hartree-Fock exchange (HFX) is computationally demanding for large systems described with high-quality basis sets. In this work, we show that excellent performance and good accuracy can nevertheless be obtained if an auxiliary density matrix is employed for the HFX calculation. Several schemes to derive an auxiliary density matrix from a high-quality density matrix are discussed. Key to the accuracy of the auxiliary density matrix methods (ADMM) is the use of a correction based on standard generalized gradient approximations for HFX. ADMM integrates seamlessly in existing HFX codes and, in particular, can be employed in linear scaling implementations. Demonstrating the performance of the method, the effect of HFX on the structure of liquid water is investigated in detail using Born-Oppenheimer molecular dynamics simulations (300 ps) of a system of 64 molecules. Representative for large systems are calculations on a solvated protein (Rubredoxin), for which ADMM outperforms the corresponding standard HFX implementation by approximately a factor 20.
Communication: Four-component density matrix renormalization group
Knecht, Stefan Reiher, Markus; Legeza, Örs
2014-01-28
We present the first implementation of the relativistic quantum chemical two- and four-component density matrix renormalization group algorithm that includes a variational description of scalar-relativistic effects and spin–orbit coupling. Numerical results based on the four-component Dirac–Coulomb Hamiltonian are presented for the standard reference molecule for correlated relativistic benchmarks: thallium hydride.
Juxtaposing density matrix and classical path-based wave packet dynamics
Aghtar, Mortaza; Liebers, Jörg; Strümpfer, Johan; Schulten, Klaus; Kleinekathöfer, Ulrich
2012-01-01
In many physical, chemical, and biological systems energy and charge transfer processes are of utmost importance. To determine the influence of the environment on these transport processes, equilibrium molecular dynamics simulations become more and more popular. From these simulations, one usually determines the thermal fluctuations of certain energy gaps, which are then either used to perform ensemble-averaged wave packet simulations, also called Ehrenfest dynamics, or to employ a density matrix approach via spectral densities. These two approaches are analyzed through energy gap fluctuations that are generated to correspond to a predetermined spectral density. Subsequently, density matrix and wave packet simulations are compared through population dynamics and absorption spectra for different parameter regimes. Furthermore, a previously proposed approach to enforce the correct long-time behavior in the wave packet simulations is probed and an improvement is proposed. PMID:22697524
Density Matrix Embedding: A Strong-Coupling Quantum Embedding Theory.
Knizia, Gerald; Chan, Garnet Kin-Lic
2013-03-12
We extend our density matrix embedding theory (DMET) [Phys. Rev. Lett.2012, 109, 186404] from lattice models to the full chemical Hamiltonian. DMET allows the many-body embedding of arbitrary fragments of a quantum system, even when such fragments are open systems and strongly coupled to their environment (e.g., by covalent bonds). In DMET, empirical approaches to strong coupling, such as link atoms or boundary regions, are replaced by a small, rigorous quantum bath designed to reproduce the entanglement between a fragment and its environment. We describe the theory and demonstrate its feasibility in strongly correlated hydrogen ring and grid models; these are not only beyond the scope of traditional embeddings but even challenge conventional quantum chemistry methods themselves. We find that DMET correctly describes the notoriously difficult symmetric dissociation of a 4 × 3 hydrogen atom grid, even when the treated fragments are as small as single hydrogen atoms. We expect that DMET will open up new ways of treating complex strongly coupled, strongly correlated systems in terms of their individual fragments.
Improved density matrix expansion for spin-unsaturated nuclei
Gebremariam, B.; Bogner, S. K.; Duguet, T.
2010-07-15
A current objective of low-energy nuclear theory is to build nonempirical nuclear energy density functionals (EDFs) from underlying internucleon interactions and many-body perturbation theory (MBPT). The density matrix expansion (DME) of Negele and Vautherin is a convenient method to map highly nonlocal Hartree-Fock expressions into the form of a quasi-local Skyrme functional with density-dependent couplings. In this work, we assess the accuracy of the DME at reproducing the nonlocal exchange (Fock) contribution to the energy. In contrast to the scalar part of the density matrix for which the original formulation of Negele and Vautherin is reasonably accurate, we demonstrate the necessity to reformulate the DME for the vector part of the density matrix, which is needed for an accurate description of spin-unsaturated nuclei. Phase-space-averaging techniques are shown to yield a significant improvement for the vector part of the density matrix compared to the original formulation of Negele and Vautherin. The key to the improved accuracy is to take into account the anisotropy that characterizes the local momentum distribution in the surface region of finite Fermi systems. Optimizing separately the DME for the central, tensor, and spin-orbit contributions to the Fock energy, one reaches a few-percent accuracy over a representative set of semi-magic nuclei. With such an accuracy at hand, one can envision using the corresponding Skyrme-like energy functional as a microscopically constrained starting point around which future phenomenological parametrizations can be built and refined.
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.
Magnesium Matrix Composite Foams-Density, Mechanical Properties, and Applications
2012-07-24
known that the effect of particle-matrix interfacial bonding is much less significant under compression compared to under tension [33,34]. One of the...parameter). Some syntactic foam composites are found to have less than 0.4 g/cc density in Figure 9. These data points belong to foams that contain...syntactic foams containing porosity only inside hollow particles. The yield strength values for various types of MMSFs, including aluminum, titanium , and
Jordan, Daniel K; Mazziotti, David A
2005-02-22
Two classes of linear-scaling methods to replace diagonalization of the one-particle Hamiltonian matrix in density functional theory are compared to each other. Purification takes a density matrix with the correct eigenfunctions and corrects the occupation numbers; density matrix minimization takes a density matrix with correct occupation numbers and corrects the eigenfunctions by rotating the orbitals. Computational comparisons are performed through modification of the MondoSCF program on water clusters and the protein endothelin. A purification scheme and a density matrix minimization scheme, based on the 1,2-contracted Schrodinger equation [D. A. Mazziotti, J. Chem. Phys. 115, 8305 (2001)] are implemented in large systems.
Random matrix approach to categorical data analysis
NASA Astrophysics Data System (ADS)
Patil, Aashay; Santhanam, M. S.
2015-09-01
Correlation and similarity measures are widely used in all the areas of sciences and social sciences. Often the variables are not numbers but are instead qualitative descriptors called categorical data. We define and study similarity matrix, as a measure of similarity, for the case of categorical data. This is of interest due to a deluge of categorical data, such as movie ratings, top-10 rankings, and data from social media, in the public domain that require analysis. We show that the statistical properties of the spectra of similarity matrices, constructed from categorical data, follow random matrix predictions with the dominant eigenvalue being an exception. We demonstrate this approach by applying it to the data for Indian general elections and sea level pressures in the North Atlantic ocean.
Random matrix approach to categorical data analysis.
Patil, Aashay; Santhanam, M S
2015-09-01
Correlation and similarity measures are widely used in all the areas of sciences and social sciences. Often the variables are not numbers but are instead qualitative descriptors called categorical data. We define and study similarity matrix, as a measure of similarity, for the case of categorical data. This is of interest due to a deluge of categorical data, such as movie ratings, top-10 rankings, and data from social media, in the public domain that require analysis. We show that the statistical properties of the spectra of similarity matrices, constructed from categorical data, follow random matrix predictions with the dominant eigenvalue being an exception. We demonstrate this approach by applying it to the data for Indian general elections and sea level pressures in the North Atlantic ocean.
Two-body density matrix of a normal Fermi fluid
NASA Astrophysics Data System (ADS)
Ristig, M. L.; Clark, J. W.
1990-05-01
The microscopic study of the two-body density matrix ρ2(r1,r2,r'1,r'2) initiated for uniform Bose fluids in an earlier paper is continued for the Fermi case. We present formal results on the structure of the generalized momentum distribution n(p,q)=Σk⁁<Ψ\\|a†k⁁+qa†p⁁-qap⁁ak⁁\\|Ψ>, and its Fourier inverse ρ2(r1,r2,r'1,r2)≡ρ2(r1,r2,r'1), based on a variational ground-state wave function of Jastrow-Slater form. The structural relations are inferred from the cluster expansions of these objects, from the asymptotic condition relating ρ2(r1,r2,r'1) to the particle density and the one-body density matrix ρ1(r1,r'1), and from formal diagrammatic connections with the Bose problem. The two-body density-matrix elements ρ2(r1,r2,r'1) are thereby expressed in closed form in terms of certain sums of irreducible cluster diagrams. Some of these diagram sums are familiar from the analogous theory of the one-body density matrix; all can be evaluated quantitatively by solving a set of Fermi-hypernetted-chain (FHNC) equations. Upon invoking the sequential relation between ρ2(r1,r2,r'1) and ρ1(r1,r'1), the corresponding result for the generalized momentum distribution n(p,q) effects a resolution into contributions from various scattering processes occurring in the many-body medium, specified by form factors that are susceptible to FHNC evaluation. This decomposition is comparable to that derived earlier for the Bose-fluid ground state but is complicated by contributions from exchange scattering and by a dynamically dressed Pauli kinematic correction. Silver has proposed a simple expression for the generalized momentum distribution n(p,q), a function which plays an essential role in his theory of final-state effects in deep-inelastic neutron scattering from the helium liquids. Based on the present microscopic treatment, the quality of Silver's estimate is assessed for the case of normal liquid He3, by evaluating the necessary distribution
Shrinkage covariance matrix approach for microarray data
NASA Astrophysics Data System (ADS)
Karjanto, Suryaefiza; Aripin, Rasimah
2013-04-01
Microarray technology was developed for the purpose of monitoring the expression levels of thousands of genes. A microarray data set typically consists of tens of thousands of genes (variables) from just dozens of samples due to various constraints including the high cost of producing microarray chips. As a result, the widely used standard covariance estimator is not appropriate for this purpose. One such technique is the Hotelling's T2 statistic which is a multivariate test statistic for comparing means between two groups. It requires that the number of observations (n) exceeds the number of genes (p) in the set but in microarray studies it is common that n < p. This leads to a biased estimate of the covariance matrix. In this study, the Hotelling's T2 statistic with the shrinkage approach is proposed to estimate the covariance matrix for testing differential gene expression. The performance of this approach is then compared with other commonly used multivariate tests using a widely analysed diabetes data set as illustrations. The results across the methods are consistent, implying that this approach provides an alternative to existing techniques.
New pole placement algorithm - Polynomial matrix approach
NASA Technical Reports Server (NTRS)
Shafai, B.; Keel, L. H.
1990-01-01
A simple and direct pole-placement algorithm is introduced for dynamical systems having a block companion matrix A. The algorithm utilizes well-established properties of matrix polynomials. Pole placement is achieved by appropriately assigning coefficient matrices of the corresponding matrix polynomial. This involves only matrix additions and multiplications without requiring matrix inversion. A numerical example is given for the purpose of illustration.
Density matrix renormalization group numerical study of the kagome antiferromagnet.
Jiang, H C; Weng, Z Y; Sheng, D N
2008-09-12
We numerically study the spin-1/2 antiferromagnetic Heisenberg model on the kagome lattice using the density-matrix renormalization group method. We find that the ground state is a magnetically disordered spin liquid, characterized by an exponential decay of spin-spin correlation function in real space and a magnetic structure factor showing system-size independent peaks at commensurate magnetic wave vectors. We obtain a spin triplet excitation gap DeltaE(S=1)=0.055+/-0.005 by extrapolation based on the large size results, and confirm the presence of gapless singlet excitations. The physical nature of such an exotic spin liquid is also discussed.
Fractional spin in reduced density-matrix functional theory.
Helbig, N; Theodorakopoulos, G; Lathiotakis, N N
2011-08-07
We study the behavior of different functionals of the one-body reduced density matrix (1RDM) for systems with fractional z-component of the total spin. We define these systems as ensembles of integer spin states. It is shown that, similarly to density functional theory, the error in the dissociation of diatomic molecules is directly related to the deviation from constancy of the atomic total energies as functions of the fractional spin. However, several functionals of the 1RDM show a size inconsistency which leads to additional errors. We also investigate the difference between a direct evaluation of the energy of an ensemble of integer-spin systems and a direct minimization of the energy of a fractional-spin system.
The problem of the universal density functional and the density matrix functional theory
Bobrov, V. B. Trigger, S. A.
2013-04-15
The analysis in this paper shows that the Hohenberg-Kohn theorem is the constellation of two statements: (i) the mathematically rigorous Hohenberg-Kohn lemma, which demonstrates that the same ground-state density cannot correspond to two different potentials of an external field, and (ii) the hypothesis of the existence of the universal density functional. Based on the obtained explicit expression for the nonrel-ativistic particle energy in a local external field, we prove that the energy of the system of more than two non-interacting electrons cannot be a functional of the inhomogeneous density. This result is generalized to the system of interacting electrons. It means that the Hohenberg-Kohn lemma cannot provide justification of the universal density functional for fermions. At the same time, statements of the density functional theory remain valid when considering any number of noninteracting ground-state bosons due to the Bose condensation effect. In the framework of the density matrix functional theory, the hypothesis of the existence of the universal density matrix functional corresponds to the cases of noninteracting particles and to interaction in the Hartree-Fock approximation.
Generalized Pauli constraints in reduced density matrix functional theory
Theophilou, Iris; Helbig, Nicole; Lathiotakis, Nektarios N.; Marques, Miguel A. L.
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.
Development and application of a density dependent matrix ...
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
Density matrix embedding in an antisymmetrized geminal power bath
Tsuchimochi, Takashi; Welborn, Matthew; Van Voorhis, Troy
2015-07-14
Density matrix embedding theory (DMET) has emerged as a powerful tool for performing wave function-in-wave function embedding for strongly correlated systems. In traditional DMET, an accurate calculation is performed on a small impurity embedded in a mean field bath. Here, we extend the original DMET equations to account for correlation in the bath via an antisymmetrized geminal power (AGP) wave function. The resulting formalism has a number of advantages. First, it allows one to properly treat the weak correlation limit of independent pairs, which DMET is unable to do with a mean-field bath. Second, it associates a size extensive correlation energy with a given density matrix (for the models tested), which AGP by itself is incapable of providing. Third, it provides a reasonable description of charge redistribution in strongly correlated but non-periodic systems. Thus, AGP-DMET appears to be a good starting point for describing electron correlation in molecules, which are aperiodic and possess both strong and weak electron correlation.
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.
NASA Astrophysics Data System (ADS)
Qi, Xianfei; Gao, Ting; Yan, Fengli
2017-09-01
We present a necessary and sufficient product criterion for bipartite quantum states based on the rank of realignment matrix of density matrix. Then, this approach is generalized to multipartite systems. We first introduce the concept of semiproduct in a similar manner to the semiseparable and prove that semiproduct is equivalent to fully product. Therefore, a quantum state is bipartite product with respect to all possible partitions implies fully product which is different from the case of separability. For pure states, it can easily be seen that several necessary and sufficient separability criteria for multipartite systems are derived as a special case of our results. Several specific examples illustrate that our criteria are convenient and operational.
Hermitian one-particle density matrix through a semiclassical gradient expansion
NASA Astrophysics Data System (ADS)
Bencheikh, K.; Räsänen, E.
2016-01-01
We carry out the semiclassical expansion of the one-particle density matrix up to the second order in {{\\hslash }}. We use the method of Grammaticos and Voros based on the Wigner transform of operators. We show that the resulting density matrix is Hermitian and idempotent in contrast with the well-known result of the semiclassical Kirzhnits expansion. Our density matrix leads to the same particle density and kinetic energy density as in the literature, and it satisfies the consistency criterion of the Euler equation. The derived Hermitian density matrix clarifies the ambiguity in the usefulness of gradient expansion approximations and might reignite the development of density functionals with semiclassical methods.
A random matrix approach to language acquisition
NASA Astrophysics Data System (ADS)
Nicolaidis, A.; Kosmidis, Kosmas; Argyrakis, Panos
2009-12-01
Since language is tied to cognition, we expect the linguistic structures to reflect patterns that we encounter in nature and are analyzed by physics. Within this realm we investigate the process of lexicon acquisition, using analytical and tractable methods developed within physics. A lexicon is a mapping between sounds and referents of the perceived world. This mapping is represented by a matrix and the linguistic interaction among individuals is described by a random matrix model. There are two essential parameters in our approach. The strength of the linguistic interaction β, which is considered as a genetically determined ability, and the number N of sounds employed (the lexicon size). Our model of linguistic interaction is analytically studied using methods of statistical physics and simulated by Monte Carlo techniques. The analysis reveals an intricate relationship between the innate propensity for language acquisition β and the lexicon size N, N~exp(β). Thus a small increase of the genetically determined β may lead to an incredible lexical explosion. Our approximate scheme offers an explanation for the biological affinity of different species and their simultaneous linguistic disparity.
Matrix product density operators: Renormalization fixed points and boundary theories
NASA Astrophysics Data System (ADS)
Cirac, J. I.; Pérez-García, D.; Schuch, N.; Verstraete, F.
2017-03-01
We consider the tensors generating matrix product states and density operators in a spin chain. For pure states, we revise the renormalization procedure introduced in (Verstraete et al., 2005) and characterize the tensors corresponding to the fixed points. We relate them to the states possessing zero correlation length, saturation of the area law, as well as to those which generate ground states of local and commuting Hamiltonians. For mixed states, we introduce the concept of renormalization fixed points and characterize the corresponding tensors. We also relate them to concepts like finite correlation length, saturation of the area law, as well as to those which generate Gibbs states of local and commuting Hamiltonians. One of the main result of this work is that the resulting fixed points can be associated to the boundary theories of two-dimensional topological states, through the bulk-boundary correspondence introduced in (Cirac et al., 2011).
Unified quantum density matrix description of coherence and polarization
NASA Astrophysics Data System (ADS)
de Lima Bernardo, Bertúlio
2017-07-01
The properties of coherence and polarization of light has been the subject of intense investigations and form the basis of many technological applications. These concepts which historically have been treated independently can now be formulated under a single classical theory. Here, we derive a quantum counterpart for this theory, with basis on a density matrix formulation, which describes jointly the coherence and polarization properties of an ensemble of photons. The method is used to show how the degree of polarization of a specific class of mixed states changes on propagation in free space, and how an interacting environment can suppress the coherence and polarization degrees of a general state. This last application can be particularly useful in the analysis of decoherence effects in optical quantum information implementations.
Reduced density matrix and order parameters of a topological insulator
NASA Astrophysics Data System (ADS)
Yu, Wing Chi; Li, Yan Chao; Sacramento, P. D.; Lin, Hai-Qing
2016-12-01
It has been recently proposed that the reduced density matrix may be used to derive the order parameter of a condensed matter system. Here we propose order parameters for the phases of a topological insulator, specifically a spinless Su-Schrieffer-Heeger (SSH) model, and consider the effect of short-range interactions. All the derived order parameters and their possible corresponding quantum phases are verified by the entanglement entropy and electronic configuration analysis results. The order parameter appropriate to the topological regions is further proved by calculating the Berry phase under twisted boundary conditions. It is found that the topological nontrivial phase is robust to the introduction of repulsive intersite interactions and can appear in the topological trivial parameter region when appropriate interactions are added.
NASA Astrophysics Data System (ADS)
Micha, David A.
This contribution deals with two approaches for localized phenomena in excited many-atom systems. The first approach develops a quantum quasi-classical treatment for the density operator, including all atoms. It is based on a partial Wigner representation and is illustrated with applications to photodissociation of NaI, and to light emission of excited Li interacting with a He cluster. This second application describes the direct dynamics with a time-dependent electronic density matrix, expanded in a basis set of atomic functions. It shows that such an approach can deal with electronically excited many-atom systems involving tens of quantum states and hundreds of classical variables. The second approach makes use of the reduced density operator description for a system in a medium. This allows for dissipative dynamics, which can be instantaneous or delayed. An application is presented for femtosecond photodesorption using a Markovian dissipation and construction of the density operator from density amplitudes, for CO/Cu(001). A second application of a reduced density operator has been made to vibrational relaxation of adsorbates, solving integrodifferential equations to compare delayed, instantaneous, and Markovian dissipation. It is concluded that delayed dissipation is needed at short times and that a Markovian treatment is suitable for the interpretation of cross-sectional measurements that involve long-term dynamics.
The "JK-only" approximation in density matrix functional and wave function theory.
Kollmar, Christian
2004-12-15
Various energy functionals applying the "JK-only" approximation which leads to two-index two-electron integrals instead of four-index two-electron integrals in the electron-electron interaction term of the electronic energy are presented. Numerical results of multiconfiguration self-consistent field calculations for the best possible "JK-only" wave function are compared to those obtained from the pair excitation multiconfiguration self-consistent (PEMCSCF) method and two versions of density matrix functional theory. One of these is derived making explicit use of some necessary conditions for N representability of the second-order density matrix. It is shown that this method models the energy functional based on the best possible "JK-only" wave function with good accuracy. The calculations also indicate that only a minor fraction of the total correlation energy is incorporated by "JK-only" approaches for larger molecules.
Huo, Pengfei; Coker, David F
2012-12-14
Powerful approximate methods for propagating the density matrix of complex systems that are conveniently described in terms of electronic subsystem states and nuclear degrees of freedom have recently been developed that involve linearizing the density matrix propagator in the difference between the forward and backward paths of the nuclear degrees of freedom while keeping the interference effects between the different forward and backward paths of the electronic subsystem described in terms of the mapping Hamiltonian formalism and semi-classical mechanics. Here we demonstrate that different approaches to developing the linearized approximation to the density matrix propagator can yield a mean-field like approximate propagator in which the nuclear variables evolve classically subject to Ehrenfest-like forces that involve an average over quantum subsystem states, and by adopting an alternative approach to linearizing we obtain an algorithm that involves classical like nuclear dynamics influenced by a quantum subsystem state dependent force reminiscent of trajectory surface hopping methods. We show how these different short time approximations can be implemented iteratively to achieve accurate, stable long time propagation and explore their implementation in different representations. The merits of the different approximate quantum dynamics methods that are thus consistently derived from the density matrix propagator starting point and different partial linearization approximations are explored in various model system studies of multi-state scattering problems and dissipative non-adiabatic relaxation in condensed phase environments that demonstrate the capabilities of these different types of approximations for treating non-adiabatic electronic relaxation, bifurcation of nuclear distributions, and the passage from nonequilibrium coherent dynamics at short times to long time thermal equilibration in the presence of a model dissipative environment.
Efficient perturbation theory to improve the density matrix renormalization group
NASA Astrophysics Data System (ADS)
Tirrito, Emanuele; Ran, Shi-Ju; Ferris, Andrew J.; McCulloch, Ian P.; Lewenstein, Maciej
2017-02-01
The density matrix renormalization group (DMRG) is one of the most powerful numerical methods available for many-body systems. It has been applied to solve many physical problems, including the calculation of ground states and dynamical properties. In this work, we develop a perturbation theory of the DMRG (PT-DMRG) to greatly increase its accuracy in an extremely simple and efficient way. Using the canonical matrix product state (MPS) representation for the ground state of the considered system, a set of orthogonal basis functions {| ψi> } is introduced to describe the perturbations to the ground state obtained by the conventional DMRG. The Schmidt numbers of the MPS that are beyond the bond dimension cutoff are used to define these perturbation terms. The perturbed Hamiltonian is then defined as H˜i j=< ψi| H ̂|ψj> ; its ground state permits us to calculate physical observables with a considerably improved accuracy compared to the original DMRG results. We benchmark the second-order perturbation theory with the help of a one-dimensional Ising chain in a transverse field and the Heisenberg chain, where the precision of the DMRG is shown to be improved O (10 ) times. Furthermore, for moderate L the errors of the DMRG and PT-DMRG both scale linearly with L-1 (with L being the length of the chain). The linear relation between the dimension cutoff of the DMRG and that of the PT-DMRG at the same precision shows a considerable improvement in efficiency, especially for large dimension cutoffs. In the thermodynamic limit we show that the errors of the PT-DMRG scale with √{L-1}. Our work suggests an effective way to define the tangent space of the ground-state MPS, which may shed light on the properties beyond the ground state. This second-order PT-DMRG can be readily generalized to higher orders, as well as applied to models in higher dimensions.
NASA Astrophysics Data System (ADS)
Wouters, Sebastian; Nakatani, Naoki; Van Neck, Dimitri; Chan, Garnet Kin-Lic
2013-08-01
The similarities between Hartree-Fock (HF) theory and the density matrix renormalization group (DMRG) are explored. Both methods can be formulated as the variational optimization of a wave-function Ansatz. Linearization of the time-dependent variational principle near a variational minimum allows to derive the random phase approximation (RPA). We show that the nonredundant parameterization of the matrix product state (MPS) tangent space [J. Haegeman, J. I. Cirac, T. J. Osborne, I. Pižorn, H. Verschelde, and F. Verstraete, Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.107.070601 107, 070601 (2011)] leads to the Thouless theorem for MPS, i.e., an explicit nonredundant parameterization of the entire MPS manifold, starting from a specific MPS reference. Excitation operators are identified, which extends the analogy between HF and DMRG to the Tamm-Dancoff approximation (TDA), the configuration interaction (CI) expansion, and coupled cluster theory. For a small one-dimensional Hubbard chain, we use a CI-MPS Ansatz with single and double excitations to improve on the ground state and to calculate low-lying excitation energies. For a symmetry-broken ground state of this model, we show that RPA-MPS allows to retrieve the Goldstone mode. We also discuss calculations of the RPA-MPS correlation energy. With the long-range quantum chemical Pariser-Parr-Pople Hamiltonian, low-lying TDA-MPS and RPA-MPS excitation energies for polyenes are obtained.
Density matrix reconstruction of a large angular momentum
NASA Astrophysics Data System (ADS)
Klose, Gerd
2001-10-01
A complete description of the quantum state of a physical system is the fundamental knowledge necessary to statistically predict the outcome of measurements. In turning this statement around, Wolfgang Pauli raised already in 1933 the question, whether an unknown quantum state could be uniquely determined by appropriate measurements-a problem that has gained new relevance in recent years. In order to harness the prospects of quantum computing, secure communication, teleportation, and the like, the development of techniques to accurately control and measure quantum states has now become a matter of practical as well as fundamental interest. However, there is no general answer to Pauli's very basic question, and quantum state reconstruction algorithms have been developed and experimentally demonstrated only for a few systems so far. This thesis presents a novel experimental method to measure the unknown and generally mixed quantum state for an angular momentum of arbitrary magnitude. The (2F + 1) x (2F + 1) density matrix describing the quantum state is hereby completely determined from a set of Stern-Gerlach measurements with (4F + 1) different orientations of the quantization axis. This protocol is implemented for laser cooled Cesium atoms in the 6S1/2(F = 4) hyperfine ground state manifold, and is applied to a number of test states prepared by optical pumping and Larmor precession. A comparison of the input and the measured states shows successful reconstructions with fidelities of about 0.95.
NASA Astrophysics Data System (ADS)
Baker, Thomas E.; Wagner, Lucas O.; Stoudenmire, E. Miles; White, Steven R.; Burke, Kieron
2014-03-01
Kohn-Sham Density Functional Theory (DFT) is a mathematically exact method that requires approximation to the exchange correlation energy which may exclude features seen in experiment or provide inadequate estimates. Meanwhile, we may use Density Matrix Renormalization Group (DMRG), a numerical method which can accurately treat strongly correlated electrons in one dimension, to find exact DFT quantities such as the Kohn-Sham potential. We use DMRG in one dimension as a benchmark to test new functionals. Further, recommendations for calculations in two and three dimensional systems are discussed as well as computational proof of principles. We graciously acknowledge the support of the Department of Energy (DE-SC0008696). L.O.W. also thanks the Korean Global Research Network Grant (No. NRF-2010-220-C00017).
NASA Astrophysics Data System (ADS)
Saini, Anshul; Stojkovic, Dejan
2016-09-01
We study time-dependent Hawking-like radiation as seen by an infalling observer during gravitational collapse of a thin shell. We calculate the occupation number of particles of which the frequencies are measured in the proper time of an infalling observer in Eddington-Finkelstein coordinates. We solve the equations for the whole process from the beginning of the collapse till the moment when the collapsing shell reaches zero radius. The radiation distribution is not thermal in the whole frequency regime, but it is approximately thermal for the wavelengths of the order of the Schwarzschild radius of the collapsing shell. After the Schwarzschild radius is crossed, the temperature increases without limits as the singularity is approached. We also calculate the density matrix associated with this radiation. It turns out that the off-diagonal correlation terms to the diagonal Hawking leading-order terms are very important. While the trace of the diagonal (Hawking) density matrix squared decreases during the evolution, the trace of the total density matrix squared remains unity at all times and all frequencies.
Shrinkage approach for EEG covariance matrix estimation.
Beltrachini, Leandro; von Ellenrieder, Nicolas; Muravchik, Carlos H
2010-01-01
We present a shrinkage estimator for the EEG spatial covariance matrix of the background activity. We show that such an estimator has some advantages over the maximum likelihood and sample covariance estimators when the number of available data to carry out the estimation is low. We find sufficient conditions for the consistency of the shrinkage estimators and results concerning their numerical stability. We compare several shrinkage schemes and show how to improve the estimator by incorporating known structure of the covariance matrix.
The origin of linear scaling Fock matrix calculation with density prescreening
Mitin, Alexander V.
2015-12-31
A theorem was proven, which reads that the number of nonzero two-electron integrals scales linearly with respect to the number of basis functions for large molecular systems. This permits to show that linear scaling property of the Fock matrix calculation with using density prescreening arises due to linear scaling properties of the number of nonzero two-electron integrals and the number of leading matrix elements of density matrix. This property is reinforced by employing the density prescreening technique. The use of the density difference prescreening further improves the linear scaling property of the Fock matrix calculation method. As a result, the linear scaling regime of the Fock matrix calculation can begin from the number of basis functions of 2000–3000 in dependence on the basis function type in molecular calculations. It was also shown that the conventional algorithm of Fock matrix calculation from stored nonzero two-electron integrals with density prescreening possesses linear scaling property.
Reduced density-matrix functional theory: Correlation and spectroscopy
Di Sabatino, S.; Romaniello, P.; Berger, J. A.; Reining, L.
2015-07-14
In this work, we explore the performance of approximations to electron correlation in reduced density-matrix functional theory (RDMFT) and of approximations to the observables calculated within this theory. Our analysis focuses on the calculation of total energies, occupation numbers, removal/addition energies, and spectral functions. We use the exactly solvable Hubbard dimer at 1/4 and 1/2 fillings as test systems. This allows us to analyze the underlying physics and to elucidate the origin of the observed trends. For comparison, we also report the results of the GW approximation, where the self-energy functional is approximated, but no further hypothesis is made concerning the approximations of the observables. In particular, we focus on the atomic limit, where the two sites of the dimer are pulled apart and electrons localize on either site with equal probability, unless a small perturbation is present: this is the regime of strong electron correlation. In this limit, using the Hubbard dimer at 1/2 filling with or without a spin-symmetry-broken ground state allows us to explore how degeneracies and spin-symmetry breaking are treated in RDMFT. We find that, within the used approximations, neither in RDMFT nor in GW, the signature of strong correlation is present, when looking at the removal/addition energies and spectral function from the spin-singlet ground state, whereas both give the exact result for the spin-symmetry broken case. Moreover, we show how the spectroscopic properties change from one spin structure to the other.
Pair 2-electron reduced density matrix theory using localized orbitals
NASA Astrophysics Data System (ADS)
Head-Marsden, Kade; Mazziotti, David A.
2017-08-01
Full configuration interaction (FCI) restricted to a pairing space yields size-extensive correlation energies but its cost scales exponentially with molecular size. Restricting the variational two-electron reduced-density-matrix (2-RDM) method to represent the same pairing space yields an accurate lower bound to the pair FCI energy at a mean-field-like computational scaling of O (r3) where r is the number of orbitals. In this paper, we show that localized molecular orbitals can be employed to generate an efficient, approximately size-extensive pair 2-RDM method. The use of localized orbitals eliminates the substantial cost of optimizing iteratively the orbitals defining the pairing space without compromising accuracy. In contrast to the localized orbitals, the use of canonical Hartree-Fock molecular orbitals is shown to be both inaccurate and non-size-extensive. The pair 2-RDM has the flexibility to describe the spectra of one-electron RDM occupation numbers from all quantum states that are invariant to time-reversal symmetry. Applications are made to hydrogen chains and their dissociation, n-acene from naphthalene through octacene, and cadmium telluride 2-, 3-, and 4-unit polymers. For the hydrogen chains, the pair 2-RDM method recovers the majority of the energy obtained from similar calculations that iteratively optimize the orbitals. The localized-orbital pair 2-RDM method with its mean-field-like computational scaling and its ability to describe multi-reference correlation has important applications to a range of strongly correlated phenomena in chemistry and physics.
Performance of the density matrix functional theory in the quantum theory of atoms in molecules.
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.
NASA Astrophysics Data System (ADS)
Mendoza-Arenas, J. J.; Franco, R.; Silva-Valencia, J.
2010-01-01
We analyze the one-dimensional Kondo necklace model, at zero temperature, with an anisotropy parameter η in the interaction of the conduction chain, by means of the density matrix renormalization group. We calculate the energy gap and estimate the quantum critical points that separate a Kondo singlet state from an antiferromagnetic state, assuming a Kosterlitz-Thouless tendency. We also observe the correlation functions and the structure factors that support our critical points. The resulting phase diagram is presented and compared to that reported previously using Lanczos calculations. It is shown that the quantum critical points vary very slowly with η , but when η approaches zero, they drop abruptly.
Implementation and testing of a frozen density matrix-divide and conquer algorithm
Ermolaeva, M.D.; Vaart, A. van der; Merz, K.M. Jr.
1999-03-25
The authors have implemented and tested a frozen density matrix (FDM) approximation to the basic divide and conquer (DC) semiempirical algorithm. Molecular dynamics and Monte Carlo simulations were performed to estimate the advantages of the method. Results were compared to those obtained from the original DC method and the combined quantum mechanical/molecular mechanical (WM/MM) method. The authors found that the FDM approximation speeds DC calculations up significantly, while only introducing small errors. They also found that the FDM DC scheme performs better than the standard QM/MM approach in terms of defining the electronic and structural properties of the systems studied herein.
Block product density matrix embedding theory for strongly correlated spin systems
NASA Astrophysics Data System (ADS)
Gunst, Klaas; Wouters, Sebastian; De Baerdemacker, Stijn; Van Neck, Dimitri
2017-05-01
Density matrix embedding theory (DMET) is a relatively new technique for the calculation of strongly correlated systems. Recently, block product DMET (BPDMET) was introduced for the study of spin systems such as the antiferromagnetic J1-J2 model on the square lattice. In this paper, we extend the variational Ansatz of BPDMET using spin-state optimization, yielding improved results. We apply the same techniques to the Kitaev-Heisenberg model on the honeycomb lattice, comparing the results when using several types of clusters. Energy profiles and correlation functions are investigated. A diagonalization in the tangent space of the variational approach yields information on the excited states and the corresponding spectral functions.
Application of Löwdin projectors to evaluate density matrix evolutions
NASA Astrophysics Data System (ADS)
Chandrakumar, N.
Projection operators are employed to evaluate functions of operators. In particular, this formalism is used to find polynomial expressions for exponential operators and thence to solve density matrix evolutions in closed analytical form. Problems explicitly treated include pulse rotation of spin-I and spin - {3}/{2} systems, spin tickling and spin interferometry on a system of two coupled spin- {1}/{2} nuclei, isotropic mixing in systems of two coupled nuclei (both spins- {1}/{2} or spins-1), and dipolar evolution in a two-spin- {1}/{2} system. The method is compared to the BCH approach for operator evolutions.
Second-Order Self-Consistent-Field Density-Matrix Renormalization Group.
Ma, Yingjin; Knecht, Stefan; Keller, Sebastian; Reiher, Markus
2017-06-13
We present a matrix-product state (MPS)-based quadratically convergent density-matrix renormalization group self-consistent-field (DMRG-SCF) approach. Following a proposal by Werner and Knowles (J. Chem. Phys. 1985, 82, 5053), our DMRG-SCF algorithm is based on a direct minimization of an energy expression which is correct to second order with respect to changes in the molecular orbital basis. We exploit a simultaneous optimization of the MPS wave function and molecular orbitals in order to achieve quadratic convergence. In contrast to previously reported (augmented Hessian) Newton-Raphson and superconfiguration-interaction algorithms for DMRG-SCF, energy convergence beyond a quadratic scaling is possible in our ansatz. Discarding the set of redundant active-active orbital rotations, the DMRG-SCF energy converges typically within two to four cycles of the self-consistent procedure.
Chiral random matrix theory for two-color QCD at high density
Kanazawa, Takuya; Yamamoto, Naoki; Wettig, Tilo
2010-04-15
We identify a non-Hermitian chiral random matrix theory that corresponds to two-color QCD at high density. We show that the partition function of the random matrix theory coincides with the partition function of the finite-volume effective theory at high density, and that the Leutwyler-Smilga-type spectral sum rules of the random matrix theory are identical to those derived from the effective theory. The microscopic Dirac spectrum of the theory is governed by the BCS gap, rather than the conventional chiral condensate. We also show that with a different choice of a parameter the random matrix theory yields the effective partition function at low density.
Energy density matrix formalism for interacting quantum systems: a quantum Monte Carlo study
Krogel, Jaron T; Kim, Jeongnim; Reboredo, Fernando A
2014-01-01
We develop an energy density matrix that parallels the one-body reduced density matrix (1RDM) for many-body quantum systems. Just as the density matrix gives access to the number density and occupation numbers, the energy density matrix yields the energy density and orbital occupation energies. The eigenvectors of the matrix provide a natural orbital partitioning of the energy density while the eigenvalues comprise a single particle energy spectrum obeying a total energy sum rule. For mean-field systems the energy density matrix recovers the exact spectrum. When correlation becomes important, the occupation energies resemble quasiparticle energies in some respects. We explore the occupation energy spectrum for the finite 3D homogeneous electron gas in the metallic regime and an isolated oxygen atom with ground state quantum Monte Carlo techniques imple- mented in the QMCPACK simulation code. The occupation energy spectrum for the homogeneous electron gas can be described by an effective mass below the Fermi level. Above the Fermi level evanescent behavior in the occupation energies is observed in similar fashion to the occupation numbers of the 1RDM. A direct comparison with total energy differences demonstrates a quantita- tive connection between the occupation energies and electron addition and removal energies for the electron gas. For the oxygen atom, the association between the ground state occupation energies and particle addition and removal energies becomes only qualitative. The energy density matrix provides a new avenue for describing energetics with quantum Monte Carlo methods which have traditionally been limited to total energies.
NASA Astrophysics Data System (ADS)
Huo, Pengfei; Coker, David F.
2011-11-01
An approach for treating dissipative, non-adiabatic quantum dynamics in general model systems at finite temperature based on linearizing the density matrix evolution in the forward-backward path difference for the environment degrees of freedom is presented. We demonstrate that the approach can capture both short time coherent quantum dynamics and long time thermal equilibration in an application to excitation energy transfer in a model photosynthetic light harvesting complex. Results are also presented for some nonadiabatic scattering models which indicate that, even though the method is based on a "mean trajectory" like scheme, it can accurately capture electronic population branching through multiple avoided crossing regions and that the approach offers a robust and reliable way to treat quantum dynamical phenomena in a wide range of condensed phase applications.
Studying genetic code by a matrix approach.
Crowder, Tanner; Li, Chi-Kwong
2010-05-01
Following Petoukhov and his collaborators, we use two length n zero-one sequences, alpha and beta, to represent a length n genetic sequence (alpha/beta) so that the columns of (alpha/beta) have the following correspondence with the nucleotides: C ~ (0/0), U ~ (1/0), G ~ (1/1), A ~ (0/1). Using the Gray code ordering to arrange alpha and beta, we build a 2(n) x 2(n) matrix C(n) including all the 4(n) length n genetic sequences. Furthermore, we use the Hamming distance of alpha and beta to construct a 2(n) x 2(n) matrix D(n). We explore structures of these matrices, refine the results in earlier papers, and propose new directions for further research.
Requist, Ryan; Pankratov, Oleg
2011-05-15
We prove that if the two-body terms in the equation of motion for the one-body reduced density matrix are approximated by ground-state functionals, the eigenvalues of the one-body reduced density matrix (occupation numbers) remain constant in time. This deficiency is related to the inability of such an approximation to account for relative phases in the two-body reduced density matrix. We derive an exact differential equation giving the functional dependence of these phases in an interacting Landau-Zener model and study their behavior in short- and long-time regimes. The phases undergo resonances whenever the occupation numbers approach the boundaries of the interval [0,1]. In the long-time regime, the occupation numbers display correlation-induced oscillations and the memory dependence of the functionals assumes a simple form.
Density matrix theory of transport and gain in quantum cascade lasers in a magnetic field
NASA Astrophysics Data System (ADS)
Savić, Ivana; Vukmirović, Nenad; Ikonić, Zoran; Indjin, Dragan; Kelsall, Robert W.; Harrison, Paul; Milanović, Vitomir
2007-10-01
A density matrix theory of electron transport and optical gain in quantum cascade lasers in an external magnetic field is formulated. Starting from a general quantum kinetic treatment, we describe the intraperiod and interperiod electron dynamics at the non-Markovian, Markovian, and Boltzmann approximation levels. Interactions of electrons with longitudinal optical phonons and classical light fields are included in the present description. The non-Markovian calculation for a prototype structure reveals a significantly different gain spectra in terms of linewidth and additional polaronic features in comparison to the Markovian and Boltzmann ones. Despite strongly controversial interpretations of the origin of the transport processes in the non-Markovian or Markovian and the Boltzmann approaches, they yield comparable values of the current densities.
Density-matrix based determination of low-energy model Hamiltonians from ab initio wavefunctions.
Changlani, Hitesh J; Zheng, Huihuo; Wagner, Lucas K
2015-09-14
We propose a way of obtaining effective low energy Hubbard-like model Hamiltonians from ab initio quantum Monte Carlo calculations for molecular and extended systems. The Hamiltonian parameters are fit to best match the ab initio two-body density matrices and energies of the ground and excited states, and thus we refer to the method as ab initio density matrix based downfolding. For benzene (a finite system), we find good agreement with experimentally available energy gaps without using any experimental inputs. For graphene, a two dimensional solid (extended system) with periodic boundary conditions, we find the effective on-site Hubbard U(∗)/t to be 1.3 ± 0.2, comparable to a recent estimate based on the constrained random phase approximation. For molecules, such parameterizations enable calculation of excited states that are usually not accessible within ground state approaches. For solids, the effective Hamiltonian enables large-scale calculations using techniques designed for lattice models.
Random matrix theory approach to vibrations near the jamming transition
NASA Astrophysics Data System (ADS)
Beltukov, Y. M.
2015-03-01
It has been shown that the dynamical matrix M describing harmonic oscillations in granular media can be represented in the form M = AA T, where the rows of the matrix A correspond to the degrees of freedom of individual granules and its columns correspond to elastic contacts between granules. Such a representation of the dynamical matrix makes it possible to estimate the density of vibrational states with the use of the random matrix theory. The found density of vibrational states is approximately constant in a wide frequency range ω- < ω < ω+, which is determined by the ratio of the number of degrees of freedom to the total number of contacts in the system, which is in good agreement with the results of the numerical experiments.
A Random Matrix Approach to Credit Risk
Guhr, Thomas
2014-01-01
We estimate generic statistical properties of a structural credit risk model by considering an ensemble of correlation matrices. This ensemble is set up by Random Matrix Theory. We demonstrate analytically that the presence of correlations severely limits the effect of diversification in a credit portfolio if the correlations are not identically zero. The existence of correlations alters the tails of the loss distribution considerably, even if their average is zero. Under the assumption of randomly fluctuating correlations, a lower bound for the estimation of the loss distribution is provided. PMID:24853864
A random matrix approach to credit risk.
Münnix, Michael C; Schäfer, Rudi; Guhr, Thomas
2014-01-01
We estimate generic statistical properties of a structural credit risk model by considering an ensemble of correlation matrices. This ensemble is set up by Random Matrix Theory. We demonstrate analytically that the presence of correlations severely limits the effect of diversification in a credit portfolio if the correlations are not identically zero. The existence of correlations alters the tails of the loss distribution considerably, even if their average is zero. Under the assumption of randomly fluctuating correlations, a lower bound for the estimation of the loss distribution is provided.
Transforming DOD Capabilities. A Matrix Approach
2003-01-01
of the Systems Approach,” Principia Cybernetica Web, 19 October 1998, <http://pespmc1.vub.ac.be/SYSAPPR.html> (15 Apr 2003). 4 LTC William H. Maglin...IDA Seminar: “Innovation and Changing Military Culture.” 23 August 2002. Heylighen F. “Basic Concepts of the Systems Approach.” Principia Cybernetica
Multivariate and matrix-variate analogues of Maxwell-Boltzmann and Raleigh densities
NASA Astrophysics Data System (ADS)
Mathai, A. M.; Princy, T.
2017-02-01
The Maxwell-Boltzmann and Raleigh densities are basic densities in many problems in Physics. A multivariate analogue and a rectangular matrix-variate analogue of these densities are explored in this article. The results may become useful in extending the usual theories, where these densities for the real scalar variable case occur, to multivariate and matrix variable situations. Various properties are studied and connection to the volumes of parallelotopes determined by p linearly independent random points in Euclidean n-space, n ≥ p, is also established. Structural decompositions of these random determinants and pathway extensions of Maxwell-Boltzmann and Raleigh densities are also considered.
Skyrmion Approach to Finite Density and Temperature
NASA Astrophysics Data System (ADS)
Park, Byung-Yoon; Riska, D. O.
We review an approach, developed over the past few years, to describe hadronic matter at finite density and temperature, whose underlying theoretical framework is the Skyrme model, an effective low energy theory rooted in large Nc QCD. In this approach matter is described by various crystal structures of skyrmions, classical topological solitons carrying baryon number, from which conventional baryons appear by quantization. Chiral and scale symmetries play a crucial role in the dynamics as described by pion, dilaton and vector meson degrees of freedom. When compressed or heated skyrmion matter describes a rich phase diagram which has strong connections with the confinement/deconfinement phase transition.
Edgar, Lowell T.; Hoying, James B.; Weiss, Jeffrey A.
2015-01-01
Mechanical interactions during angiogenesis, i.e., traction applied by neovessels to the extracellular matrix and the corresponding deformation, are important regulators of growth and neovascularization. We have previously designed, implemented, and validated a coupled model of angiogenesis in which a discrete microvessel growth model interacts with a continuous finite element mesh through the application of local remodeling sprout stresses (Edgar et al. in Biomech Model Mechanobiol, 2014). However, the initial implementation of this framework does not take matrix density into account when determined these remodeling stresses and is therefore insufficient for the study of angiogenesis within heterogeneous matrix environments such as those found in vivo. The objective of this study was to implement sensitivity to matrix density in the active stress generation within AngioFE in order to allow the study of angiogenic growth within a heterogeneous density environment. We accomplished this by scaling active sprout stresses relative to local matrix density using a scaling factor previously determined from experimental data. We then exercised the new functionality of the model by simulating angiogenesis within four different scenarios: homogeneous density, a narrow gap model, and matrix density gradient, and a construct subjected to repeated loading/unloading and preconditioning. These numerical experiments predicted heterogeneous matrix density in the initially homogeneous case, the closure and alignment of microvessels along a low-density gap, the formation of a unique cap-like structure during angiogenesis within a density gradient, and the alignment of microvessels in the absence of applied load due to preconditioning. The result of these in silico investigations demonstrate how matrix heterogeneity affects neovascularization and matrix deformation and provides a platform for studying angiogenesis in complicated and multi-faceted mechanical environments that
High-harmonic spectra from time-dependent two-particle reduced-density-matrix theory
NASA Astrophysics Data System (ADS)
Lackner, Fabian; Březinová, Iva; Sato, Takeshi; Ishikawa, Kenichi L.; Burgdörfer, Joachim
2017-03-01
The ab initio description of the nonlinear response of many-electron systems to strong-laser fields remains a major challenge. In order to address larger systems, alternative methods need to be developed that bypass the exponential scaling with particle number inherent to conventional wave-function-based approaches. In this paper we present a fully three-dimensional implementation of the time-dependent two-particle reduced-density-matrix (TD-2RDM) method for many-electron atoms. We benchmark this approach by a comparison with multiconfigurational time-dependent Hartree-Fock results for the harmonic spectra of beryllium and neon. We show that the TD-2RDM is very well suited to describe the nonlinear atomic response and to reveal the influence of electron-correlation effects.
Quantum Monte Carlo with density matrix: potential energy curve derived properties.
Bonfim, Víctor S; Borges, Nádia M; Martins, João B L; Gargano, Ricardo; Politi, José Roberto Dos S
2017-04-01
In this work, we used diffusion quantum Monte Carlo with density matrix (d-DMC) and variational quantum Monte Carlo (d-VMC) to determine the potential energy curve (PEC) and obtain the spectroscopic constants of H2 molecule in the ground state, in order to evaluate the capability of these methods to provide an accurate PEC description. These quantum Monte Carlo methods build with density matrix are new approaches to conventional quantum Monte Carlo methods based on wave function formed by product of α and β determinants. To investigate the robustness of d-DMC, we performed calculations with two different basis sets and analyzed the influence of the size of these sets on results. To the best of our knowledge, this is the first study that shows the dissociation energy and rotational constant obtained from d-QMC. We found that the quality of PEC described by the d-DMC is essentially coincident with the most accurate results available in the literature, regardless of the complexity of basis set employed.
Density matrix perturbation theory for magneto-optical response of periodic insulators
NASA Astrophysics Data System (ADS)
Lebedeva, Irina; Tokatly, Ilya; Rubio, Angel
2015-03-01
Density matrix perturbation theory offers an ideal theoretical framework for the description of response of solids to arbitrary electromagnetic fields. In particular, it allows to consider perturbations introduced by uniform electric and magnetic fields under periodic boundary conditions, though the corresponding potentials break the translational invariance of the Hamiltonian. We have implemented the density matrix perturbation theory in the open-source Octopus code on the basis of the efficient Sternheimer approach. The procedures for responses of different order to electromagnetic fields, including electric polarizability, orbital magnetic susceptibility and magneto-optical response, have been developed and tested by comparison with the results for finite systems and for wavefunction-based perturbation theory, which is already available in the code. Additional analysis of the orbital magneto-optical response is performed on the basis of analytical models. Symmetry limitations to observation of the magneto-optical response are discussed. The financial support from the Marie Curie Fellowship PIIF-GA-2012-326435 (RespSpatDisp) is gratefully acknowledged.
The reduced density matrix method and the role of three-index representability conditions
NASA Astrophysics Data System (ADS)
Braams, Bastiaan J.; Zhao, Zhengji; Fukuda, Mituhiro; Overton, Michael L.; Percus, Jerome K.
2004-03-01
The variational approach for electronic structure based on the two-body reduced density matrix is studied, incorporating two representability conditions beyond the previously used P, Q and G conditions. The additional conditions (called T1 and T2 here) are implicit in work of R. M. Erdahl and extend the well-known three-index diagonal conditions also known as the Weinhold-Wilson inequalities. Calculations of the ground state energy and the dipole moment are reported for 47 different systems, in each case using an STO-6G basis set and comparing with Hartree-Fock, SDCI, BD(T), CCSD(T) and full CI calculations [2]. It is found that the use of the T1 and T2 conditions gives a significant improvement over just the P, Q and G conditions, and provides in all cases that we have studied more accurate results than the other mentioned approximations. [1] R. M. Erdahl, Int. J. Quantum Chem. 13, 697--718 (1978). [2] Zhengji Zhao, Bastiaan J. Braams, Mituhiro Fukuda, Michael L. Overton and Jerome K. Percus: "The reduced density matrix method and the role of three-index representability conditions". Accepted for publication in Journal of Chemical Physics.
A state interaction spin-orbit coupling density matrix renormalization group method.
Sayfutyarova, Elvira R; Chan, Garnet Kin-Lic
2016-06-21
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.
Metal-insulator transition in disordered systems from the one-body density matrix
NASA Astrophysics Data System (ADS)
Olsen, Thomas; Resta, Raffaele; Souza, Ivo
2017-01-01
The insulating state of matter can be probed by means of a ground state geometrical marker, which is closely related to the modern theory of polarization (based on a Berry phase). In the present work we show that this marker can be applied to determine the metal-insulator transition in disordered systems. In particular, for noninteracting systems the geometrical marker can be obtained from the configurational average of the norm-squared one-body density matrix, which can be calculated within open as well as periodic boundary conditions. This is in sharp contrast to a classification based on the static conductivity, which is only sensible within periodic boundary conditions. We exemplify the method by considering a simple lattice model, known to have a metal-insulator transition as a function of the disorder strength, and demonstrate that the transition point can be obtained accurately from the one-body density matrix. The approach has a general ab initio formulation and could in principle be applied to realistic disordered materials by standard electronic structure methods.
NASA Astrophysics Data System (ADS)
Longbiao, Li
2015-12-01
The matrix multicracking evolution of cross-ply ceramic-matrix composites (CMCs) has been investigated using energy balance approach. The multicracking of cross-ply CMCs was classified into five modes, i.e., (1) mode 1: transverse multicracking; (2) mode 2: transverse multicracking and matrix multicracking with perfect fiber/matrix interface bonding; (3) mode 3: transverse multicracking and matrix multicracking with fiber/matrix interface debonding; (4) mode 4: matrix multicracking with perfect fiber/matrix interface bonding; and (5) mode 5: matrix multicracking with fiber/matrix interface debonding. The stress distributions of four cracking modes, i.e., mode 1, mode 2, mode 3 and mode 5, are analysed using shear-lag model. The matrix multicracking evolution of mode 1, mode 2, mode 3 and mode 5, has been determined using energy balance approach. The effects of ply thickness and fiber volume fraction on matrix multicracking evolution of cross-ply CMCs have been investigated.
Density matrix of radiation of a black hole with a fluctuating horizon
NASA Astrophysics Data System (ADS)
Iofa, Mikhail Z.
2016-09-01
The density matrix of Hawking radiation is calculated in the model of a black hole with a fluctuating horizon. Quantum fluctuations smear the classical horizon of a black hole and modify the density matrix of radiation producing the off-diagonal elements. The off-diagonal elements may store information on correlations between the radiation and the black hole. The smeared density matrix was constructed by convolution of the density matrix calculated with the instantaneous horizon with the Gaussian distribution over the instantaneous horizons. The distribution has the extremum at the classical radius of the black hole and the width of order of the Planck length. Calculations were performed in the model of a black hole formed by the thin collapsing shell which follows a trajectory that is a solution of the matching equations connecting the interior and exterior geometries.
The single-particle density matrix of a quantum bright soliton from the coordinate Bethe ansatz
NASA Astrophysics Data System (ADS)
Ayet, Alex; Brand, Joachim
2017-02-01
We present a novel approach for computing reduced density matrices for superpositions of eigenstates of a Bethe-ansatz solvable model by direct integration of the wave function in coordinate representation. A diagrammatic approach is developed to keep track of relevant terms and identify symmetries, which helps to reduce the number of terms that have to be evaluated numerically. As a first application we compute with modest numerical resources the single-particle density matrix and its eigenvalues including the condensate fraction for a quantum bright soliton with up to N = 10 bosons. The latter are constructed as superpositions of string-type Bethe-ansatz eigenstates of nonrelativistic bosons in one spatial dimension with attractive contact interaction. Upon delocalising the superposition in momentum space we find that the condensate fraction reaches maximum values larger than 97% with weak particle-number dependence in the range of particles studied. The presented approach is suitable for studying time-dependent problems and generalises to higher-order correlation functions.
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...
The transfer matrix approach to circular graphene quantum dots
NASA Astrophysics Data System (ADS)
Chau Nguyen, H.; Nguyen, Nhung T. T.; Nguyen, V. Lien
2016-07-01
We adapt the transfer matrix (T-matrix) method originally designed for one-dimensional quantum mechanical problems to solve the circularly symmetric two-dimensional problem of graphene quantum dots. Similar to one-dimensional problems, we show that the generalized T-matrix contains rich information about the physical properties of these quantum dots. In particular, it is shown that the spectral equations for bound states as well as quasi-bound states of a circular graphene quantum dot and related quantities such as the local density of states and the scattering coefficients are all expressed exactly in terms of the T-matrix for the radial confinement potential. As an example, we use the developed formalism to analyse physical aspects of a graphene quantum dot induced by a trapezoidal radial potential. Among the obtained results, it is in particular suggested that the thermal fluctuations and electrostatic disorders may appear as an obstacle to controlling the valley polarization of Dirac electrons.
Linear-scaling density matrix perturbation treatment of electric fields in solids.
Xiang, H J; Yang, Jinlong; Hou, J G; Zhu, Qingshi
2006-12-31
We develop a novel linear-scaling [O(N)] algorithm for calculating the optical dielectric constant and Born effective charge. Our method relies on the fact that only the sum of the nondiagonal parts of the electric field perturbation in solids contributes to the first-order derivative density matrix, which can then be obtained through the density-matrix perturbation method. The optical dielectric constant of amorphous SiO(2) is computed using a realistic model for the first time.
A Problem-Centered Approach to Canonical Matrix Forms
ERIC Educational Resources Information Center
Sylvestre, Jeremy
2014-01-01
This article outlines a problem-centered approach to the topic of canonical matrix forms in a second linear algebra course. In this approach, abstract theory, including such topics as eigenvalues, generalized eigenspaces, invariant subspaces, independent subspaces, nilpotency, and cyclic spaces, is developed in response to the patterns discovered…
A Problem-Centered Approach to Canonical Matrix Forms
ERIC Educational Resources Information Center
Sylvestre, Jeremy
2014-01-01
This article outlines a problem-centered approach to the topic of canonical matrix forms in a second linear algebra course. In this approach, abstract theory, including such topics as eigenvalues, generalized eigenspaces, invariant subspaces, independent subspaces, nilpotency, and cyclic spaces, is developed in response to the patterns discovered…
NASA Astrophysics Data System (ADS)
Cheng, Wei; Xu, Fang; Li, Hua; Wang, Gang
2014-04-01
Given the density matrix of a bipartite quantum state, could we decide whether it is separable, free entangled, or PPT entangled? Here, we give a negative answer to this question by providing a lot of concrete examples of density matrices, some of which are well known. We find that both separability and distillability are dependent on the decomposition of the density matrix. To be more specific, we show that if a given matrix is considered as the density operators of different composite systems, their entanglement properties might be different. In the case of density matrices, we can look them as both and bipartite quantum states and show that their entanglement properties (i.e., separable, free entangled, or PPT entangled) are completely irrelevant to each other.
Symmetry-conserving purification of quantum states within the density matrix renormalization group
Nocera, Alberto; Alvarez, Gonzalo
2016-01-28
The density matrix renormalization group (DMRG) algorithm was originally designed to efficiently compute the zero-temperature or ground-state properties of one-dimensional strongly correlated quantum systems. The development of the algorithm at finite temperature has been a topic of much interest, because of the usefulness of thermodynamics quantities in understanding the physics of condensed matter systems, and because of the increased complexity associated with efficiently computing temperature-dependent properties. The ancilla method is a DMRG technique that enables the computation of these thermodynamic quantities. In this paper, we review the ancilla method, and improve its performance by working on reduced Hilbert spaces andmore » using canonical approaches. Furthermore we explore its applicability beyond spins systems to t-J and Hubbard models.« less
2017-01-01
We present a second-order N-electron valence state perturbation theory (NEVPT2) based on a density matrix renormalization group (DMRG) reference wave function that exploits a Cholesky decomposition of the two-electron repulsion integrals (CD-DMRG-NEVPT2). With a parameter-free multireference perturbation theory approach at hand, the latter allows us to efficiently describe static and dynamic correlation in large molecular systems. We demonstrate the applicability of CD-DMRG-NEVPT2 for spin-state energetics of spin-crossover complexes involving calculations with more than 1000 atomic basis functions. We first assess, in a study of a heme model, the accuracy of the strongly and partially contracted variant of CD-DMRG-NEVPT2 before embarking on resolving a controversy about the spin ground state of a cobalt tropocoronand complex. PMID:28094988
Symmetry-conserving purification of quantum states within the density matrix renormalization group
Nocera, Alberto; Alvarez, Gonzalo
2016-01-28
The density matrix renormalization group (DMRG) algorithm was originally designed to efficiently compute the zero-temperature or ground-state properties of one-dimensional strongly correlated quantum systems. The development of the algorithm at finite temperature has been a topic of much interest, because of the usefulness of thermodynamics quantities in understanding the physics of condensed matter systems, and because of the increased complexity associated with efficiently computing temperature-dependent properties. The ancilla method is a DMRG technique that enables the computation of these thermodynamic quantities. In this paper, we review the ancilla method, and improve its performance by working on reduced Hilbert spaces and using canonical approaches. Furthermore we explore its applicability beyond spins systems to t-J and Hubbard models.
Freitag, Leon; Knecht, Stefan; Angeli, Celestino; Reiher, Markus
2017-02-14
We present a second-order N-electron valence state perturbation theory (NEVPT2) based on a density matrix renormalization group (DMRG) reference wave function that exploits a Cholesky decomposition of the two-electron repulsion integrals (CD-DMRG-NEVPT2). With a parameter-free multireference perturbation theory approach at hand, the latter allows us to efficiently describe static and dynamic correlation in large molecular systems. We demonstrate the applicability of CD-DMRG-NEVPT2 for spin-state energetics of spin-crossover complexes involving calculations with more than 1000 atomic basis functions. We first assess, in a study of a heme model, the accuracy of the strongly and partially contracted variant of CD-DMRG-NEVPT2 before embarking on resolving a controversy about the spin ground state of a cobalt tropocoronand complex.
Pižorn, Iztok; Verstraete, Frank
2012-02-10
The numerical renormalization group (NRG) is rephrased as a variational method with the cost function given by the sum of all the energies of the effective low-energy Hamiltonian. This allows us to systematically improve the spectrum obtained by NRG through sweeping. The ensuing algorithm has a lot of similarities to the density matrix renormalization group (DMRG) when targeting many states, and this synergy of NRG and DMRG combines the best of both worlds and extends their applicability. We illustrate this approach with simulations of a quantum spin chain and a single impurity Anderson model where the accuracy of the effective eigenstates is greatly enhanced as compared to the NRG, especially in the transition to the continuum limit.
NASA Astrophysics Data System (ADS)
Ito, Fumiyuki
2010-12-01
The supermolecule approach has been used to model molecules embedded in solid argon matrix, wherein interaction between the guest and the host atoms in the first solvation shell is evaluated with the use of density functional calculations. Structural stability and simulated spectra have been obtained for formic acid dimer (FAD)-Arn (n = 21-26) clusters. The calculations at the B971/6-31++G(3df,3pd) level have shown that the tetrasubstitutional site on Ar(111) plane is likely to incorporate FAD most stably, in view of consistency with the matrix shifts available experimentally.
Distinguishing chaotic time series from noise: A random matrix approach
NASA Astrophysics Data System (ADS)
Ye, Bin; Chen, Jianxing; Ju, Chen; Li, Huijun; Wang, Xuesong
2017-03-01
Deterministically chaotic systems can often give rise to random and unpredictable behaviors which make the time series obtained from them to be almost indistinguishable from noise. Motivated by the fact that data points in a chaotic time series will have intrinsic correlations between them, we propose a random matrix theory (RMT) approach to identify the deterministic or stochastic dynamics of the system. We show that the spectral distributions of the correlation matrices, constructed from the chaotic time series, deviate significantly from the predictions of random matrix ensembles. On the contrary, the eigenvalue statistics for a noisy signal follow closely those of random matrix ensembles. Numerical results also indicate that the approach is to some extent robust to additive observational noise which pollutes the data in many practical situations. Our approach is efficient in recognizing the continuous chaotic dynamics underlying the evolution of the time series.
Matrix product approach for the asymmetric random average process
NASA Astrophysics Data System (ADS)
Zielen, F.; Schadschneider, A.
2003-04-01
We consider the asymmetric random average process which is a one-dimensional stochastic lattice model with nearest-neighbour interaction but continuous and unbounded state variables. First, the explicit functional representations, so-called beta densities, of all local interactions leading to steady states of product measure form are rigorously derived. This also completes an outstanding proof given in a previous publication. Then we present an alternative solution for the processes with factorized stationary states by using a matrix product ansatz. Due to continuous state variables we obtain a matrix algebra in the form of a functional equation which can be solved exactly.
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.
Matrix density mediates polarization and lumen formation of endothelial sprouts in VEGF gradients.
Shamloo, Amir; Heilshorn, Sarah C
2010-11-21
Endothelial cell (EC) sprouting morphogenesis is a critical step during angiogenesis, the formation of new blood vessels from existing conduits. Here, three-dimensional sprouting morphogenesis was examined using in vitro microfluidic devices that enabled the separate and simultaneous tuning of biomechanical and soluble biochemical stimuli. Quantitative analysis of endothelial sprout formation demonstrated that the ability of vascular endothelial growth factor (VEGF) to regulate stable sprout formation was mediated by the density of the surrounding collagen/fibronectin matrix. The coordinated migration and proliferation of multiple ECs to form stable sprouts were enhanced at intermediate matrix densities (1.2-1.9 mg ml(-1)), while lower densities resulted in uncoordinated migration (0.3-0.7 mg ml(-1)) and higher densities resulted in broad cell clusters that did not elongate (2.7 mg ml(-1)). Within the permissive range of matrix biomechanics, higher density matrices resulted in shorter, thicker, and slower-growing sprouts. The sprouts in higher density matrices also were more likely to polarize towards higher VEGF concentrations, included more cells per cross-sectional area, and demonstrated more stable lumen formation compared to sprouts in lower density matrices. These results quantitatively demonstrate that matrix density mediates VEGF-induced sprout polarization and lumen formation, potentially by regulating the balance between EC migration rate and proliferation rate.
Construct order parameters from the reduced density matrix spectra
Gu, Shi-Jian; Yu, Wing Chi; Lin, Hai-Qing
2013-09-15
In this paper, we try to establish a connection between a quantum information concept, i.e., the mutual information, and the conventional order parameter in condensed matter physics. We show that non-vanishing mutual information between two subsystems separated by a long distance means the existence of long-range orders in the system. By analyzing the spectra of the reduced density matrices that are used to calculate the mutual information, we show how to derive the local order operators that identify various ordered phases in condensed matter physics. -- Highlights: •Discussed the relation between long-range order and the mutual information (MI). •Pointed out how to check the existence of long-range order from MI. •Proposed a scheme to derive the diagonal and off-diagonal order parameter. •Gave three examples to show the effectiveness of the scheme.
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.
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.
Shell Model Approach to Nuclear Level Density
NASA Astrophysics Data System (ADS)
Horoi, Mihai
2000-04-01
Nuclear level densities (NLD) are traditionally estimated using variations of Fermi Gas Formula (FGF) or combinatoric techniques. Recent investigations using Monte Carlo Shell Model (MCSM) techniques indicate that a shell model description of NLD may be an accurate and stable approach. Full shell model calculations of NLD are very difficult. We calculated the NLD for all nuclei in the sd shell and show that the results can be described by a single particle combinatoric model, which depends on two parameters similar to FGF. We further investigated other models and find that a sum of gaussians with means and variances given by French and Ratcliff averages (Phys. Rev. C 3, 94(1971)) is able to accurately describe shell model NLD, even when shell effects are present. The contribution of the spurious center-of-mass motion to the shell model NLD is also discussed.
A Surrogate Measure of Cortical Bone Matrix Density by Long T2-Suppressed MRI
Seifert, Alan C.; Li, Cheng; Wehrli, Suzanne L.; Wehrli, Felix W.
2015-01-01
Magnetic resonance has the potential to image and quantify two pools of water within bone: free water within the Haversian pore system (transverse relaxation time, T2 > 1 ms), and water hydrogen-bonded to matrix collagen (T2 ~ 300–400 µs). While total bone water concentration quantified by MRI has been shown to scale with porosity, greater insight into bone matrix density and porosity may be gained by relaxation-based separation of bound and pore water fractions. The objective of this study was to evaluate a recently developed surrogate measurement for matrix density, single adiabatic inversion recovery (SIR) zero echo-time (ZTE) MRI, in human bone. Specimens of tibial cortical bone from 15 donors (27–97 y/o, eight female and seven male) were examined at 9.4T field strength using two methods: (1) 1H ZTE MRI, to capture total 1H signal, and (2) 1H SIR-ZTE MRI, to selectively image matrix-associated 1H signal. Total water, bone matrix, and bone mineral densities were also quantified gravimetrically, and porosity was measured by micro-CT. ZTE apparent total water 1H concentration was 32.7±3.2 M (range: 28.5–40.3 M), and was correlated positively with porosity (R2 = 0.80) and negatively with matrix and mineral densities (R2 = 0.90 and 0.82, respectively). SIR-ZTE apparent bound water 1H concentration was 32.9±3.9 M (range: 24.4–39.8 M), and its correlations were opposite to those of apparent total water: negative with porosity (R2 = 0.73) and positive with matrix density (R2 = 0.74) and mineral density (R2 = 0.72). Porosity was strongly correlated with gravimetric matrix density (R2 = 0.91, negative) and total water density (R2 = 0.92, positive). The strong correlations of SIR-ZTE-derived apparent bound water 1H concentration with ground-truth measurements suggest that this quantitative solid-state MRI method provides a nondestructive surrogate measure of bone matrix density. PMID:26085307
A Surrogate Measure of Cortical Bone Matrix Density by Long T2 -Suppressed MRI.
Seifert, Alan C; Li, Cheng; Wehrli, Suzanne L; Wehrli, Felix W
2015-12-01
Magnetic resonance has the potential to image and quantify two pools of water within bone: free water within the Haversian pore system (transverse relaxation time, T2 > 1 ms), and water hydrogen-bonded to matrix collagen (T2 ∼ 300 to 400 μs). Although total bone water concentration quantified by MRI has been shown to scale with porosity, greater insight into bone matrix density and porosity may be gained by relaxation-based separation of bound and pore water fractions. The objective of this study was to evaluate a recently developed surrogate measurement for matrix density, single adiabatic inversion recovery (SIR) zero echo-time (ZTE) MRI, in human bone. Specimens of tibial cortical bone from 15 donors (aged 27 to 97 years; 8 female and 7 male) were examined at 9.4T field strength using two methods: (1) (1)H ZTE MRI, to capture total (1)H signal, and (2) (1)H SIR-ZTE MRI, to selectively image matrix-associated (1)H signal. Total water, bone matrix, and bone mineral densities were also quantified gravimetrically, and porosity was measured by micro-CT. ZTE apparent total water (1)H concentration was 32.7 ± 3.2 M (range 28.5 to 40.3 M), and was correlated positively with porosity (R(2) = 0.80) and negatively with matrix and mineral densities (R(2) = 0.90 and 0.82, respectively). SIR-ZTE apparent bound water (1)H concentration was 32.9 ± 3.9 M (range 24.4 to 39.8 M), and its correlations were opposite to those of apparent total water: negative with porosity (R(2) = 0.73) and positive with matrix density (R(2) = 0.74) and mineral density (R(2) = 0.72). Porosity was strongly correlated with gravimetric matrix density (R(2) = 0.91, negative) and total water density (R(2) = 0.92, positive). The strong correlations of SIR-ZTE-derived apparent bound water (1)H concentration with ground-truth measurements suggest that this quantitative solid-state MRI method provides a nondestructive surrogate measure of bone matrix density
A Contemporary Matrix Approach to Defining Shared Governance.
ERIC Educational Resources Information Center
Davenport, Richard; Daniels, Elaine; Jones, James; Kesseler, Roger; Mowrey, Merlyn
This paper outlines a matrix approach to shared governance developed at Central Michigan University (CMU), designed to help faculty and administrators focus on specific decision areas and to define existing roles more clearly. The process began at CMU in spring 1998 with the formation of an ad hoc committee on governance which surveyed faculty and…
Smallwood, D.O.
1995-08-07
It is shown that the usual method for computing 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 inputs and outputs. The modified form of Cholesky decomposition used is G{sub zz} = LCL{prime}, where G is the cross spectral density matrix of inputs and outputs, L is a lower; triangular matrix with ones on the diagonal, and C is a diagonal matrix, and the symbol {prime} denotes the conjugate transpose. If a diagonal element of C is zero, the off diagonal elements in the corresponding column of L are set to zero. It is shown that the results can be equivalently obtained using singular value decomposition (SVD) of G{sub zz}. The formulation as a SVD problem suggests a way to order the inputs when a natural physical order of the inputs is absent.
Liu, C; Liu, J; Yao, Y X; Wu, P; Wang, C Z; Ho, K M
2016-10-11
We recently proposed the correlation matrix renormalization (CMR) theory to treat the electronic correlation effects [Phys. Rev. B 2014, 89, 045131 and Sci. Rep. 2015, 5, 13478] in ground state total energy calculations of molecular systems using the Gutzwiller variational wave function (GWF). By adopting a number of approximations, the computational effort of the CMR can be reduced to a level similar to Hartree-Fock calculations. This paper reports our recent progress in minimizing the error originating from some of these approximations. We introduce a novel sum-rule correction to obtain a more accurate description of the intersite electron correlation effects in total energy calculations. Benchmark calculations are performed on a set of molecules to show the reasonable accuracy of the method.
Density-matrix based determination of low-energy model Hamiltonians from ab initio wavefunctions
Changlani, Hitesh J.; Zheng, Huihuo; Wagner, Lucas K.
2015-09-14
We propose a way of obtaining effective low energy Hubbard-like model Hamiltonians from ab initio quantum Monte Carlo calculations for molecular and extended systems. The Hamiltonian parameters are fit to best match the ab initio two-body density matrices and energies of the ground and excited states, and thus we refer to the method as ab initio density matrix based downfolding. For benzene (a finite system), we find good agreement with experimentally available energy gaps without using any experimental inputs. For graphene, a two dimensional solid (extended system) with periodic boundary conditions, we find the effective on-site Hubbard U{sup ∗}/t to be 1.3 ± 0.2, comparable to a recent estimate based on the constrained random phase approximation. For molecules, such parameterizations enable calculation of excited states that are usually not accessible within ground state approaches. For solids, the effective Hamiltonian enables large-scale calculations using techniques designed for lattice models.
Yanai, Takeshi; Saitow, Masaaki; Xiong, Xiao-Gen; Chalupský, Jakub; Kurashige, Yuki; Guo, Sheng; Sharma, Sandeep
2017-10-10
We present the development of the multistate multireference second-order perturbation theory (CASPT2) with multiroot references, which are described using the density matrix renormalization group (DMRG) method to handle a large active space. The multistate first-order wave functions are expanded into the internally contracted (IC) basis of the single-state single-reference (SS-SR) scheme, which is shown to be the most feasible variant to use DMRG references. The feasibility of the SS-SR scheme comes from two factors: first, it formally does not require the fourth-order transition reduced density matrix (TRDM) and second, the computational complexity scales linearly with the number of the reference states. The extended multistate (XMS) treatment is further incorporated, giving suited treatment of the zeroth-order Hamiltonian despite the fact that the SS-SR based IC basis is not invariant with respect to the XMS rotation. In addition, the state-specific fourth-order reduced density matrix (RDM) is eliminated in an approximate fashion using the cumulant reconstruction formula, as also done in the previous state-specific DMRG-cu(4)-CASPT2 approach. The resultant method, referred to as DMRG-cu(4)-XMS-CASPT2, uses the RDMs and TRDMs of up to third-order provided by the DMRG calculation. The multistate potential energy curves of the photoisomerization of diarylethene derivatives with CAS(26e,24o) are presented to illustrate the applicability of our theoretical approach.
Nonequilibrium density-matrix description of steady-state quantum transport.
Dhar, Abhishek; Saito, Keiji; Hänggi, Peter
2012-01-01
With this work we investigate the stationary nonequilibrium density matrix of current carrying nonequilibrium steady states of in-between quantum systems that are connected to reservoirs. We describe the analytical procedure to obtain the explicit result for the reduced density matrix of quantum transport when the system, the connecting reservoirs, and the system-reservoir interactions are described by quadratic Hamiltonians. Our procedure is detailed for both electronic transport described by the tight-binding Hamiltonian and for phonon transport described by harmonic Hamiltonians. For the special case of weak system-reservoir couplings, a more detailed description of the steady-state density matrix is obtained. Several paradigm transport setups for interelectrode electron transport and low-dimensional phonon heat flux are elucidated.
Nonmonotonic Recursive Polynomial Expansions for Linear Scaling Calculation of the Density Matrix.
Rubensson, Emanuel H
2011-05-10
As it stands, density matrix purification is a powerful tool for linear scaling electronic structure calculations. The convergence is rapid and depends only weakly on the band gap. However, as will be shown in this letter, there is room for improvements. The key is to allow for nonmonotonicity in the recursive polynomial expansion. On the basis of this idea, new purification schemes are proposed that require only half the number of matrix-matrix multiplications compared to previous schemes. The speedup is essentially independent of the location of the chemical potential and increases with decreasing band gap.
Matrix sublimation method for the formation of high-density amorphous ice
NASA Astrophysics Data System (ADS)
Kouchi, A.; Hama, T.; Kimura, Y.; Hidaka, H.; Escribano, R.; Watanabe, N.
2016-08-01
A novel method for the formation of amorphous ice involving matrix sublimation has been developed. A CO-rich CO:H2O mixed ice was deposited at 8-10 K under ultra-high vacuum condition, which was then allowed to warm. After the sublimation of matrix CO at 35 K, amorphous ice remained. The amorphous ice formed exhibits a highly porous microscale texture; however, it also rather exhibits a density similar to that of high-density amorphous ice formed under high pressure. Furthermore, unlike conventional vapor-deposited amorphous ice, the amorphous ice is stable up to 140 K, where it transforms directly to cubic ice Ic.
Entangled electron and nuclear spin states in 15N@C60: Density matrix tomography
NASA Astrophysics Data System (ADS)
Scherer, Werner; Mehring, Michael
2008-02-01
Procedures of the preparation and detection of entangled electron-nuclear spin states in N15@C60 by combining electron spin resonance and electron nuclear double resonance pulse techniques are presented. A quantitative evaluation of the complete density matrix is obtained by a special density matrix tomography. All four Bell states of a two qubit subsystem were analyzed and experimental decoherence times are presented. In addition, we estimate a quantum critical temperature of Tq=7.76K for this system at an electron spin resonance frequency of 95GHz.
Progressive delamination in polymer matrix composite laminates: A new approach
NASA Technical Reports Server (NTRS)
Chamis, C. C.; Murthy, P. L. N.; Minnetyan, L.
1992-01-01
A new approach independent of stress intensity factors and fracture toughness parameters has been developed and is described for the computational simulation of progressive delamination in polymer matrix composite laminates. The damage stages are quantified based on physics via composite mechanics while the degradation of the laminate behavior is quantified via the finite element method. The approach accounts for all types of composite behavior, laminate configuration, load conditions, and delamination processes starting from damage initiation, to unstable propagation, and to laminate fracture. Results of laminate fracture in composite beams, panels, plates, and shells are presented to demonstrate the effectiveness and versatility of this new approach.
Random Vector and Matrix Theories: A Renormalization Group Approach
NASA Astrophysics Data System (ADS)
Zinn-Justin, Jean
2014-09-01
Random matrices in the large N expansion and the so-called double scaling limit can be used as toy models for quantum gravity: 2D quantum gravity coupled to conformal matter. This has generated a tremendous expansion of random matrix theory, tackled with increasingly sophisticated mathematical methods and number of matrix models have been solved exactly. However, the somewhat paradoxical situation is that either models can be solved exactly or little can be said. Since the solved models display critical points and universal properties, it is tempting to use renormalization group ideas to determine universal properties, without solving models explicitly. Initiated by Br\\'ezin and Zinn-Justin, the approach has led to encouraging results, first for matrix integrals and then quantum mechanics with matrices, but has not yet become a universal tool as initially hoped. In particular, general quantum field theories with matrix fields require more detailed investigations. To better understand some of the encountered difficulties, we first apply analogous ideas to the simpler O(N) symmetric vector models, models that can be solved quite generally in the large N limit. Unlike other attempts, our method is a close extension of Br\\'ezin and Zinn-Justin. Discussing vector and matrix models with similar approximation scheme, we notice that in all cases (vector and matrix integrals, vector and matrix path integrals in the local approximation), at leading order, non-trivial fixed points satisfy the same universal algebraic equation, and this is the main result of this work. However, its precise meaning and role have still to be better understood.
Edgar, Lowell T.; Underwood, Clayton J.; Guilkey, James E.; Hoying, James B.; Weiss, Jeffrey A.
2014-01-01
Angiogenesis is regulated by the local microenvironment, including the mechanical interactions between neovessel sprouts and the extracellular matrix (ECM). However, the mechanisms controlling the relationship of mechanical and biophysical properties of the ECM to neovessel growth during sprouting angiogenesis are just beginning to be understood. In this research, we characterized the relationship between matrix density and microvascular topology in an in vitro 3D organ culture model of sprouting angiogenesis. We used these results to design and calibrate a computational growth model to demonstrate how changes in individual neovessel behavior produce the changes in vascular topology that were observed experimentally. Vascularized gels with higher collagen densities produced neovasculatures with shorter vessel lengths, less branch points, and reduced network interconnectivity. The computational model was able to predict these experimental results by scaling the rates of neovessel growth and branching according to local matrix density. As a final demonstration of utility of the modeling framework, we used our growth model to predict several scenarios of practical interest that could not be investigated experimentally using the organ culture model. Increasing the density of the ECM significantly reduced angiogenesis and network formation within a 3D organ culture model of angiogenesis. Increasing the density of the matrix increases the stiffness of the ECM, changing how neovessels are able to deform and remodel their surroundings. The computational framework outlined in this study was capable of predicting this observed experimental behavior by adjusting neovessel growth rate and branching probability according to local ECM density, demonstrating that altering the stiffness of the ECM via increasing matrix density affects neovessel behavior, thereby regulated vascular topology during angiogenesis. PMID:24465500
Computing the Density Matrix in Electronic Structure Theory on Graphics Processing Units.
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.
Prevention of accidental exposure in radiotherapy: the risk matrix approach.
Vilaragut, J J; Duménigo, C; Delgado, J M; Morales, J; McDonnell, J D; Ferro, R; Ortiz López, P; Ramírez, M L; Pérez Mulas, A; Papadopulos, S; Gonçalves, M; López Morones, R; Sánchez Cayuela, C; Cascajo Castresana, A; Somoano, F; Álvarez, C; Guillén, A; Rodríguez, M; Pereira, P P; Nader, A
2013-02-01
Knowledge and lessons from past accidental exposures in radiotherapy are very helpful in finding safety provisions to prevent recurrence. Disseminating lessons is necessary but not sufficient. There may be additional latent risks for other accidental exposures, which have not been reported or have not occurred, but are possible and may occur in the future if not identified, analyzed, and prevented by safety provisions. Proactive methods are available for anticipating and quantifying risk from potential event sequences. In this work, proactive methods, successfully used in industry, have been adapted and used in radiotherapy. Risk matrix is a tool that can be used in individual hospitals to classify event sequences in levels of risk. As with any anticipative method, the risk matrix involves a systematic search for potential risks; that is, any situation that can cause an accidental exposure. The method contributes new insights: The application of the risk matrix approach has identified that another group of less catastrophic but still severe single-patient events may have a higher probability, resulting in higher risk. The use of the risk matrix approach for safety assessment in individual hospitals would provide an opportunity for self-evaluation and managing the safety measures that are most suitable to the hospital's own conditions.
Kinetic equations for a density matrix describing nonlinear effects in spectral line wings
Parkhomenko, A. I. Shalagin, A. M.
2011-11-15
Kinetic quantum equations are derived for a density matrix with collision integrals describing nonlinear effects in spectra line wings. These equations take into account the earlier established inequality of the spectral densities of Einstein coefficients for absorption and stimulated radiation emission by a two-level quantum system in the far wing of a spectral line in the case of frequent collisions. The relationship of the absorption and stimulated emission probabilities with the characteristics of radiation and an elementary scattering event is found.
Alternative Approaches to High Energy Density Fusion
NASA Astrophysics Data System (ADS)
Hammer, J.
2016-10-01
This paper explores selected approaches to High Energy Density (HED) fusion, beginning with discussion of ignition requirements at the National Ignition Facility (NIF). The needed improvements to achieve ignition are closely tied to the ability to concentrate energy in the implosion, manifested in the stagnation pressure, Pstag. The energy that must be assembled in the imploded state to ignite varies roughly as Pstag-2, so among other requirements, there is a premium on reaching higher Pstag to achieve ignition with the available laser energy. The U.S. inertial confinement fusion program (ICF) is pursuing higher Pstag on NIF through improvements to capsule stability and symmetry. One can argue that recent experiments place an approximate upper bound on the ultimate ignition energy requirement. Scaling the implosions consistently in spatial, temporal and energy scales shows that implosions of the demonstrated quality ignite robustly at 9-15 times the current energy of NIF. While lasers are unlikely to reach that bounding energy, it appears that pulsed-power sources could plausibly do so, giving a range of paths forward for ICF depending on success in improving energy concentration. In this paper, I show the scaling arguments then discuss topics from my own involvement in HED fusion. The recent Viewfactor experiments at NIF have shed light on both the observed capsule drive deficit and errors in the detailed modelling of hohlraums. The latter could be important factors in the inability to achieve the needed symmetry and energy concentration. The paper then recounts earlier work in Fast Ignition and the uses of pulsed-power for HED and fusion applications. It concludes with a description of a method for improving pulsed-power driven hohlraums that could potentially provide a factor of 10 in energy at NTF-like drive conditions and reach the energy bound for indirect drive ICF.
Wen, Xiaotong; Rangarajan, Govindan; Ding, Mingzhou
2013-08-28
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.
Collagen Matrix Density Drives the Metabolic Shift in Breast Cancer Cells.
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 Â© 2016 The Authors. Published by Elsevier B.V. All rights reserved.
Approach of high density coal preparation method
Yang, Y.; Chen, Q.
1996-12-31
Density difference of aged anthracite coal of high density and discard is less than that of general coal and discard; conventional separation methods are difficult to be used. For the special coal, coal dry beneficiation technology with air-dense medium fluidized bed has obvious superiority over other separation methods.
A Quasi-Likelihood Approach to Nonnegative Matrix Factorization.
Devarajan, Karthik; Cheung, Vincent C K
2016-08-01
A unified approach to nonnegative matrix factorization based on the theory of generalized linear models is proposed. This approach embeds a variety of statistical models, including the exponential family, within a single theoretical framework and provides a unified view of such factorizations from the perspective of quasi-likelihood. Using this framework, a family of algorithms for handling signal-dependent noise is developed and its convergence proved using the expectation-maximization algorithm. In addition, a measure to evaluate the goodness of fit of the resulting factorization is described. The proposed methods allow modeling of nonlinear effects using appropriate link functions and are illustrated using an application in biomedical signal processing.
Exact and approximate many-body dynamics with stochastic one-body density matrix evolution
Lacroix, Denis
2005-06-01
We show that the dynamics of interacting fermions can be exactly replaced by a quantum jump theory in the many-body density matrix space. In this theory, jumps occur between densities formed of pairs of Slater determinants, D{sub ab}= vertical bar {phi}{sub a}><{phi}{sub b} vertical bar, where each state evolves according to the stochastic Schroedinger equation given by O. Juillet and Ph. Chomaz [Phys. Rev. Lett. 88, 142503 (2002)]. A stochastic Liouville-von Neumann equation is derived as well as the associated. Bogolyubov-Born-Green-Kirwood-Yvon hierarchy. Due to the specific form of the many-body density along the path, the presented theory is equivalent to a stochastic theory in one-body density matrix space, in which each density matrix evolves according to its own mean-field augmented by a one-body noise. Guided by the exact reformulation, a stochastic mean-field dynamics valid in the weak coupling approximation is proposed. This theory leads to an approximate treatment of two-body effects similar to the extended time-dependent Hartree-Fock scheme. In this stochastic mean-field dynamics, statistical mixing can be directly considered and jumps occur on a coarse-grained time scale. Accordingly, numerical effort is expected to be significantly reduced for applications.
Progressive fracture of polymer matrix composite structures: A new approach
NASA Technical Reports Server (NTRS)
Chamis, C. C.; Murthy, P. L. N.; Minnetyan, L.
1992-01-01
A new approach independent of stress intensity factors and fracture toughness parameters has been developed and is described for the computational simulation of progressive fracture of polymer matrix composite structures. The damage stages are quantified based on physics via composite mechanics while the degradation of the structural behavior is quantified via the finite element method. The approach account for all types of composite behavior, structures, load conditions, and fracture processes starting from damage initiation, to unstable propagation and to global structural collapse. Results of structural fracture in composite beams, panels, plates, and shells are presented to demonstrate the effectiveness and versatility of this new approach. Parameters and guidelines are identified which can be used as criteria for structural fracture, inspection intervals, and retirement for cause. Generalization to structures made of monolithic metallic materials are outlined and lessons learned in undertaking the development of new approaches, in general, are summarized.
Coe, Jeremy P; Almeida, Nuno M S; Paterson, Martin J
2017-09-02
We investigate if a range of challenging spin systems can be described sufficiently well using Monte Carlo configuration interaction (MCCI) and the density matrix renormalization group (DMRG) in a way that heads toward a more "black box" approach. Experimental results and other computational methods are used for comparison. The gap between the lowest doublet and quartet state of methylidyne (CH) is first considered. We then look at a range of first-row transition metal monocarbonyls: MCO when M is titanium, vanadium, chromium, or manganese. For these MCO systems we also employ partially spin restricted open-shell coupled-cluster (RCCSD). We finally investigate the high-spin low-lying states of the iron dimer, its cation and its anion. The multireference character of these molecules is also considered. We find that these systems can be computationally challenging with close low-lying states and often multireference character. For this more straightforward application and for the basis sets considered, we generally find qualitative agreement between DMRG and MCCI. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.
Reduced-density-matrix spectrum and block entropy of permutationally invariant many-body systems.
Salerno, Mario; Popkov, Vladislav
2010-07-01
Spectral properties of the reduced density matrix (RDM) of permutational invariant quantum many-body systems are investigated. The RDM block diagonalization which accounts for all symmetries of the Hamiltonian is achieved. The analytical expression of the RDM spectrum is provided for arbitrary parameters and rigorously proved in the thermodynamical limit. The existence of several sum rules and recurrence relations among RDM eigenvalues is also demonstrated and the distribution function of RDM eigenvalues (including degeneracies) characterized. In particular, we prove that the distribution function approaches a two-dimensional Gaussian in the limit of large subsystem sizes n>1. As a physical application we discuss the von Neumann entropy (VNE) of a block of size n for a system of hard-core bosons on a complete graph, as a function of n and of the temperature T. The occurrence of a crossover of VNE from purely logarithmic behavior at T=0 to a purely linear behavior in n for T≥Tc, is demonstrated.
A transition matrix approach to the Davenport gryo calibration scheme
NASA Technical Reports Server (NTRS)
Natanson, G. A.
1998-01-01
The in-flight gyro calibration scheme commonly used by NASA Goddard Space Flight Center (GSFC) attitude ground support teams closely follows an original version of the Davenport algorithm developed in the late seventies. Its basic idea is to minimize the least-squares differences between attitudes gyro- propagated over the course of a maneuver and those determined using post- maneuver sensor measurements. The paper represents the scheme in a recursive form by combining necessary partials into a rectangular matrix, which is propagated in exactly the same way as a Kalman filters square transition matrix. The nontrivial structure of the propagation matrix arises from the fact that attitude errors are not included in the state vector, and therefore their derivatives with respect to estimated a parameters do not appear in the transition matrix gyro defined in the conventional way. In cases when the required accuracy can be achieved by a single iteration, representation of the Davenport gyro calibration scheme in a recursive form allows one to discard each gyro measurement immediately after it was used to propagate the attitude and state transition matrix. Another advantage of the new approach is that it utilizes the same expression for the error sensitivity matrix as that used by the Kalman filter. As a result the suggested modification of the Davenport algorithm made it possible to reuse software modules implemented in the Kalman filter estimator, where both attitude errors and gyro calibration parameters are included in the state vector. The new approach has been implemented in the ground calibration utilities used to support the Tropical Rainfall Measuring Mission (TRMM). The paper analyzes some preliminary results of gyro calibration performed by the TRMM ground attitude support team. It is demonstrated that an effect of the second iteration on estimated values of calibration parameters is negligibly small, and therefore there is no need to store processed gyro data
Fourier-Legendre expansion of the one-electron density matrix of ground-state two-electron atoms
NASA Astrophysics Data System (ADS)
Ragot, Sébastien; Ruiz, María Belén
2008-09-01
The density matrix ρ(r,r') of a spherically symmetric system can be expanded as a Fourier-Legendre series of Legendre polynomials Pl(cosθ=rṡr'/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 ρ(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 Pl(cosθ)=cosθ. 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 ρ(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.
Analysis of gene set using shrinkage covariance matrix approach
NASA Astrophysics Data System (ADS)
Karjanto, Suryaefiza; Aripin, Rasimah
2013-09-01
Microarray methodology has been exploited for different applications such as gene discovery and disease diagnosis. This technology is also used for quantitative and highly parallel measurements of gene expression. Recently, microarrays have been one of main interests of statisticians because they provide a perfect example of the paradigms of modern statistics. In this study, the alternative approach to estimate the covariance matrix has been proposed to solve the high dimensionality problem in microarrays. The extension of traditional Hotelling's T2 statistic is constructed for determining the significant gene sets across experimental conditions using shrinkage approach. Real data sets were used as illustrations to compare the performance of the proposed methods with other methods. The results across the methods are consistent, implying that this approach provides an alternative to existing techniques.
On the ``Matrix Approach'' to Interacting Particle Systems
NASA Astrophysics Data System (ADS)
de Sanctis, L.; Isopi, M.
2004-04-01
Derrida et al. and Schütz and Stinchcombe gave algebraic formulas for the correlation functions of the partially asymmetric simple exclusion process. Here we give a fairly general recipe of how to get these formulas and extend them to the whole time evolution (starting from the generator of the process), for a certain class of interacting systems. We then analyze the algebraic relations obtained to show that the matrix approach does not work with some models such as the voter and the contact processes.
Infections on Temporal Networks—A Matrix-Based Approach
Koher, Andreas; Lentz, Hartmut H. K.; Hövel, Philipp; Sokolov, Igor M.
2016-01-01
We extend the concept of accessibility in temporal networks to model infections with a finite infectious period such as the susceptible-infected-recovered (SIR) model. This approach is entirely based on elementary matrix operations and unifies the disease and network dynamics within one algebraic framework. We demonstrate the potential of this formalism for three examples of networks with high temporal resolution: networks of social contacts, sexual contacts, and livestock-trade. Our investigations provide a new methodological framework that can be used, for instance, to estimate the epidemic threshold, a quantity that determines disease parameters, for which a large-scale outbreak can be expected. PMID:27035128
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.
T-Matrix Approach to Strongly Coupled QGP
NASA Astrophysics Data System (ADS)
Liu, Shuai Y. F.; Rapp, Ralf
2017-01-01
Based on a thermodynamic T-matrix approach we extract the potential V between two static charges in the quark-gluon plasma (QGP) from ts to the pertinent lattice-QCD free energy. With suitable relativistic corrections we utilize this new potential to compute heavy-quark transport coefficients and compare the results to previous calculations using either F or U as potential. We then discuss a generalization of the T-matrix re-summation to a “matrix log” re-summation of t-channel diagrams for the grand partition function of the QGP in the Luttinger-Ward skeleton diagram formalism. With V as a non-perturbative driving kernel in the light-parton sector, we obtain the QGP equation of state from ts to lattice-QCD data. The resulting light-parton spectral functions are characterized by large thermal widths at small momenta, indicating the dissolution of quasi-particles in a strongly coupled QGP.
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
NASA Astrophysics Data System (ADS)
Nemes, Csaba; Barcza, Gergely; Nagy, Zoltán; Legeza, Örs; Szolgay, Péter
2014-06-01
In the numerical analysis of strongly correlated quantum lattice models one of the leading algorithms developed to balance the size of the effective Hilbert space and the accuracy of the simulation is the density matrix renormalization group (DMRG) algorithm, in which the run-time is dominated by the iterative diagonalization of the Hamilton operator. As the most time-dominant step of the diagonalization can be expressed as a list of dense matrix operations, the DMRG is an appealing candidate to fully utilize the computing power residing in novel kilo-processor architectures. In the paper a smart hybrid CPU-GPU implementation is presented, which exploits the power of both CPU and GPU and tolerates problems exceeding the GPU memory size. Furthermore, a new CUDA kernel has been designed for asymmetric matrix-vector multiplication to accelerate the rest of the diagonalization. Besides the evaluation of the GPU implementation, the practical limits of an FPGA implementation are also discussed.
Matrix formalism of excursion set theory: A new approach to statistics of dark matter halo counting
NASA Astrophysics Data System (ADS)
Nikakhtar, Farnik; Baghram, Shant
2017-08-01
Excursion set theory (EST) is an analytical framework to study the large-scale structure of the Universe. EST introduces a procedure to calculate the number density of structures by relating the cosmological linear perturbation theory to the nonlinear structures in late time. In this work, we introduce a novel approach to reformulate the EST in matrix formalism. We propose that the matrix representation of EST will facilitate the calculations in this framework. The method is to discretize the two-dimensional plane of variance and density contrast of EST, where the trajectories for each point in the Universe lived there. The probability of having a density contrast in a chosen variance is represented by a probability ket. Naturally, the concept of the transition matrix pops up to define the trajectories. We also define the probability transition rate which is used to obtain the first up-crossing of trajectories and the number count of the structures. In this work we show that the discretization let us study the non-Markov processes by forcing them to look like a Wiener process. Also we discuss that the zero drift processes with Gaussian and also non-Gaussian initial conditions can be studied by this formalism. The continuous limit of the formalism is discussed, and the known Fokker-Planck dispersion equation is recovered. Finally we show that the probability of the most massive progenitors can be extracted in this framework.
NASA Astrophysics Data System (ADS)
Liang, Wenkel; Isborn, Christine M.; Li, Xiaosong
2009-11-01
The calculation of doubly excited states is one of the major problems plaguing the modern day excited state workhorse methodology of linear response time dependent Hartree-Fock (TDHF) and density function theory (TDDFT). We have previously shown that the use of a resonantly tuned field within real-time TDHF and TDDFT is able to simultaneously excite both the α and β electrons to achieve the two-electron excited states of minimal basis H2 and HeH+ [C. M. Isborn and X. Li, J. Chem. Phys. 129, 204107 (2008)]. We now extend this method to many electron systems with the use of our Car-Parrinello density matrix search (CP-DMS) with a first-principles fictitious mass method for wave function optimization [X. Li, C. L. Moss, W. Liang, and Y. Feng, J. Chem. Phys. 130, 234115 (2009)]. Real-time TDHF/TDDFT is used during the application of the laser field perturbation, driving the electron density toward the doubly excited state. The CP-DMS method then converges the density to the nearest stationary state. We present these stationary state doubly excited state energies and properties at the HF and DFT levels for H2, HeH+, lithium hydride, ethylene, and butadiene.
NASA Astrophysics Data System (ADS)
Yanai, Takeshi; Kurashige, Yuki; Neuscamman, Eric; Chan, Garnet Kin-Lic
2010-01-01
We describe the joint application of the density matrix renormalization group and canonical transformation theory to multireference quantum chemistry. The density matrix renormalization group provides the ability to describe static correlation in large active spaces, while the canonical transformation theory provides a high-order description of the dynamic correlation effects. We demonstrate the joint theory in two benchmark systems designed to test the dynamic and static correlation capabilities of the methods, namely, (i) total correlation energies in long polyenes and (ii) the isomerization curve of the [Cu2O2]2+ core. The largest complete active spaces and atomic orbital basis sets treated by the joint DMRG-CT theory in these systems correspond to a (24e,24o) active space and 268 atomic orbitals in the polyenes and a (28e,32o) active space and 278 atomic orbitals in [Cu2O2]2+.
NASA Astrophysics Data System (ADS)
Kanazawa, Takuya; Wettig, Tilo
2014-10-01
We generalize QCD at asymptotically large isospin chemical potential to an arbitrary even number of flavors. We also allow for small quark chemical potentials, which stress the coincident Fermi surfaces of the paired quarks and lead to a sign problem in Monte Carlo simulations. We derive the corresponding low-energy effective theory in both p- and ɛ-expansion and quantify the severity of the sign problem. We construct the random matrix theory describing our physical situation and show that it can be mapped to a known random matrix theory at low baryon density so that new insights can be gained without additional calculations. In particular, we explain the Silver Blaze phenomenon at high isospin density. We also introduce stressed singular values of the Dirac operator and relate them to the pionic condensate. Finally we comment on extensions of our work to two-color QCD.
van der Spoel, D; Berendsen, H J
1996-01-01
In this work we give an overview of the methodologies required to compute the rate of proton transfer in hydrogen bonded systems in solution. Using ab initio or density functional methods we determine proton potentials of a truncated system as a function of proton-donor proton-acceptor distance as well as nonbonding parameters. By classical molecular dynamics we evaluate a swarm of proton potentials with the proton fixed in the reactant well. The rate of proton transfer is calculated perturbatively using the Density Matrix Evolution (DME) method, going beyond the Born Oppenheimer approximation. The method is illustrated by two examples: hydrogen malonate and the active center of HIV-1 protease.
Testing the density matrix expansion against ab initio calculations of trapped neutron drops
Bogner, S. K.; Hergert, H.; Furnstahl, R. J.; Kortelainen, Erno M; Stoitsov, M. V.; Maris, Pieter; Vary, J. P.
2011-01-01
Microscopic input to a universal nuclear energy density functional can be provided through the density matrix expansion (DME), which has recently been revived and improved. Several DME implementation strategies are tested for neutron drop systems in harmonic traps by comparing to Hartree-Fock (HF) and ab initio no-core full configuration (NCFC) calculations with a model interaction (Minnesota potential). The new DME with exact treatment of Hartree contributions is found to best reproduce HF results and supplementing the functional with fit Skyrme-like contact terms shows systematic improvement toward the full NCFC results.
Distance matrix-based approach to protein structure prediction.
Kloczkowski, Andrzej; Jernigan, Robert L; Wu, Zhijun; Song, Guang; Yang, Lei; Kolinski, Andrzej; Pokarowski, Piotr
2009-03-01
Much structural information is encoded in the internal distances; a distance matrix-based approach can be used to predict protein structure and dynamics, and for structural refinement. Our approach is based on the square distance matrix D = [r(ij)(2)] containing all square distances between residues in proteins. This distance matrix contains more information than the contact matrix C, that has elements of either 0 or 1 depending on whether the distance r (ij) is greater or less than a cutoff value r (cutoff). We have performed spectral decomposition of the distance matrices D = sigma lambda(k)V(k)V(kT), in terms of eigenvalues lambda kappa and the corresponding eigenvectors v kappa and found that it contains at most five nonzero terms. A dominant eigenvector is proportional to r (2)--the square distance of points from the center of mass, with the next three being the principal components of the system of points. By predicting r (2) from the sequence we can approximate a distance matrix of a protein with an expected RMSD value of about 7.3 A, and by combining it with the prediction of the first principal component we can improve this approximation to 4.0 A. We can also explain the role of hydrophobic interactions for the protein structure, because r is highly correlated with the hydrophobic profile of the sequence. Moreover, r is highly correlated with several sequence profiles which are useful in protein structure prediction, such as contact number, the residue-wise contact order (RWCO) or mean square fluctuations (i.e. crystallographic temperature factors). We have also shown that the next three components are related to spatial directionality of the secondary structure elements, and they may be also predicted from the sequence, improving overall structure prediction. We have also shown that the large number of available HIV-1 protease structures provides a remarkable sampling of conformations, which can be viewed as direct structural information about the
Derivation of the density matrix of a single photon produced in parametric down-conversion
Kolenderski, Piotr; Wasilewski, Wojciech
2009-07-15
We discuss an effective numerical method of density matrix determination of fiber coupled single photon generated in process of spontaneous parametric down conversion in type I noncollinear configuration. The presented theory has been successfully applied in case of source utilized to demonstrate the experimental characterization of spectral state of single photon, what was reported in Wasilewski, Kolenderski, and Frankowski [Phys. Rev. Lett. 99, 123601 (2007)].
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.
Density-matrix method applied to mode coupling in lenslike fibers
NASA Astrophysics Data System (ADS)
Maeda, K.; Hamasaki, J.
1980-04-01
Mode conversion due to random refractive-index fluctuations of a lossless multimode waveguide is considered. An equation of motion for an average density matrix, which describes wave phenomena in statistically identical waveguides is derived. This equation includes the coupled power equation given by Marcuse, and also describes evolution of correlations between propagating modes. Using this equation, mode-conversion characteristics among degenerate modes in a lenslike fiber are obtained for several correlation lengths and variances of the refractive-index fluctuations.
Effective field theory during inflation: Reduced density matrix and its quantum master equation
NASA Astrophysics Data System (ADS)
Boyanovsky, D.
2015-07-01
We study the power spectrum of super-Hubble fluctuations of an inflatonlike scalar field, the "system," coupled to another scalar field, the "environment" during de Sitter inflation. We obtain the reduced density matrix for the inflaton fluctuations by integrating out the environmental degrees of freedom. These are considered to be massless and conformally coupled to gravity as a proxy to describe degrees of freedom that remain sub-Hubble all throughout inflation. The time evolution of the density matrix is described by a quantum master equation, which describes the decay of the vacuum state, the production of particles and correlated pairs and quantum entanglement between super and sub-Hubble degrees of freedom. The quantum master equation provides a nonperturbative resummation of secular terms from self-energy (loop) corrections to the inflaton fluctuations. In the case studied here these are Sudakov-type double logarithms which result in the decay of the power spectrum of inflaton fluctuations upon horizon crossing with a concomitant violation of scale invariance. The reduced density matrix and its quantum master equation furnish a powerful nonperturbative framework to study the effective field theory of long wavelength fluctuations by tracing short wavelength degrees of freedom.
NASA Astrophysics Data System (ADS)
Buchman, Omri; Baer, Roi
2017-09-01
The one-body density matrix (OBDM) is a fundamental contraction of the Bose-Einstein condensate wave function, encapsulating its one-body properties. It serves as a major analysis tool with which the condensed component of the density can be identified. Despite its cardinal importance, calculating the ground-state OBDM of trapped interacting bosons is a challenge and to date OBDM calculations have been published only for homogeneous systems or for trapped weakly interacting bosons. In this paper we discuss an approach for computing the OBDM based on a double-walker diffusion Monte Carlo random walk coupled with a stochastic permanent calculation. We here describe the method and study some of its statistical convergence and properties applying it to some model systems.
Partitioned density functional approach for a Lennard-Jones fluid.
Zhou, Shiqi
2003-12-01
The existing classical density functional approach for nonuniform Lennard-Jones fluid, which is based on dividing the Lennard-Jones interaction potential into a short-range, repulsive part, and a smoothly varying, long-range, attractive tail, was improved by dividing the bulk second-order direct correlation function into strongly density-depending short-range part and weakly density-depending long-range part. The latter is treated by functional perturbation expansion truncated at the lowest order whose accuracy depends on how weakly the long-range part depends on the bulk density. The former is treated by the truncated functional perturbation expansion which is rewritten in the form of the simple weighted density approximation and incorporates the omitted higher-order terms by applying Lagrangian theorem of differential calculus to the reformulated form. The two approximations are put into the density profile equation of the density functional theory formalism to predict the density distribution for Lennard-Jones fluid in contact with a hard wall or between two hard walls within the whole density range for reduced temperature T(*)=1.35 and a density point for reduced temperature T(*)=1. The present partitioned density functional theory performs much better than several previous density functional perturbation theory approaches and a recently proposed bridge density functional approximation.
Stoitsov, M. V.; Kortelainen, Erno M; Bogner, S. K.; Duguet, T.; Furnstahl, R. J.; Gebremariam, B.; Schunck, N.
2010-01-01
In a recent series of papers, Gebremariam, Bogner, and Duguet derived a microscopically-based nuclear energy density functional by applying the Density Matrix Expansion (DME) to the Hartree-Fock energy obtained from chiral effective field theory (EFT) two- and three-nucleon interactions. Due to the structure of the chiral interactions, each coupling in the DME functional is given as the sum of a coupling constant arising from zero-range contact interactions and a coupling function of the density arising from the finite-range pion exchanges. Since the contact contributions have essentially the same structure as those entering empirical Skyrme functionals, a microscopically guided Skyrme phenomenology has been suggested in which the contact terms in the DME functional are released for optimization to finite-density observables to capture short-range correlation energy contributions from beyond Hartree-Fock. The present paper is the first attempt to assess the ability of the newly suggested DME functional, which has a much richer set of density dependencies than traditional Skyrme functionals, to generate sensible and stable results for nuclear applications. The results of the first proof-of-principle calculations are given, and numerous practical issues related to the implementation of the new functional in existing Skyrme codes are discussed. Using a restricted singular value decomposition (SVD) optimization procedure, it is found that the new DME functional gives numerically stable results and exhibits a small but systematic reduction in {chi}^{2} compared to standard Skyrme functionals, thus justifying its suitability for future global optimizations and large-scale calculations.
Stoitsov, M.; Kortelainen, M.; Schunck, N.; Bogner, S. K.; Gebremariam, B.; Duguet, T.
2010-11-15
In a recent series of articles, Gebremariam, Bogner, and Duguet derived a microscopically based nuclear energy density functional by applying the density matrix expansion (DME) to the Hartree-Fock energy obtained from chiral effective field theory two- and three-nucleon interactions. Owing to the structure of the chiral interactions, each coupling in the DME functional is given as the sum of a coupling constant arising from zero-range contact interactions and a coupling function of the density arising from the finite-range pion exchanges. Because the contact contributions have essentially the same structure as those entering empirical Skyrme functionals, a microscopically guided Skyrme phenomenology has been suggested in which the contact terms in the DME functional are released for optimization to finite-density observables to capture short-range correlation energy contributions from beyond Hartree-Fock. The present article is the first attempt to assess the ability of the newly suggested DME functional, which has a much richer set of density dependencies than traditional Skyrme functionals, to generate sensible and stable results for nuclear applications. The results of the first proof-of-principle calculations are given, and numerous practical issues related to the implementation of the new functional in existing Skyrme codes are discussed. Using a restricted singular value decomposition optimization procedure, it is found that the new DME functional gives numerically stable results and exhibits a small but systematic reduction of our test {chi}{sup 2} function compared to standard Skyrme functionals, thus justifying its suitability for future global optimizations and large-scale calculations.
NASA Astrophysics Data System (ADS)
Parson, William W.; Warshel, Arieh
2004-01-01
The dispersed-polaron (spin-boson) model is reviewed briefly and then used to develop a density-matrix model for studies of electron transfer in condensed phases. The frequencies and Franck-Condon factors for solvent vibrational modes that are coupled to electron transfer are obtained from molecular dynamics (MD) simulations by the dispersed-polaron treatment. Microscopic rate constants for vibrational relaxations, dephasing and coherence transfer between the solvent modes are obtained by fitting the time dependence of the solvent coordinates in the density-matrix treatment to the corresponding time dependence obtained from molecular-dynamics simulations with a classical linear-response approximation. This is done by adjusting a single parameter, the time constant for thermal equilibration of the two lowest levels of a solvent mode ( T10). The model thus focuses on the coupling between solvent modes, rather than on the more widely studied coupling of solute modes by the thermal bath. The resulting density-matrix model is used to examine vibronic coupling in the initial electron-transfer step in photosynthetic bacterial reaction centers. Values of T10 in the range of 1-2 ps are consistent with molecular-dynamics simulations of the time-dependent energy gap between the reactant and product states (P* and P +B -), and also with the damping of coherent vibrational motions that are seen experimentally after excitation of reaction centers with a short pulse of light. In both the density-matrix model and the MD simulations, the autocorrelation function of the energy gap also has a decay component with a time constant of about 50 fs, which we ascribe to the group dephasing of oscillatory motions at many different frequencies. This component is insensitive to vibrational relaxations and is largely irrelevant to the electron-transfer dynamics. Using values of T10 in the range of 1-2 ps, a model with five vibrational modes reproduces the main features of electron transfer
Two functions of the density matrix and their relation to the chemical bond
NASA Astrophysics Data System (ADS)
Schmider, Hartmut L.; Becke, Axel D.
2002-02-01
We examine and compare two previously introduced functions of the one-particle density matrix that are suitable to represent its off-diagonal structure in a condensed form and that have illustrative connections to the nature of the chemical bond. One of them, the Localized-Orbital Locator (LOL) [J. Molec. Struct. (THEOCHEM) 527, 51 (2000)], is based only on the noninteracting kinetic-energy density τ and the charge density ρ at a point, and gives an intuitive measure of the relative speed of electrons in its vicinity. Alternatively, LOL focuses on regions that are dominated by single localized orbitals. The other one, the Parity Function P [J. Chem. Phys. 105, 11134 (1996)], is a section through the Wigner phase-space function at zero momentum, and contains information about the phase of the interference of atomiclike orbital contributions from bound centers. In this paper, we discuss the way in which these functions condense information in the density matrix, and illustrate on a variety of examples of unusual chemical bonds how they can help to understand the nature of "covalence."
Analysis of the segmented contraction of basis functions using density matrix theory.
Custodio, Rogério; Gomes, André Severo Pereira; Sensato, Fabrício Ronil; Trevas, Júlio Murilo Dos Santos
2006-11-30
A particular formulation based on density matrix (DM) theory at the Hartree-Fock level of theory and the description of the atomic orbitals as integral transforms is introduced. This formulation leads to a continuous representation of the density matrices as functions of a generator coordinate and to the possibility of plotting either the continuous or discrete density matrices as functions of the exponents of primitive Gaussian basis functions. The analysis of these diagrams provides useful information allowing: (a) the determination of the most important primitives for a given orbital, (b) the core-valence separation, and (c) support for the development of contracted basis sets by the segmented method. Copyright 2006 Wiley Periodicals, Inc.
Density hysteresis of heavy water confined in a nanoporous silica matrix
Zhang, Yang; Faraone, Antonio; Kamitakahara, William; Liu, Kao-Hsiang; Mou, Chung-Yuan; Leao, Juscelino B; Chang, Sung C; Chen, Sow-hsin H
2011-01-01
A neutron scattering technique was developed to measure the density of heavy water confined in a nanoporous silica matrix in a temperature-pressure range, from 300 to 130 K and from 1 to 2,900 bars, where bulk water will crystalize. We observed a prominent hysteresis phenomenon in the measured density profiles between warming and cooling scans above 1,000 bars. We inter- pret this hysteresis phenomenon as support (although not a proof) of the hypothetical existence of a first-order liquid liquid phase transition of water that would exist in the macroscopic system if crystallization could be avoided in the relevant phase region. Moreover, the density data we obtained for the confined heavy water under these conditions are valuable to large communities in biology and earth and planetary sciences interested in phenomena in which nanometer-sized water layers are involved.
Density hysteresis of heavy water confined in a nanoporous silica matrix
Zhang, Yang; Faraone, Antonio; Kamitakahara, William A.; Liu, Kao-Hsiang; Mou, Chung-Yuan; Leão, Juscelino B.; Chang, Sung; Chen, Sow-Hsin
2011-01-01
A neutron scattering technique was developed to measure the density of heavy water confined in a nanoporous silica matrix in a temperature-pressure range, from 300 to 130 K and from 1 to 2,900 bars, where bulk water will crystalize. We observed a prominent hysteresis phenomenon in the measured density profiles between warming and cooling scans above 1,000 bars. We interpret this hysteresis phenomenon as support (although not a proof) of the hypothetical existence of a first-order liquid–liquid phase transition of water that would exist in the macroscopic system if crystallization could be avoided in the relevant phase region. Moreover, the density data we obtained for the confined heavy water under these conditions are valuable to large communities in biology and earth and planetary sciences interested in phenomena in which nanometer-sized water layers are involved. PMID:21746898
NASA Astrophysics Data System (ADS)
Roemelt, Michael
2015-07-01
Spin Orbit Coupling (SOC) is introduced to molecular ab initio density matrix renormalization group (DMRG) calculations. In the presented scheme, one first approximates the electronic ground state and a number of excited states of the Born-Oppenheimer (BO) Hamiltonian with the aid of the DMRG algorithm. Owing to the spin-adaptation of the algorithm, the total spin S is a good quantum number for these states. After the non-relativistic DMRG calculation is finished, all magnetic sublevels of the calculated states are constructed explicitly, and the SOC operator is expanded in the resulting basis. To this end, spin orbit coupled energies and wavefunctions are obtained as eigenvalues and eigenfunctions of the full Hamiltonian matrix which is composed of the SOC operator matrix and the BO Hamiltonian matrix. This treatment corresponds to a quasi-degenerate perturbation theory approach and can be regarded as the molecular equivalent to atomic Russell-Saunders coupling. For the evaluation of SOC matrix elements, the full Breit-Pauli SOC Hamiltonian is approximated by the widely used spin-orbit mean field operator. This operator allows for an efficient use of the second quantized triplet replacement operators that are readily generated during the non-relativistic DMRG algorithm, together with the Wigner-Eckart theorem. With a set of spin-orbit coupled wavefunctions at hand, the molecular g-tensors are calculated following the scheme proposed by Gerloch and McMeeking. It interprets the effective molecular g-values as the slope of the energy difference between the lowest Kramers pair with respect to the strength of the applied magnetic field. Test calculations on a chemically relevant Mo complex demonstrate the capabilities of the presented method.
Roemelt, Michael
2015-07-28
Spin Orbit Coupling (SOC) is introduced to molecular ab initio density matrix renormalization group (DMRG) calculations. In the presented scheme, one first approximates the electronic ground state and a number of excited states of the Born-Oppenheimer (BO) Hamiltonian with the aid of the DMRG algorithm. Owing to the spin-adaptation of the algorithm, the total spin S is a good quantum number for these states. After the non-relativistic DMRG calculation is finished, all magnetic sublevels of the calculated states are constructed explicitly, and the SOC operator is expanded in the resulting basis. To this end, spin orbit coupled energies and wavefunctions are obtained as eigenvalues and eigenfunctions of the full Hamiltonian matrix which is composed of the SOC operator matrix and the BO Hamiltonian matrix. This treatment corresponds to a quasi-degenerate perturbation theory approach and can be regarded as the molecular equivalent to atomic Russell-Saunders coupling. For the evaluation of SOC matrix elements, the full Breit-Pauli SOC Hamiltonian is approximated by the widely used spin-orbit mean field operator. This operator allows for an efficient use of the second quantized triplet replacement operators that are readily generated during the non-relativistic DMRG algorithm, together with the Wigner-Eckart theorem. With a set of spin-orbit coupled wavefunctions at hand, the molecular g-tensors are calculated following the scheme proposed by Gerloch and McMeeking. It interprets the effective molecular g-values as the slope of the energy difference between the lowest Kramers pair with respect to the strength of the applied magnetic field. Test calculations on a chemically relevant Mo complex demonstrate the capabilities of the presented method.
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 ψ(t) = < ψ | A(t) | ψ > . This includes quantum quenches. The generalization to (non-)thermal mixed state dynamics 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.
Controlled-surface-wettability-based fabrication of hydrogel substrates with matrix tethering density variations
NASA Astrophysics Data System (ADS)
Rahman, Md. Mahmudur; Lee, Donghee; Bhagirath, Divya; Zhao, Xiangshan; Band, Vimla; Ryu, Sangjin
2014-03-01
It is widely accepted that cells behave differently responding to the stiffness of extracellular matrix (ECM). Such observations were made by culturing cells on hydrogel substrates of tunable stiffness. However, it was recently proposed that cells actually sense how strongly they are tethered to ECM, not the local stiffness of ECM. To investigate the hypothesis, we develop constant-stiffness hydrogel substrates with varying matrix tethering density (the number of anchoring sites between the gel and the ECM protein molecules). We fabricate polyacrylamide gel of static stiffness and conjugate ECM proteins to the gel using a cross-linker. When treating the gel with the cross-linker, we control positioning of cross-linker solutions with different concentrations using superhydrophobic barriers on glass, functionalize the gel by pressing it to the aligned cross-linker solutions, and conjugate an ECM protein of constant concentration to the gel. We expect that the gel will be functionalized to different degrees depending on the concentration distribution of the cross-linker and thus the gel will have variations of matrix tethering density even with constant ECM protein concentration. We acknowledge support from Bioengineering for Human Health grant of UNL-UNMC.
Effect of bone graft density on in vitro cell behavior with enamel matrix derivative.
Miron, Richard J; Caluseru, Oana M; Guillemette, Vincent; Zhang, Yufeng; Buser, Daniel; Chandad, Fatiha; Sculean, Anton
2015-09-01
Bone replacement grafting materials play an important role in regenerative dentistry. Despite a large array of tested bone-grafting materials, little information is available comparing the effects of bone graft density on in vitro cell behavior. Therefore, the aim of the present study is to compare the effects of cells seeded on bone grafts at low and high density in vitro for osteoblast adhesion, proliferation, and differentiation. The response of osteoblasts to the presence of a growth factor (enamel matrix derivative, (EMD)) in combination with low (8 mg per well) or high (100 mg per well) bone grafts (BG; natural bone mineral, Bio-Oss®) density, was studied and compared for osteoblast cell adhesion, proliferation, and differentiation as assessed by real-time PCR. Standard tissue culture plastic was used as a control with and without EMD. The present study demonstrates that in vitro testing of bone-grafting materials is largely influenced by bone graft seeding density. Osteoblast adhesion was up to 50 % lower when cells were seeded on high-density BG when compared to low-density BG and control tissue culture plastic. Furthermore, proliferation was affected in a similar manner whereby cell proliferation on high-density BG (100 mg/well) was significantly increased when compared to that on low-density BG (8 mg/well). In contrast, cell differentiation was significantly increased on high-density BG as assessed by real-time PCR for markers collagen 1 (Col 1), alkaline phosphatase (ALP), and osteocalcin (OC) as well as alizarin red staining. The effects of EMD on osteoblast adhesion, proliferation, and differentiation further demonstrated that the bone graft seeding density largely controls in vitro results. EMD significantly increased cell attachment only on high-density BG, whereas EMD was able to further stimulate cell proliferation and differentiation of osteoblasts on control culture plastic and low-density BG when compared to high-density BG. The results
Non-Hermitian random matrix models: Free random variable approach
Janik, R.A.,; Nowak, M.A., ||; Papp, G.,; Wambach, J.,; Zahed, I., |
1997-04-01
Using the standard concepts of free random variables, we show that for a large class of non-Hermitian random matrix models, the support of the eigenvalue distribution follows from their Hermitian analogs using a conformal transformation. We also extend the concepts of free random variables to the class of non-Hermitian matrices, and apply them to the models discussed by Ginibre-Girko (elliptic ensemble) [J. Ginibre, J. Math. Phys. {bold 6}, 1440 (1965); V. L. Girko, {ital Spectral Theory of Random Matrices} (in Russian) (Nauka, Moscow, 1988)] and Mahaux-Weidenm{umlt u}ller (chaotic resonance scattering) [C. Mahaux and H. A. Weidenm{umlt u}ller, {ital Shell-model Approach to Nuclear Reactions} (North-Holland, Amsterdam, 1969)]. {copyright} {ital 1997} {ital The American Physical Society}
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.
Adiabatic approximation in time-dependent reduced-density-matrix functional theory
Requist, Ryan; Pankratov, Oleg
2010-04-15
With the aim of describing real-time electron dynamics, we introduce an adiabatic approximation for the equation of motion of the one-body reduced density matrix (one-matrix). The eigenvalues of the one-matrix, which represent the occupation numbers of single-particle orbitals, are obtained from the constrained minimization of the instantaneous ground-state energy functional rather than from their dynamical equations. The performance of the approximation vis-a-vis nonadiabatic effects is assessed in real-time simulations of a two-site Hubbard model. Due to Landau-Zener-type transitions, the system evolves into a nonstationary state with persistent oscillations in the observables. The amplitude of the oscillations displays a strongly nonmonotonic dependence on the strength of the electron-electron interaction and the rate of variation of the external potential. We interpret an associated resonance behavior in the phase of the oscillations in terms of 'scattering' with spectator energy levels. To clarify the motivation for the minimization condition, we derive a sequence of energy functionals E{sub v}{sup (n)}, for which the corresponding sequence of minimizing one-matrices is asymptotic to the exact one-matrix in the adiabatic limit.
Cawkwell, M J; Wood, M A; Niklasson, Anders M N; Mniszewski, S M
2014-12-09
The algorithm developed in Cawkwell, M. J. et al. J. Chem. Theory Comput. 2012 , 8 , 4094 for the computation of the density matrix in electronic structure theory on a graphics processing unit (GPU) using the second-order spectral projection (SP2) method [ Niklasson, A. M. N. Phys. Rev. B 2002 , 66 , 155115 ] has been efficiently parallelized over multiple GPUs on a single compute node. The parallel implementation provides significant speed-ups with respect to the single GPU version with no loss of accuracy. The performance and accuracy of the parallel GPU-based algorithm is compared with the performance of the SP2 algorithm and traditional matrix diagonalization methods on a multicore central processing unit (CPU).
Random matrix model of QCD at finite density and the nature of the quenched limit
Stephanov, M.A.
1996-06-01
We use a random matrix model to study chiral symmetry breaking in QCD at finite chemical potential {mu}. We solve the model and compute the eigenvalue density of the Dirac matrix on a complex plane. A naive {open_quote}{open_quote}replica trick{close_quote}{close_quote} fails for {mu}{ne}0; we find that quenched QCD is not a simple {ital n}{r_arrow}0 limit of QCD with {ital n} quarks. It is the limit of a theory with 2{ital n} quarks: {ital n} quarks with original action and {ital n} quarks with conjugate action. The results agree with earlier studies of lattice QCD at {mu}{ne}0 and provide a simple analytical explanation of a long-standing puzzle. {copyright} {ital 1996 The American Physical Society.}
NASA Astrophysics Data System (ADS)
Chen, Xin
2014-04-01
Understanding the roles of the temporary and spatial structures of quantum functional noise in open multilevel quantum molecular systems attracts a lot of theoretical interests. I want to establish a rigorous and general framework for functional quantum noises from the constructive and computational perspectives, i.e., how to generate the random trajectories to reproduce the kernel and path ordering of the influence functional with effective Monte Carlo methods for arbitrary spectral densities. This construction approach aims to unify the existing stochastic models to rigorously describe the temporary and spatial structure of Gaussian quantum noises. In this paper, I review the Euclidean imaginary time influence functional and propose the stochastic matrix multiplication scheme to calculate reduced equilibrium density matrices (REDM). In addition, I review and discuss the Feynman-Vernon influence functional according to the Gaussian quadratic integral, particularly its imaginary part which is critical to the rigorous description of the quantum detailed balance. As a result, I establish the conditions under which the influence functional can be interpreted as the average of exponential functional operator over real-valued Gaussian processes for open multilevel quantum systems. I also show the difference between the local and nonlocal phonons within this framework. With the stochastic matrix multiplication scheme, I compare the normalized REDM with the Boltzmann equilibrium distribution for open multilevel quantum systems.
Chen, Xin
2014-04-21
Understanding the roles of the temporary and spatial structures of quantum functional noise in open multilevel quantum molecular systems attracts a lot of theoretical interests. I want to establish a rigorous and general framework for functional quantum noises from the constructive and computational perspectives, i.e., how to generate the random trajectories to reproduce the kernel and path ordering of the influence functional with effective Monte Carlo methods for arbitrary spectral densities. This construction approach aims to unify the existing stochastic models to rigorously describe the temporary and spatial structure of Gaussian quantum noises. In this paper, I review the Euclidean imaginary time influence functional and propose the stochastic matrix multiplication scheme to calculate reduced equilibrium density matrices (REDM). In addition, I review and discuss the Feynman-Vernon influence functional according to the Gaussian quadratic integral, particularly its imaginary part which is critical to the rigorous description of the quantum detailed balance. As a result, I establish the conditions under which the influence functional can be interpreted as the average of exponential functional operator over real-valued Gaussian processes for open multilevel quantum systems. I also show the difference between the local and nonlocal phonons within this framework. With the stochastic matrix multiplication scheme, I compare the normalized REDM with the Boltzmann equilibrium distribution for open multilevel quantum systems.
Quantum correlations in different density-matrix representations of spin-1/2 open chain
NASA Astrophysics Data System (ADS)
Fel'dman, E. B.; Zenchuk, A. I.
2012-07-01
We consider quantum correlations in a spin-1/2 open chain of N nodes with the XY Hamiltonian using different bases for the density-matrix representation and the initial state with a single polarized node. These bases of our choice are the following: (i) the basis of eigenvectors of the fermion operators which appears naturally through the Jordan-Wigner transformation (this representation of the density matrix is referred to as the β representation); (ii) its Fourier representation (c representation of the density matrix); and (iii) the basis of eigenvectors of the operators Ijz (the z projection of the jth spin, j=1,⋯,N). Although for the short chains (a few nodes) the qualitative behavior of the entanglement and the discord are very similar (the difference is quantitative), this is not valid for longer chains (N≳10). In this case, there are qualitative and quantitative distinctions between the entanglement and the discord in all three cases. We underline the three most important features: (i) the quantum discord is static in the β representation, where the entanglement is identical to zero; (ii) in the c representation, the concurrence may be nonzero only between the nearest neighbors (with a single exception), while the discord is nonzero between any two nodes; and (iii) there is so-called “echo” in the evolution of the discord, which is not observed in the evolution of the concurrence. Using different bases, we may choose the preferable behavior of quantum correlations which allows a given quantum system to be more flexible in applications.
Parker, Shane M.; Shiozaki, Toru
2014-12-07
We extend the active space decomposition method, recently developed by us, to more than two active sites using the density matrix renormalization group algorithm. The fragment wave functions are described by complete or restricted active-space wave functions. Numerical results are shown on a benzene pentamer and a perylene diimide trimer. It is found that the truncation errors in our method decrease almost exponentially with respect to the number of renormalization states M, allowing for numerically exact calculations (to a few μE{sub h} or less) with M = 128 in both cases. This rapid convergence is because the renormalization steps are used only for the interfragment electron correlation.
Applying the density matrix expansion with coordinate-space chiral interactions
NASA Astrophysics Data System (ADS)
Dyhdalo, A.; Bogner, S. K.; Furnstahl, R. J.
2017-05-01
We apply the density matrix expansion (DME) at Hartree-Fock level with long-range chiral effective field theory interactions defined in coordinate space up to next-to-next-to-leading order. We consider chiral potentials both with and without explicit Δ isobars. The challenging algebra associated with applying the DME to three-nucleon forces is tamed using a new organization scheme, which will also facilitate generalizations. We include local regulators on the interactions to mitigate the effects of singular potentials on the DME couplings and simplify the optimization of generalized Skyrme-like functionals.
Analysis of NMR self-diffusion measurements by a density matrix calculation
NASA Astrophysics Data System (ADS)
Stepišnik, J.
1981-04-01
The density matrix formalism with the Magnus expansion of the time evolution operator is used to study the nmr response in a pulsed magnetic field gradient (mfg) spin-echo experiment. The results show that the spin-echo cannot only measure the self-diffusion coefficient but can determine the spectrum of the single-particle velocity autocorrelation function as well. The proper combination of rf and mfg pulse sequences are proposed for measuring self-diffusion in spin systems with strong dipolar coupling where the classical method fails.
NASA Astrophysics Data System (ADS)
Schmider, Hartmut; Smith, Vedene H., Jr.; Weyrich, Wolf
1992-06-01
For the beryllium atom, it is demonstrated that coherent form factors F(k) can be insufficient for inferring the one-particle reduced density matrix (ODM). The description in terms of reciprocal form factors B(s) as the complementary momentum-space property is compared with the results for a least-squares fit to F(k) data. A virtually complete description of the true ODM may be obtained by using a combined data set, as can be shown by representing the ODM in spherically averaged form.
Density-matrix-power functional: Performance for finite systems and the homogeneous electron gas
NASA Astrophysics Data System (ADS)
Lathiotakis, N. N.; Sharma, S.; Dewhurst, J. K.; Eich, F. G.; Marques, M. A. L.; Gross, E. K. U.
2009-04-01
An exchange-correlation energy functional involving fractional power of the one-body reduced density matrix [S. Sharma, J. K. Dewhurst, N. N. Lathiotakis, and E. K. U. Gross, Phys. Rev. B 78, 201103(R) (2008)] is applied to finite systems and to the homogeneous electron gas. The performance of the functional is assessed for the correlation and atomization energies of a large set of molecules and for the correlation energy of the homogeneous electron gas. High accuracy is found for these two very different types of systems.
Highly linear high-density vector quantiser and vector-matrix multiplier
NASA Astrophysics Data System (ADS)
Pedroni, V. A.
1994-06-01
Simplicity is a key factor in the development of high-density systems. The authors discuss a balanced, four-quadrant, fully-analogue vector-matrix multiplier (VMM) and a vector quantiser (VQ) which require very small silicon area for their implementations, while presenting high linearity, a totally flexible input dynamic range, a symmetric power consumption behaviour, and are inherently suitable for parallel operation. The circuits require only four transistors per synapse in the VMM and two in the VQ, plus two (small) refresh transistors.
Differential cross sections and spin density matrix elements for the reaction gamma p -> p omega
M. Williams, D. Applegate, M. Bellis, C.A. Meyer
2009-12-01
High-statistics differential cross sections and spin density matrix elements for the reaction gamma p -> p omega have been measured using the CLAS at Jefferson Lab for center-of-mass (CM) energies from threshold up to 2.84 GeV. Results are reported in 112 10-MeV wide CM energy bins, each subdivided into cos(theta_CM) bins of width 0.1. These are the most precise and extensive omega photoproduction measurements to date. A number of prominent structures are clearly present in the data. Many of these have not previously been observed due to limited statistics in earlier measurements.
A practical guide to density matrix embedding theory in quantum chemistry
Wouters, Sebastian; Jimenez-Hoyos, Carlos A.; Sun, Qiming; ...
2016-05-09
Density matrix embedding theory (DMET) (Knizia, G.; Chan, G. K.-L. Phys. Rev. Lett. 2012, 109, 186404) provides a theoretical framework to treat finite fragments in the presence of a surrounding molecular or bulk environment, even when there is significant correlation or entanglement between the two. In this work, we give a practically oriented and explicit description of the numerical and theoretical formulation of DMET. Here, we also describe in detail how to perform self-consistent DMET optimizations. We explore different embedding strategies with and without a self-consistency condition in hydrogen rings, beryllium rings, and a sample SN2 reaction.
Parker, Shane M; Shiozaki, Toru
2014-12-07
We extend the active space decomposition method, recently developed by us, to more than two active sites using the density matrix renormalization group algorithm. The fragment wave functions are described by complete or restricted active-space wave functions. Numerical results are shown on a benzene pentamer and a perylene diimide trimer. It is found that the truncation errors in our method decrease almost exponentially with respect to the number of renormalization states M, allowing for numerically exact calculations (to a few μE(h) or less) with M = 128 in both cases. This rapid convergence is because the renormalization steps are used only for the interfragment electron correlation.
A Collective Neurodynamic Optimization Approach to Nonnegative Matrix Factorization.
Fan, Jianchao; Wang, Jun
2017-10-01
Nonnegative matrix factorization (NMF) is an advanced method for nonnegative feature extraction, with widespread applications. However, the NMF solution often entails to solve a global optimization problem with a nonconvex objective function and nonnegativity constraints. This paper presents a collective neurodynamic optimization (CNO) approach to this challenging problem. The proposed collective neurodynamic system consists of a population of recurrent neural networks (RNNs) at the lower level and a particle swarm optimization (PSO) algorithm with wavelet mutation at the upper level. The RNNs act as search agents carrying out precise local searches according to their neurodynamics and initial conditions. The PSO algorithm coordinates and guides the RNNs with updated initial states toward global optimal solution(s). A wavelet mutation operator is added to enhance PSO exploration diversity. Through iterative interaction and improvement of the locally best solutions of RNNs and global best positions of the whole population, the population-based neurodynamic systems are almost sure able to achieve the global optimality for the NMF problem. It is proved that the convergence of the group-best state to the global optimal solution with probability one. The experimental results substantiate the efficacy and superiority of the CNO approach to bound-constrained global optimization with several benchmark nonconvex functions and NMF-based clustering with benchmark data sets in comparison with the state-of-the-art algorithms.
Control-matrix approach to stellarator design and control
Mynick, H.E.; Pomphrey, N.
2000-02-09
The full space Z always equal to {l{underscore}brace}Zj=1,..Nz{r{underscore}brace} of independent variables defining a stellarator configuration is large. To find attractive design points in this space, or to understand operational flexibility about a given design point, one needs insight into the topography in Z-space of the physics figures of merit Pi which characterize the machine performance, and means of determining those directions in Z-space which give one independent control over the Pi, as well as those which affect none of them, and so are available for design flexibility. The control matrix (CM) approach described here provides a mathematical means of obtaining these. In this work, the authors describe the CM approach and use it in studying some candidate Quasi-Axisymmetric (QA) stellarator configurations the NCSX design group has been considering. In the process of the analysis, a first exploration of the topography of the configuration space in the vicinity of these candidate systems has been performed, whose character is discussed.
Capillary condensation in pores with rough walls: a density functional approach.
Bryk, P; Rzysko, W; Malijevsky, Al; Sokołowski, S
2007-09-01
The effect of surface roughness of slit-like pore walls on the capillary condensation of a spherical particles and short chains is studied. The gas molecules interact with the substrate by a Lennard-Jones (9,3) potential. The rough layer at each pore wall has a variable thickness and density and consists of a disordered quenched matrix of spherical particles. The system is described in the framework of a density functional approach and using computer simulations. The contribution due to attractive van der Waals interactions between adsorbate molecules is described by using first-order mean spherical approximation and mean-field approximation.
NASA Astrophysics Data System (ADS)
Silvi, Pietro; Calarco, Tommaso; Morigi, Giovanna; Montangero, Simone
2014-03-01
Ions of the same charge inside confining potentials can form crystalline structures which can be controlled by means of the ion density and of the external trap parameters. In particular, a linear chain of trapped ions exhibits a transition to a zigzag equilibrium configuration, which is controlled by the strength of the transverse confinement. Studying this phase transition in the quantum regime is a challenging problem, even when employing numerical methods to simulate microscopically quantum many-body systems. Here we present a compact analytical treatment to map the original long-range problem into a short-range quantum field theory on a lattice. We provide a complete numerical architecture, based on the density matrix renormalization group, to address the effective quantum ϕ4 model. This technique is instrumental in giving a complete characterization of the phase diagram, as well as pinpointing the universality class of the criticality.
A new approach for estimating the density of liquids.
Sakagami, T; Fuchizaki, K; Ohara, K
2016-10-05
We propose a novel approach with which to estimate the density of liquids. The approach is based on the assumption that the systems would be structurally similar when viewed at around the length scale (inverse wavenumber) of the first peak of the structure factor, unless their thermodynamic states differ significantly. The assumption was implemented via a similarity transformation to the radial distribution function to extract the density from the structure factor of a reference state with a known density. The method was first tested using two model liquids, and could predict the densities within an error of several percent unless the state in question differed significantly from the reference state. The method was then applied to related real liquids, and satisfactory results were obtained for predicted densities. The possibility of applying the method to amorphous materials is discussed.
Leptogenesis with heavy neutrino flavours: from density matrix to Boltzmann equations
Blanchet, Steve; Bari, Pasquale Di; Jones, David A.; Marzola, Luca E-mail: pdb1d08@soton.ac.uk E-mail: daj1g08@soton.ac.uk
2013-01-01
Leptogenesis with heavy neutrino flavours is discussed within a density matrix formalism. We write the density matrix equation, describing the generation of the matter-antimatter asymmetry, for an arbitrary choice of the right-handed (RH) neutrino masses. For hierarchical RH neutrino masses lying in the fully flavoured regimes, this reduces to multiple-stage Boltzmann equations. In this case we recover and extend results previously derived within a quantum state collapse description. We confirm the generic existence of phantom terms. However, taking into account the effect of gauge interactions, we show that they are washed out at the production with a wash-out rate that is halved compared to that one acting on the total asymmetry. In the N{sub 1}-dominated scenario they cancel without contributing to the final baryon asymmetry. In other scenarios they do not in general and they have to be taken into account. We also confirm that there is a (orthogonal) component in the asymmetry produced by the heavier RH neutrinos which completely escapes the washout from the lighter RH neutrinos and show that phantom terms additionally contribute to it. The other (parallel) component is washed out with the usual exponential factor, even for weak washout. Finally, as an illustration, we study the two RH neutrino model in the light of the above findings, showing that phantom terms can contribute to the final asymmetry also in this case.
Effects of Extracellular Matrix Density and Mesenchymal Stem Cells on Neovascularization In Vivo
Kniazeva, Ekaterina; Kachgal, Suraj
2011-01-01
Aberrant angiogenesis is common to a variety of diseases in which alterations in tissue mechanical properties also occur. A fundamental understanding of the interdependence of angiogenesis and tissue structural properties may enhance the development of therapeutic strategies. We previously established that increasing extracellular matrix density inhibits capillary morphogenesis in three-dimensional tissues in vitro, and that addition of human mesenchymal stem cells (MSCs) partially rescues a healthy angiogenic phenotype. This study's goal was to investigate if these effects can be recapitulated in vivo. Human umbilical vein endothelial cells, MSCs, or a mixture of both was suspended in fibrin gel precursor solutions of 5, 10, and 15 mg/mL concentrations and injected subcutaneously into SCID mice. Neovascularization was assessed in tissue constructs retrieved at 3, 7, and 21 days by quantifying vessel numbers, perfusion, thickness, maturity, and perivascular collagen deposition. The data show that changing extracellular matrix density inhibits capillary morphogenesis in vivo in a manner consistent with that observed in vitro. Delivery of both human umbilical vein endothelial cells and MSCs produced more robust and mature vessels than delivery of either cell type alone in all tissue concentrations. PMID:20979533
Low excitations of 16O using generalized density matrix random phase approximation GDRPA
NASA Astrophysics Data System (ADS)
Taqi, Ali H.; Radhi, R. A.; Hussein, Adil M.
2014-07-01
The random phase approximation (RPA) equations based on the generalized density matrix (GDM), the so-called GDRPA are reformulated in a more compact matrix form, which renders the method especially suitable for realistic nuclear structure calculations. The GDRPA Hamiltonian is expressed in terms of the one-body particle-particle (pp) and hole-hole (hh) density matrices, and the nuclear force contributes not only in the particle-hole (ph) channel, as in normal ph-RPA, but also in the pp and hh channels. The Hamiltonian is diagonalized iteratively starting from initial guess values and the iterating process is carried out until self-consistency is achieved. The calculation in the model space 1p, 1d and 2s using Warburton and Brown interaction WBP is performed for 16O. The GDRPA in the ph shell model calculations is tested, by comparing the energy eigenvalues and the electron scattering form factors with the results of the normal RPA and with the available experimental data.
Leptogenesis with heavy neutrino flavours: from density matrix to Boltzmann equations
NASA Astrophysics Data System (ADS)
Blanchet, Steve; Di Bari, Pasquale; Jones, David A.; Marzola, Luca
2013-01-01
Leptogenesis with heavy neutrino flavours is discussed within a density matrix formalism. We write the density matrix equation, describing the generation of the matter-antimatter asymmetry, for an arbitrary choice of the right-handed (RH) neutrino masses. For hierarchical RH neutrino masses lying in the fully flavoured regimes, this reduces to multiple-stage Boltzmann equations. In this case we recover and extend results previously derived within a quantum state collapse description. We confirm the generic existence of phantom terms. However, taking into account the effect of gauge interactions, we show that they are washed out at the production with a wash-out rate that is halved compared to that one acting on the total asymmetry. In the N1-dominated scenario they cancel without contributing to the final baryon asymmetry. In other scenarios they do not in general and they have to be taken into account. We also confirm that there is a (orthogonal) component in the asymmetry produced by the heavier RH neutrinos which completely escapes the washout from the lighter RH neutrinos and show that phantom terms additionally contribute to it. The other (parallel) component is washed out with the usual exponential factor, even for weak washout. Finally, as an illustration, we study the two RH neutrino model in the light of the above findings, showing that phantom terms can contribute to the final asymmetry also in this case.
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.
Relativistic density-dependent Hartree-Fock approach for finite nuclei
Shi, H.; Chen, B.; Ma, Z. |
1995-07-01
The nucleon self-energy obtained from the Dirac Brueckner-Hartree-Fock calculation is parametrized by introducing density-dependent coupling constants of isoscalar mesons in the relativistic Hartree-Fock (RHF) approach. The RHF calculations with density-dependent coupling constants not only reproduce the nuclear matter saturation properties, but also provide a good starting point to study finite nuclei properties. The relativistic density-dependent Hartree-Fock (RDHF) approach contains the features of the relativistic {ital G} matrix and in the meantime simplifies the calculation. The ground state properties of spherical nuclei calculated in the RDHF are in good agreement with the experimental data. The contribution of isovector mesons {pi} and {rho}, especially the contribution of the tensor coupling of {rho} meson, are discussed in this paper.
SivaRanjan, Uppala; Ramachandran, Ramesh
2014-02-07
A quantum-mechanical model integrating the concepts of reduced density matrix and effective Hamiltonians is proposed to explain the multi-spin effects observed in rotational resonance (R{sup 2}) nuclear magnetic resonance (NMR) experiments. Employing this approach, the spin system of interest is described in a reduced subspace inclusive of its coupling to the surroundings. Through suitable model systems, the utility of our theory is demonstrated and verified with simulations emerging from both analytic and numerical methods. The analytic results presented in this article provide an accurate description/interpretation of R{sup 2} experimental results and could serve as a test-bed for distinguishing coherent/incoherent effects in solid-state NMR.
A discrete approach for modeling cell-matrix adhesions
NASA Astrophysics Data System (ADS)
Escribano, J.; Sánchez, M. T.; García-Aznar, J. M.
2014-06-01
During recent years the interaction between the extracellular matrix and the cytoskeleton of the cell has been object of numerous studies due to its importance in cell migration processes. These interactions are performed through protein clutches, known as focal adhesions. For migratory cells these focal adhesions along with force generating processes in the cytoskeleton are responsible for the formation of protrusion structures like lamellipodia or filopodia. Much is known about these structures: the different proteins that conform them, the players involved in their formation or their role in cell migration. Concretely, growth-cone filopodia structures have attracted significant attention because of their role as cell sensors of their surrounding environment and its complex behavior. On this matter, a vast myriad of mathematical models has been presented to explain its mechanical behavior. In this work, we aim to study the mechanical behavior of these structures through a discrete approach. This numerical model provides an individual analysis of the proteins involved including spatial distribution, interaction between them, and study of different phenomena, such as clutches unbinding or protein unfolding.
A cantilever-free approach to dot-matrix nanoprinting
Brown, Keith A.; Eichelsdoerfer, Daniel J.; Shim, Wooyoung; Rasin, Boris; Radha, Boya; Liao, Xing; Schmucker, Abrin L.; Liu, Guoliang; Mirkin, Chad A.
2013-01-01
Scanning probe lithography (SPL) is a promising candidate approach for desktop nanofabrication, but trade-offs in throughput, cost, and resolution have limited its application. The recent development of cantilever-free scanning probe arrays has allowed researchers to define nanoscale patterns in a low-cost and high-resolution format, but with the limitation that these are duplication tools where each probe in the array creates a copy of a single pattern. Here, we report a cantilever-free SPL architecture that can generate 100 nanometer-scale molecular features using a 2D array of independently actuated probes. To physically actuate a probe, local heating is used to thermally expand the elastomeric film beneath a single probe, bringing it into contact with the patterning surface. Not only is this architecture simple and scalable, but it addresses fundamental limitations of 2D SPL by allowing one to compensate for unavoidable imperfections in the system. This cantilever-free dot-matrix nanoprinting will enable the construction of surfaces with chemical functionality that is tuned across the nano- and macroscales. PMID:23861495
Chebyshev matrix product state approach for time evolution
NASA Astrophysics Data System (ADS)
Halimeh, Jad C.; Kolley, Fabian; McCulloch, Ian P.
2015-09-01
We present and test a new algorithm for time-evolving quantum many-body systems initially proposed by Holzner et al. [Phys. Rev. B 83, 195115 (2011), 10.1103/PhysRevB.83.195115]. The approach is based on merging the matrix product state (MPS) formalism with the method of expanding the time-evolution operator in Chebyshev polynomials. We calculate time-dependent observables of a system of hardcore bosons quenched under the Bose-Hubbard Hamiltonian on a one-dimensional lattice. We compare the new algorithm to more standard methods using the MPS architecture. We find that the Chebyshev method gives numerically exact results for small times. However, the reachable times are smaller than the ones obtained with the other state-of-the-art methods. We further extend the new method using a spectral-decomposition-based projective scheme that utilizes an effective bandwidth significantly smaller than the full bandwidth, leading to longer evolution times than the nonprojective method and more efficient information storage, data compression, and less computational effort.
Perturbative approach to covariance matrix of the matter power spectrum
Mohammed, Irshad; Seljak, Uros; Vlah, Zvonimir
2016-12-14
Here, we evaluate the covariance matrix of the matter power spectrum using perturbation theory up to dominant terms at 1-loop order and compare it to numerical simulations. We decompose the covariance matrix into the disconnected (Gaussian) part, trispectrum from the modes outside the survey (beat coupling or super-sample variance), and trispectrum from the modes inside the survey, and show how the different components contribute to the overall covariance matrix. We find the agreement with the simulations is at a 10\\% level up to $k \\sim 1 h {\\rm Mpc^{-1}}$. We also show that all the connected components are dominated by the large-scale modes ($k<0.1 h {\\rm Mpc^{-1}}$), regardless of the value of the wavevectors $k,\\, k'$ of the covariance matrix, suggesting that one must be careful in applying the jackknife or bootstrap methods to the covariance matrix. We perform an eigenmode decomposition of the connected part of the covariance matrix, showing that at higher $k$ it is dominated by a single eigenmode. Furthermore, the full covariance matrix can be approximated as the disconnected part only, with the connected part being treated as an external nuisance parameter with a known scale dependence, and a known prior on its variance for a given survey volume. Finally, we provide a prescription for how to evaluate the covariance matrix from small box simulations without the need to simulate large volumes.
Perturbative approach to covariance matrix of the matter power spectrum
Mohammed, Irshad; Seljak, Uros; Vlah, Zvonimir
2016-12-14
Here, we evaluate the covariance matrix of the matter power spectrum using perturbation theory up to dominant terms at 1-loop order and compare it to numerical simulations. We decompose the covariance matrix into the disconnected (Gaussian) part, trispectrum from the modes outside the survey (beat coupling or super-sample variance), and trispectrum from the modes inside the survey, and show how the different components contribute to the overall covariance matrix. We find the agreement with the simulations is at a 10\\% level up tomore » $$k \\sim 1 h {\\rm Mpc^{-1}}$$. We also show that all the connected components are dominated by the large-scale modes ($$k<0.1 h {\\rm Mpc^{-1}}$$), regardless of the value of the wavevectors $$k,\\, k'$$ of the covariance matrix, suggesting that one must be careful in applying the jackknife or bootstrap methods to the covariance matrix. We perform an eigenmode decomposition of the connected part of the covariance matrix, showing that at higher $k$ it is dominated by a single eigenmode. Furthermore, the full covariance matrix can be approximated as the disconnected part only, with the connected part being treated as an external nuisance parameter with a known scale dependence, and a known prior on its variance for a given survey volume. Finally, we provide a prescription for how to evaluate the covariance matrix from small box simulations without the need to simulate large volumes.« less
Perturbative approach to covariance matrix of the matter power spectrum
Mohammed, Irshad; Seljak, Uros; Vlah, Zvonimir
2016-06-30
We evaluate the covariance matrix of the matter power spectrum using perturbation theory up to dominant terms at 1-loop order and compare it to numerical simulations. We decompose the covariance matrix into the disconnected (Gaussian) part, trispectrum from the modes outside the survey (beat coupling or super-sample variance), and trispectrum from the modes inside the survey, and show how the different components contribute to the overall covariance matrix. We find the agreement with the simulations is at a 10\\% level up to $k \\sim 1 h {\\rm Mpc^{-1}}$. We show that all the connected components are dominated by the large-scale modes ($k<0.1 h {\\rm Mpc^{-1}}$), regardless of the value of the wavevectors $k,\\, k'$ of the covariance matrix, suggesting that one must be careful in applying the jackknife or bootstrap methods to the covariance matrix. We perform an eigenmode decomposition of the connected part of the covariance matrix, showing that at higher $k$ it is dominated by a single eigenmode. The full covariance matrix can be approximated as the disconnected part only, with the connected part being treated as an external nuisance parameter with a known scale dependence, and a known prior on its variance for a given survey volume. Finally, we provide a prescription for how to evaluate the covariance matrix from small box simulations without the need to simulate large volumes.
Perturbative approach to covariance matrix of the matter power spectrum
NASA Astrophysics Data System (ADS)
Mohammed, Irshad; Seljak, Uroš; Vlah, Zvonimir
2017-04-01
We evaluate the covariance matrix of the matter power spectrum using perturbation theory up to dominant terms at 1-loop order and compare it to numerical simulations. We decompose the covariance matrix into the disconnected (Gaussian) part, trispectrum from the modes outside the survey (supersample variance) and trispectrum from the modes inside the survey, and show how the different components contribute to the overall covariance matrix. We find the agreement with the simulations is at a 10 per cent level up to k ˜ 1 h Mpc-1. We show that all the connected components are dominated by the large-scale modes (k < 0.1 h Mpc-1), regardless of the value of the wave vectors k, k΄ of the covariance matrix, suggesting that one must be careful in applying the jackknife or bootstrap methods to the covariance matrix. We perform an eigenmode decomposition of the connected part of the covariance matrix, showing that at higher k, it is dominated by a single eigenmode. The full covariance matrix can be approximated as the disconnected part only, with the connected part being treated as an external nuisance parameter with a known scale dependence, and a known prior on its variance for a given survey volume. Finally, we provide a prescription for how to evaluate the covariance matrix from small box simulations without the need to simulate large volumes.
NASA Astrophysics Data System (ADS)
Jacobs, Verne; Kutana, Alex
The frequency-dependent transition rates for single-photon and multi-photon processes in quantized many-electron systems are evaluated using a reduced-density-matrix approach. We provide a fundamental quantum-mechanical foundation for systematic spectral simulations. A perturbation expansion of the frequency-domain Liouville-space self-energy operator is introduced for detailed evaluations of the spectral-line shapes. In the diagonal-resolvent (isolated-line) and short-memory-time (Markov) approximations, the lowest-order contributions to the spectral-line widths and shifts associated with environmental electron-photon and electron-phonon interactions are systematically evaluated. Our description is directly applicable to electromagnetic processes in a wide variety of many-electron systems, without premature approximations. In particular, our approach can be applied to investigate quantum optical phenomena involving electrons in both bulk and nanoscale semiconductor materials entirely from first principles, using a single-electron basis set obtained from density functional theory as a starting point for a many-electron description. Work supported by the Office of Naval Research through the Basic Research Program at The Naval Research Laboratory. A portion of this work was performed under the ASEE post doc program at NRL.
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.
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
Johnson, Christopher D; Worrall, Fred
2007-06-01
This paper reports the preparation and properties of a new low density granular absorbent material based on a zeolite/vermiculite composite. The composite prepared addresses a number of important issues relating to the use of zeolites in environmental and waste management applications. The material prepared has large particle size due to binderless adhesion of zeolite crystals within the protective lamellar matrix provided by the vermiculite granule. Additionally, the porous nature of new material ensures that it outperforms natural zeolite grains in ion-exchange tests. The material was shown to have a low bulk density (0.75 g cm(-3)) adding the benefit that the majority of grains float on water for over 15 h. The conclusion of the study is that the use of composite matrices enable the preparation of materials which show the physical properties of the host, (e.g., granular and low density), whilst maintaining the powder-like properties (e.g., high ion-exchange and small crystal size) of the active component. The resulting material can be easily handled and separated from aqueous waste streams using either flotation or exploiting its granular nature.
NASA Astrophysics Data System (ADS)
Putaja, A.; Eich, F. G.; Baldsiefen, T.; Räsänen, E.
2016-03-01
Physically valid and numerically efficient approximations for the exchange and correlation energy are critical for reduced-density-matrix-functional theory to become a widely used method in electronic structure calculations. Here we examine the physical limits of power functionals of the form f (n ,n') =(nn')α for the scaling function in the exchange-correlation energy. To this end we obtain numerically the minimizing momentum distributions for the three- and two-dimensional homogeneous electron gas, respectively. In particular, we examine the limiting values for the power α to yield physically sound solutions that satisfy the Lieb-Oxford lower bound for the exchange-correlation energy and exclude pinned states with the condition n (k )<1 for all wave vectors k . The results refine the constraints previously obtained from trial momentum distributions. We also compute the values for α that yield the exact correlation energy and its kinetic part for both the three- and two-dimensional electron gas. In both systems, narrow regimes of validity and accuracy are found at α ≳0.6 and at rs≳10 for the density parameter, corresponding to relatively low densities.
Simple Approach to Renormalize the Cabibbo-Kobayashi-Maskawa Matrix
Kniehl, Bernd A.; Sirlin, Alberto
2006-12-01
We present an on-shell scheme to renormalize the Cabibbo-Kobayashi-Maskawa (CKM) matrix. It is based on a novel procedure to separate the external-leg mixing corrections into gauge-independent self-mass and gauge-dependent wave function renormalization contributions, and to implement the on-shell renormalization of the former with nondiagonal mass counterterm matrices. Diagonalization of the complete mass matrix leads to an explicit CKM counterterm matrix, which automatically satisfies all the following important properties: it is gauge independent, preserves unitarity, and leads to renormalized amplitudes that are nonsingular in the limit in which any two fermions become mass degenerate.
Quasi-particle energy spectra in local reduced density matrix functional theory
Lathiotakis, Nektarios N.; Helbig, Nicole; Rubio, Angel
2014-10-28
Recently, we introduced [N. N. Lathiotakis, N. Helbig, A. Rubio, and N. I. Gidopoulos, Phys. Rev. A 90, 032511 (2014)] local reduced density matrix functional theory (local RDMFT), a theoretical scheme capable of incorporating static correlation effects in Kohn-Sham equations. Here, we apply local RDMFT to molecular systems of relatively large size, as a demonstration of its computational efficiency and its accuracy in predicting single-electron properties from the eigenvalue spectrum of the single-particle Hamiltonian with a local effective potential. We present encouraging results on the photoelectron spectrum of molecular systems and the relative stability of C{sub 20} isotopes. In addition, we propose a modelling of the fractional occupancies as functions of the orbital energies that further improves the efficiency of the method useful in applications to large systems and solids.
A Practical Guide to Density Matrix Embedding Theory in Quantum Chemistry.
Wouters, Sebastian; Jiménez-Hoyos, Carlos A; Sun, Qiming; Chan, Garnet K-L
2016-06-14
Density matrix embedding theory (DMET) (Knizia, G.; Chan, G. K.-L. Phys. Rev. Lett. 2012, 109, 186404) provides a theoretical framework to treat finite fragments in the presence of a surrounding molecular or bulk environment, even when there is significant correlation or entanglement between the two. In this work, we give a practically oriented and explicit description of the numerical and theoretical formulation of DMET. We also describe in detail how to perform self-consistent DMET optimizations. We explore different embedding strategies with and without a self-consistency condition in hydrogen rings, beryllium rings, and a sample SN2 reaction. The source code for the calculations in this work can be obtained from https://github.com/sebwouters/qc-dmet .
Baryogenesis from L -violating Higgs-doublet decay in the density-matrix formalism
NASA Astrophysics Data System (ADS)
Hambye, Thomas; Teresi, Daniele
2017-07-01
We compute in the density-matrix formalism the baryon asymmetry generated by the decay of the Higgs doublet into a right-handed (RH) neutrino and a Standard Model lepton. The emphasis is put on the baryon asymmetry produced by the total lepton-number violating decay. From the derivation of the corresponding evolution equations, and from their integration, we find that this contribution is fully relevant for large parts of the parameter space. This confirms the results found recently in the C P -violating decay formalism with thermal corrections and shows in particular that the lepton-number violating processes are important not only for high-scale leptogenesis but also when the RH-neutrino masses are in the GeV range. For large values of the Yukawa couplings, we also find that the strong washout is generically much milder for this total lepton-number violating part than for the usual RH-neutrino oscillation flavor part.
N-leg spin-S Heisenberg ladders: A density-matrix renormalization group study
NASA Astrophysics Data System (ADS)
Ramos, F. B.; Xavier, J. C.
2014-03-01
We investigate the N-leg spin-S Heisenberg ladders by using the density matrix renormalization group method. We present estimates of the spin gap Δs and of the ground-state energy per site e∞N in the thermodynamic limit for ladders with widths up to six legs and spin S≤5/2. We also estimate the ground-state energy per site e∞2D for the infinite two-dimensional spin-S Heisenberg model. Our results support that for ladders with semi-integer spins the spin excitation is gapless for N odd and gapped for N even, whereas for integer spin ladders the spin gap is nonzero, independent of the number of legs. Those results agree with the well-known conjectures of Haldane and Sénéchal-Sierra for chains and ladders, respectively. We also observe edge states for ladders with N odd, similar to what happens in spin chains.
Density matrix renormalization group study of triangular Kitaev-Heisenberg model
NASA Astrophysics Data System (ADS)
Sota, Shigetoshi; Sjinjo, Kazuya; Shirakawa, Tomonori; Tohyama, Takami; Yunoki, Seiji
2015-03-01
Topological insulator has been one of the most active subjects in the current condensed matter physics. For most of topological insulators electron correlations are considered to be not essential. However, in the case where electron correlations are strong, novel phases such as a spin liquid phase can emerge in competition with a spin-orbit coupling. Here, using the density matrix renormalization group method, we investigate magnetic phase of a triangular Kitaev-Heisenberg (quantum compass) model that contains a spin-orbital interaction and spin frustration in the antiferromagnetic region. The triangular Kitaev-Heisenberg model is regarded as a dual model of the honeycomb Kitaev-Heisenberg model that is usually employed to discuss A2CuO3 (A=Na, K). Systematically calculating ground state energy, entanglement entropy, entanglement spectrum, and spin-spin correlation functions, we discuss the duality between the triangular and the honeycomb Kitaev-Heisenberg model as well as the ground state magnetic phases.
A note on the high temperature expansion of the density matrix for the isotropic Heisenberg chain
NASA Astrophysics Data System (ADS)
Tsuboi, Zengo
2007-04-01
Göhmann, Klümper and Seel derived the multiple integral formula of the density matrix of the XXZ Heisenberg chain at finite temperatures. We have applied the high temperature expansion (HTE) method to isotropic case of their formula in a finite magnetic field and obtained coefficients for several short-range correlation functions. For example, we have succeeded to obtain the coefficients of the HTE of the third neighbor correlation function <σjzσj+3z> for zero magnetic field up to the order of 25. These results expand our previous results on the emptiness formation probability [Z. Tsuboi, M. Shiroishi, J. Phys. A: Math. Gen. 38 (2005) L363-L370, condmat/0502569.] to more general correlation functions.
NASA Astrophysics Data System (ADS)
Ghosh, Debashree; Hachmann, Johannes; Yanai, Takeshi; Chan, Garnet Kin-Lic
2008-04-01
In previous work we have shown that the density matrix renormalization group (DMRG) enables near-exact calculations in active spaces much larger than are possible with traditional complete active space algorithms. Here, we implement orbital optimization with the DMRG to further allow the self-consistent improvement of the active orbitals, as is done in the complete active space self-consistent field (CASSCF) method. We use our resulting DMRG-CASSCF method to study the low-lying excited states of the all-trans polyenes up to C24H26 as well as β-carotene, correlating with near-exact accuracy the optimized complete π-valence space with up to 24 active electrons and orbitals, and analyze our results in the light of the recent discovery from resonance Raman experiments of new optically dark states in the spectrum.
NASA Astrophysics Data System (ADS)
Hachmann, Johannes; Cardoen, Wim; Chan, Garnet Kin-Lic
2006-10-01
We have devised a local ab initio density matrix renormalization group algorithm to describe multireference correlations in large systems. For long molecules that are extended in one of their spatial dimensions, we can obtain an exact characterization of correlation, in the given basis, with a cost that scales only quadratically with the size of the system. The reduced scaling is achieved solely through integral screening and without the construction of correlation domains. We demonstrate the scaling, convergence, and robustness of the algorithm in polyenes and hydrogen chains. We converge to exact correlation energies (in the sense of full configuration interaction, with 1-10μEh precision) in all cases and correlate up to 100 electrons in 100 active orbitals. We further use our algorithm to obtain exact energies for the metal-insulator transition in hydrogen chains and compare and contrast our results with those from conventional quantum chemical methods.
Hu, Weifeng; Chan, Garnet Kin-Lic
2015-07-14
We describe and extend the formalism of state-specific analytic density matrix renormalization group (DMRG) energy gradients, first used by Liu et al. [J. Chem. Theor. Comput. 2013, 9, 4462]. We introduce a DMRG wave function maximum overlap following technique to facilitate state-specific DMRG excited-state optimization. Using DMRG configuration interaction (DMRG-CI) gradients, we relax the low-lying singlet states of a series of trans-polyenes up to C20H22. Using the relaxed excited-state geometries, as well as correlation functions, we elucidate the exciton, soliton, and bimagnon ("single-fission") character of the excited states, and find evidence for a planar conical intersection.
NASA Astrophysics Data System (ADS)
Mukhopadhyay, S.; Ramasesha, S.
2009-08-01
We have used the density matrix renormalization group (DMRG) method to study the linear and nonlinear optical responses of first generation nitrogen based dendrimers with donor acceptor groups. We have employed Pariser-Parr-Pople Hamiltonian to model the interacting π electrons in these systems. Within the DMRG method we have used an innovative scheme to target excited states with large transition dipole to the ground state. This method reproduces exact optical gaps and polarization in systems where exact diagonalization of the Hamiltonian is possible. We have used a correction vector method which tacitly takes into account the contribution of all excited states, to obtain the ground state polarizibility, first hyperpolarizibility, and two photon absorption cross sections. We find that the lowest optical excitations as well as the lowest excited triplet states are localized. It is interesting to note that the first hyperpolarizibility saturates more rapidly with system size compared to linear polarizibility unlike that of linear polyenes.
Energy density functional study of nuclear matrix elements for neutrinoless ββ decay.
Rodríguez, Tomás R; Martínez-Pinedo, Gabriel
2010-12-17
We present an extensive study of nuclear matrix elements (NME) for the neutrinoless double-beta decay of the nuclei 48Ca, 76Ge, 82Se, 96Zr, 100Mo, 116Cd, 124Sn, 128Te, 130Te, 136Xe, and 150Nd based on state-of-the-art energy density functional methods using the Gogny D1S functional. Beyond-mean-field effects are included within the generating coordinate method with particle number and angular momentum projection for both initial and final ground states. We obtain a rather constant value for the NMEs around 4.7 with the exception of 48Ca and 150Nd, where smaller values are found. We analyze the role of deformation and pairing in the evaluation of the NME and present detailed results for the decay of 150Nd.
Density matrix model for polarons in a terahertz quantum dot cascade laser
NASA Astrophysics Data System (ADS)
Burnett, Benjamin A.; Williams, Benjamin S.
2014-10-01
A density matrix based method is introduced for computation of steady-state dynamics in quantum cascade systems of arbitrary size, which incorporates an optical field coherently. The method is applied to a model terahertz quantum dot cascade laser system, where a means of treating coherent electron-optical-phonon coupling is also introduced. Results predict a strong increase in the upper state lifetime and operating temperature as compared to traditional well-based terahertz quantum cascade lasers. However, new complications also arise, including multiple peaks in the gain spectrum due to strong electron-phonon coupling, and strong parasitic subthreshold current channels that arise due to reduced dephasing. It is anticipated that novel design schemes will be necessary for such lasers to become a reality.
Mukhopadhyay, S; Ramasesha, S
2009-08-21
We have used the density matrix renormalization group (DMRG) method to study the linear and nonlinear optical responses of first generation nitrogen based dendrimers with donor acceptor groups. We have employed Pariser-Parr-Pople Hamiltonian to model the interacting pi electrons in these systems. Within the DMRG method we have used an innovative scheme to target excited states with large transition dipole to the ground state. This method reproduces exact optical gaps and polarization in systems where exact diagonalization of the Hamiltonian is possible. We have used a correction vector method which tacitly takes into account the contribution of all excited states, to obtain the ground state polarizibility, first hyperpolarizibility, and two photon absorption cross sections. We find that the lowest optical excitations as well as the lowest excited triplet states are localized. It is interesting to note that the first hyperpolarizibility saturates more rapidly with system size compared to linear polarizibility unlike that of linear polyenes.
Low-density, high-strength intermetallic matrix composites by XD (trademark) synthesis
NASA Technical Reports Server (NTRS)
Kumar, K. S.; Dipietro, M. S.; Brown, S. A.; Whittenberger, J. D.
1991-01-01
A feasibility study was conducted to evaluate the potential of particulate composites based on low-density, L1(sub 2) trialuminide matrices for high-temperature applications. The compounds evaluated included Al22Fe3Ti8 (as a multiphase matrix), Al67Ti25Cr8, and Al66Ti25Mn9. The reinforcement consisted of TiB2 particulates. The TiB2 composites were processed by ingot and powder metallurgy techniques. Microstructural characterization and mechanical testing were performed in the hot-pressed and hot-isostatic-pressed condition. The casting were sectioned and isothermally forged into pancakes. All the materials were tested in compression as a function of temperature, and at high temperatures as a function of strain rate. The test results are discussed.
Alcohol outlet density and violence: A geographically weighted regression approach.
Cameron, Michael P; Cochrane, William; Gordon, Craig; Livingston, Michael
2016-05-01
We investigate the relationship between outlet density (of different types) and violence (as measured by police activity) across the North Island of New Zealand, specifically looking at whether the relationships vary spatially. We use New Zealand data at the census area unit (approximately suburb) level, on police-attended violent incidents and outlet density (by type of outlet), controlling for population density and local social deprivation. We employed geographically weighted regression to obtain both global average and locally specific estimates of the relationships between alcohol outlet density and violence. We find that bar and night club density, and licensed club density (e.g. sports clubs) have statistically significant and positive relationships with violence, with an additional bar or night club is associated with nearly 5.3 additional violent events per year, and an additional licensed club associated with 0.8 additional violent events per year. These relationships do not show significant spatial variation. In contrast, the effects of off-licence density and restaurant/café density do exhibit significant spatial variation. However, the non-varying effects of bar and night club density are larger than the locally specific effects of other outlet types. The relationships between outlet density and violence vary significantly across space for off-licences and restaurants/cafés. These results suggest that in order to minimise alcohol-related harms, such as violence, locally specific policy interventions are likely to be necessary. [Cameron MP, Cochrane W, Gordon C, Livingston M. Alcohol outlet density and violence: A geographically weighted regression approach. Drug Alcohol Rev 2016;35:280-288]. © 2015 Australasian Professional Society on Alcohol and other Drugs.
Andrews, Lester
2004-02-20
Metal hydrides are of considerable importance in chemical synthesis as intermediates in catalytic hydrogenation reactions. Transition metal atoms react with dihydrogen to produce metal dihydrides or dihydrogen complexes and these may be trapped in solid matrix samples for infrared spectroscopic study. The MH(2) or M(H(2)) molecules so formed react further to form higher MH(4), (H(2))MH(2), or M(H(2))(2), and MH(6), (H(2))(2)MH(2), or M(H(2))(3) hydrides or complexes depending on the metal. In this critical review these transition metal and dihydrogen reaction products are surveyed for Groups 3 though 12 and the contrasting behaviour in Groups 6 and 10 is discussed. Minimum energy structures and vibrational frequencies predicted by Density Functional Theory agree with the experimental results, strongly supporting the identification of novel binary transition metal hydride species, which the matrix-isolation method is well-suited to investigate. 104 references are cited.
NASA Astrophysics Data System (ADS)
Nakatani, Naoki; Wouters, Sebastian; Van Neck, Dimitri; Chan, Garnet Kin-Lic
2014-01-01
Linear response theory for the density matrix renormalization group (DMRG-LRT) was first presented in terms of the DMRG renormalization projectors [J. J. Dorando, J. Hachmann, and G. K.-L. Chan, J. Chem. Phys. 130, 184111 (2009)]. Later, with an understanding of the manifold structure of the matrix product state (MPS) ansatz, which lies at the basis of the DMRG algorithm, a way was found to construct the linear response space for general choices of the MPS gauge in terms of the tangent space vectors [J. Haegeman, J. I. Cirac, T. J. Osborne, I. Pižorn, H. Verschelde, and F. Verstraete, Phys. Rev. Lett. 107, 070601 (2011)]. These two developments led to the formulation of the Tamm-Dancoff and random phase approximations (TDA and RPA) for MPS. This work describes how these LRTs may be efficiently implemented through minor modifications of the DMRG sweep algorithm, at a computational cost which scales the same as the ground-state DMRG algorithm. In fact, the mixed canonical MPS form implicit to the DMRG sweep is essential for efficient implementation of the RPA, due to the structure of the second-order tangent space. We present ab initio DMRG-TDA results for excited states of polyenes, the water molecule, and a [2Fe-2S] iron-sulfur cluster.
TIEG1-NULL OSTEOCYTES DISPLAY DEFECTS IN THEIR MORPHOLOGY, DENSITY AND SURROUNDING BONE MATRIX
Haddad, Oualid; Hawse, John R.; Subramaniam, Malayannan; Spelsberg, Thomas C.; Bensamoun, Sabine F.
2011-01-01
Through the development of TGFβ-inducible early gene-1 (TIEG1) knockout (KO) mice, we have demonstrated that TIEG1 plays an important role in osteoblast-mediated bone mineralization, and in bone resistance to mechanical strain. To further investigate the influence of TIEG1 in skeletal maintenance, osteocytes were analyzed by transmission electron microscopy using TIEG1 KO and wild-type mouse femurs at one, three and eight months of age. The results revealed an age-dependent change in osteocyte surface and density, suggesting a role for TIEG1 in osteocyte development. Moreover, there was a decrease in the amount of hypomineralized bone matrix surrounding the osteocytes in TIEG1 KO mice relative to wild-type controls. While little is known about the function or importance of this hypomineralized bone matrix immediately adjacent to osteocytes, this study reveals significant differences in this bone microenvironment and suggests that osteocyte function may be compromised in the absence of TIEG1 expression. PMID:22121306
Nakatani, Naoki; Wouters, Sebastian; Van Neck, Dimitri; Chan, Garnet Kin-Lic
2014-01-14
Linear response theory for the density matrix renormalization group (DMRG-LRT) was first presented in terms of the DMRG renormalization projectors [J. J. Dorando, J. Hachmann, and G. K.-L. Chan, J. Chem. Phys. 130, 184111 (2009)]. Later, with an understanding of the manifold structure of the matrix product state (MPS) ansatz, which lies at the basis of the DMRG algorithm, a way was found to construct the linear response space for general choices of the MPS gauge in terms of the tangent space vectors [J. Haegeman, J. I. Cirac, T. J. Osborne, I. Pižorn, H. Verschelde, and F. Verstraete, Phys. Rev. Lett. 107, 070601 (2011)]. These two developments led to the formulation of the Tamm-Dancoff and random phase approximations (TDA and RPA) for MPS. This work describes how these LRTs may be efficiently implemented through minor modifications of the DMRG sweep algorithm, at a computational cost which scales the same as the ground-state DMRG algorithm. In fact, the mixed canonical MPS form implicit to the DMRG sweep is essential for efficient implementation of the RPA, due to the structure of the second-order tangent space. We present ab initio DMRG-TDA results for excited states of polyenes, the water molecule, and a [2Fe-2S] iron-sulfur cluster.
The variational two-electron reduced-density-matrix method for extended systems
NASA Astrophysics Data System (ADS)
Rubin, Nicholas C.
In this thesis we develop the variational two-electron reduced-density-matrix method for extended systems. Extended systems are represented in two ways: i) lattice models describing the dominant valence electronic structure with periodic boundaries to account for their extended nature and ii) a crystalline-orbital basis built from atomic orbitals using the generalization of molecular orbital theory to polymers. The first part of this thesis (Ch. 3--4) examines the performance of the variational 2-RDM method on lattice systems with tunable electron correlation. The first of these systems is the classic Hubbard model with linear and ladder lattice topologies. Because electron correlation functions, such as charge- and spin-ordering, are linear functions of the 2-RDM, the difference in electronic structure between one- and quasi-one-dimensional systems is accurately characterized. The second model contains only two-body interactions and is unique among typical spin models in that it does not have a mean-field reference wave function. The ground state wave functions from all Hamiltonians in the model have the same 1-electron reduced density matrix; consequently, one-electron theories are largely inapplicable. The superconducting eta-pairing ground states make the model a unique tool for demonstrating the necessary N-representability in highly correlated environments. The second part of this thesis (Ch. 5--6) develops a formalism for modeling materials by solving the full Schrodinger equation. Crystalline-orbital Hartree-Fock provides a set of orbitals and integral tensors for the variational 2-RDM method. We demonstrate that time-reversal symmetry, which is implicitly included in position space electronic structure calculations, must be explicitly included as an N-representability constraint on the 2-RDM when using a momentum space basis. The necessity of these equality constraints is demonstrated by the accurate recovery of the binding energy of two polymers and the
One plus two-body random matrix ensembles with parity: Density of states and parity ratios
Vyas, Manan; Srivastava, P. C.; Kota, V. K. B.
2011-06-15
One plus two-body embedded Gaussian orthogonal ensemble of random matrices with parity [EGOE(1+2)-{pi}] generated by a random two-body interaction (modeled by GOE in two-particle spaces) in the presence of a mean field for spinless identical fermion systems is defined, generalizing the two-body ensemble with parity analyzed by Papenbrock and Weidenmueller [Phys. Rev. C 78, 054305 (2008)], in terms of two mixing parameters and a gap between the positive ({pi}=+) and negative ({pi}=-) parity single-particle (sp) states. Numerical calculations are used to demonstrate, using realistic values of the mixing parameters appropriate for some nuclei, that the EGOE(1+2)-{pi} ensemble generates Gaussian form (with corrections) for fixed parity eigenvalue densities (i.e., state densities). The random matrix model also generates many features in parity ratios of state densities that are similar to those predicted by a method based on the Fermi-gas model for nuclei. We have also obtained, by applying the formulation due to Chang et al. [Ann. Phys. (NY) 66, 137 (1971)], a simple formula for the spectral variances defined over fixed-(m{sub 1},m{sub 2}) spaces, where m{sub 1} is the number of fermions in the positive parity sp states and m{sub 2} is the number of fermions in the negative parity sp states. Similarly, using the binary correlation approximation, in the dilute limit, we have derived expressions for the lowest two-shape parameters. The smoothed densities generated by the sum of fixed-(m{sub 1},m{sub 2}) Gaussians with lowest two-shape corrections describe the numerical results in many situations. The model also generates preponderance of positive parity ground states for small values of the mixing parameters, and this is a feature seen in nuclear shell-model results.
This abstract describes the approach implemented in EPA's version of Positive Matrix Factorization (EPA PMF) to estimate uncertainties in the modeled solutions. Details are provided regarding sources of uncertainty in constrained factor analytic models and how these approaches a...
NASA Astrophysics Data System (ADS)
Merker, L.; Weichselbaum, A.; Costi, T. A.
2012-08-01
Recent developments in the numerical renormalization group (NRG) allow the construction of the full density matrix (FDM) of quantum impurity models [see A. Weichselbaum and J. von Delft, Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.99.076402 99, 076402 (2007)] by using the completeness of the eliminated states introduced by F. B. Anders and A. Schiller [F. B. Anders and A. Schiller, Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.95.196801 95, 196801 (2005)]. While these developments prove particularly useful in the calculation of transient response and finite-temperature Green's functions of quantum impurity models, they may also be used to calculate thermodynamic properties. In this paper, we assess the FDM approach to thermodynamic properties by applying it to the Anderson impurity model. We compare the results for the susceptibility and specific heat to both the conventional approach within NRG and to exact Bethe ansatz results. We also point out a subtlety in the calculation of the susceptibility (in a uniform field) within the FDM approach. Finally, we show numerically that for the Anderson model, the susceptibilities in response to a local and a uniform magnetic field coincide in the wide-band limit, in accordance with the Clogston-Anderson compensation theorem.
An Infrastructureless Approach to Estimate Vehicular Density in Urban Environments
Sanguesa, Julio A.; Fogue, Manuel; Garrido, Piedad; Martinez, Francisco J.; Cano, Juan-Carlos; Calafate, Carlos T.; Manzoni, Pietro
2013-01-01
In Vehicular Networks, communication success usually depends on the density of vehicles, since a higher density allows having shorter and more reliable wireless links. Thus, knowing the density of vehicles in a vehicular communications environment is important, as better opportunities for wireless communication can show up. However, vehicle density is highly variable in time and space. This paper deals with the importance of predicting the density of vehicles in vehicular environments to take decisions for enhancing the dissemination of warning messages between vehicles. We propose a novel mechanism to estimate the vehicular density in urban environments. Our mechanism uses as input parameters the number of beacons received per vehicle, and the topological characteristics of the environment where the vehicles are located. Simulation results indicate that, unlike previous proposals solely based on the number of beacons received, our approach is able to accurately estimate the vehicular density, and therefore it could support more efficient dissemination protocols for vehicular environments, as well as improve previously proposed schemes. PMID:23435054
Density matrix renormalization group study of the Anyon-Hubbard model
NASA Astrophysics Data System (ADS)
Arcila-Forero, J.; Franco, R.; Silva-Valencia, J.
2016-02-01
Recently optical lattices allow us to observe phase transition without the uncertainty posed by complex materials, and the simulations of these systems are an excellent bridge between materials-based condensed matter physics and cold atoms. In this way, the computational physics related to many-body problems have increased in importance. Using the density matrix renormalization group method, we studied a Hubbard model for anyons, which is an equivalent to a variant of the Bose-Hubbard model in which the bosonic hopping depends on the local density. This is an exact mapping between anyons and bosons in one dimension. The anyons interlope between bosons and fermions. For two anyons under particle exchange, the wave function acquires a fractional phase eiθ . We conclude that this system exhibits two phases: Mott-insulator and superfluid. We present the phase diagram for some angles. The Mott lobe increases with an increase of the statistical. We observed a reentrance phase transition for all lobes. We showed that the model studied is in the same universality class as the Bose-Hubbard model with two-body interactions.
NASA Astrophysics Data System (ADS)
Gavryusev, V.; Signoles, A.; Ferreira-Cao, M.; Zürn, G.; Hofmann, C. S.; Günter, G.; Schempp, H.; Robert-de-Saint-Vincent, M.; Whitlock, S.; Weidemüller, M.
2016-08-01
We present combined measurements of the spatially resolved optical spectrum and the total excited-atom number in an ultracold gas of three-level atoms under electromagnetically induced transparency conditions involving high-lying Rydberg states. The observed optical transmission of a weak probe laser at the center of the coupling region exhibits a double peaked spectrum as a function of detuning, while the Rydberg atom number shows a comparatively narrow single resonance. By imaging the transmitted light onto a charge-coupled-device camera, we record hundreds of spectra in parallel, which are used to map out the spatial profile of Rabi frequencies of the coupling laser. Using all the information available we can reconstruct the full one-body density matrix of the three-level system, which provides the optical susceptibility and the Rydberg density as a function of spatial position. These results help elucidate the connection between three-level interference phenomena, including the interplay of matter and light degrees of freedom and will facilitate new studies of many-body effects in optically driven Rydberg gases.
SCDM-k: Localized orbitals for solids via selected columns of the density matrix
NASA Astrophysics Data System (ADS)
Damle, Anil; Lin, Lin; Ying, Lexing
2017-04-01
The recently developed selected columns of the density matrix (SCDM) method (Damle et al. 2015, [16]) is a simple, robust, efficient and highly parallelizable method for constructing localized orbitals from a set of delocalized Kohn-Sham orbitals for insulators and semiconductors with Γ point sampling of the Brillouin zone. In this work we generalize the SCDM method to Kohn-Sham density functional theory calculations with k-point sampling of the Brillouin zone, which is needed for more general electronic structure calculations for solids. We demonstrate that our new method, called SCDM-k, is by construction gauge independent and a natural way to describe localized orbitals. SCDM-k computes localized orbitals without the use of an optimization procedure, and thus does not suffer from the possibility of being trapped in a local minimum. Furthermore, the computational complexity of using SCDM-k to construct orthogonal and localized orbitals scales as O (Nlog N) where N is the total number of k-points in the Brillouin zone. SCDM-k is therefore efficient even when a large number of k-points are used for Brillouin zone sampling. We demonstrate the numerical performance of SCDM-k using systems with model potentials in two and three dimensions.
Hybrid-space density matrix renormalization group study of the doped two-dimensional Hubbard model
NASA Astrophysics Data System (ADS)
Ehlers, G.; White, S. R.; Noack, R. M.
2017-03-01
The performance of the density matrix renormalization group (DMRG) is strongly influenced by the choice of the local basis of the underlying physical lattice. We demonstrate that, for the two-dimensional Hubbard model, the hybrid-real-momentum-space formulation of the DMRG is computationally more efficient than the standard real-space formulation. In particular, we show that the computational cost for fixed bond dimension of the hybrid-space DMRG is approximately independent of the width of the lattice, in contrast to the real-space DMRG, for which it is proportional to the width squared. We apply the hybrid-space algorithm to calculate the ground state of the doped two-dimensional Hubbard model on cylinders of width four and six sites; at n =0.875 filling, the ground state exhibits a striped charge-density distribution with a wavelength of eight sites for both U /t =4.0 and 8.0 . We find that the strength of the charge ordering depends on U /t and on the boundary conditions. Furthermore, we investigate the magnetic ordering as well as the decay of the static spin, charge, and pair-field correlation functions.
Li, Zhao; Xu, Heming; Li, Shujuan; Li, Qijun; Zhang, Wenji; Ye, Tiantian; Yang, Xinggang; Pan, Weisan
2014-01-30
The study was aimed to develop a novel gastro-floating multiparticulate system based on a porous and low-density matrix core with excellent floatability. The gastro-floating pellets (GFP) were composed of a porous matrix core, a drug loaded layer (DIP and HPMC), a sub-coating layer (HPMC) and a retarding layer (Eudragit(®) NE 30D). The porous matrix cores were evaluated in specific. EC was chosen as the matrix membrane for its rigidity and minimal expansion to large extent. The porous matrix core was achieved by the complete release of the bulk water soluble excipient from the EC coated beads, and mannitol was selected as the optimal water soluble excipient. SEM photomicrographs confirmed the structure of porous matrix cores. The compositions of GFP were investigated and optimized by orthogonal array design. The optimized formulation could sustain the drug release for 12h and float on the dissolution medium for at least 12h without lag time to float. The pharmacokinetic study was conducted in beagle dogs, and the relative bioavailability of the test preparation was 193.11±3.43%. In conclusion, the novel gastro-floating pellets can be developed as a promising approach for the gastro-retentive drug delivery systems.
Random matrix approach to the distribution of genomic distance.
Alexeev, Nikita; Zograf, Peter
2014-08-01
The cycle graph introduced by Bafna and Pevzner is an important tool for evaluating the distance between two genomes, that is, the minimal number of rearrangements needed to transform one genome into another. We interpret this distance in topological terms and relate it to the random matrix theory. Namely, the number of genomes at a given 2-break distance from a fixed one (the Hultman number) is represented by a coefficient in the genus expansion of a matrix integral over the space of complex matrices with the Gaussian measure. We study generating functions for the Hultman numbers and prove that the two-break distance distribution is asymptotically normal.
A novel approach for FE-SEM imaging of wood-matrix polymer interface in a biocomposite.
Singh, Adya P; Anderson, Ross; Park, Byung-Dae; Nuryawan, Arif
2013-01-01
Understanding the interface between polymer and biomass in composite products is important for developing high performance products, as the quality of adhesion at the interface determines composite properties. For example, with greater stiffness compared to polymer matrix, such as that of high density polyethylene, the wood component enhances stiffness of wood-polymer composites, provided there is good adhesion between composite components. However, in composites made from wood flour (wood particles) and synthetic resins it is often difficult to clearly resolve particle-matrix interfaces in the conventionally employed microscopy method that involves SEM examination of fractured faces of composites. We developed a novel approach, where composites made from high density polyethylene and wood flour were examined and imaged with a FE-SEM (field emission scanning electron microscope) in transverse sections cut through the composites. Improved definition of the interface was achieved using this approach, which enabled a more thorough comparison to be made of the features of the interface between wood particles and the matrix in composites with and without a coupling agent, as it was possible to clearly resolve the interfaces for particles of all sizes, from large particles consisting of many cells down to tiny cell wall fragments, particularly in composites that did not incorporate the coupling agent used to enhance particle adhesion with the matrix polymer. The method developed would be suitable particularly for high definition SEM imaging of a wide range of composites made combining wood and agricultural residues with synthetic polymers.
Kussmann, Jörg; Luenser, Arne; Beer, Matthias; Ochsenfeld, Christian
2015-03-07
An analytical method to calculate the molecular vibrational Hessian matrix at the self-consistent field level is presented. By analysis of the multipole expansions of the relevant derivatives of Coulomb-type two-electron integral contractions, we show that the effect of the perturbation on the electronic structure due to the displacement of nuclei decays at least as r{sup −2} instead of r{sup −1}. The perturbation is asymptotically local, and the computation of the Hessian matrix can, in principle, be performed with O(N) complexity. Our implementation exhibits linear scaling in all time-determining steps, with some rapid but quadratic-complexity steps remaining. Sample calculations illustrate linear or near-linear scaling in the construction of the complete nuclear Hessian matrix for sparse systems. For more demanding systems, scaling is still considerably sub-quadratic to quadratic, depending on the density of the underlying electronic structure.
A Simple Approach to Dot Matrix Printing of Foreign Scripts.
ERIC Educational Resources Information Center
Becker, Donald A.
1985-01-01
Outlines the structure of a printer driven program that converts Romanized texts, composed with the aid of standard word-processing software, into codes that enable a dot matrix printer to produce high-quality printouts in various non-Roman scripts. (Author/SED)
Coupled Mode Formalism: Connecting Phasor, Matrix, and Geometrical Approaches
2014-05-30
the map’s cyclical re-use of a fixed range of longitude co-ordinates. This is somewhat analogous to the situation in solid state physics in which the...1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 III COUPLED STATES : MATRIX FORM...4 IV COUPLED STATES : GEOMETRIC FORM . . . . . . . . . . . . . . . . . . . . . . . . . . 5 Normal form
Exploring multicollinearity using a random matrix theory approach.
Feher, Kristen; Whelan, James; Müller, Samuel
2012-01-01
Clustering of gene expression data is often done with the latent aim of dimension reduction, by finding groups of genes that have a common response to potentially unknown stimuli. However, what is poorly understood to date is the behaviour of a low dimensional signal embedded in high dimensions. This paper introduces a multicollinear model which is based on random matrix theory results, and shows potential for the characterisation of a gene cluster's correlation matrix. This model projects a one dimensional signal into many dimensions and is based on the spiked covariance model, but rather characterises the behaviour of the corresponding correlation matrix. The eigenspectrum of the correlation matrix is empirically examined by simulation, under the addition of noise to the original signal. The simulation results are then used to propose a dimension estimation procedure of clusters from data. Moreover, the simulation results warn against considering pairwise correlations in isolation, as the model provides a mechanism whereby a pair of genes with `low' correlation may simply be due to the interaction of high dimension and noise. Instead, collective information about all the variables is given by the eigenspectrum.
Yao, Rutao; Ramachandra, Ranjith M.; Mahajan, Neeraj; Rathod, Vinay; Gunasekar, Noel; Panse, Ashish; Ma, Tianyu; Jian, Yiqiang; Yan, Jianhua; Carson, Richard E.
2012-01-01
To achieve optimal PET image reconstruction through better system modeling, we developed a system matrix that is based on the probability density function for each line of response (LOR-PDF). The LOR-PDFs are grouped by LOR-to-detector incident angles to form a highly compact system matrix. The system matrix was implemented in the MOLAR list mode reconstruction algorithm for a small animal PET scanner. The impact of LOR-PDF on reconstructed image quality was assessed qualitatively as well as quantitatively in terms of contrast recovery coefficient (CRC) and coefficient of variance (COV), and its performance was compared with a fixed Gaussian (iso-Gaussian) line spread function. The LOR-PDFs of 3 coincidence signal emitting sources, 1) ideal positron emitter that emits perfect back-to-back γ rays (γγ) in air; 2) fluorine-18 (18F) nuclide in water; and 3) oxygen-15 (15O) nuclide in water, were derived, and assessed with simulated and experimental phantom data. The derived LOR-PDFs showed anisotropic and asymmetric characteristics dependent on LOR-detector angle, coincidence emitting source, and the medium, consistent with common PET physical principles. The comparison of the iso-Gaussian function and LOR-PDF showed that: 1) without positron range and acolinearity effects, the LOR-PDF achieved better or similar trade-offs of contrast recovery and noise for objects of 4-mm radius or larger, and this advantage extended to smaller objects (e.g. 2-mm radius sphere, 0.6-mm radius hot-rods) at higher iteration numbers; and 2) with positron range and acolinearity effects, the iso-Gaussian achieved similar or better resolution recovery depending on the significance of positron range effect. We conclude that the 3-D LOR-PDF approach is an effective method to generate an accurate and compact system matrix. However, when used directly in expectation-maximization based list-mode iterative reconstruction algorithms such as MOLAR, its superiority is not clear. For this
NASA Astrophysics Data System (ADS)
Şener, Melih K.; Schulten, Klaus
2002-03-01
We develop a random matrix model approach to study static disorder in pigment-protein complexes in photosynthetic organisms. As a case study, we examine the ring of B850 bacteriochlorophylls in the peripheral light-harvesting complex of Rhodospirillum molischianum, formulated in terms of an effective Hamiltonian describing the collective electronic excitations of the system. We numerically examine and compare various models of disorder and observe that both the density of states and the absorption spectrum of the model show remarkable spectral universality. For the case of unitary disorder, we develop a method to analytically evaluate the density of states of the ensemble using the supersymmetric formulation of random matrix theory. Succinct formulas that can be readily applied in future studies are provided in an appendix.
Sener, Melih K; Schulten, Klaus
2002-03-01
We develop a random matrix model approach to study static disorder in pigment-protein complexes in photosynthetic organisms. As a case study, we examine the ring of B850 bacteriochlorophylls in the peripheral light-harvesting complex of Rhodospirillum molischianum, formulated in terms of an effective Hamiltonian describing the collective electronic excitations of the system. We numerically examine and compare various models of disorder and observe that both the density of states and the absorption spectrum of the model show remarkable spectral universality. For the case of unitary disorder, we develop a method to analytically evaluate the density of states of the ensemble using the supersymmetric formulation of random matrix theory. Succinct formulas that can be readily applied in future studies are provided in an appendix.
Open-Ended Recursive Approach for the Calculation of Multiphoton Absorption Matrix Elements
2015-01-01
We present an implementation of single residues for response functions to arbitrary order using a recursive approach. Explicit expressions in terms of density-matrix-based response theory for the single residues of the linear, quadratic, cubic, and quartic response functions are also presented. These residues correspond to one-, two-, three- and four-photon transition matrix elements. The newly developed code is used to calculate the one-, two-, three- and four-photon absorption cross sections of para-nitroaniline and para-nitroaminostilbene, making this the first treatment of four-photon absorption in the framework of response theory. We find that the calculated multiphoton absorption cross sections are not very sensitive to the size of the basis set as long as a reasonably large basis set with diffuse functions is used. The choice of exchange–correlation functional, however, significantly affects the calculated cross sections of both charge-transfer transitions and other transitions, in particular, for the larger para-nitroaminostilbene molecule. We therefore recommend the use of a range-separated exchange–correlation functional in combination with the augmented correlation-consistent double-ζ basis set aug-cc-pVDZ for the calculation of multiphoton absorption properties. PMID:25821415
Open-Ended Recursive Approach for the Calculation of Multiphoton Absorption Matrix Elements.
Friese, Daniel H; Beerepoot, Maarten T P; Ringholm, Magnus; Ruud, Kenneth
2015-03-10
We present an implementation of single residues for response functions to arbitrary order using a recursive approach. Explicit expressions in terms of density-matrix-based response theory for the single residues of the linear, quadratic, cubic, and quartic response functions are also presented. These residues correspond to one-, two-, three- and four-photon transition matrix elements. The newly developed code is used to calculate the one-, two-, three- and four-photon absorption cross sections of para-nitroaniline and para-nitroaminostilbene, making this the first treatment of four-photon absorption in the framework of response theory. We find that the calculated multiphoton absorption cross sections are not very sensitive to the size of the basis set as long as a reasonably large basis set with diffuse functions is used. The choice of exchange-correlation functional, however, significantly affects the calculated cross sections of both charge-transfer transitions and other transitions, in particular, for the larger para-nitroaminostilbene molecule. We therefore recommend the use of a range-separated exchange-correlation functional in combination with the augmented correlation-consistent double-ζ basis set aug-cc-pVDZ for the calculation of multiphoton absorption properties.
NASA Astrophysics Data System (ADS)
Lim, S. P.; Sheng, D. N.
2016-07-01
A many-body localized (MBL) state is a new state of matter emerging in a disordered interacting system at high-energy densities through a disorder-driven dynamic phase transition. The nature of the phase transition and the evolution of the MBL phase near the transition are the focus of intense theoretical studies with open issues in the field. We develop an entanglement density matrix renormalization group (En-DMRG) algorithm to accurately target highly excited states for MBL systems. By studying the one-dimensional Heisenberg spin chain in a random field, we demonstrate the accuracy of the method in obtaining energy eigenstates and the corresponding statistical results of quantum states in the MBL phase. Based on large system simulations by En-DMRG for excited states, we demonstrate some interesting features in the entanglement entropy distribution function, which is characterized by two peaks: one at zero and another one at the quantized entropy S =ln2 with an exponential decay tail on the S >ln2 side. Combining En-DMRG with exact diagonalization simulations, we demonstrate that the transition from the MBL phase to the delocalized ergodic phase is driven by rare events where the locally entangled spin pairs develop power-law correlations. The corresponding phase diagram contains an intermediate or crossover regime, which has power-law spin-z correlations resulting from contributions of the rare events. We discuss the physical picture for the numerical observations in this regime, where various distribution functions are distinctly different from results deep in the ergodic and MBL phases for finite-size systems. Our results may provide new insights for understanding the phase transition in such systems.
Assessing modularity using a random matrix theory approach.
Feher, Kristen; Whelan, James; Müller, Samuel
2011-09-26
Random matrix theory (RMT) is well suited to describing the emergent properties of systems with complex interactions amongst their constituents through their eigenvalue spectrums. Some RMT results are applied to the problem of clustering high dimensional biological data with complex dependence structure amongst the variables. It will be shown that a gene relevance or correlation network can be constructed by choosing a correlation threshold in a principled way, such that it corresponds to a block diagonal structure in the correlation matrix, if such a structure exists. The structure is then found using community detection algorithms, but with parameter choice guided by RMT predictions. The resulting clustering is compared to a variety of hierarchical clustering outputs and is found to the most generalised result, in that it captures all the features found by the other considered methods.
2D Mueller matrix approach for tissue complete polarization characterization
NASA Astrophysics Data System (ADS)
Fanjul-Vélez, F.; Arce-Diego, J.-L.; Romanov, O. G.; Tolstik, A. L.; Ormachea, O.
2007-06-01
The use of optical techniques in medical praxis allows practitioners to improve their tools. This improvement is realized in two main aspects, treatment and characterization of biological tissue. The former deals with methods like Photodynamic Therapy (PDT), Low Intensity Laser Therapy (LILT) or Hyperthermia. Tissue characterization by optical means is more challenging. The idea is to obtain images from biological tissues with a non-contact, non-invasive and safe procedure. The drawbacks of conventional imaging techniques, like X-Ray with its ionising radiation or ultrasound with the needed contact, are then avoided. Some of these optical techniques are for instance Confocal Microscopy or Optical Coherence Tomography (OCT). The inclusion of the analysis of light polarization can increase the contrast in these images. In this work, polarization information via the Mueller matrix of the target tissue in 2D is proposed as an improved way of characterization. This matrix contains all the polarization properties of tissue, including depolarisation, so a more complete analysis can be carried out. A polarimeter, composed by linear polarizers and rotators, as long as a CCD camera, is proposed to measure 2D Mueller matrix in concrete points of a biological tissue. The importance of these diagnosis methods is crucial in preliminary detection of diseases, like cancer.
NASA Astrophysics Data System (ADS)
Habershon, Scott
2013-09-01
We introduce a new approach for calculating quantum time-correlation functions and time-dependent expectation values in many-body thermal systems; both electronically adiabatic and non-adiabatic cases can be treated. Our approach uses a path integral simulation to sample an initial thermal density matrix; subsequent evolution of this density matrix is equivalent to solution of the time-dependent Schrödinger equation, which we perform using a linear expansion of Gaussian wavepacket basis functions which evolve according to simple classical-like trajectories. Overall, this methodology represents a formally exact approach for calculating time-dependent quantum properties; by introducing approximations into both the imaginary-time and real-time propagations, this approach can be adapted for complex many-particle systems interacting through arbitrary potentials. We demonstrate this method for the spin Boson model, where we find good agreement with numerically exact calculations. We also discuss future directions of improvement for our approach with a view to improving accuracy and efficiency.
NASA Astrophysics Data System (ADS)
Giesbertz, K. J. H.; Gritsenko, O. V.; Baerends, E. J.
2012-03-01
Adiabatic response time-dependent density functional theory (TDDFT) suffers from the restriction to basically an occupied → virtual single excitation formulation. Adiabatic time-dependent density matrix functional theory allows to break away from this restriction. Problematic excitations for TDDFT, viz. bonding-antibonding, double, charge transfer, and higher excitations, are calculated along the bond-dissociation coordinate of the prototype molecules H2 and HeH+ using the recently developed adiabatic linear response phase-including (PI) natural orbital theory (PINO). The possibility to systematically increase the scope of the calculation from excitations out of (strongly) occupied into weakly occupied ("virtual") natural orbitals to larger ranges of excitations is explored. The quality of the PINO response calculations is already much improved over TDDFT even when the severest restriction is made, to virtually the size of the TDDFT diagonalization problem (only single excitation out of occupied orbitals plus all diagonal doubles). Further marked improvement is obtained with moderate extension to allow for excitation out of the lumo and lumo+1, which become fractionally occupied in particular at longer distances due to left-right correlation effects. In the second place the interpretation of density matrix response calculations is elucidated. The one-particle reduced density matrix response for an excitation is related to the transition density matrix to the corresponding excited state. The interpretation of the transition density matrix in terms of the familiar excitation character (single excitations, double excitations of various types, etc.) is detailed. The adiabatic PINO theory is shown to successfully resolve the problematic cases of adiabatic TDDFT when it uses a proper PI orbital functional such as the PILS functional.
Giesbertz, K J H; Gritsenko, O V; Baerends, E J
2012-03-07
Adiabatic response time-dependent density functional theory (TDDFT) suffers from the restriction to basically an occupied → virtual single excitation formulation. Adiabatic time-dependent density matrix functional theory allows to break away from this restriction. Problematic excitations for TDDFT, viz. bonding-antibonding, double, charge transfer, and higher excitations, are calculated along the bond-dissociation coordinate of the prototype molecules H(2) and HeH(+) using the recently developed adiabatic linear response phase-including (PI) natural orbital theory (PINO). The possibility to systematically increase the scope of the calculation from excitations out of (strongly) occupied into weakly occupied ("virtual") natural orbitals to larger ranges of excitations is explored. The quality of the PINO response calculations is already much improved over TDDFT even when the severest restriction is made, to virtually the size of the TDDFT diagonalization problem (only single excitation out of occupied orbitals plus all diagonal doubles). Further marked improvement is obtained with moderate extension to allow for excitation out of the lumo and lumo+1, which become fractionally occupied in particular at longer distances due to left-right correlation effects. In the second place the interpretation of density matrix response calculations is elucidated. The one-particle reduced density matrix response for an excitation is related to the transition density matrix to the corresponding excited state. The interpretation of the transition density matrix in terms of the familiar excitation character (single excitations, double excitations of various types, etc.) is detailed. The adiabatic PINO theory is shown to successfully resolve the problematic cases of adiabatic TDDFT when it uses a proper PI orbital functional such as the PILS functional.
Entanglement or separability: the choice of how to factorize the algebra of a density matrix
NASA Astrophysics Data System (ADS)
Thirring, W.; Bertlmann, R. A.; Köhler, P.; Narnhofer, H.
2011-10-01
Quantum entanglement has become a resource for the fascinating developments in quantum information and quantum communication during the last decades. It quantifies a certain nonclassical correlation property of a density matrix representing the quantum state of a composite system. We discuss the concept of how entanglement changes with respect to different factorizations of the algebra which describes the total quantum system. Depending on the considered factorization a quantum state appears either entangled or separable. For pure states we always can switch unitarily between separability and entanglement, however, for mixed states a minimal amount of mixedness is needed. We discuss our general statements in detail for the familiar case of qubits, the GHZ states, Werner states and Gisin states, emphasizing their geometric features. As theorists we use and play with this free choice of factorization, which for an experimentalist is often naturally fixed. For theorists it offers an extension of the interpretations and is adequate to generalizations, as we point out in the examples of quantum teleportation and entanglement swapping.
Application of variational reduced-density-matrix theory to organic molecules
NASA Astrophysics Data System (ADS)
Gidofalvi, Gergely; Mazziotti, David A.
2005-03-01
Variational calculation of the two-electron reduced-density matrix (2-RDM), using a new first-order algorithm [D. A. Mazziotti, Phys. Rev. Lett. 93, 213001 (2004)], is applied to medium-sized organic molecules. The calculations reveal systematic trends in the accuracy of the energy with well-known chemical concepts such as hybridization, electronegativity, and atomic size. Furthermore, correlation energies from hydrocarbon chains indicate that the calculation of the 2-RDM subject to two-positivity conditions is size extensive, that is, the energy grows linearly with the number of electrons. Because organic molecules have a well-defined set of functional groups, we employ the trends in energy accuracy of the functional groups to design a correction to the 2-RDM energy for an arbitrary organic molecule. We apply the 2-RDM calculations with the functional-group correction to a large set of organic molecules with different functional groups. Energies with millihartree accuracy are obtained both at equilibrium and nonequilibrium geometries.
Analytical nuclear derivatives for the parametric two-electron reduced density matrix method
NASA Astrophysics Data System (ADS)
Valentine, Andrew J. S.; Mazziotti, David A.
2017-10-01
Efficient and accurate nuclear gradients are essential to performing molecular optimizations. Here for the first time we present analytical nuclear gradients for the parametric two-electron reduced-density-matrix method (p2-RDM), which uses the 2-RDM as the primary variable in calculations in lieu of the many-electron wavefunction. While numerical gradients require six energy evaluations for each atom, analytical gradients require only a single calculation for each geometry sampled. We present benchmark p2-RDM geometry optimizations that show analytical gradients reduce CPU times by as much as 80%, even for small molecules. We also use p2-RDM to evaluate the bond length alternation (BLA), or the difference in length between adjacent single and double bonds, of trans-polyacetylene (PA). We find that the BLA in the extrapolated limit to be 0.080 Å, in agreement with experiment and closely mirroring the prediction of the more expensive coupled-cluster with single and double excitations with perturbative triples (CCSD(T)).
Extended density-matrix model applied to silicon-based terahertz quantum cascade lasers
NASA Astrophysics Data System (ADS)
Dinh, T. V.; Valavanis, A.; Lever, L. J. M.; Ikonić, Z.; Kelsall, R. W.
2012-06-01
Silicon-based terahertz quantum cascade lasers (QCLs) offer potential advantages over existing III-V devices. Although coherent electron transport effects are known to be important in QCLs, they have never been considered in Si-based device designs. We describe a density-matrix transport model that is designed to be more general than those in previous studies and to require less a priori knowledge of electronic band structure, allowing its use in semiautomated design procedures. The basis of the model includes all states involved in interperiod transport, and our steady-state solution extends beyond the rotating-wave approximation by including dc and counterpropagating terms. We simulate the potential performance of bound-to-continuum Ge/SiGe QCLs and find that devices with 4-5-nm-thick barriers give the highest simulated optical gain. We also examine the effects of interdiffusion between Ge and SiGe layers; we show that if it is taken into account in the design, interdiffusion lengths of up to 1.5 nm do not significantly affect the simulated device performance.
Permutationally Invariant Part of a Density Matrix and Nonseparability of N-Qubit States
NASA Astrophysics Data System (ADS)
Gao, Ting; Yan, Fengli; van Enk, S. J.
2014-05-01
We consider the concept of "the permutationally invariant (PI) part of a density matrix," which has proven very useful for both efficient quantum state estimation and entanglement characterization of N-qubit systems. We show here that the concept is, in fact, basis dependent but that this basis dependence makes it an even more powerful concept than has been appreciated so far. By considering the PI part ρPI of a general (mixed) N-qubit state ρ, we obtain (i) strong bounds on quantitative nonseparability measures, (ii) a whole hierarchy of multipartite separability criteria (one of which entails a sufficient criterion for genuine N-partite entanglement) that can be experimentally determined by just 2N +1 measurement settings, (iii) a definition of an efficiently measurable degree of separability, which can be used for quantifying a novel aspect of decoherence of N qubits, and (iv) an explicit example that shows there are, for increasing N, genuinely N-partite entangled states lying closer and closer to the maximally mixed state. Moreover, we show that if the PI part of a state is k nonseparable, then so is the actual state. We further argue to add as requirement on any multipartite entanglement measure E that it satisfy E(ρ)≥E(ρPI), even though the operation that maps ρ→ρPI is not local.
Cao, Haihui; Ackerman, Jerome L; Hrovat, Mirko I; Graham, Lila; Glimcher, Melvin J; Wu, Yaotang
2008-12-01
The density of the organic matrix of bone substance is a critical parameter necessary to clinically evaluate and distinguish structural and metabolic pathological conditions such as osteomalacia in adults and rickets in growing children. Water- and fat-suppressed proton projection MRI (WASPI) was developed as a noninvasive means to obtain this information. In this study, a density calibration phantom was developed to convert WASPI intensity to true bone matrix density. The phantom contained a specifically designed poly(ethylene oxide)/poly(methyl methacrylate) (PEO/PMMA) blend, whose MRI properties (T(1), T(2), and resonance linewidth) were similar to those of solid bone matrix (collagen, tightly bound water, and other immobile molecules), minimizing the need to correct for differences in T(1) and/or T(2) relaxation between the phantom and the subject. Cortical and trabecular porcine bone specimens were imaged using WASPI with the calibration phantom in the field of view (FOV) as a stable intensity reference. Gravimetric and amino acid analyses were carried out on the same specimens after WASPI, and the chemical results were found to be highly correlated (r(2) = 0.98 and 0.95, respectively) to the WASPI intensity. By this procedure the WASPI intensity can be used to obtain the true bone matrix mass density in g cm(-3).
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).
Random Matrix Theory Approach to Chaotic Coherent Perfect Absorbers.
Li, Huanan; Suwunnarat, Suwun; Fleischmann, Ragnar; Schanz, Holger; Kottos, Tsampikos
2017-01-27
We employ random matrix theory in order to investigate coherent perfect absorption (CPA) in lossy systems with complex internal dynamics. The loss strength γ_{CPA} and energy E_{CPA}, for which a CPA occurs, are expressed in terms of the eigenmodes of the isolated cavity-thus carrying over the information about the chaotic nature of the target-and their coupling to a finite number of scattering channels. Our results are tested against numerical calculations using complex networks of resonators and chaotic graphs as CPA cavities.
Random Matrix Theory Approach to Chaotic Coherent Perfect Absorbers
NASA Astrophysics Data System (ADS)
Li, Huanan; Suwunnarat, Suwun; Fleischmann, Ragnar; Schanz, Holger; Kottos, Tsampikos
2017-01-01
We employ random matrix theory in order to investigate coherent perfect absorption (CPA) in lossy systems with complex internal dynamics. The loss strength γCPA and energy ECPA, for which a CPA occurs, are expressed in terms of the eigenmodes of the isolated cavity—thus carrying over the information about the chaotic nature of the target—and their coupling to a finite number of scattering channels. Our results are tested against numerical calculations using complex networks of resonators and chaotic graphs as CPA cavities.
NASA Astrophysics Data System (ADS)
Alvarez, G.
2009-09-01
The purpose of this paper is (i) to present a generic and fully functional implementation of the density-matrix renormalization group (DMRG) algorithm, and (ii) to describe how to write additional strongly-correlated electron models and geometries by using templated classes. Besides considering general models and geometries, the code implements Hamiltonian symmetries in a generic way and parallelization over symmetry-related matrix blocks. Program summaryProgram title: DMRG++ Catalogue identifier: AEDJ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDJ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: See file LICENSE No. of lines in distributed program, including test data, etc.: 15 795 No. of bytes in distributed program, including test data, etc.: 83 454 Distribution format: tar.gz Programming language: C++, MPI Computer: PC, HP cluster Operating system: Any, tested on Linux Has the code been vectorized or parallelized?: Yes RAM: 1 GB (256 MB is enough to run included test) Classification: 23 External routines: BLAS and LAPACK Nature of problem: Strongly correlated electrons systems, display a broad range of important phenomena, and their study is a major area of research in condensed matter physics. In this context, model Hamiltonians are used to simulate the relevant interactions of a given compound, and the relevant degrees of freedom. These studies rely on the use of tight-binding lattice models that consider electron localization, where states on one site can be labeled by spin and orbital degrees of freedom. The calculation of properties from these Hamiltonians is a computational intensive problem, since the Hilbert space over which these Hamiltonians act grows exponentially with the number of sites on the lattice. Solution method: The DMRG is a numerical variational technique to study quantum many body Hamiltonians. For one-dimensional and quasi one-dimensional systems, the
Constrained Perturbation Regularization Approach for Signal Estimation Using Random Matrix Theory
NASA Astrophysics Data System (ADS)
Suliman, Mohamed; Ballal, Tarig; Kammoun, Abla; Al-Naffouri, Tareq Y.
2016-12-01
In this supplementary appendix we provide proofs and additional extensive simulations that complement the analysis of the main paper (constrained perturbation regularization approach for signal estimation using random matrix theory).
Chen, Zhenhua; Chen, Xun; Wu, Wei
2013-04-28
In this series, the n-body reduced density matrix (n-RDM) approach for nonorthogonal orbitals and their applications to ab initio valence bond (VB) methods are presented. As the first paper of this series, Hamiltonian matrix elements between internally contracted VB wave functions are explicitly provided by means of nonorthogonal orbital based RDM approach. To this end, a more generalized Wick's theorem, called enhanced Wick's theorem, is presented both in arithmetical and in graphical forms, by which the deduction of expressions for the matrix elements between internally contracted VB wave functions is dramatically simplified, and the matrix elements are finally expressed in terms of tensor contractions of electronic integrals and n-RDMs of the reference VB self-consistent field wave function. A string-based algorithm is developed for the purpose of evaluating n-RDMs in an efficient way. Using the techniques presented in this paper, one is able to develop new methods and efficient algorithms for nonorthogonal orbital based many-electron theory much easier than by use of the first quantized formulism.
Random Matrix Approach to Quantum Adiabatic Evolution Algorithms
NASA Technical Reports Server (NTRS)
Boulatov, Alexei; Smelyanskiy, Vadier N.
2004-01-01
We analyze the power of quantum adiabatic evolution algorithms (Q-QA) for solving random NP-hard optimization problems within a theoretical framework based on the random matrix theory (RMT). We present two types of the driven RMT models. In the first model, the driving Hamiltonian is represented by Brownian motion in the matrix space. We use the Brownian motion model to obtain a description of multiple avoided crossing phenomena. We show that the failure mechanism of the QAA is due to the interaction of the ground state with the "cloud" formed by all the excited states, confirming that in the driven RMT models. the Landau-Zener mechanism of dissipation is not important. We show that the QAEA has a finite probability of success in a certain range of parameters. implying the polynomial complexity of the algorithm. The second model corresponds to the standard QAEA with the problem Hamiltonian taken from the Gaussian Unitary RMT ensemble (GUE). We show that the level dynamics in this model can be mapped onto the dynamics in the Brownian motion model. However, the driven RMT model always leads to the exponential complexity of the algorithm due to the presence of the long-range intertemporal correlations of the eigenvalues. Our results indicate that the weakness of effective transitions is the leading effect that can make the Markovian type QAEA successful.
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.
Validation of density-functional versus density-functional+U approaches for oxide ultrathin films
NASA Astrophysics Data System (ADS)
Barcaro, Giovanni; Thomas, Iorwerth Owain; Fortunelli, Alessandro
2010-03-01
A comparison between available experimental information and the predictions of density-functional and density-functional+U approaches is presented for oxide ultrathin films grown on single-crystal metal surfaces. Prototypical examples of monolayer phases of an ionic oxide (ZnO), a late transition metal oxide (NiO), and an early transition metal oxide (TiO2) are considered. The aim is to validate the theoretical approaches, focusing on the prediction of structural features and the reproduction of scanning tunneling microscopy images, rationalized in terms of the local density of states of the systems. It is found that it is possible to reasonably estimate the optimal lattice constant of ultrathin supported films and that the inclusion of the Hubbard U term appreciably improves the accuracy of theoretical predictions, especially in the case of nonpolar ultrathin phases of a transition metal oxide. Moreover, the optimal value of U for the oxide layer at the interface with the metal support is found to differ from that appropriate for the bulk oxide, as a consequence of the intermixing of oxide and support electronic states and screening effects.
NASA Astrophysics Data System (ADS)
DePrince, A. Eugene; Mazziotti, David A.
2010-01-01
The parametric variational two-electron reduced-density-matrix (2-RDM) method is applied to computing electronic correlation energies of medium-to-large molecular systems by exploiting the spatial locality of electron correlation within the framework of the cluster-in-molecule (CIM) approximation [S. Li et al., J. Comput. Chem. 23, 238 (2002); J. Chem. Phys. 125, 074109 (2006)]. The 2-RDMs of individual molecular fragments within a molecule are determined, and selected portions of these 2-RDMs are recombined to yield an accurate approximation to the correlation energy of the entire molecule. In addition to extending CIM to the parametric 2-RDM method, we (i) suggest a more systematic selection of atomic-orbital domains than that presented in previous CIM studies and (ii) generalize the CIM method for open-shell quantum systems. The resulting method is tested with a series of polyacetylene molecules, water clusters, and diazobenzene derivatives in minimal and nonminimal basis sets. Calculations show that the computational cost of the method scales linearly with system size. We also compute hydrogen-abstraction energies for a series of hydroxyurea derivatives. Abstraction of hydrogen from hydroxyurea is thought to be a key step in its treatment of sickle cell anemia; the design of hydroxyurea derivatives that oxidize more rapidly is one approach to devising more effective treatments.
Husowitz, B; Talanquer, V
2007-02-07
Density functional theory is used to explore the solvation properties of a spherical solute immersed in a supercritical diatomic fluid. The solute is modeled as a hard core Yukawa particle surrounded by a diatomic Lennard-Jones fluid represented by two fused tangent spheres using an interaction site approximation. The authors' approach is particularly suitable for thoroughly exploring the effect of different interaction parameters, such as solute-solvent interaction strength and range, solvent-solvent long-range interactions, and particle size, on the local solvent structure and the solvation free energy under supercritical conditions. Their results indicate that the behavior of the local coordination number in homonuclear diatomic fluids follows trends similar to those reported in previous studies for monatomic fluids. The local density augmentation is particularly sensitive to changes in solute size and is affected to a lesser degree by variations in the solute-solvent interaction strength and range. The associated solvation free energies exhibit a nonmonotonous behavior as a function of density for systems with weak solute-solvent interactions. The authors' results suggest that solute-solvent interaction anisotropies have a major influence on the nature and extent of local solvent density inhomogeneities and on the value of the solvation free energies in supercritical solutions of heteronuclear molecules.
Density matrix embedding theory studies of the two-dimensional Hubbard model
NASA Astrophysics Data System (ADS)
Zheng, Bo-Xiao
Density matrix embedding theory (DMET) provides a quantum embedding framework to compute the electronic structure in strongly correlated lattice systems. It has been applied to various model Hamiltonians and ab initio systems. In this talk, I will review the results obtained in the two-dimensional one-band Hubbard model using DMET. Over the last years, we mapped a calibrated ground-state phase diagram of the two-dimensional Hubbard model, concerning magnetic, superconducting and various inhomogeneous phases. Based on the results from this work, as well as the consistent data from other numerical methods, we are able to conclude that many parts of the Hubbard phase diagram is already settled up to an accurate energy scale of 0.001t. Recently, by using large-scale auxiliary-field quantum Monte Carlo (AFQMC) in the impurity problem, we are able to treat much larger embedded clusters at half-filling (and with the constrained path approximation at non-half-filling), which provides a deeper understanding on the finite-size effects of energy and observables in both quantum embedding and finite cluster numerical methods. Finally, we systematically investigated the putative inhomogeneous phases in the underdoped, strong coupling Hubbard model, proposing new inhomogeneous patterns as strong candidates for the ground state. Reference: [1] Bo-Xiao Zheng, Garnet K.-L. Chan, arXiv:1504.01784 [2] J.P.F. Leblanc, Andrey E. Antipov, et al., arXiv:1505.02290 We acknowledge funding from the US Department of Energy, Office of Science, through DE-SC0008624 and DE-SC0010530. This work was also performed as part of the Simons Collaboration on the Many Electron Problem, sponsored by the Simons Foundation.
Dissipative quantum molecular dynamics in gases and condensed media: A density matrix treatment
NASA Astrophysics Data System (ADS)
Leathers, Andrew S.
We present a study of dissipative quantum molecular dynamics, covering several different methods of treating the dissipation. We use a reduced density matrix framework, which leads to coupled integro-differential equations in time. We then develop a numerical algorithm for solving these equations. This algorithm is tested by comparing the results to a solved model. The method is then applied to the vibrational relaxation of adsorbates on metal surfaces. We also use this model to test approximations which transform the integro-differential equations into simpler integral equations. Our results compare well to experiment, and demonstrate the need for a full treatment without approximations. This model is then expanded to allow for electronic relaxation, as well as excitation by a light pulse. The electronic relaxation occurs on a different time scale, and is treated differently than the vibrational relaxation. Our method is shown to be general enough to handle both cases. Our next model is light-induced electron transfer in a metal cluster on a semiconductor surface. We consider both direct electronic excitation causing electron transfer, as well as indirect transfer, where there is excitation to an intermediate state which is coupled to the electron transferred state. Our results indicate vibrational relaxation plays a small role in the direct transfer dynamics, but is still important in the indirect case. Finally, we present a mixed quantum-classical study of the effect of initial conditions, with the goal of moving towards a method capable of treating dissipation in both quantum and mixed quatum-classical systems. (Full text of this dissertation may be available via the University of Florida Libraries web site. Please check http://www.uflib.ufl.edu/etd.html)
Harris, Travis V.; Morokuma, Keiji; Kurashige, Yuki; Yanai, Takeshi
2014-02-07
The applicability of ab initio multireference wavefunction-based methods to the study of magnetic complexes has been restricted by the quickly rising active-space requirements of oligonuclear systems and dinuclear complexes with S > 1 spin centers. Ab initio density matrix renormalization group (DMRG) methods built upon an efficient parameterization of the correlation network enable the use of much larger active spaces, and therefore may offer a way forward. Here, we apply DMRG-CASSCF to the dinuclear complexes [Fe{sub 2}OCl{sub 6}]{sup 2−} and [Cr{sub 2}O(NH{sub 3}){sub 10}]{sup 4+}. After developing the methodology through systematic basis set and DMRG M testing, we explore the effects of extended active spaces that are beyond the limit of conventional methods. We find that DMRG-CASSCF with active spaces including the metal d orbitals, occupied bridging-ligand orbitals, and their virtual double shells already capture a major portion of the dynamic correlation effects, accurately reproducing the experimental magnetic coupling constant (J) of [Fe{sub 2}OCl{sub 6}]{sup 2−} with (16e,26o), and considerably improving the smaller active space results for [Cr{sub 2}O(NH{sub 3}){sub 10}]{sup 4+} with (12e,32o). For comparison, we perform conventional MRCI+Q calculations and find the J values to be consistent with those from DMRG-CASSCF. In contrast to previous studies, the higher spin states of the two systems show similar deviations from the Heisenberg spectrum, regardless of the computational method.
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.
Neurotrophic Keratopathy: Therapeutic Approach Using a Novel Matrix Regenerating Agent.
Guerra, Marta; Marques, Sara; Quadrado Gil, João; Campos, Joana; Ramos, Paula; Rosa, Andreia Martins; Quadrado, Maria João; Murta, Joaquim Neto
2017-09-14
To evaluate the efficacy and tolerance of a new matrix-regenerating agent (RGTA), Cacicol(®), a polymer that mimics heparan sulfates bound to extracellular matrix proteins, avoiding its proteolysis, to treat neurotrophic keratopathy (NK). Uncontrolled prospective clinical study performed between January 2014 and May 2016. Twenty-five patients (25 eyes) with corneal neurotrophic ulcers, nonresponsive to at least 2 weeks of conservative therapy, were treated with Cacicol, instilled once/twice a week. During follow-up, slit-lamp examination, anterior segment photography, fluorescein-dye testing, and best-corrected visual acuity were analyzed. Ulcer evolution was evaluated using image analysis software (ImageJ(®)) and healing defined as decrease of the corneal ulcer area. An independent observer measured ulcer area. All patients had complete corneal healing within an average of 4.13 ± 2.32 weeks. Mean ulcer area decreased significantly (P = 0.001) from 16.51% ± 18.56% (1st day) to 8.68% ± 11.25% at the 7th day and to 4.73% ± 10.75% at the 14th day. Compared with day 1, mean ulcer area decreased 60.24% after 7 days (P = 0.001), 54.92% after 14 days (P = 0.059), and 83.00% after 21 days (P = 0.003). Two cases of recurrence (8.0%) were registered. No systemic or local side effects were noticed. The new regenerating agent, Cacicol, represents an effective and safe therapy to treat NK.
Random matrix approach to cross correlations in financial data
NASA Astrophysics Data System (ADS)
Plerou, Vasiliki; Gopikrishnan, Parameswaran; Rosenow, Bernd; Amaral, Luís A.; Guhr, Thomas; Stanley, H. Eugene
2002-06-01
We analyze cross correlations between price fluctuations of different stocks using methods of random matrix theory (RMT). Using two large databases, we calculate cross-correlation matrices
Random matrix approach to the dynamics of stock inventory variations
NASA Astrophysics Data System (ADS)
Zhou, Wei-Xing; Mu, Guo-Hua; Kertész, János
2012-09-01
It is well accepted that investors can be classified into groups owing to distinct trading strategies, which forms the basic assumption of many agent-based models for financial markets when agents are not zero-intelligent. However, empirical tests of these assumptions are still very rare due to the lack of order flow data. Here we adopt the order flow data of Chinese stocks to tackle this problem by investigating the dynamics of inventory variations for individual and institutional investors that contain rich information about the trading behavior of investors and have a crucial influence on price fluctuations. We find that the distributions of cross-correlation coefficient Cij have power-law forms in the bulk that are followed by exponential tails, and there are more positive coefficients than negative ones. In addition, it is more likely that two individuals or two institutions have a stronger inventory variation correlation than one individual and one institution. We find that the largest and the second largest eigenvalues (λ1 and λ2) of the correlation matrix cannot be explained by random matrix theory and the projections of investors' inventory variations on the first eigenvector u(λ1) are linearly correlated with stock returns, where individual investors play a dominating role. The investors are classified into three categories based on the cross-correlation coefficients CV R between inventory variations and stock returns. A strong Granger causality is unveiled from stock returns to inventory variations, which means that a large proportion of individuals hold the reversing trading strategy and a small part of individuals hold the trending strategy. Our empirical findings have scientific significance in the understanding of investors' trading behavior and in the construction of agent-based models for emerging stock markets.
Random matrix approach to cross correlations in financial data.
Plerou, Vasiliki; Gopikrishnan, Parameswaran; Rosenow, Bernd; Amaral, Luís A Nunes; Guhr, Thomas; Stanley, H Eugene
2002-06-01
We analyze cross correlations between price fluctuations of different stocks using methods of random matrix theory (RMT). Using two large databases, we calculate cross-correlation matrices C of returns constructed from (i) 30-min returns of 1000 US stocks for the 2-yr period 1994-1995, (ii) 30-min returns of 881 US stocks for the 2-yr period 1996-1997, and (iii) 1-day returns of 422 US stocks for the 35-yr period 1962-1996. We test the statistics of the eigenvalues lambda(i) of C against a "null hypothesis"--a random correlation matrix constructed from mutually uncorrelated time series. We find that a majority of the eigenvalues of C fall within the RMT bounds [lambda(-),lambda(+)] for the eigenvalues of random correlation matrices. We test the eigenvalues of C within the RMT bound for universal properties of random matrices and find good agreement with the results for the Gaussian orthogonal ensemble of random matrices-implying a large degree of randomness in the measured cross-correlation coefficients. Further, we find that the distribution of eigenvector components for the eigenvectors corresponding to the eigenvalues outside the RMT bound display systematic deviations from the RMT prediction. In addition, we find that these "deviating eigenvectors" are stable in time. We analyze the components of the deviating eigenvectors and find that the largest eigenvalue corresponds to an influence common to all stocks. Our analysis of the remaining deviating eigenvectors shows distinct groups, whose identities correspond to conventionally identified business sectors. Finally, we discuss applications to the construction of portfolios of stocks that have a stable ratio of risk to return.
Random matrix approach to quantum adiabatic evolution algorithms
Boulatov, A.; Smelyanskiy, V.N.
2005-05-15
We analyze the power of the quantum adiabatic evolution algorithm (QAA) for solving random computationally hard optimization problems within a theoretical framework based on random matrix theory (RMT). We present two types of driven RMT models. In the first model, the driving Hamiltonian is represented by Brownian motion in the matrix space. We use the Brownian motion model to obtain a description of multiple avoided crossing phenomena. We show that nonadiabatic corrections in the QAA are due to the interaction of the ground state with the 'cloud' formed by most of the excited states, confirming that in driven RMT models, the Landau-Zener scenario of pairwise level repulsions is not relevant for the description of nonadiabatic corrections. We show that the QAA has a finite probability of success in a certain range of parameters, implying a polynomial complexity of the algorithm. The second model corresponds to the standard QAA with the problem Hamiltonian taken from the RMT Gaussian unitary ensemble (GUE). We show that the level dynamics in this model can be mapped onto the dynamics in the Brownian motion model. For this reason, the driven GUE model can also lead to polynomial complexity of the QAA. The main contribution to the failure probability of the QAA comes from the nonadiabatic corrections to the eigenstates, which only depend on the absolute values of the transition amplitudes. Due to the mapping between the two models, these absolute values are the same in both cases. Our results indicate that this 'phase irrelevance' is the leading effect that can make both the Markovian- and GUE-type QAAs successful.
Nakatani, Naoki; Chan, Garnet Kin-Lic
2013-04-07
We investigate tree tensor network states for quantum chemistry. Tree tensor network states represent one of the simplest generalizations of matrix product states and the density matrix renormalization group. While matrix product states encode a one-dimensional entanglement structure, tree tensor network states encode a tree entanglement structure, allowing for a more flexible description of general molecules. We describe an optimal tree tensor network state algorithm for quantum chemistry. We introduce the concept of half-renormalization which greatly improves the efficiency of the calculations. Using our efficient formulation we demonstrate the strengths and weaknesses of tree tensor network states versus matrix product states. We carry out benchmark calculations both on tree systems (hydrogen trees and π-conjugated dendrimers) as well as non-tree molecules (hydrogen chains, nitrogen dimer, and chromium dimer). In general, tree tensor network states require much fewer renormalized states to achieve the same accuracy as matrix product states. In non-tree molecules, whether this translates into a computational savings is system dependent, due to the higher prefactor and computational scaling associated with tree algorithms. In tree like molecules, tree network states are easily superior to matrix product states. As an illustration, our largest dendrimer calculation with tree tensor network states correlates 110 electrons in 110 active orbitals.
Coherent states/density functional theory approach to molecular dynamics
NASA Astrophysics Data System (ADS)
Tsereteli, Kakha; Yan, Yun-an; Morales, Jorge A.
2006-03-01
We present a combined coherent states (CS)/density functional theory approach to molecular dynamics within the electron nuclear dynamics framework. Nuclei are described by a product of narrow, frozen Gaussian wave packets that is approximately separable into translational, rotational, and vibrational CS parts. Electrons are described by a single-determinantal Thouless CS in a time-dependent Kohn-Sham fashion. This novel approach improves several features of the Car-Parrinello method by providing an ab initio CS Lagrangian, a quasi-classical CS description for the nuclei, and a non-redundant representation of a general electronic single-determinantal state. Preliminary simulations of the H + + H 2 reaction at ELab = 30 eV are also presented.
Simulation of sprays using a Lagrangian filtered density function approach
NASA Astrophysics Data System (ADS)
Liu, Wanjiao; Garrick, Sean
2013-11-01
Sprays and atomization have wide applications in industry, including combustion/engines, pharmaceutics and agricultural spraying. Due to the complexity of the underlying processes, much of the underlying phenomena are not fully understood. Numerical simulation may provide ways to investigate atomization and spray dynamics. Large eddy simulation (LES) is a practical approach to flow simulation as it resolves only the large-scale structures while modeling the sub-grid scale (SGS) effects. We combine a filtered density function (FDF) based approach with a Lagrangian volume-of-fluid method to perform LES. This resulting methodology is advantageous in that it has no diffusive or dissipative numerical errors, and the highly non-linear surface tension force appears in closed form thus the modeling of the SGS surface tension is not needed when simulating turbulent, multiphase flows. We present the methodology and some results for the simulation of multiphase jets.
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.
Kussmann, Jörg; Ochsenfeld, Christian
2007-11-28
A density matrix-based time-dependent self-consistent field (D-TDSCF) method for the calculation of dynamic polarizabilities and first hyperpolarizabilities using the Hartree-Fock and Kohn-Sham density functional theory approaches is presented. The D-TDSCF method allows us to reduce the asymptotic scaling behavior of the computational effort from cubic to linear for systems with a nonvanishing band gap. The linear scaling is achieved by combining a density matrix-based reformulation of the TDSCF equations with linear-scaling schemes for the formation of Fock- or Kohn-Sham-type matrices. In our reformulation only potentially linear-scaling matrices enter the formulation and efficient sparse algebra routines can be employed. Furthermore, the corresponding formulas for the first hyperpolarizabilities are given in terms of zeroth- and first-order one-particle reduced density matrices according to Wigner's (2n+1) rule. The scaling behavior of our method is illustrated for first exemplary calculations with systems of up to 1011 atoms and 8899 basis functions.
Approaches to 100 Gbit/sq. in. recording density
NASA Technical Reports Server (NTRS)
Kryder, Mark H.
1994-01-01
A recording density of 10 Gbit/sq. in. is being pursued by a number of companies and universities in the National Storage Industry Consortium. It is widely accepted that this goal will be achieved in the laboratory within a few years. In this paper approaches to achieving 100 Gbit/sq. in. storage densities are considered. A major obstacle to continued scaling of magnetic recording to higher densities is that as the bit size is reduced, the grain size in the magnetic media must be reduced in order that media noise does not become so large that the signal to noise ratio (SNR) degrades sufficiently to make detection impossible. At 100 Gbit/sq. in., the bit size is only 0.006 square micrometers, which, in order to achieve 30 dB SNR, requires a grain size of about 2.5 nm. Such small grains are subject to thermal instability, and the recorded information will degrade over time unless the magnetic anisotropy of the materials used is increased significantly, or the media thickness is made much larger than expected on the basis of scaling today's longitudinal media thickness.
A Wigner Monte Carlo approach to density functional theory
Sellier, J.M. Dimov, I.
2014-08-01
In order to simulate quantum N-body systems, stationary and time-dependent density functional theories rely on the capacity of calculating the single-electron wave-functions of a system from which one obtains the total electron density (Kohn–Sham systems). In this paper, we introduce the use of the Wigner Monte Carlo method in ab-initio calculations. This approach allows time-dependent simulations of chemical systems in the presence of reflective and absorbing boundary conditions. It also enables an intuitive comprehension of chemical systems in terms of the Wigner formalism based on the concept of phase-space. Finally, being based on a Monte Carlo method, it scales very well on parallel machines paving the way towards the time-dependent simulation of very complex molecules. A validation is performed by studying the electron distribution of three different systems, a Lithium atom, a Boron atom and a hydrogenic molecule. For the sake of simplicity, we start from initial conditions not too far from equilibrium and show that the systems reach a stationary regime, as expected (despite no restriction is imposed in the choice of the initial conditions). We also show a good agreement with the standard density functional theory for the hydrogenic molecule. These results demonstrate that the combination of the Wigner Monte Carlo method and Kohn–Sham systems provides a reliable computational tool which could, eventually, be applied to more sophisticated problems.
Fragment approach to constrained density functional theory calculations using Daubechies wavelets.
Ratcliff, Laura E; Genovese, Luigi; Mohr, Stephan; Deutsch, Thierry
2015-06-21
In a recent paper, we presented a linear scaling Kohn-Sham density functional theory (DFT) code based on Daubechies wavelets, where a minimal set of localized support functions are optimized in situ and therefore adapted to the chemical properties of the molecular system. Thanks to the systematically controllable accuracy of the underlying basis set, this approach is able to provide an optimal contracted basis for a given system: accuracies for ground state energies and atomic forces are of the same quality as an uncontracted, cubic scaling approach. This basis set offers, by construction, a natural subset where the density matrix of the system can be projected. In this paper, we demonstrate the flexibility of this minimal basis formalism in providing a basis set that can be reused as-is, i.e., without reoptimization, for charge-constrained DFT calculations within a fragment approach. Support functions, represented in the underlying wavelet grid, of the template fragments are roto-translated with high numerical precision to the required positions and used as projectors for the charge weight function. We demonstrate the interest of this approach to express highly precise and efficient calculations for preparing diabatic states and for the computational setup of systems in complex environments.
Fragment Approach to Constrained Density Functional Theory Calculations using Daubechies Wavelets
Ratcliff, Laura E.; Genovese, Luigi; Mohr, Stephan; Deutsch, Thierry
2015-06-21
In a recent paper, we presented a linear scaling Kohn-Sham density functional theory (DFT) code based on Daubechies wavelets, where a minimal set of localized support functions are optimized in situ and therefore adapted to the chemical properties of the molecular system. Thanks to the systematically controllable accuracy of the underlying basis set, this approach is able to provide an optimal contracted basis for a given system: accuracies for ground state energies and atomic forces are of the same quality as an uncontracted, cubic scaling approach. This basis set offers, by construction, a natural subset where the density matrix of the system can be projected. In this paper, we demonstrate the flexibility of this minimal basis formalism in providing a basis set that can be reused as-is, i.e., without reoptimization, for charge-constrained DFT calculations within a fragment approach. Support functions, represented in the underlying wavelet grid, of the template fragments are roto-translated with high numerical precision to the required positions and used as projectors for the charge weight function. We demonstrate the interest of this approach to express highly precise and efficient calculations for preparing diabatic states and for the computational setup of systems in complex environments.
Fragment approach to constrained density functional theory calculations using Daubechies wavelets
Ratcliff, Laura E.; Genovese, Luigi; Mohr, Stephan; Deutsch, Thierry
2015-06-21
In a recent paper, we presented a linear scaling Kohn-Sham density functional theory (DFT) code based on Daubechies wavelets, where a minimal set of localized support functions are optimized in situ and therefore adapted to the chemical properties of the molecular system. Thanks to the systematically controllable accuracy of the underlying basis set, this approach is able to provide an optimal contracted basis for a given system: accuracies for ground state energies and atomic forces are of the same quality as an uncontracted, cubic scaling approach. This basis set offers, by construction, a natural subset where the density matrix of the system can be projected. In this paper, we demonstrate the flexibility of this minimal basis formalism in providing a basis set that can be reused as-is, i.e., without reoptimization, for charge-constrained DFT calculations within a fragment approach. Support functions, represented in the underlying wavelet grid, of the template fragments are roto-translated with high numerical precision to the required positions and used as projectors for the charge weight function. We demonstrate the interest of this approach to express highly precise and efficient calculations for preparing diabatic states and for the computational setup of systems in complex environments.
A theoretical validation of the B-matrix spatial distribution approach to diffusion tensor imaging.
Borkowski, Karol; Kłodowski, Krzysztof; Figiel, Henryk; Krzyżak, Artur Tadeusz
2017-02-01
The recently presented B-matrix Spatial Distribution (BSD) approach is a calibration technique which derives the actual distribution of the B-matrix in space. It is claimed that taking into account the spatial variability of the B-matrix improves the accuracy of diffusion tensor imaging (DTI). The purpose of this study is to verify this approach theoretically through computer simulations. Assuming three different spatial distributions of the B-matrix, diffusion weighted signals were calculated for the six orientations of a model anisotropic phantom. Subsequently two variants of the BSD calibration were performed for each of the three cases; one with the assumption of high uniformity of the model phantom (uBSD-DTI) and the other taking into account imperfections in phantom structure (BSD-DTI). Several cases of varying degrees of phantom uniformity were analyzed and the distributions of the B-matrix obtained were used for the calculation of the diffusion tensor of a model isotropic phantom. The results were compared with standard diffusion tensor calculation. The simulations confirmed the improvement of accuracy in the determination of the diffusion tensor after the calibration. BSD-DTI improves accuracy independent of both the degree of uniformity of the phantom and the inhomogeneity of the B-matrix. In cases of a relatively good uniformity of the phantom and minor distortions in the spatial distribution of the B-matrix, the uBSD-DTI approach is sufficient.
How Fast Can Networks Synchronize? A Random Matrix Theory Approach
NASA Astrophysics Data System (ADS)
Timme, Marc; Wolf, Fred; Geisel, Theo
2004-03-01
Pulse-coupled oscillators constitute a paradigmatic class of dynamical systems interacting on networks because they model a variety of biological systems including flashing fireflies and chirping crickets as well as pacemaker cells of the heart and neural networks. Synchronization is one of the most simple and most prevailing kinds of collective dynamics on such networks. Here we study collective synchronization [1] of pulse-coupled oscillators interacting on asymmetric random networks. Using random matrix theory we analytically determine the speed of synchronization in such networks in dependence on the dynamical and network parameters [2]. The speed of synchronization increases with increasing coupling strengths. Surprisingly, however, it stays finite even for infinitely strong interactions. The results indicate that the speed of synchronization is limited by the connectivity of the network. We discuss the relevance of our findings to general equilibration processes on complex networks. [5mm] [1] M. Timme, F. Wolf, T. Geisel, Phys. Rev. Lett. 89:258701 (2002). [2] M. Timme, F. Wolf, T. Geisel, cond-mat/0306512 (2003).
Different approaches for extracting information from the co-occurrence matrix.
Nanni, Loris; Brahnam, Sheryl; Ghidoni, Stefano; Menegatti, Emanuele; Barrier, Tonya
2013-01-01
In 1979 Haralick famously introduced a method for analyzing the texture of an image: a set of statistics extracted from the co-occurrence matrix. In this paper we investigate novel sets of texture descriptors extracted from the co-occurrence matrix; in addition, we compare and combine different strategies for extending these descriptors. The following approaches are compared: the standard approach proposed by Haralick, two methods that consider the co-occurrence matrix as a three-dimensional shape, a gray-level run-length set of features and the direct use of the co-occurrence matrix projected onto a lower dimensional subspace by principal component analysis. Texture descriptors are extracted from the co-occurrence matrix evaluated at multiple scales. Moreover, the descriptors are extracted not only from the entire co-occurrence matrix but also from subwindows. The resulting texture descriptors are used to train a support vector machine and ensembles. Results show that our novel extraction methods improve the performance of standard methods. We validate our approach across six medical datasets representing different image classification problems using the Wilcoxon signed rank test. The source code used for the approaches tested in this paper will be available at: http://www.dei.unipd.it/wdyn/?IDsezione=3314&IDgruppo_pass=124&preview=.
Different Approaches for Extracting Information from the Co-Occurrence Matrix
Nanni, Loris; Brahnam, Sheryl; Ghidoni, Stefano; Menegatti, Emanuele; Barrier, Tonya
2013-01-01
In 1979 Haralick famously introduced a method for analyzing the texture of an image: a set of statistics extracted from the co-occurrence matrix. In this paper we investigate novel sets of texture descriptors extracted from the co-occurrence matrix; in addition, we compare and combine different strategies for extending these descriptors. The following approaches are compared: the standard approach proposed by Haralick, two methods that consider the co-occurrence matrix as a three-dimensional shape, a gray-level run-length set of features and the direct use of the co-occurrence matrix projected onto a lower dimensional subspace by principal component analysis. Texture descriptors are extracted from the co-occurrence matrix evaluated at multiple scales. Moreover, the descriptors are extracted not only from the entire co-occurrence matrix but also from subwindows. The resulting texture descriptors are used to train a support vector machine and ensembles. Results show that our novel extraction methods improve the performance of standard methods. We validate our approach across six medical datasets representing different image classification problems using the Wilcoxon signed rank test. The source code used for the approaches tested in this paper will be available at: http://www.dei.unipd.it/wdyn/?IDsezione=3314&IDgruppo_pass=124&preview=. PMID:24386228
A space efficient flexible pivot selection approach to evaluate determinant and inverse of a matrix.
Jafree, Hafsa Athar; Imtiaz, Muhammad; Inayatullah, Syed; Khan, Fozia Hanif; Nizami, Tajuddin
2014-01-01
This paper presents new simple approaches for evaluating determinant and inverse of a matrix. The choice of pivot selection has been kept arbitrary thus they reduce the error while solving an ill conditioned system. Computation of determinant of a matrix has been made more efficient by saving unnecessary data storage and also by reducing the order of the matrix at each iteration, while dictionary notation [1] has been incorporated for computing the matrix inverse thereby saving unnecessary calculations. These algorithms are highly class room oriented, easy to use and implemented by students. By taking the advantage of flexibility in pivot selection, one may easily avoid development of the fractions by most. Unlike the matrix inversion method [2] and [3], the presented algorithms obviate the use of permutations and inverse permutations.
Levorson, Erica J.; Mountziaris, Paschalia M.; Hu, Olivia; Kasper, F. Kurtis
2014-01-01
This study investigated the coculture of chondrocytes and mesenchymal stem cells (MSCs) on electrospun fibrous polymer scaffolds to produce polymer/extracellular matrix (ECM) hybrid constructs with the objective of reducing the number of chondrocytes necessary to produce ample cartilage-like ECM within the scaffolds. To generate these hybrid constructs, electrospun poly(ɛ-caprolactone) fibrous scaffolds were seeded at both high and low initial densities with five different ratios of chondrocytes to MSCs: 1:0, 1:1, 1:3, 1:5, and 0:1, and cultured for 7, 14, and 21 days. Glycosaminoglycan production and distribution within the three coculture groups was similar to quantities generated by chondrocyte-only controls. Conversely, as the concentration of chondrocytes was increased, the collagen content of the constructs also increased at each time point, with a 1:1 chondrocyte to MSC ratio approximating the collagen production of chondrocytes alone. Histological staining suggested that cocultured constructs mimicked the well-distributed ECM patterns of chondrocyte generated constructs, while improving greatly over the restricted distribution of matrix within MSC-only constructs. These results support the capacity of cocultures of chondrocytes and MSCs to generate cartilaginous matrix within a polymeric scaffold. Further, the inclusion of MSCs in these cocultures enables the reduction of chondrocytes needed to produce cell-generated ECM. PMID:24007559
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
Kaminski, S; Jakobi, A; Wilhelm, Chr
2014-12-01
This paper is intended to identify the uncertainties of activities in environmental samples measured with gamma-ray spectrometry that result from uncertainties in matrix composition, density and geometrical dimensions of the sample. For that purpose efficiencies were calculated for a wide range of environmental matrices such as fresh and ashed food samples, water samples and soil samples. Compositions were mainly taken from literature. Densities and geometry parameters were varied in a range occurring in practice. Considered energies cover a range from 46.5keV to 2000keV. Finally, a couple of recommendations in respect to gamma-ray spectrometric measurements of environmental samples are given.
NASA Technical Reports Server (NTRS)
Pototzky, Anthony S.
2008-01-01
A simple matrix polynomial approach is introduced for approximating unsteady aerodynamics in the s-plane and ultimately, after combining matrix polynomial coefficients with matrices defining the structure, a matrix polynomial of the flutter equations of motion (EOM) is formed. A technique of recasting the matrix-polynomial form of the flutter EOM into a first order form is also presented that can be used to determine the eigenvalues near the origin and everywhere on the complex plane. An aeroservoelastic (ASE) EOM have been generalized to include the gust terms on the right-hand side. The reasons for developing the new matrix polynomial approach are also presented, which are the following: first, the "workhorse" methods such as the NASTRAN flutter analysis lack the capability to consistently find roots near the origin, along the real axis or accurately find roots farther away from the imaginary axis of the complex plane; and, second, the existing s-plane methods, such as the Roger s s-plane approximation method as implemented in ISAC, do not always give suitable fits of some tabular data of the unsteady aerodynamics. A method available in MATLAB is introduced that will accurately fit generalized aerodynamic force (GAF) coefficients in a tabular data form into the coefficients of a matrix polynomial form. The root-locus results from the NASTRAN pknl flutter analysis, the ISAC-Roger's s-plane method and the present matrix polynomial method are presented and compared for accuracy and for the number and locations of roots.
NASA Astrophysics Data System (ADS)
Miura, Shinichi; Okazaki, Susumu
2001-09-01
In this paper, the path integral molecular dynamics (PIMD) method has been extended to employ an efficient approximation of the path action referred to as the pair density matrix approximation. Configurations of the isomorphic classical systems were dynamically sampled by introducing fictitious momenta as in the PIMD based on the standard primitive approximation. The indistinguishability of the particles was handled by a pseudopotential of particle permutation that is an extension of our previous one [J. Chem. Phys. 112, 10 116 (2000)]. As a test of our methodology for Boltzmann statistics, calculations have been performed for liquid helium-4 at 4 K. We found that the PIMD with the pair density matrix approximation dramatically reduced the computational cost to obtain the structural as well as dynamical (using the centroid molecular dynamics approximation) properties at the same level of accuracy as that with the primitive approximation. With respect to the identical particles, we performed the calculation of a bosonic triatomic cluster. Unlike the primitive approximation, the pseudopotential scheme based on the pair density matrix approximation described well the bosonic correlation among the interacting atoms. Convergence with a small number of discretization of the path achieved by this approximation enables us to construct a method of avoiding the problem of the vanishing pseudopotential encountered in the calculations by the primitive approximation.
Liquid water simulations with the density fragment interaction approach.
Hu, Xiangqian; Jin, Yingdi; Zeng, Xiancheng; Hu, Hao; Yang, Weitao
2012-06-07
We reformulate the density fragment interaction (DFI) approach [Fujimoto and Yang, J. Chem. Phys., 2008, 129, 054102.] to achieve linear-scaling quantum mechanical calculations for large molecular systems. Two key approximations are developed to improve the efficiency of the DFI approach and thus enable the calculations for large molecules: the electrostatic interactions between fragments are computed efficiently by means of polarizable electrostatic-potential-fitted atomic charges; and frozen fragment pseudopotentials, similar to the effective fragment potentials that can be fitted from interactions between small molecules, are employed to take into account the Pauli repulsion effect among fragments. Our reformulated and parallelized DFI method demonstrates excellent parallel performance based on the benchmarks for the system of 256 water molecules. Molecular dynamics simulations for the structural properties of liquid water also show a qualitatively good agreement with experimental measurements including the heat capacity, binding energy per water molecule, and the radial distribution functions of atomic pairs of O-O, O-H, and H-H. With this approach, large-scale quantum mechanical simulations for water and other liquids become feasible.
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
Radisavljević, Maja; Kamceva, Tina; Vukićević, Iva; Nisavić, Marija; Milovanović, Milan; Petković, Marijana
2013-01-01
We compare the quality and reliability of laser desorption and ionisation mass spectra of FeCl3 acquired without the assistance of the matrix with the spectra acquired with different organic matrix molecules. Generally, inorganic salts tend to form clusters upon laser irradiation, the signals of which can be easily distinguished from ions arising from the matrix. In the presence of a matrix, cluster ions are, however, mostly suppressed. We have compared the number of analyte signals, accuracy of determination of isotope composition of the analyte and the sensitivity of FeCl3 detection between different approaches. The results obtained imply that the sensitivity of mass spectrometric analysis of FeCl3 is somewhat higher when matrices are applied than in the matrix-free approach. Among all matrices tested in this work, F20TPP seems to be the most promising for further applications as a matrix for mass spectrometry of inorganic salts.
A new approach to calculate the transport matrix in RF cavities
Eidelman, Yu.; Mokhov, N.; Nagaitsev, S.; Solyak, N.; /Fermilab
2011-03-01
A realistic approach to calculate the transport matrix in RF cavities is developed. It is based on joint solution of equations of longitudinal and transverse motion of a charged particle in an electromagnetic field of the linac. This field is a given by distribution (measured or calculated) of the component of the longitudinal electric field on the axis of the linac. New approach is compared with other matrix methods to solve the same problem. The comparison with code ASTRA has been carried out. Complete agreement for tracking results for a TESLA-type cavity is achieved. A corresponding algorithm will be implemented into the MARS15 code. A realistic approach to calculate the transport matrix in RF cavities is developed. Complete agreement for tracking results with existed code ASTRA is achieved. New algorithm will be implemented into MARS15 code.
Soltan, Ahmed; McGovern, Brian; Drakakis, Emmanuel; Neil, Mark; Maaskant, Pleun; Akhter, Mahbub; Lee, Jun Su; Degenaar, Patrick
2017-04-01
Optical neuron stimulation arrays are important for both in-vitro biology and retinal prosthetic biomedical applications. Hence, in this work, we present an 8100 pixel high radiance photonic stimulator. The chip module vertically combines custom made gallium nitride μ LEDs with a CMOS application specific integrated circuit. This is designed with active pixels to ensure random access and to allow continuous illumination of all required pixels. The μLEDs have been assembled on the chip using a solder ball flip-chip bonding technique which has allowed for reliable and repeatable manufacture. We have evaluated the performance of the matrix by measuring the different factors including the static, dynamic power consumption, the illumination, and the current consumption by each LED. We show that the power consumption is within a range suitable for portable use. Finally, the thermal behavior of the matrix is monitored and the matrix proved to be thermally stable.
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.
Oberhofer, Harald; Blumberger, Jochen
2010-12-28
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.
NASA Astrophysics Data System (ADS)
Bencheikh, K.; van Zyl, B. P.; Berkane, K.
2016-08-01
The semiclassical ℏ expansion of the one-particle density matrix for a two-dimensional Fermi gas is calculated within the Wigner transform method of B. Grammaticos and A. Voros [Ann. Phys. (N.Y.) 123, 359 (1979), 10.1016/0003-4916(79)90343-9], originally developed in the context of nuclear physics. The method of Grammaticos and Voros has the virtue of preserving both the Hermiticity and idempotency of the density matrix to all orders in the ℏ expansion. As a topical application, we use our semiclassical expansion to go beyond the local-density approximation for the construction of the total dipole-dipole interaction energy functional of a two-dimensional, spin-polarized dipolar Fermi gas. We find a finite, second-order gradient correction to the Hartree-Fock energy, which takes the form ɛ (∇ρ ) 2/√{ρ } , with ɛ being small (|ɛ |≪1 ) and negative. We test the quality of the corrected energy by comparing it with the exact results available for harmonic confinement. Even for small particle numbers, the gradient correction to the dipole-dipole energy provides a significant improvement over the local-density approximation.
2017-01-01
The use of a nanoparticle (NP)-based antitumor drug carrier has been an emerging strategy for selectively delivering the drugs to the tumor area and, thus, reducing the side effects that are associated with a high systemic dose of antitumor drugs. Precise control of drug loading and release is critical so as to maximize the therapeutic index of the NPs. Here, we propose a simple method of synthesizing NPs with tunable drug release while maintaining their loading ability, by varying the polymer matrix density of amine- or carboxyl-functionalized hydrogel NPs. We find that the NPs with a loose matrix released more cisplatin, with up to a 33 times faster rate. Also, carboxyl-functionalized NPs loaded more cisplatin and released it at a faster rate than amine-functionalized NPs. We performed detailed Monte Carlo computer simulations that elucidate the relation between the matrix density and drug release kinetics. We found good agreement between the simulation model and the experimental results for drug release as a function of time. Also, we compared the cellular uptake between amine-functionalized NPs and carboxyl-functionalized NPs, as a higher cellular uptake of NPs leads to improved cisplatin delivery. The amine-functionalized NPs can deliver 3.5 times more cisplatin into cells than the carboxyl-functionalized NPs. The cytotoxic efficacy of both the amine-functionalized NPs and the carboxyl-functionalized NPs showed a strong correlation with the cisplatin release profile, and the latter showed a strong correlation with the NP matrix density. PMID:28782048
Quantum dynamics of finite atomic and molecular systems through density matrix methods
NASA Astrophysics Data System (ADS)
Thorndyke, Brian
We develop a mixed quantum-classical formulation to describe the dynamics of few- and many-body atomic systems by applying a partial Wigner transform over the quantum Liouville equation of motion. In this approach, the density operator becomes a function in quasiclassical phase space, while remaining an operator over a subset of quantal variables. By taking appropriate limits and introducing an effective potential, we derive equations of motion describing quasiclassical nuclear trajectories coupled to quantal electronic evolution. We also introduce a variable timestep procedure to account for the disparity between slow nuclear motion and fast electronic fluctuations. Our mixed quantum-classical method is applied to the study of three simple one-dimensional two-state models. The first model represents the photoinduced desorption of an alkali atom from a metal surface, where near-resonant electron transfer is important. A second model explores a binary collision under conditions where two avoided crossings are present. The third model follows the photoinduced dissociation of the sodium iodide complex, whose long-range attractive surface results in oscillations of internuclear distance. Quantities such as state populations and quantum coherence are computed, and found to be in excellent agreement with precise quantal results obtained through fast Fourier transform grid methods. Having validated our approach, we turn to the study of alkali atoms embedded in rare gas clusters, treating the alkali atom-rare gas interactions with l-dependent semi-local pseudopotentials. Light emission from the electronic motion of the alkali atom is derived in the semiclassical limit, and computational methods to render the simulation feasible for a many-atom cluster are discussed. The formalism is applied to lithium atoms in helium clusters, where the cluster configuration and the electronic population dynamics of the lithium atom are monitored over time. We study both the ground and
One-particle density matrix occupation spectrum of many-body localized states after a global quench
NASA Astrophysics Data System (ADS)
Lezama, Talía L. M.; Bera, Soumya; Schomerus, Henning; Heidrich-Meisner, Fabian; Bardarson, Jens H.
2017-08-01
The emergent integrability of the many-body localized phase is naturally understood in terms of localized quasiparticles. As a result, the occupations of the one-particle density matrix in eigenstates show a Fermi-liquid-like discontinuity. Here, we show that in the steady state reached at long times after a global quench from a perfect density-wave state, this occupation discontinuity is absent, reminiscent of a Fermi liquid at a finite temperature, while the full occupation function remains strongly nonthermal. We discuss how one can understand this as a consequence of the local structure of the density-wave state and the resulting partial occupation of quasiparticles. This partial occupation can be controlled by tuning the initial state and can be described by an effective temperature.
Y. Wu; L. Pan; K. Pruess
2004-03-16
Modeling fracture-matrix interaction within a complex multiple phase flow system is a key issue for fractured reservoir simulation. Commonly used mathematical models for dealing with such interactions employ a dual- or multiple-continuum concept, in which fractures and matrix are represented as overlapping, different, but interconnected continua, described by parallel sets of conservation equations. The conventional single-point upstream weighting scheme, in which the fracture relative permeability is used to represent the counterpart at the fracture-matrix interface, is the most common scheme by which to estimate flow mobility for fracture-matrix flow terms. However, such a scheme has a serious flaw, which may lead to unphysical solutions or significant numerical errors. To overcome the limitation of the conventional upstream weighting scheme, this paper presents a physically based modeling approach for estimating physically correct relative permeability in calculating multiphase flow between fractures and the matrix, using continuity of capillary pressure at the fracture-matrix interface. The proposed approach has been implemented into two multiphase reservoir simulators and verified using analytical solutions and laboratory experimental data. The new method is demonstrated to be accurate, numerically efficient, and easy to implement in dual- or multiple-continuum models.
Wu, Yu-Shu; Pan, Lehua; Pruess, Karsten
2004-03-15
Modeling fracture-matrix interaction within a complex multiple phase flow system is a key issue for fractured reservoir simulation. Commonly used mathematical models for dealing with such interactions employ a dual- or multiple-continuum concept, in which fractures and matrix are represented as overlapping, different, but interconnected continua, described by parallel sets of conservation equations. The conventional single-point upstream weighting scheme, in which the fracture relative permeability is used to represent the counterpart at the fracture-matrix interface, is the most common scheme by which to estimate flow mobility for fracture-matrix flow terms. However, such a scheme has a serious flaw, which may lead to unphysical solutions or significant numerical errors. To overcome the limitation of the conventional upstream weighting scheme, this paper presents a physically based modeling approach for estimating physically correct relative permeability in calculating multiphase flow between fractures and the matrix, using continuity of capillary pressure at the fracture-matrix interface. The proposed approach has been implemented into two multiphase reservoir simulators and verified using analytical solutions and laboratory experimental data. The new method is demonstrated to be accurate, numerically efficient, and easy to implement in dual- or multiple-continuum models.
Annihilating Filter-Based Low-Rank Hankel Matrix Approach for Image Inpainting.
Jin, Kyong Hwan; Ye, Jong Chul
2015-11-01
In this paper, we propose a patch-based image inpainting method using a low-rank Hankel structured matrix completion approach. The proposed method exploits the annihilation property between a shift-invariant filter and image data observed in many existing inpainting algorithms. In particular, by exploiting the commutative property of the convolution, the annihilation property results in a low-rank block Hankel structure data matrix, and the image inpainting problem becomes a low-rank structured matrix completion problem. The block Hankel structured matrices are obtained patch-by-patch to adapt to the local changes in the image statistics. To solve the structured low-rank matrix completion problem, we employ an alternating direction method of multipliers with factorization matrix initialization using the low-rank matrix fitting algorithm. As a side product of the matrix factorization, locally adaptive dictionaries can be also easily constructed. Despite the simplicity of the algorithm, the experimental results using irregularly subsampled images as well as various images with globally missing patterns showed that the proposed method outperforms existing state-of-the-art image inpainting methods.
NASA Astrophysics Data System (ADS)
Hine, N. D. M.; Haynes, P. D.; Mostofi, A. A.; Payne, M. C.
2010-09-01
We present calculations of formation energies of defects in an ionic solid (Al2O3) extrapolated to the dilute limit, corresponding to a simulation cell of infinite size. The large-scale calculations required for this extrapolation are enabled by developments in the approach to parallel sparse matrix algebra operations, which are central to linear-scaling density-functional theory calculations. The computational cost of manipulating sparse matrices, whose sizes are determined by the large number of basis functions present, is greatly improved with this new approach. We present details of the sparse algebra scheme implemented in the ONETEP code using hierarchical sparsity patterns, and demonstrate its use in calculations on a wide range of systems, involving thousands of atoms on hundreds to thousands of parallel processes.
Hine, N D M; Haynes, P D; Mostofi, A A; Payne, M C
2010-09-21
We present calculations of formation energies of defects in an ionic solid (Al(2)O(3)) extrapolated to the dilute limit, corresponding to a simulation cell of infinite size. The large-scale calculations required for this extrapolation are enabled by developments in the approach to parallel sparse matrix algebra operations, which are central to linear-scaling density-functional theory calculations. The computational cost of manipulating sparse matrices, whose sizes are determined by the large number of basis functions present, is greatly improved with this new approach. We present details of the sparse algebra scheme implemented in the ONETEP code using hierarchical sparsity patterns, and demonstrate its use in calculations on a wide range of systems, involving thousands of atoms on hundreds to thousands of parallel processes.
Very high cell density perfusion of CHO cells anchored in a non-woven matrix-based bioreactor.
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
NASA Astrophysics Data System (ADS)
Kobayashi, Masato; Nakai, Hiromi
2006-03-01
We numerically assess the method for obtaining second-order Møller-Plesset (MP2) energy from the Hartree-Fock density matrix (DM) recently proposed by Surján [Surján, Chem. Phys. Lett. 406 (2005) 318]. It is confirmed that Surján's method, referred to as DM-Laplace MP2, can obtain MP2 energy accurately by means of appropriate integral quadrature and a matrix exponential evaluation scheme. Numerical tests reveal that the Euler-Maclaurin and the Romberg numerical integration schemes can achieve milli-hartree accuracy with small quadrature points. This Letter also indicates the possibility of the application of DM-Laplace MP2 to linear-scaling self-consistent field techniques, which give approximate DM.
Lishev, St.; Yordanov, D. Shivarova, A.
2015-04-08
Concepts for the extraction of volume-produced negative hydrogen ions from a rf matrix source (a matrix of small-radius discharges with a planar-coil inductive driving) are presented and discussed based on experimental results for the current densities of the extracted ions and the co-extracted electrons. The experiment has been carried out in a single discharge of the source: a rf discharge with a radius of 2.25 cm inductively driven by a 3.5-turn planar coil. The length of the discharge tube, the area of the reference electrode inserted in the discharge volume, the discharge modes, the magnetic filter and its position along the discharge length, the position of the permanent magnets for the separation of the co-extracted electrons from the extracted ions in the extraction device and the bias applied to its first electrode are considered as factors influencing the extracted currents of negative ions.
Filtered density function approach for reactive transport in groundwater
NASA Astrophysics Data System (ADS)
Suciu, Nicolae; Schüler, Lennart; Attinger, Sabine; Knabner, Peter
2016-04-01
Spatial filtering may be used in coarse-grained simulations (CGS) of reactive transport in groundwater, similar to the large eddy simulations (LES) in turbulence. The filtered density function (FDF), stochastically equivalent to a probability density function (PDF), provides a statistical description of the sub-grid, unresolved, variability of the concentration field. Besides closing the chemical source terms in the transport equation for the mean concentration, like in LES-FDF methods, the CGS-FDF approach aims at quantifying the uncertainty over the whole hierarchy of heterogeneity scales exhibited by natural porous media. Practically, that means estimating concentration PDFs on coarse grids, at affordable computational costs. To cope with the high dimensionality of the problem in case of multi-component reactive transport and to reduce the numerical diffusion, FDF equations are solved by particle methods. But, while trajectories of computational particles are modeled as stochastic processes indexed by time, the concentration's heterogeneity is modeled as a random field, with multi-dimensional, spatio-temporal sets of indices. To overcome this conceptual inconsistency, we consider FDFs/PDFs of random species concentrations weighted by conserved scalars and we show that their evolution equations can be formulated as Fokker-Planck equations describing stochastically equivalent processes in concentration-position spaces. Numerical solutions can then be approximated by the density in the concentration-position space of an ensemble of computational particles governed by the associated Itô equations. Instead of sequential particle methods we use a global random walk (GRW) algorithm, which is stable, free of numerical diffusion, and practically insensitive to the increase of the number of particles. We illustrate the general FDF approach and the GRW numerical solution for a reduced complexity problem consisting of the transport of a single scalar in groundwater
A Synthetic Approach to the Transfer Matrix Method in Classical and Quantum Physics
ERIC Educational Resources Information Center
Pujol, O.; Perez, J. P.
2007-01-01
The aim of this paper is to propose a synthetic approach to the transfer matrix method in classical and quantum physics. This method is an efficient tool to deal with complicated physical systems of practical importance in geometrical light or charged particle optics, classical electronics, mechanics, electromagnetics and quantum physics. Teaching…
Bojanić, Nemanja; Fišteš, Aleksandar; Rakić, Dušan; Takači, Aleksandar; Došenović, Tatjana
2017-05-01
The breakage matrix approach is a mathematical tool to relate input and output particle size distribution from a milling operation. Adjustment of the break release in the flour milling process is extremely important because it affects granulation and quality characteristics of the stock and hence the total results and balance of the mill. In this study the breakage matrix approach has been used for the purpose of controlling the release on the front passages of the break system in the flour milling process. It has been established that, for any particle size distribution of wheat, it is possible to predict break releases together with the distribution of the release size fractions by using the breakage matrices. Also, the reversibility of this approach is examined, that is the possibility to identify the wheat particle size distribution that would result in desired break releases and/or the desired yields of different sized intermediate stocks under the given set of milling conditions. It is confirmed that the breakage matrix approach can be successfully used to predict the break releases. The reverse breakage matrix concept allows the determination of the wheat particle size distribution which would result in a targeted break release. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.
A Synthetic Approach to the Transfer Matrix Method in Classical and Quantum Physics
ERIC Educational Resources Information Center
Pujol, O.; Perez, J. P.
2007-01-01
The aim of this paper is to propose a synthetic approach to the transfer matrix method in classical and quantum physics. This method is an efficient tool to deal with complicated physical systems of practical importance in geometrical light or charged particle optics, classical electronics, mechanics, electromagnetics and quantum physics. Teaching…
Xie, Hang; Jiang, Feng; Tian, Heng; Zheng, Xiao; Kwok, Yanho; Chen, Shuguang; Yam, ChiYung; Yan, YiJing; Chen, Guanhua
2012-07-28
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)], 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.
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.
Nonextensive random matrix theory approach to mixed regular-chaotic dynamics.
Abul-Magd, A Y
2005-06-01
We apply Tsallis' q -indexed entropy to formulate a nonextensive random matrix theory, which may be suitable for systems with mixed regular-chaotic dynamics. The joint distribution of the matrix elements is given by folding the corresponding quantity in the conventional random matrix theory by a distribution of the inverse matrix-element variance. It keeps the basis invariance of the standard theory but violates the independence of the matrix elements. We consider the subextensive regime of q more than unity in which the transition from the Wigner to the Poisson statistics is expected to start. We calculate the level density for different values of the entropic index. Our results are consistent with an analogous calculation by Tsallis and collaborators. We calculate the spacing distribution for mixed systems with and without time-reversal symmetry. Comparing the result of calculation to a numerical experiment shows that the proposed nonextensive model provides a satisfactory description for the initial stage of the transition from chaos towards the Poisson statistics.
An entropy-driven matrix completion (E-MC) approach to complex network mapping
NASA Astrophysics Data System (ADS)
Koochakzadeh, Ali; Pal, Piya
2016-05-01
Mapping the topology of a complex network in a resource-efficient manner is a challenging problem with applications in internet mapping, social network inference, and so forth. We propose a new entropy driven algorithm leveraging ideas from matrix completion, to map the network using monitors (or sensors) which, when placed on judiciously selected nodes, are capable of discovering their immediate neighbors. The main challenge is to maximize the portion of discovered network using only a limited number of available monitors. To this end, (i) a new measure of entropy or uncertainty is associated with each node, in terms of the currently discovered edges incident on that node, and (ii) a greedy algorithm is developed to select a candidate node for monitor placement based on its entropy. Utilizing the fact that many complex networks of interest (such as social networks), have a low-rank adjacency matrix, a matrix completion algorithm, namely 1-bit matrix completion, is combined with the greedy algorithm to further boost its performance. The low rank property of the network adjacency matrix can be used to extrapolate a portion of missing edges, and consequently update the node entropies, so as to efficiently guide the network discovery algorithm towards placing monitors on the nodes that can turn out to be more informative. Simulations performed on a variety of real world networks such as social networks and peer networks demonstrate the superior performance of the matrix-completion guided approach in discovering the network topology.
Parkhomenko, A I; Shalagin, Anatolii M
2011-11-30
Using the eikonal approximation, we have calculated effective collision frequencies in density-matrix kinetic equations describing nonlinear effects in the wings of spectral lines. We have established the relation between the probabilities of absorption and stimulated emission and the characteristics of the radiation and elementary scattering event. The example of the power interaction potential shows that quantum mechanical calculation of the collision frequencies in the eikonal approximation and previously known spectral line wing theory give similar results for the probability of radiation absorption.
Wu, Yu-Shu; Pruess, Karsten
2004-05-04
Modeling fracture-matrix interaction within a multiple-phase flow system is a key issue for fractured reservoir simulation. Commonly used mathematical models for dealing with such interactions employ dual- or multiple-continuum concepts, in which fractures and matrix are represented as overlapping, different, but interconnected continua, described by parallel sets of conservation equations. The conventional single-point upstream weighting scheme is most commonly used to estimate flow mobility for fracture-matrix flow. However, such a scheme may have serious limitations or flaws, which lead to unphysical solutions or significant numerical errors. To overcome the limitations of the conventional upstream weighting scheme, this paper presents a physically based modeling approach for estimating physically correct relative permeability in calculating multiphase flow between fractures and the matrix, using continuity of capillary pressure at the fracture-matrix interface. The proposed approach has been implemented into two multiphase reservoir simulators and verified using analytical solutions and laboratory experimental data. The new method is demonstrated to be accurate, numerically efficient, and easy to implement in dual- or multiple-continuum reservoir simulators.
Density Induced Phase Transitions in the Schwinger Model: A Study with Matrix Product States
NASA Astrophysics Data System (ADS)
Bañuls, Mari Carmen; Cichy, Krzysztof; Cirac, J. Ignacio; Jansen, Karl; Kühn, Stefan
2017-02-01
We numerically study the zero temperature phase structure of the multiflavor Schwinger model at nonzero chemical potential. Using matrix product states, we reproduce analytical results for the phase structure for two flavors in the massless case and extend the computation to the massive case, where no analytical predictions are available. Our calculations allow us to locate phase transitions in the mass-chemical potential plane with great precision and provide a concrete example of tensor networks overcoming the sign problem in a lattice gauge theory calculation.
Influence of Hemp Fibers Pre-processing on Low Density Polyethylene Matrix Composites Properties
NASA Astrophysics Data System (ADS)
Kukle, S.; Vidzickis, R.; Zelca, Z.; Belakova, D.; Kajaks, J.
2016-04-01
In present research with short hemp fibres reinforced LLDPE matrix composites with fibres content in a range from 30 to 50 wt% subjected to four different pre-processing technologies were produced and such their properties as tensile strength and elongation at break, tensile modulus, melt flow index, micro hardness and water absorption dynamics were investigated. Capillary viscosimetry was used for fluidity evaluation and melt flow index (MFI) evaluated for all variants. MFI of fibres of two pre-processing variants were high enough to increase hemp fibres content from 30 to 50 wt% with moderate increase of water sorption capability.
NASA Astrophysics Data System (ADS)
Thorvaldsen, Andreas J.; Ruud, Kenneth; Kristensen, Kasper; Jørgensen, Poul; Coriani, Sonia
2008-12-01
A general method is presented for the calculation of molecular properties to arbitrary order at the Kohn-Sham density functional level of theory. The quasienergy and Lagrangian formalisms are combined to derive response functions and their residues by straightforward differentiation of the quasienergy derivative Lagrangian using the elements of the density matrix in the atomic orbital representation as variational parameters. Response functions and response equations are expressed in the atomic orbital basis, allowing recent advances in the field of linear-scaling methodology to be used. Time-dependent and static perturbations are treated on an equal footing, and atomic basis sets that depend on the applied frequency-dependent perturbations may be used, e.g., frequency-dependent London atomic orbitals. The 2n+1 rule may be applied if computationally favorable, but alternative formulations using higher-order perturbed density matrices are also derived. These may be advantageous in order to minimize the number of response equations that needs to be solved, for instance, when one of the perturbations has many components, as is the case for the first-order geometrical derivative of the hyperpolarizability.
NASA Astrophysics Data System (ADS)
Weisse, A.; Bursill, R. J.; Hamer, C. J.; Weihong, Zheng
2006-04-01
The phase diagram of the two-leg t-Jz ladder is explored, using the density-matrix renormalization group method. Results are obtained for energy gaps, electron density profiles, and correlation functions for the half filled and quarter filled cases. The effective Lagrangian velocity parameter vρ is shown to vanish at half filling. The behavior of the one-hole gap in the Nagaoka limit is investigated, and found to disagree with theoretical predictions. A tentative phase diagram is presented, which is quite similar to the full t-J ladder, but scaled up by a factor of about 2 in coupling. Near half filling a Luther-Emery phase is found, which may be expected to show superconducting correlations, while near quarter filling the system appears to be in a Tomonaga-Luttinger phase.
NASA Astrophysics Data System (ADS)
Gibson, Joshua W.; Johnson, Bruce R.
2006-02-01
A theoretical analysis of recent experiments measuring the 782nm surface-enhanced Raman scattering of p-mercaptoaniline bound to silver nanoshells of different core and shell radii [J. B. Jackson and N. J. Halas, Proc. Natl. Acad. Sci. U.S.A. 101, 17930 (2004)] is performed. Electronic structure Hartree-Fock and density-functional theory calculations for Ag salts of p-mercaptoaniline are used to characterize observed vibrational modes and configuration-interaction singles calculations are carried out to examine excited states. Multimode vibronic density-matrix calculations are then made including one excited electronic state, using a classical description of the strong local fields and a phenomenological treatment of relaxations. The spectral behavior as a function of both nanoshell surface-plasmon resonance position and molecular electronic spacing is examined.
Perturbation approach to multifractal dimensions for certain critical random-matrix ensembles.
Bogomolny, E; Giraud, O
2011-09-01
Fractal dimensions of eigenfunctions for various critical random matrix ensembles are investigated in perturbation series in the regimes of strong and weak multifractality. In both regimes, we obtain expressions similar to those of the critical banded random matrix ensemble extensively discussed in the literature. For certain ensembles, the leading-order term for weak multifractality can be calculated within standard perturbation theory. For other models, such a direct approach requires modifications, which are briefly discussed. Our analytical formulas are in good agreement with numerical calculations.
A New Approach of Designing Superalloys for Low Density
NASA Technical Reports Server (NTRS)
MacKay, Rebecca A.; Gabb, Timothy P.; Smialek, James L.; Nathal, Michael V.
2010-01-01
New low-density single-crystal (LDS) alloy, have bee. developed for turbine blade applications, which have the potential for significant improvements in the thrust-to-weight ratio over current production superalloys. An innovative alloying strategy was wed to achieve alloy density reductions, high-temperature creep resistance, microstructural stability, and cyclic oxidation resistance. The alloy design relies on molybdenum as a potent. lower-density solid-solution strengthener in the nickel-based superalloy. Low alloy density was also achieved with modest rhenium levels tmd the absence of tungsten. Microstructural, physical mechanical, and environmental testing demonstrated the feasibility of this new LDS superalloy design.
A Delphi-matrix approach to SEA and its application within the tourism sector in Taiwan
Kuo, N.-W. . E-mail: ibis@ntcn.edu.tw; Hsiao, T.-Y.; Yu, Y.-H.
2005-04-15
Strategic Environmental Assessment (SEA) is a procedural tool and within the framework of SEA, several different types of analytical methods can be used in the assessment. However, the impact matrix used currently in Taiwan has some disadvantages. Hence, a Delphi-matrix approach to SEA is proposed here to improve the performance of Taiwan's SEA. This new approach is based on the impact matrix combination with indicators of sustainability, and then the Delphi method is employed to collect experts' opinions. In addition, the assessment of National Floriculture Park Plan and Taiwan Flora 2008 Program is taken as an example to examine this new method. Although international exhibition is one of the important tourism (economic) activities, SEA is seldom about tourism sector. Finally, the Delphi-matrix approach to SEA for tourism development plan is established containing eight assessment topics and 26 corresponding categories. In summary, three major types of impacts: resources' usages, pollution emissions, and local cultures change are found. Resources' usages, such as water, electricity, and natural gas demand, are calculated on a per capita basis. Various forms of pollution resulting from this plan, such as air, water, soil, waste, and noise, are also identified.
Analytical O (αs) corrections to the beam frame double-spin density matrix elements of e+e-→t t ¯
NASA Astrophysics Data System (ADS)
Kaldamäe, L.; Groote, S.; Körner, J. G.
2016-12-01
We provide analytical results for the O (αs) corrections to the double-spin density matrix elements in the reaction e+e-→t t ¯ . These concern the elements l l , l t , l n , t t , t n , and n n of the double-spin density matrix elements where l , t , n stand for longitudinal, transverse and normal orientations with respect to the beam frame spanned by the electron and the top quark momentum.
Investigations of turbulent scalar fields using probability density function approach
NASA Technical Reports Server (NTRS)
Gao, Feng
1991-01-01
Scalar fields undergoing random advection have attracted much attention from researchers in both the theoretical and practical sectors. Research interest spans from the study of the small scale structures of turbulent scalar fields to the modeling and simulations of turbulent reacting flows. The probability density function (PDF) method is an effective tool in the study of turbulent scalar fields, especially for those which involve chemical reactions. It has been argued that a one-point, joint PDF approach is the one to choose from among many simulation and closure methods for turbulent combustion and chemically reacting flows based on its practical feasibility in the foreseeable future for multiple reactants. Instead of the multi-point PDF, the joint PDF of a scalar and its gradient which represents the roles of both scalar and scalar diffusion is introduced. A proper closure model for the molecular diffusion term in the PDF equation is investigated. Another direction in this research is to study the mapping closure method that has been recently proposed to deal with the PDF's in turbulent fields. This method seems to have captured the physics correctly when applied to diffusion problems. However, if the turbulent stretching is included, the amplitude mapping has to be supplemented by either adjusting the parameters representing turbulent stretching at each time step or by introducing the coordinate mapping. This technique is still under development and seems to be quite promising. The final objective of this project is to understand some fundamental properties of the turbulent scalar fields and to develop practical numerical schemes that are capable of handling turbulent reacting flows.
Ranucci, C S; Moghe, P V
2001-02-01
The regulation of cell motility by ligand density on substrates with variable microtopography is not well understood. In this report, we studied the adhesion and motility behavior of HepG2 cells on microtextured poly(glycolic-co-lactic)acid (PGLA) copolymer substrates, whose surface bioactivity was differentially modified through the adsorption of 0-5.5 ng/cm(2) collagen. Microtextured PGLA substrates were fabricated as thin films with a uniform surface distribution of micropores of median size of 3.1 +/- 1.5 microm and three-dimensional root mean squared roughness of 0.253 microm. Even in the absence of collagen, cells on microtextured substrates responded to substrate topography by exhibiting a 200% increase in adhesion strength compared with untextured controls and ventral localization of the intracellular adhesion protein vinculin. Further enhancement in adhesion strength (420% over untextured, untreated substrates) was demonstrated with bioactivated, microtextured surfaces, indicating that cell adhesion responses to topography and surface ligand density were cooperative. Our motility studies of cells on untextured substrates adsorbed with different levels of collagen demonstrated that a classical biphasic relationship between the cell population averaged migration rate, mu, and the collagen ligand density was preserved. However, comparison of cell motility responses between untextured and microtextured substrates indicates that the motility versus ligand density curve shifted, such that equivalent levels of cell motility were achieved at lower ligand density on microtextured surfaces. Furthermore, the maximum mu values achieved on the microtextured substrates exceeded those on untextured substrates by twofold. Taken together, we show that the magnitude of subcellular scale microtexture of a polymer substrate can sensitize the cell motility responsiveness to substrate ligand concentration; we suggest that the underlying mechanisms involve alteration in the
Sorption on deformable solids. Density functional theory approach.
Berim, Gersh O; Ruckenstein, Eli
2011-11-17
A modified density functional theory is proposed to describe fluid adsorption and absorption by a solid, the density of which is nonhomogeneous near the interface. The density distribution of the solid is not provided by apriori assumptions, but is obtained via the minimization of an appropriate thermodynamic potential. The theory considers a mixture of two components in a slitlike pore. One of them, the fluid, is in contact with a reservoir containing the same kind of molecules and can be described through a grand canonical ensemble. The other component has strong interactions between its molecules. As a consequence, it forms a solid in the slit which can be treated as a canonical ensemble of a fixed number of molecules. The theory predicts both an intrinsic (in the absence of fluid) change in the solid density near the interface and a solid density variation as the fluid density in the reservoir is changed. In addition, it reveals that the oscillations that occur in the fluid density when the solid density is uniform are damped by the nonuniform solid. The theory provides the amounts of fluid adsorbed as well as absorbed by the solid.
Predicting Fish Densities in Lotic Systems: a Simple Modeling Approach
Fish density models are essential tools for fish ecologists and fisheries managers. However, applying these models can be difficult because of high levels of model complexity and the large number of parameters that must be estimated. We designed a simple fish density model and te...
Predicting Fish Densities in Lotic Systems: a Simple Modeling Approach
Fish density models are essential tools for fish ecologists and fisheries managers. However, applying these models can be difficult because of high levels of model complexity and the large number of parameters that must be estimated. We designed a simple fish density model and te...
Two-electron Reduced-Density-Matrix Mechanics: With Application to Many-electron Atoms and Molecules
NASA Astrophysics Data System (ADS)
Mazziotti, David
2010-03-01
In 1959 Charles Coulson popularized the challenge of computing the ground-state energy as a functional of the two-electron reduced density matrix (2-RDM) without the many-electron wavefunction. Recently, theoretical and computational advances have led to two classes of 2-RDM methods [1]: (i) the variational calculation of the 2-RDM subject to approximate N-representability conditions and (ii) the non-variational calculation of the 2-RDM from the anti-Hermitian contracted Schr"odinger equation. I will develop the background for the 2-RDM methods, discuss recent theoretical and computational advances, and present some applications, including the detection of poly-radical correlation in polyaromatic acene and aryne chains, the study of protonated acetylene and malonaldehyde beyond the Born-Oppenheimer approximation, and the computation of activation energies in pericyclic reactions of open- and closed-shell molecular species. [4pt] [1] ``Two-electron Reduced-Density-Matrix Mechanics with Application to Many-electron Atoms and Molecules,'' edited by D. A. Mazziotti, Advances in Chemical Physics Vol. 134 (Wiley, New York, 2007).
Giesbertz, K. J. H.; Gritsenko, O. V.; Baerends, E. J.
2014-05-14
Recently, we have demonstrated that the problems finding a suitable adiabatic approximation in time-dependent one-body reduced density matrix functional theory can be remedied by introducing an additional degree of freedom to describe the system: the phase of the natural orbitals [K. J. H. Giesbertz, O. V. Gritsenko, and E. J. Baerends, Phys. Rev. Lett. 105, 013002 (2010); K. J. H. Giesbertz, O. V. Gritsenko, and E. J. Baerends, J. Chem. Phys. 133, 174119 (2010)]. In this article we will show in detail how the frequency-dependent response equations give the proper static limit (ω → 0), including the perturbation in the chemical potential, which is required in static response theory to ensure the correct number of particles. Additionally we show results for the polarizability for H{sub 2} and compare the performance of two different two-electron functionals: the phase-including Löwdin–Shull functional and the density matrix form of the Löwdin–Shull functional.
Spin alignment and density matrix measurement in sup 28 Si + sup 12 C orbiting reaction
Ray, A.; Shapira, D.; Halbert, M.L.; Gomez del Campo, J.; Kim, H.J. ); Sullivan, J.P. . Cyclotron Inst.); Shivakumar, B.; Mitchell, J. . Wright Nuclear Structure Lab.)
1990-01-01
Gamma-ray angular correlations have been measured for the strongly damped reactions {sup 12}C({sup 28}Si,{sup 12}C){sup 28}Si between {theta}{sub cm} = (120{degree} {minus} 160{degree}) for E{sub cm} = 43.5 and 48 MeV. We find that the density matrices for the {sup 12}C(2{sub 1}{sup +}) and {sup 28}Si states are almost diagonal with respect to the direction of motion of the outgoing particle. The measured density matrices and spin alignments are consistent with the picture of formation of a long-lived dinuclear complex undergoing orbiting, bending and wriggling motions, but not with those obtained from statistical compound nucleus or sticking model calculations. 17 refs., 2 figs., 1 tab.
Increasing the power density when using inert matrix fuels to reduce production of transuranics
Recktenwald, G.D.; Deinert, M.R.
2013-07-01
Reducing the production of transuranics is a goal of most advanced nuclear fuel cycles. One way to do this is to recycle the transuranics into the same reactors that are currently producing them using an inert matrix fuel. In previous work we have modeled such a reactor where 72%, of the core is comprised of standard enriched uranium fuel pins, with the remaining 28% fuel made from Yttria stabilized zirconium, in which transuranics are loaded. A key feature of this core is that all of the transuranics produced by the uranium fuel assemblies are later burned in inert matrix fuel assemblies. It has been shown that this system can achieve reductions in transuranic waste of more than 86%. The disadvantage of such a system is that the core power rating must be significantly lower than a standard pressurized water reactor. One reason for the lower power is that high burnup of the uranium fuel precludes a critical level of reactivity at the end of the campaign. Increasing the uranium enrichment and changing the pin pitch are two ways to increase burnup while maintaining criticality. In this paper we use MCNPX and a linear reactivity model to quantify the effect of these two parameters on the end of campaign reactivity. Importantly, we show that in the region of our proposed reactor, enrichment increases core reactivity by 0.02 per percent uranium 235 and pin pitch increases reactivity by 0.02 per mm. Reactivity is lost at a rate of 0.005 per MWd/kgIHM uranium burnup. (authors)
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.
Shrinkage covariance matrix approach based on robust trimmed mean in gene sets detection
NASA Astrophysics Data System (ADS)
Karjanto, Suryaefiza; Ramli, Norazan Mohamed; Ghani, Nor Azura Md; Aripin, Rasimah; Yusop, Noorezatty Mohd
2015-02-01
Microarray involves of placing an orderly arrangement of thousands of gene sequences in a grid on a suitable surface. The technology has made a novelty discovery since its development and obtained an increasing attention among researchers. The widespread of microarray technology is largely due to its ability to perform simultaneous analysis of thousands of genes in a massively parallel manner in one experiment. Hence, it provides valuable knowledge on gene interaction and function. The microarray data set typically consists of tens of thousands of genes (variables) from just dozens of samples due to various constraints. Therefore, the sample covariance matrix in Hotelling's T2 statistic is not positive definite and become singular, thus it cannot be inverted. In this research, the Hotelling's T2 statistic is combined with a shrinkage approach as an alternative estimation to estimate the covariance matrix to detect significant gene sets. The use of shrinkage covariance matrix overcomes the singularity problem by converting an unbiased to an improved biased estimator of covariance matrix. Robust trimmed mean is integrated into the shrinkage matrix to reduce the influence of outliers and consequently increases its efficiency. The performance of the proposed method is measured using several simulation designs. The results are expected to outperform existing techniques in many tested conditions.
Density matrix spectra and order parameters in the 1D extended Hubbard model
NASA Astrophysics Data System (ADS)
Yu, Wing Chi; Gu, Shi-Jian; Lin, Hai-Qing
2016-09-01
Without any knowledge of the symmetry existing in a system, we derive the exact forms of the order parameters which show long-range correlations in the ground state of the one-dimensional (1D) extended Hubbard model using a quantum information approach. Our work demonstrates that the quantum information approach can help us to find the explicit form of the order parameter, which could not be derived systematically via traditional methods in the condensed matter theory.
Beer, Matthias; Ochsenfeld, Christian
2008-06-14
A density matrix-based Laplace reformulation of coupled-perturbed self-consistent field (CPSCF) theory is presented. It allows a direct, instead of iterative, solution for the integral-independent part of the density matrix-based CPSCF (D-CPSCF) equations [J. Kussmann and C. Ochsenfeld, J. Chem. Phys. 127, 054103 (2007)]. In this way, the matrix-multiplication overhead compared to molecular orbital-based solutions is reduced to a minimum, while at the same time, the linear-scaling behavior of D-CPSCF theory is preserved. The present Laplace-based equation solver is expected to be of general applicability.
Simon, Aude; Iftner, Christophe; Mascetti, Joëlle; Spiegelman, Fernand
2015-03-19
The present theoretical study aims at investigating the effects of an argon matrix on the structures, energetics, dynamics, and infrared (IR) spectra of small water clusters (H2O)n (n = 1-6). The potential energy surface is obtained from a hybrid self-consistent charge density functional-based tight binding/force-field approach (SCC-DFTB/FF) in which the water clusters are treated at the SCC-DFTB level and the matrix is modeled at the FF level by a cluster consisting of ∼340 Ar atoms with a face centered cubic (fcc) structure, namely (H2O)n/Ar. With respect to a pure FF scheme, this allows a quantum description of the molecular system embedded in the matrix, along with all-atom geometry optimization and molecular dynamics (MD) simulations of the (H2O)n/Ar system. Finite-temperature IR spectra are derived from the MD simulations. The SCC-DFTB/FF scheme is first benchmarked on (H2O)Arn clusters against correlated wave function results and DFT calculations performed in the present work, and against FF data available in the literature. Regarding (H2O)n/Ar systems, the geometries of the water clusters are found to adapt to the fcc environment, possibly leading to intermolecular distortion and matrix perturbation. Several energetical quantities are estimated to characterize the water clusters in the matrix. In the particular case of the water hexamer, substitution and insertion energies for the prism, bag, and cage are found to be lower than that for the 6-member ring isomer. Finite-temperature MD simulations show that the water monomer has a quasifree rotation motion at 13 K, in agreement with experimental data. In the case of the water dimer, the only large-amplitude motion is a distortion-rotation intermolecular motion, whereas only vibration motions around the nuclei equilibrium positions are observed for clusters with larger sizes. Regarding the IR spectra, we find that the matrix environment leads to redshifts of the stretching modes and almost no shift of the
NASA Astrophysics Data System (ADS)
Schuetrumpf, B.; Nazarewicz, W.; Reinhard, P.-G.
2017-08-01
Background: The central depression of nucleonic density, i.e., a reduction of density in the nuclear interior, has been attributed to many factors. For instance, bubble structures in superheavy nuclei are believed to be due to the electrostatic repulsion. In light nuclei, the mechanism behind the density reduction in the interior has been discussed in terms of shell effects associated with occupations of s orbits. Purpose: The main objective of this work is to reveal mechanisms behind the formation of central depression in nucleonic densities in light and heavy nuclei. To this end, we introduce several measures of the internal nucleonic density. Through the statistical analysis, we study the information content of these measures with respect to nuclear matter properties. Method: We apply nuclear density functional theory with Skyrme functionals. Using the statistical tools of linear least square regression, we inspect correlations between various measures of central depression and model parameters, including nuclear matter properties. We study bivariate correlations with selected quantities as well as multiple correlations with groups of parameters. Detailed correlation analysis is carried out for 34Si for which a bubble structure has been reported recently, 48Ca, and N =82 , 126, and 184 isotonic chains. Results: We show that the central depression in medium-mass nuclei is very sensitive to shell effects, whereas for superheavy systems it is firmly driven by the electrostatic repulsion. An appreciable semibubble structure in proton density is predicted for 294Og, which is currently the heaviest nucleus known experimentally. Conclusion: Our correlation analysis reveals that the central density indicators in nuclei below 208Pb carry little information on parameters of nuclear matter; they are predominantly driven by shell structure. On the other hand, in the superheavy nuclei there exists a clear relationship between the central nucleonic density and symmetry energy.
On the scaling of avaloids and turbulence with the average density approaching the density limit
NASA Astrophysics Data System (ADS)
Antar, G. Y.; Counsell, G.; Ahn, J.-W.
2005-08-01
This article is dedicated to the characterization of turbulent transport in the scrape-off layer of the Mega Ampère Spherical Tokamak [A. Sykes et al., Phys. Plasmas 8, 2101 (2001)] as a function of the average density (nL). The aim is to answer a renewed interest in this subject since the bursty character of turbulence in the scrape-off layer was shown to be caused by large-scale events with high radial velocity reaching about 1/10th of the sound speed called avaloids [G. Antar et al., Phys. Rev. Lett 87, 065001 (2001)]. With increasing density, turbulence and transport increase nonlinearly at the midplane while remaining almost unchanged in the target region. Using various and complementary statistical analyses, the existence of a "critical" density, at nL/nG≃0.35 is emphasized; nG is the Greenwald density. Both above and below this density, intermittency decreases and avaloids play a decreasing role in the particle radial transport. This is interpreted as caused by the interplay between avaloids and the surrounding turbulent structures which mix them more efficiently with increasing density as the level of the background turbulence increases. The scaling of the different quantities with respect to the normalized density is obtained. It reveals that not only the level of turbulence and transport increase, but also the radial velocity and length scales. This increases the coupling between the hot plasma edge and the cold scrape-off layer that may explain the disruptive instability occurring at high densities.
On the scaling of avaloids and turbulence with the average density approaching the density limit
Antar, G.Y.; Counsell, G.; Ahn, J.-W.
2005-08-15
This article is dedicated to the characterization of turbulent transport in the scrape-off layer of the Mega Ampere Spherical Tokamak [A. Sykes et al., Phys. Plasmas 8, 2101 (2001)] as a function of the average density (n{sub L}). The aim is to answer a renewed interest in this subject since the bursty character of turbulence in the scrape-off layer was shown to be caused by large-scale events with high radial velocity reaching about 1/10th of the sound speed called avaloids [G. Antar et al., Phys. Rev. Lett 87, 065001 (2001)]. With increasing density, turbulence and transport increase nonlinearly at the midplane while remaining almost unchanged in the target region. Using various and complementary statistical analyses, the existence of a 'critical' density, at n{sub L}/n{sub G}{approx_equal}0.35 is emphasized; n{sub G} is the Greenwald density. Both above and below this density, intermittency decreases and avaloids play a decreasing role in the particle radial transport. This is interpreted as caused by the interplay between avaloids and the surrounding turbulent structures which mix them more efficiently with increasing density as the level of the background turbulence increases. The scaling of the different quantities with respect to the normalized density is obtained. It reveals that not only the level of turbulence and transport increase, but also the radial velocity and length scales. This increases the coupling between the hot plasma edge and the cold scrape-off layer that may explain the disruptive instability occurring at high densities.
Positron accumulation effect in particles embedded in a low-density matrix
Dryzek, Jerzy; Siemek, Krzysztof
2015-02-07
Systematic studies of the so-called positron accumulation effect for samples with particles embedded in a matrix are reported. This effect is related to energetic positrons which penetrate inhomogeneous medium. Due to differences in the linear absorption coefficient, different amounts of positrons are accumulated and annihilate in the identical volume of both materials. Positron lifetime spectroscopy and Doppler broadening of the annihilation line using Na-22 positrons were applied to the studies of the epoxy resin samples with embedded micro-sized particles of transition metals, i.e., Ni, Sn, Mo, W, and nonmetal particles, i.e., Si and NaF. The significant difference between the determined fraction of positrons annihilating in the particles and the particle volume fraction indicates the positron accumulation effect. The simple phenomenological model and Monte Carlo simulations are able to describe the main features of the obtained dependencies. The aluminum alloy with embedded Sn nanoparticles is also considered for demonstration differences between the accumulation and another related effect, i.e., the positron affinity.
On the GPI approach with unknown inertia matrix in robot manipulators
NASA Astrophysics Data System (ADS)
Arteaga-Pérez, Marco A.; Gutiérrez-Giles, Alejandro
2014-04-01
This article discusses the design of generalised proportional integral observers for the tracking control of robot manipulators. The unknown, possibly state-dependent, additive nonlinearity influencing the input-output description, in terms of the tracking error dynamics is modelled for observer construction purposes, as an absolutely bounded, additive, unknown time-varying perturbation input signal. A disadvantage of the approach lies in the fact that the system inertia matrix is usually required for implementation. In this work, it is shown how the approach can be modified to avoid the use of the inertia matrix when it is unknown. A set of experiments with three different test beds is carried out to show the good performance of the proposed algorithm.
Nested-observation error covariance matrix in 1dVAR approach
NASA Astrophysics Data System (ADS)
Park, C.; Heidinger, A. K.
2010-12-01
Cloud-top Height (CTH) information is critical parameter derived from satellites. In recognition of this, CTH algorithms were included in the algorithm package developed by the NOAA GOES-R Algorithm Working Group (AWG) for application to the Advanced Baseline lmager (ABI). The ABI Cloud Height Algorithm (ACHA) uses an optimal estimation (OE) method with nested observations from three infrared channels (11, 12, 13.3 μm). The retrieval accuracy of this approach is highly dependent on the proper specification of the background error covariance and the observation error covariance matrices. The study introduces a new method to estimate all elements (including off-diagonal terms) of the observation error and its covariance matrix. In this study, we will demonstrate how proper specification of the off-diagonal terms in observation error covariance matrix with nested observation data set improves the ACHA approach. This improvement will be demonstrated through comparisons with CALIPSO, CLOUDSAT and MODIS CTH products.
NASA Astrophysics Data System (ADS)
Schrodt, F. I.; Shan, H.; Kattge, J.; Reich, P.; Banerjee, A.; Reichstein, M.
2012-12-01
With the advent of remotely sensed data and coordinated efforts to create global databases, the ecological community has progressively become more data-intensive. However, in contrast to other disciplines, statistical ways of handling these large data sets, especially the gaps which are inherent to them, are lacking. Widely used theoretical approaches, for example model averaging based on Akaike's information criterion (AIC), are sensitive to missing values. Yet, the most common way of handling sparse matrices - the deletion of cases with missing data (complete case analysis) - is known to severely reduce statistical power as well as inducing biased parameter estimates. In order to address these issues, we present novel approaches to gap filling in large ecological data sets using matrix factorization techniques. Factorization based matrix completion was developed in a recommender system context and has since been widely used to impute missing data in fields outside the ecological community. Here, we evaluate the effectiveness of probabilistic matrix factorization techniques for imputing missing data in ecological matrices using two imputation techniques. Hierarchical Probabilistic Matrix Factorization (HPMF) effectively incorporates hierarchical phylogenetic information (phylogenetic group, family, genus, species and individual plant) into the trait imputation. Kernelized Probabilistic Matrix Factorization (KPMF) on the other hand includes environmental information (climate and soils) into the matrix factorization through kernel matrices over rows and columns. We test the accuracy and effectiveness of HPMF and KPMF in filling sparse matrices, using the TRY database of plant functional traits (http://www.try-db.org). TRY is one of the largest global compilations of plant trait databases (750 traits of 1 million plants), encompassing data on morphological, anatomical, biochemical, phenological and physiological features of plants. However, despite of unprecedented
Charged- and neutral-pion production in the S-matrix approach
Malafaia, V.; Pena, M. T.; Elster, Ch.; Adam, J. Jr.
2006-10-15
The S-matrix approach is used to calculate both charged- and neutral-pion production in nucleon-nucleon (NN) scattering near threshold. The irreducible pion-rescattering diagram, direct production mechanism, {delta} isobars in intermediate states, and Z diagrams mediated by heavy isoscalar mesons are included in the calculation. For the NN distortions, we considered a realistic interaction, within the Bonn family of potentials, which describes the nucleonic inelasticities above the pion production energy threshold.
Villanueva, Idalis; Bishop, Nikki L.
2009-01-01
The ability to encapsulate cells over a range of cell densities is important toward mimicking cell densities of native tissues and rationally designing strategies where cell source and/or cell numbers are clinically limited. Our preliminary findings demonstrate that survival of freshly isolated adult bovine chondrocytes dramatically decreases when photoencapsulated in poly(ethylene glycol) hydrogels at low densities (4 million cells/mL). During enzymatic digestion of cartilage, chondrocytes undergo a harsh change in their microenvironment. We hypothesize that the absence of exogenous antioxidants, the hyposmotic environment, and the loss of a protective pericellular matrix (PCM) increase chondrocytes' susceptibility to free radical damage during photoencapsulation. Incorporation of antioxidants and serum into the encapsulation medium improved cell survival twofold compared to phosphate-buffered saline. Increasing medium osmolarity from 330 to 400 mOsm (physiological) improved cell survival by 40% and resulted in ∼2-fold increase in adenosine triphosphate (ATP) production 24 h postencapsulation. However, cell survival was only temporary. Allowing cells to reproduce some PCM before photoencapsulation in 400 mOsm medium resulted in superior cell survival during and postencapsulation for up to 15 days. In summary, the combination of antioxidants, physiological osmolarity, and the development of some PCM result in an improved robustness against free radical damage during photoencapsulation. PMID:19331581
Villanueva, Idalis; Bishop, Nikki L; Bryant, Stephanie J
2009-10-01
The ability to encapsulate cells over a range of cell densities is important toward mimicking cell densities of native tissues and rationally designing strategies where cell source and/or cell numbers are clinically limited. Our preliminary findings demonstrate that survival of freshly isolated adult bovine chondrocytes dramatically decreases when photoencapsulated in poly(ethylene glycol) hydrogels at low densities (4 million cells/mL). During enzymatic digestion of cartilage, chondrocytes undergo a harsh change in their microenvironment. We hypothesize that the absence of exogenous antioxidants, the hyposmotic environment, and the loss of a protective pericellular matrix (PCM) increase chondrocytes' susceptibility to free radical damage during photoencapsulation. Incorporation of antioxidants and serum into the encapsulation medium improved cell survival twofold compared to phosphate-buffered saline. Increasing medium osmolarity from 330 to 400 mOsm (physiological) improved cell survival by 40% and resulted in approximately 2-fold increase in adenosine triphosphate (ATP) production 24 h postencapsulation. However, cell survival was only temporary. Allowing cells to reproduce some PCM before photoencapsulation in 400 mOsm medium resulted in superior cell survival during and postencapsulation for up to 15 days. In summary, the combination of antioxidants, physiological osmolarity, and the development of some PCM result in an improved robustness against free radical damage during photoencapsulation.
NASA Astrophysics Data System (ADS)
Kurashige, Yuki; Yanai, Takeshi
2009-06-01
This article presents an efficient and parallelized implementation of the density matrix renormalization group (DMRG) algorithm for quantum chemistry calculations. The DMRG method as a large-scale multireference electronic structure model is by nature particularly efficient for one-dimensionally correlated systems, while the present development is oriented toward applications for polynuclear transition metal compounds, in which the macroscopic one-dimensional structure of electron correlation is absent. A straightforward extension of the DMRG algorithm is proposed with further improvements and aggressive optimizations to allow its application with large multireference active space, which is often demanded for metal compound calculations. Special efficiency is achieved by making better use of sparsity and symmetry in the operator and wave function representations. By accomplishing computationally intensive DMRG calculations, the authors have found that a large number of renormalized basis states are required to represent high entanglement of the electron correlation for metal compound applications, and it is crucial to adopt auxiliary perturbative correction to the projected density matrix during the DMRG sweep optimization in order to attain proper convergence to the solution. Potential energy curve calculations for the Cr2 molecule near the known equilibrium precisely predicted the full configuration interaction energies with a correlation space of 24 electrons in 30 orbitals [denoted by (24e,30o)]. The energies are demonstrated to be accurate to 0.6mEh (the error from the extrapolated best value) when as many as 10 000 renormalized basis states are employed for the left and right DMRG block representations. The relative energy curves for [Cu2O2]2+ along the isomerization coordinate were obtained from DMRG and other correlated calculations, for which a fairly large orbital space (32e,62o) is modeled as a full correlation space. The DMRG prediction nearly overlaps
An Extreme Learning Machine Approach to Density Estimation Problems.
Cervellera, Cristiano; Maccio, Danilo
2017-01-17
In this paper, we discuss how the extreme learning machine (ELM) framework can be effectively employed in the unsupervised context of multivariate density estimation. In particular, two algorithms are introduced, one for the estimation of the cumulative distribution function underlying the observed data, and one for the estimation of the probability density function. The algorithms rely on the concept of $F$-discrepancy, which is closely related to the Kolmogorov-Smirnov criterion for goodness of fit. Both methods retain the key feature of the ELM of providing the solution through random assignment of the hidden feature map and a very light computational burden. A theoretical analysis is provided, discussing convergence under proper hypotheses on the chosen activation functions. Simulation tests show how ELMs can be successfully employed in the density estimation framework, as a possible alternative to other standard methods.
An information theory approach to the density of the earth
NASA Technical Reports Server (NTRS)
Graber, M. A.
1977-01-01
Information theory can develop a technique which takes experimentally determined numbers and produces a uniquely specified best density model satisfying those numbers. A model was generated using five numerical parameters: the mass of the earth, its moment of inertia, three zero-node torsional normal modes (L = 2, 8, 26). In order to determine the stability of the solution, six additional densities were generated, in each of which the period of one of the three normal modes was increased or decreased by one standard deviation. The superposition of the seven models is shown. It indicates that current knowledge of the torsional modes is sufficient to specify the density in the upper mantle but that the lower mantle and core will require smaller standard deviations before they can be accurately specified.
The density of states approach for the simulation of finite density quantum field theories
NASA Astrophysics Data System (ADS)
Langfeld, K.; Lucini, B.; Rago, A.; Pellegrini, R.; Bongiovanni, L.
2015-07-01
Finite density quantum field theories have evaded first principle Monte-Carlo simulations due to the notorious sign-problem. The partition function of such theories appears as the Fourier transform of the generalised density-of-states, which is the probability distribution of the imaginary part of the action. With the advent of Wang-Landau type simulation techniques and recent advances [1], the density-of-states can be calculated over many hundreds of orders of magnitude. Current research addresses the question whether the achieved precision is high enough to reliably extract the finite density partition function, which is exponentially suppressed with the volume. In my talk, I review the state-of-play for the high precision calculations of the density-of-states as well as the recent progress for obtaining reliable results from highly oscillating integrals. I will review recent progress for the Z3 quantum field theory for which results can be obtained from the simulation of the dual theory, which appears to free of a sign problem.
Crystallization induced by multiple seeds: dynamical density functional approach.
Neuhaus, T; Schmiedeberg, M; Löwen, H
2013-12-01
Using microscopic dynamical density functional theory, we calculate the dynamical formation of polycrystals by following the crystal growth around multiple crystalline seeds imposed to an undercooled fluid. Depending on the undercooling and the size ratio as well as the relative crystal orientation of two neighboring seeds, three possibilities of the final state emerge, namely no crystallization at all, formation of a monocrystal, or two crystallites separated by a curved grain boundary. Our results, which are obtained for two-dimensional hard disk systems using a fundamental-measure density functional, shed new light on the particle-resolved structure and growth of polycrystalline material in general.
Sousa, João Carlos; Costa, Manuel João; Palha, Joana Almeida
2010-03-01
The biochemistry and molecular biology of the extracellular matrix (ECM) is difficult to convey to students in a classroom setting in ways that capture their interest. The understanding of the matrix's roles in physiological and pathological conditions study will presumably be hampered by insufficient knowledge of its molecular structure. Internet-available resources can bridge the division between the molecular details and ECM's biological properties and associated processes. This article presents an approach to teach the ECM developed for first year medical undergraduates who, working in teams: (i) Explore a specific molecular component of the matrix, (ii) identify a disease in which the component is implicated, (iii) investigate how the component's structure/function contributes to ECM' supramolecular organization in physiological and in pathological conditions, and (iv) share their findings with colleagues. The approach-designated i-cell-MATRIX-is focused on the contribution of individual components to the overall organization and biological functions of the ECM. i-cell-MATRIX is student centered and uses 5 hours of class time. Summary of results and take home message: A "1-minute paper" has been used to gather student feedback on the impact of i-cell-MATRIX. Qualitative analysis of student feedback gathered in three consecutive years revealed that students appreciate the approach's reliance on self-directed learning, the interactivity embedded and the demand for deeper insights on the ECM. Learning how to use internet biomedical resources is another positive outcome. Ninety percent of students recommend the activity for subsequent years. i-cell-MATRIX is adaptable by other medical schools which may be looking for an approach that achieves higher student engagement with the ECM. Copyright © 2010 International Union of Biochemistry and Molecular Biology, Inc.
Shenvi, Neil; van Aggelen, Helen; Yang, Yang; Yang, Weitao; Schwerdtfeger, Christine; Mazziotti, David
2013-08-07
Tensor hypercontraction is a method that allows the representation of a high-rank tensor as a product of lower-rank tensors. In this paper, we show how tensor hypercontraction can be applied to both the electron repulsion integral tensor and the two-particle excitation amplitudes used in the parametric 2-electron reduced density matrix (p2RDM) algorithm. Because only O(r) auxiliary functions are needed in both of these approximations, our overall algorithm can be shown to scale as O(r(4)), where r is the number of single-particle basis functions. We apply our algorithm to several small molecules, hydrogen chains, and alkanes to demonstrate its low formal scaling and practical utility. Provided we use enough auxiliary functions, we obtain accuracy similar to that of the standard p2RDM algorithm, somewhere between that of CCSD and CCSD(T).
Jacquod, Ph
2004-04-16
Two particles, initially in a product state, become entangled when they come together and start to interact. Using semiclassical methods, we calculate the time evolution of the corresponding reduced density matrix rho(1), obtained by integrating out the degrees of freedom of one of the particles. We find that entanglement generation sensitively depends (i) on the interaction potential, especially on its strength and range, and (ii) on the nature of the underlying classical dynamics. Under general statistical assumptions, and for short-ranged interaction potentials, we find that P(t) decays exponentially fast in a chaotic environment, whereas it decays only algebraically in a regular system. In the chaotic case, the decay rate is given by the golden rule spreading of one-particle states due to the two-particle coupling, but cannot exceed the system's Lyapunov exponent.
Chan, Garnet Kin-Lic; Van Voorhis, Troy
2005-05-22
We describe the theory and implementation of two extensions to the density-matrix renormalization-group (DMRG) algorithm in quantum chemistry: (i) to work with an underlying nonorthogonal one-particle basis (using a biorthogonal formulation) and (ii) to use non-Hermitian and complex operators and complex wave functions, which occur naturally in biorthogonal formulations. Using these developments, we carry out ground-state calculations on ethene, butadiene, and hexatriene, in a polarized atomic-orbital basis. The description of correlation in these systems using a localized nonorthogonal basis is improved over molecular-orbital DMRG calculations, and comparable to or better than coupled-cluster calculations, although we encountered numerical problems associated with non-Hermiticity. We believe that the non-Hermitian DMRG algorithm may further become useful in conjunction with other non-Hermitian Hamiltonians, for example, similarity-transformed coupled-cluster Hamiltonians.
Das, Mousumi
2014-03-28
We studied the nature of the ground state and low-lying excited states of armchair polyacene oligomers (Polyphenanthrene) within long-range Pariser-Parr-Pople model Hamiltonian with up to 14 monomers using symmetrized density matrix renormalization group technique. The ground state of all armchair polyacenes studied is found to be singlet. The results show that lowest singlet dipole allowed excited state has higher energy for armchair polyacenes as compared to linear fused polyacenes. Moreover, unlike linear fused polyacenes, the lowest singlet excited state of these oligomers is always found to lie below the lowest dipole forbidden two-photon state indicating that these armchair polyacene oligomers strongly fluoresce. The calculations of low-lying excitations on singly and triply electron doped armchair polyacene oligomers show a low energy band with strong transition dipole moment that coupled to charge conductivity. This implies armchair polyacene posses novel field-effect transistor properties.
Dual Approach To Superquantile Estimation And Applications To Density Fitting
2016-06-01
optimization on second-order epi-splines to arrive at incrementally better approximations of superquantile values. With these improved estimates, we...samples of various heavy-tailed distributions. 14. SUBJECT TERMS probability density estimation, epi-splines, optimization , risk quantification...superquantiles and superexpectations, we apply constrained optimization on second-order epi-splines to arrive at incrementally better approximations of
The nutrient density approach to healthy eating: challenges and opportunities
USDA-ARS?s Scientific Manuscript database
The term 'nutrient density' for foods/beverages has been used loosely to promote the Dietary Guidelines for Americans. The 2010 Dietary Guidelines for Americans defined 'all vegetables, fruits, whole grains, fat-free or low-fat milk and milk products, seafood, lean meats and poultry, eggs, beans and...
Lin, Huizi A; Gupta, Michelle S; Varma, Devika M; Gilchrist, M Lane; Nicoll, Steven B
2016-01-01
Engineered constructs represent a promising treatment for replacement of nucleus pulposus (NP) tissue. Recently, photocrosslinked hydrogels comprised of methacrylated carboxymethylcellulose (CMC) were shown to support chondrogenic differentiation of encapsulated human mesenchymal stem cells (hMSCs) and promote accumulation of NP-like extracellular matrix (ECM). The objective of this study was to investigate the influence of CMC crosslinking density, by varying macromer concentration and modification (i.e., methacrylation) percentage, on NP-like differentiation of encapsulated hMSCs. Constructs of lower macromer concentration (2%, w/v) exhibited significantly greater collagen II accumulation, more homogeneous distribution of ECM macromolecules, and a temporal increase in mechanical properties compared to hydrogels of higher macromer concentration (4%, w/v). Constructs of higher modification percentage (25%) gave rise to significantly elevated collagen II content and the formation of cell clusters within the matrix relative to samples of lower modification percentage (10% and 15%). These differences in functional ECM accumulation and distribution are likely attributed to the distinct crosslinked network structures of the various hydrogel formulations. Overall, CMC constructs of lower macromer concentration and modification percentage were most promising as scaffolds for NP tissue engineering based on functional ECM assembly. Optimization of such hydrogel fabrication parameters may lead to the development of clinically relevant tissue-engineered NP replacements.
Transfer-matrix approach for finite-difference time-domain simulation of periodic structures.
Deinega, Alexei; Belousov, Sergei; Valuev, Ilya
2013-11-01
Optical properties of periodic structures can be calculated using the transfer-matrix approach, which establishes a relation between amplitudes of the wave incident on a structure with transmitted or reflected waves. The transfer matrix can be used to obtain transmittance and reflectance spectra of finite periodic structures as well as eigenmodes of infinite structures. Traditionally, calculation of the transfer matrix is performed in the frequency domain and involves linear algebra. In this work, we present a technique for calculation of the transfer matrix using the finite-difference time-domain (FDTD) method and show the way of its implementation in FDTD code. To illustrate the performance of our technique we calculate the transmittance spectra for opal photonic crystal slabs consisting of multiple layers of spherical scatterers. Our technique can be used for photonic band structure calculations. It can also be combined with existing FDTD methods for the analysis of periodic structures at an oblique incidence, as well as for modeling point sources in a periodic environment.
Transfer-matrix approach for finite-difference time-domain simulation of periodic structures
NASA Astrophysics Data System (ADS)
Deinega, Alexei; Belousov, Sergei; Valuev, Ilya
2013-11-01
Optical properties of periodic structures can be calculated using the transfer-matrix approach, which establishes a relation between amplitudes of the wave incident on a structure with transmitted or reflected waves. The transfer matrix can be used to obtain transmittance and reflectance spectra of finite periodic structures as well as eigenmodes of infinite structures. Traditionally, calculation of the transfer matrix is performed in the frequency domain and involves linear algebra. In this work, we present a technique for calculation of the transfer matrix using the finite-difference time-domain (FDTD) method and show the way of its implementation in FDTD code. To illustrate the performance of our technique we calculate the transmittance spectra for opal photonic crystal slabs consisting of multiple layers of spherical scatterers. Our technique can be used for photonic band structure calculations. It can also be combined with existing FDTD methods for the analysis of periodic structures at an oblique incidence, as well as for modeling point sources in a periodic environment.
NASA Astrophysics Data System (ADS)
Leathers, Andrew S.; Micha, David A.; Kilin, Dmitri S.
2009-10-01
The interaction of an excited adsorbate with a medium undergoing electronic and vibrational transitions leads to fast dissipation due to electronic energy relaxation and slow (or delayed) dissipation from vibrational energy relaxation. A theoretical and computational treatment of these phenomena has been done in terms of a reduced density matrix satisfying a generalized Liouville-von Neumann equation, with instantaneous dissipation constructed from state-to-state transition rates, and delayed dissipation given by a memory term derived from the time-correlation function (TCF) of atomic displacements in the medium. Two representative applications are presented here, where electronic excitation may enhance vibrational relaxation of an adsorbate. They involve femtosecond excitation of (a) a CO molecule adsorbed on the Cu(001) metal surface and (b) a metal cluster on a semiconductor surface, Ag3Si(111):H, both electronically excited by visible light and undergoing electron transfer and dissipative dynamics by electronic and vibrational relaxations. Models have been parametrized in both cases from electronic structure calculations and known TCFs for the medium, which are slowly decaying in case (a) and fast decaying in case (b). This requires different numerical procedures in the solution of the integrodifferential equations for the reduced density matrix, which have been solved with an extension of the Runge-Kutta algorithm. Results for the populations of vibronic states versus time show that they oscillate due to vibrational coupling through dissipative interaction with the substrate and show quantum coherence. The total population of electronic states is, however, little affected by vibrational motions. Vibrational relaxation is important only at very long times to establish thermal equilibrium.
The nutrient density approach to healthy eating: challenges and opportunities.
Nicklas, Theresa A; Drewnowski, Adam; O'Neil, Carol E
2014-12-01
The term 'nutrient density' for foods/beverages has been used loosely to promote the Dietary Guidelines for Americans. The 2010 Dietary Guidelines for Americans defined 'all vegetables, fruits, whole grains, fat-free or low-fat milk and milk products, seafood, lean meats and poultry, eggs, beans and peas (legumes), and nuts and seeds that are prepared without added solid fats, added sugars, and sodium' as nutrient dense. The 2010 Dietary Guidelines for Americans further states that nutrient-dense foods and beverages provide vitamins, minerals and other substances that may have positive health effects with relatively few (kilo)calories or kilojoules. Finally, the definition states nutrients and other beneficial substances have not been 'diluted' by the addition of energy from added solid fats, added sugars or by the solid fats naturally present in the food. However, the Dietary Guidelines Advisory Committee and other scientists have failed to clearly define 'nutrient density' or to provide criteria or indices that specify cut-offs for foods that are nutrient dense. Today, 'nutrient density' is a ubiquitous term used in the scientific literature, policy documents, marketing strategies and consumer messaging. However, the term remains ambiguous without a definitive or universal definition. Classifying or ranking foods according to their nutritional content is known as nutrient profiling. The goal of the present commentary is to address the research gaps that still exist before there can be a consensus on how best to define nutrient density, highlight the situation in the USA and relate this to wider, international efforts in nutrient profiling.
Unified approach to nuclear densities from exotic atoms
NASA Astrophysics Data System (ADS)
Friedman, E.
2009-09-01
Parameters of nuclear density distributions are derived from least-squares fits to strong interaction observables in exotic atoms. Global analyses of antiprotonic and pionic atoms show reasonably good agreement between the two types of probes regarding the average behaviour of root-mean-square radii of the neutron distributions. Apparent conflict regarding the shape of the neutron distribution is attributed to different radial sensitivities of these two probes.
Wang, Guoli; Ebrahimi, Nader
2014-01-01
Non-negative matrix factorization (NMF) is a powerful machine learning method for decomposing a high-dimensional nonnegative matrix V into the product of two nonnegative matrices, W and H, such that V ∼ W H. It has been shown to have a parts-based, sparse representation of the data. NMF has been successfully applied in a variety of areas such as natural language processing, neuroscience, information retrieval, image processing, speech recognition and computational biology for the analysis and interpretation of large-scale data. There has also been simultaneous development of a related statistical latent class modeling approach, namely, probabilistic latent semantic indexing (PLSI), for analyzing and interpreting co-occurrence count data arising in natural language processing. In this paper, we present a generalized statistical approach to NMF and PLSI based on Renyi's divergence between two non-negative matrices, stemming from the Poisson likelihood. Our approach unifies various competing models and provides a unique theoretical framework for these methods. We propose a unified algorithm for NMF and provide a rigorous proof of monotonicity of multiplicative updates for W and H. In addition, we generalize the relationship between NMF and PLSI within this framework. We demonstrate the applicability and utility of our approach as well as its superior performance relative to existing methods using real-life and simulated document clustering data. PMID:25821345
Devarajan, Karthik; Wang, Guoli; Ebrahimi, Nader
2015-04-01
Non-negative matrix factorization (NMF) is a powerful machine learning method for decomposing a high-dimensional nonnegative matrix V into the product of two nonnegative matrices, W and H, such that V ∼ W H. It has been shown to have a parts-based, sparse representation of the data. NMF has been successfully applied in a variety of areas such as natural language processing, neuroscience, information retrieval, image processing, speech recognition and computational biology for the analysis and interpretation of large-scale data. There has also been simultaneous development of a related statistical latent class modeling approach, namely, probabilistic latent semantic indexing (PLSI), for analyzing and interpreting co-occurrence count data arising in natural language processing. In this paper, we present a generalized statistical approach to NMF and PLSI based on Renyi's divergence between two non-negative matrices, stemming from the Poisson likelihood. Our approach unifies various competing models and provides a unique theoretical framework for these methods. We propose a unified algorithm for NMF and provide a rigorous proof of monotonicity of multiplicative updates for W and H. In addition, we generalize the relationship between NMF and PLSI within this framework. We demonstrate the applicability and utility of our approach as well as its superior performance relative to existing methods using real-life and simulated document clustering data.
NASA Technical Reports Server (NTRS)
Poe, C. C., Jr.
1988-01-01
A method was previously developed to predict the fracture toughness (stress intensity factor at failure) of composites in terms of the elastic constants and the tensile failing strain of the fibers. The method was applied to boron/aluminum composites made with various proportions of 0 to + or - 45 deg plies. Predicted values of fracture toughness were in gross error because widespread yielding of the aluminum matrix made the compliance very nonlinear. An alternate method was developed to predict the strain intensity factor at failure rather than the stress intensity factor because the singular strain field was not affected by yielding as much as the stress field. Strengths of specimens containing crack-like slits were calculated from predicted failing strains using uniaxial stress-strain curves. Predicted strengths were in good agreement with experimental values, even for the very nonlinear laminates that contained only + or - 45 deg plies. This approach should be valid for other metal matrix composites that have continuous fibers.
Modeling limit languages via limit adjacency matrix and Yusof-Goode approaches
NASA Astrophysics Data System (ADS)
Lim, Wen Li, Yusof, Yuhani
2015-05-01
Limit language was introduced by Goode and Pixton in 2004 under the framework of formal language theory. It is a subset of splicing languages which is restricted to the molecules that will be presented in the splicing system after the reaction of biochemical has run to its completion. In this paper, limit adjacency matrix will be introduced to model the existence of limit languages from splicing languages. Besides, it can be used to characterize the splicing language in terms of active persistent, adult/inert and transient properties based on Yusof-Goode splicing system. In this paper, some examples and theorems that have been formulated via limit adjacency matrix approach will be presented too.
2011-01-01
Homogeneous Condensation in High Density Gas Expansions (Postprint) 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Ryan Jansen ...Prescribed by ANSI Std. 239.18 A Lagrangian–Eulerian approach to modeling homogeneous condensation in high density gas expansions Ryan Jansen , Natalia...Lagrangian–Eulerian approach to modeling homogeneous condensation in high density gas expansions Ryan Jansen ,1 Natalia Gimelshein,2 Sergey Gimelshein,2
NASA Astrophysics Data System (ADS)
Nakatani, Naoki; Guo, Sheng
2017-03-01
This paper describes an interface between the density matrix renormalization group (DMRG) method and the complete active-space self-consistent field (CASSCF) method and its analytical gradient, as well as an extension to the second-order perturbation theory (CASPT2) method. This interfacing allows large active-space multi-reference computations to be easily performed. The interface and its extension are both implemented in terms of reduced density matrices (RDMs) which can be efficiently computed via the DMRG sweep algorithm. We also present benchmark results showing that, in practice, the DMRG-CASSCF calculations scale with active-space size in a polynomial manner in the case of quasi-1D systems. Geometry optimization of a binuclear iron-sulfur cluster using the DMRG-CASSCF analytical gradient is demonstrated, indicating that the inclusion of the valence p-orbitals of sulfur and double-shell d-orbitals of iron lead to non-negligible changes in the geometry compared to the results of small active-space calculations. With the exception of the selection of M values, many computational settings in these practical DMRG calculations have been tuned and black-boxed in our interface, and so the resulting DMRG-CASSCF and DMRG-CASPT2 calculations are now available to novice users as a common tool to compute strongly correlated electronic wavefunctions.
Murphy, E; FitzGerald, O; Saxne, T; Bresnihan, B
2002-11-01
Chondromalacia patellae is a potentially disabling disorder characterised by features of patellar cartilage degradation. To evaluate markers of cartilage and bone turnover in patients with chondromalacia patellae. 18 patients with chondromalacia patellae were studied. Serum cartilage oligomeric matrix protein (s-COMP) and bone sialoprotein (s-BSP) levels were measured by enzyme linked immunosorbent assay (ELISA) and compared with those of age and sex matched healthy control subjects. Periarticular bone mineral density (BMD) of both knee joints was assessed by dual energy x ray absorptiometry (DXA). s-COMP levels were significantly raised in all patients with chondromalacia patellae compared with healthy control subjects (p=0.0001). s-BSP levels did not differ significantly between the groups (p=0.41). BMD of the patella was significantly reduced in patients with chondromalacia patellae compared with the control subjects (p=0.016). In patients with bilateral chondromalacia patellae, BMD of the patella was lower in the more symptomatic knee joint (p=0.005). Changes in periarticular BMD were localised to the patella and were not present in femoral regions. Neither s-COMP (p=0.18) nor s-BSP (p=0.40) levels correlated with patellar BMD. Increased s-COMP levels, reflecting cartilage degradation, and reduced BMD localised to the patella may represent clinically useful markers in the diagnosis and monitoring of patients with chondromalacia patellae. Measures of cartilage degradation did not correlate with loss of patellar bone density, suggesting dissociated pathophysiological mechanisms.
Ohyabu, Yoshimi; Yunoki, Shunji; Hatayama, Hirosuke; Teranishi, Yoshikazu
2013-11-01
Collagen-based 3-D hydrogels often lack sufficient mechanical strength for tissue engineering. We developed a method for fabrication of high-density collagen fibril matrix (CFM) gels from concentrated solutions of uncleaved gelatin (UCG). Denatured random-coil UCG exhibited more rapid and efficient renaturation into collagen triple-helix than cleaved gelatin (CG) over a broad range of setting temperatures. The UCG solution formed opaque gels with high-density reconstituted collagen fibrils at 28-32 °C and transparent gels similar to CG at <25 °C. The unique gelation properties of UCG enabled the encapsulation of cultured cells in CFM of high solid volume (>5%) and elasticity (1.28 ± 0.15 kPa at 5% and 4.82 ± 0.38 kPa at 8%) with minimal cell loss. The elastic modulus of these gels was higher than that of conventional CFM containing 0.5% collagen. High-strength CFM may provide more durable hydrogels for tissue engineering and regenerative medicine.
Continuation of probability density functions using a generalized Lyapunov approach
NASA Astrophysics Data System (ADS)
Baars, S.; Viebahn, J. P.; Mulder, T. E.; Kuehn, C.; Wubs, F. W.; Dijkstra, H. A.
2017-05-01
Techniques from numerical bifurcation theory are very useful to study transitions between steady fluid flow patterns and the instabilities involved. Here, we provide computational methodology to use parameter continuation in determining probability density functions of systems of stochastic partial differential equations near fixed points, under a small noise approximation. Key innovation is the efficient solution of a generalized Lyapunov equation using an iterative method involving low-rank approximations. We apply and illustrate the capabilities of the method using a problem in physical oceanography, i.e. the occurrence of multiple steady states of the Atlantic Ocean circulation.
Nuclear clustering in the energy density functional approach
Ebran, J.-P.; Khan, E.; Nikšić, T.; Vretenar, D.
2015-10-15
Nuclear Energy Density Functionals (EDFs) are a microscopic tool of choice extensively used over the whole chart to successfully describe the properties of atomic nuclei ensuing from their quantum liquid nature. In the last decade, they also have proved their ability to deal with the cluster phenomenon, shedding a new light on its fundamental understanding by treating on an equal footing both quantum liquid and cluster aspects of nuclei. Such a unified microscopic description based on nucleonic degrees of freedom enables to tackle the question pertaining to the origin of the cluster phenomenon and emphasizes intrinsic mechanisms leading to the emergence of clusters in nuclei.
First Measurements of the 1̂, 2̂, and 3̂ Spin Density Matrix Elements in γp ->pφ using CLAS at JLab
NASA Astrophysics Data System (ADS)
Vernarsky, Brian
2012-10-01
In an effort towards a ``complete'' experiment for the φ meson, we present studies from two experiments with unpolarized targets, one using a circularly polarized photon beam (g1c) and one using a linearly polarized photon beam (g8b), both carried out using the CEBAF Large Acceptance Spectrometer (CLAS) at Jefferson Lab. The experiments were analyzed using an extended maximum likelihood fit to the cross section with partial wave amplitudes. New likelihood functions were calculated to account for the polarization of the photon beams. The results of these fits are then used to project out the spin density matrix for the φ. First measurements of the 1̂, 2̂, and 3̂ spin density matrix elements will be presented using this method. As a check, we compare to another method, Schilling's method, which fits the decay angular distribution with a function that uses the spin density matrix elements as parameters.
Hielscher, Abigail C; Gerecht, Sharon
2012-12-01
A major paradigm shift in cancer research is the emergence of multidisciplinary approaches to investigate complex cell behaviors, to elucidate regulatory mechanisms and to identify therapeutic targets. Recently, efforts are focused on the engineering of complex in vitro models, which more accurately recapitulate the growth and progression of cancer. These strategies have proven vital for investigating and targeting the events that control tumor angiogenesis. In this review, we explore how the emerging engineering approaches are being used to unlock the complex mechanisms regulating tumor angiogenesis. Emphasis is placed on models using natural and synthetic biomaterials to generate scaffolds mimicking the extracellular matrix, which is known to play a critical role in angiogenesis. While the models presented in this review are revolutionary, improvements are still necessary and concepts for advancing and perfecting engineering approaches for modeling tumor angiogenesis are proposed. Overall, the marriage between disparate scientific fields is expected to yield significant improvements in our understanding and treatment of cancer.
A new approach to mass spectrometer measurements of thermospheric density
NASA Technical Reports Server (NTRS)
Melfi, L. T., Jr.; Brock, F. J.; Brown, C. A., Jr.
1974-01-01
The gas sampling problem in satellite and high velocity probes was investigated by applying the theory of a drifting Maxwellian gas. A lens system using a free stream ion source was developed and experimentally evaluated over the pressure range of 0.00001 to 0.01 N/m sq (approx. 10 to the minus 7th power to 0.0001 torr). The source has high beam transparency, which minimizes gas-surface collisions within, or near, the ionization volume. It is shown that for high ion energy (60 eV), the extracted ion beam has an on-axis energy spread of less than 4 eV, and that 90 percent of the ions are within 2.5 deg of the beam axis. It is concluded that the molecular beam mass spectrometer concept, developed for gas density measurements in the upper atmosphere, substantially reduces gas-surface scattering and gas-surface reactions in the sample, and preserves the integrity of the gas sample during the analysis process. Studies show that both the Scout and Delta launch vehicles have adequate volume, control, velocity, and data acquisition capability necessary to obtain thermospheric number density in real time.
Tabacchi, G; Hutter, J; Mundy, C
2005-04-07
A combined linear response--frozen electron density model has been implemented in a molecular dynamics scheme derived from an extended Lagrangian formalism. This approach is based on a partition of the electronic charge distribution into a frozen region described by Kim-Gordon theory, and a response contribution determined by the instaneous ionic configuration of the system. The method is free from empirical pair-potentials and the parameterization protocol involves only calculations on properly chosen subsystems. They apply this method to a series of alkali halides in different physical phases and are able to reproduce experimental structural and thermodynamic properties with an accuracy comparable to Kohn-Sham density functional calculations.
Matrix approach to discrete fractional calculus II: Partial fractional differential equations
NASA Astrophysics Data System (ADS)
Podlubny, Igor; Chechkin, Aleksei; Skovranek, Tomas; Chen, YangQuan; Vinagre Jara, Blas M.
2009-05-01
A new method that enables easy and convenient discretization of partial differential equations with derivatives of arbitrary real order (so-called fractional derivatives) and delays is presented and illustrated on numerical solution of various types of fractional diffusion equation. The suggested method is the development of Podlubny's matrix approach [I. Podlubny, Matrix approach to discrete fractional calculus, Fractional Calculus and Applied Analysis 3 (4) (2000) 359-386]. Four examples of numerical solution of fractional diffusion equation with various combinations of time-/space-fractional derivatives (integer/integer, fractional/integer, integer/fractional, and fractional/fractional) with respect to time and to the spatial variable are provided in order to illustrate how simple and general is the suggested approach. The fifth example illustrates that the method can be equally simply used for fractional differential equations with delays. A set of MATLAB routines for the implementation of the method as well as sample code used to solve the examples have been developed.
Vernarsky, Brian J.
2014-01-01
In an effort towards a ''complete'' experiment for the ω meson, we present studies from an experiment with an unpolarized target and a circularly polarized photon beam (g1c), carried out using the CEBAF Large Acceptance Spectrometer (CLAS) at Jefferson Lab. The experiment was analyzed using an extended maximum likelihood fit with partial wave amplitudes. New likelihood functions were calculated to account for the polarization of the photon beam. Both circular and linear polarizations are explored. The results of these fits are then used to project out the spin density matrix for the {omega}. First measurements of the {rho}{sup 3} spin density matrix elements will be presented using this method.
Energy density and stress: A new approach to teaching electromagnetism
NASA Astrophysics Data System (ADS)
Herrmann, F.
1989-08-01
By introducing the electromagnetic field in the customary way, ideas are promoted that do not correspond to those of contemporary physics: on the one hand, ideas that stem from pre-Maxwellian times when interactions were still conceived as actions at a distance and, on the other hand, ideas that can be understood only from the point of view that the electromagnetic field is carried by a medium. A part of a course in electromagnetism is sketched in which, from the beginning, the electromagnetic field is presented as a system in its own right and the local quantities energy density and stress are put into the foreground. In this way, justice is done to the views of modern physics and, moreover, the field becomes conceptually simpler.
A Sparse Matrix Approach for Simultaneous Quantification of Nystagmus and Saccade
NASA Technical Reports Server (NTRS)
Kukreja, Sunil L.; Stone, Lee; Boyle, Richard D.
2012-01-01
The vestibulo-ocular reflex (VOR) consists of two intermingled non-linear subsystems; namely, nystagmus and saccade. Typically, nystagmus is analysed using a single sufficiently long signal or a concatenation of them. Saccade information is not analysed and discarded due to insufficient data length to provide consistent and minimum variance estimates. This paper presents a novel sparse matrix approach to system identification of the VOR. It allows for the simultaneous estimation of both nystagmus and saccade signals. We show via simulation of the VOR that our technique provides consistent and unbiased estimates in the presence of output additive noise.
Berkolaiko, G.; Kuipers, J.
2013-11-15
To study electronic transport through chaotic quantum dots, there are two main theoretical approaches. One involves substituting the quantum system with a random scattering matrix and performing appropriate ensemble averaging. The other treats the transport in the semiclassical approximation and studies correlations among sets of classical trajectories. There are established evaluation procedures within the semiclassical evaluation that, for several linear and nonlinear transport moments to which they were applied, have always resulted in the agreement with random matrix predictions. We prove that this agreement is universal: any semiclassical evaluation within the accepted procedures is equivalent to the evaluation within random matrix theory. The equivalence is shown by developing a combinatorial interpretation of the trajectory sets as ribbon graphs (maps) with certain properties and exhibiting systematic cancellations among their contributions. Remaining trajectory sets can be identified with primitive (palindromic) factorisations whose number gives the coefficients in the corresponding expansion of the moments of random matrices. The equivalence is proved for systems with and without time reversal symmetry.
Correlation and volatility in an Indian stock market: A random matrix approach
NASA Astrophysics Data System (ADS)
Kulkarni, Varsha; Deo, Nivedita
2007-11-01
We examine the volatility of an Indian stock market in terms of correlation of stocks and quantify the volatility using the random matrix approach. First we discuss trends observed in the pattern of stock prices in the Bombay Stock Exchange for the three-year period 2000 2002. Random matrix analysis is then applied to study the relationship between the coupling of stocks and volatility. The study uses daily returns of 70 stocks for successive time windows of length 85 days for the year 2001. We compare the properties of matrix C of correlations between price fluctuations in time regimes characterized by different volatilities. Our analyses reveal that (i) the largest (deviating) eigenvalue of C correlates highly with the volatility of the index, (ii) there is a shift in the distribution of the components of the eigenvector corresponding to the largest eigenvalue across regimes of different volatilities, (iii) the inverse participation ratio for this eigenvector anti-correlates significantly with the market fluctuations and finally, (iv) this eigenvector of C can be used to set up a Correlation Index, CI whose temporal evolution is significantly correlated with the volatility of the overall market index.
NASA Astrophysics Data System (ADS)
Berkolaiko, G.; Kuipers, J.
2013-11-01
To study electronic transport through chaotic quantum dots, there are two main theoretical approaches. One involves substituting the quantum system with a random scattering matrix and performing appropriate ensemble averaging. The other treats the transport in the semiclassical approximation and studies correlations among sets of classical trajectories. There are established evaluation procedures within the semiclassical evaluation that, for several linear and nonlinear transport moments to which they were applied, have always resulted in the agreement with random matrix predictions. We prove that this agreement is universal: any semiclassical evaluation within the accepted procedures is equivalent to the evaluation within random matrix theory. The equivalence is shown by developing a combinatorial interpretation of the trajectory sets as ribbon graphs (maps) with certain properties and exhibiting systematic cancellations among their contributions. Remaining trajectory sets can be identified with primitive (palindromic) factorisations whose number gives the coefficients in the corresponding expansion of the moments of random matrices. The equivalence is proved for systems with and without time reversal symmetry.
NASA Astrophysics Data System (ADS)
Moroz, Pavel
Growing fossil fuels consumption compels researchers to find new alternative pathways to produce energy. Along with new materials for the conversion of different types of energy into electricity innovative methods for efficient processing of energy sources are also introduced. The main criteria for the success of such materials and methods are the low cost and compelling performance. Among different types of materials semiconductor nanocrystals are considered as promising candidates for the role of the efficient and cheap absorbers for solar energy applications. In addition to the anticipated cost reduction, the integration of nanocrystals (NC) into device architectures is inspired by the possibility of tuning the energy of electrical charges in NCs via nanoparticle size. However, the stability of nanocrystals in photovoltaic devices is limited by the stability of organic ligands which passivate the surface of semiconductors to preserve quantum confinement. The present work introduces a new strategy for low-temperature processing of colloidal nanocrystals into all-inorganic films: semiconductor matrix encapsulated nanocrystal arrays (SMENA). This methodology goes beyond the traditional ligand-interlinking scheme and relies on the encapsulation of morphologically-defined nanocrystal arrays into a matrix of a wide-band gap semiconductor, which preserves optoelectronic properties of individual nanoparticles. Fabricated solids exhibit excellent thermal stability, which is attributed to the heteroepitaxial structure of nanocrystal-matrix interfaces. The main characteristics and properties of these solids were investigated and compared with ones of traditionally fabricated nanocrystal films using standard spectroscopic, optoelectronic and electronic techniques. As a proof of concept, we. We also characterized electron transport phenomena in different types of nanocrystal films using all-optical approach. By measuring excited carrier lifetimes in either ligand-linked or
Mass balance modelling of contaminants in river basins: application of the flexible matrix approach.
Warren, Christopher; Mackay, Don; Whelan, Mick; Fox, Kay
2007-07-01
It is useful to have available a variety of catchment-scale water quality models that range in complexity, spatial resolution and data requirements. In a previous paper [Warren, C., Mackay, D., Whelan, M., Fox, K., 2005. Mass balance modelling of contaminants in river basins: a flexible matrix approach. Chemosphere 61, 1458-1467] a series of simple to intermediately complex mass balance models was presented which can be used for tiered exposure assessments in river basins. The connectivity of the segments is expressed using a matrix that permits flexibility in application, enabling the model to be re-segmented and applied to different catchments as required. In this paper, the intermediate models, QWASI matrix-rate constant (QMX-R) and QWASI matrix-fugacity (QMX-F) are used to estimate concentrations of linear alkylbenzene sulfonates (LAS) in the rivers Aire and Calder, UK, and of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in the Fraser River basin, Canada. The results compare satisfactorily with monitoring data, suggesting that these QWASI-based models for exposure and risk assessment may be applicable under data-limited conditions. The use of QWASI-based models for regulatory purposes in an evaluative river system is also discussed with reference to assessments of para-dichlorobenzene (pDCB), trichloroethylene (TCE), bis(2-ethylhexyl) phthalate (DEHP) and toluene. It is shown that multi-media QWASI model predictions can be usefully depicted graphically on chemical space diagrams and used to highlight regions in which advection, partitioning to sediments and volatilization may be important determinants of chemical fate in river systems.
Rimayi, Cornelius; Odusanya, David; Mtunzi, Fanyana; Tsoka, Shepherd
2015-01-01
This paper investigates the efficiency of application of four different multivariate calibration techniques, namely matrix-matched internal standard (MMIS), matrix-matched external standard (MMES), solvent-only internal standard (SOIS) and solvent-only external standard (SOES) on the detection and quantification of 20 organochlorine compounds from high, low and blank matrix water sample matrices by Gas Chromatography-Mass Spectrometry (GC-MS) coupled to solid phase extraction (SPE). Further statistical testing, using Statistical Package for the Social Science (SPSS) by applying MANOVA, T-tests and Levene's F tests indicates that matrix composition has a more significant effect on the efficiency of the analytical method than the calibration method of choice. Matrix effects are widely described as one of the major sources of errors in GC-MS multiresidue analysis. Descriptive and inferential statistics proved that the matrix-matched internal standard calibration was the best approach to use for samples of varying matrix composition as it produced the most precise average mean recovery of 87% across all matrices tested. The use of an internal standard calibration overall produced more precise total recoveries than external standard calibration, with mean values of 77% and 64% respectively. The internal standard calibration technique produced a particularly high overall standard deviation of 38% at 95% confidence level indicating that it is less robust than the external standard calibration method which had an overall standard error of 32% at 95% confidence level. Overall, the matrix-matched external standard calibration proved to be the best calibration approach for analysis of low matrix samples which consisted of the real sample matrix as it had the most precise recovery of 98% compared to other calibration approaches for the low-matrix samples.
Nonpharmacological approaches for reducing serum low-density lipoprotein cholesterol.
Griffin, Bruce A
2014-07-01
To reinforce the key role of diet and lifestyle modification as the first-line treatment for the reduction of raised serum low-density lipoprotein cholesterol (LDL-C) and prevention of cardiovascular disease. Also, to counter recent claims that the current dietary guidelines for the treatment of cardiovascular disease have misplaced emphasis on the importance of removing dietary saturated fat instead of sugar. This review provides new insight into the effects of diet and lifestyle factors with established efficacy in lowering serum LDL-C. This includes energy-restricted weight loss and new findings on the effects of alternative day fasting; novel metabolic and molecular effects of replacing palmitic acid with oleic acid; evidence for a dose-response relationship between the intake of dietary stanols and LDL-C; and identification of a unique metabolic pathway for the excretion of cholesterol. The review reports new evidence for the efficacy of alternate day fasting, reassurance that the current dietary guidelines are not misguided by recommending removal of saturated fat, that a high intake of dietary stanols can achieve a reduction in LDL-C of up to 18%, and describes a pathway of cholesterol excretion that may help to explain variation in the response of serum LDL-C to dietary fat and cholesterol.
Murphy, E; FitzGerald, O; Saxne, T; Bresnihan, B
2002-01-01
Background: Chondromalacia patellae is a potentially disabling disorder characterised by features of patellar cartilage degradation. Objective: To evaluate markers of cartilage and bone turnover in patients with chondromalacia patellae. Methods: 18 patients with chondromalacia patellae were studied. Serum cartilage oligomeric matrix protein (s-COMP) and bone sialoprotein (s-BSP) levels were measured by enzyme linked immunosorbent assay (ELISA) and compared with those of age and sex matched healthy control subjects. Periarticular bone mineral density (BMD) of both knee joints was assessed by dual energy x ray absorptiometry (DXA). Results: s-COMP levels were significantly raised in all patients with chondromalacia patellae compared with healthy control subjects (p=0.0001). s-BSP levels did not differ significantly between the groups (p=0.41). BMD of the patella was significantly reduced in patients with chondromalacia patellae compared with the control subjects (p=0.016). In patients with bilateral chondromalacia patellae, BMD of the patella was lower in the more symptomatic knee joint (p=0.005). Changes in periarticular BMD were localised to the patella and were not present in femoral regions. Neither s-COMP (p=0.18) nor s-BSP (p=0.40) levels correlated with patellar BMD. Conclusions: Increased s-COMP levels, reflecting cartilage degradation, and reduced BMD localised to the patella may represent clinically useful markers in the diagnosis and monitoring of patients with chondromalacia patellae. Measures of cartilage degradation did not correlate with loss of patellar bone density, suggesting dissociated pathophysiological mechanisms. PMID:12379520
A quasi-likelihood approach to non-negative matrix factorization
Devarajan, Karthik; Cheung, Vincent C.K.
2017-01-01
A unified approach to non-negative matrix factorization based on the theory of generalized linear models is proposed. This approach embeds a variety of statistical models, including the exponential family, within a single theoretical framework and provides a unified view of such factorizations from the perspective of quasi-likelihood. Using this framework, a family of algorithms for handling signal-dependent noise is developed and its convergence proven using the Expectation-Maximization algorithm. In addition, a measure to evaluate the goodness-of-fit of the resulting factorization is described. The proposed methods allow modeling of non-linear effects via appropriate link functions and are illustrated using an application in biomedical signal processing. PMID:27348511
Tuminaro, Raymond S.; Perego, Mauro; Tezaur, Irina Kalashnikova; Salinger, Andrew G.; Price, Stephen
2016-10-06
A multigrid method is proposed that combines ideas from matrix dependent multigrid for structured grids and algebraic multigrid for unstructured grids. It targets problems where a three-dimensional mesh can be viewed as an extrusion of a two-dimensional, unstructured mesh in a third dimension. Our motivation comes from the modeling of thin structures via finite elements and, more specifically, the modeling of ice sheets. Extruded meshes are relatively common for thin structures and often give rise to anisotropic problems when the thin direction mesh spacing is much smaller than the broad direction mesh spacing. Within our approach, the first few multigrid hierarchy levels are obtained by applying matrix dependent multigrid to semicoarsen in a structured thin direction fashion. After sufficient structured coarsening, the resulting mesh contains only a single layer corresponding to a two-dimensional, unstructured mesh. Algebraic multigrid can then be employed in a standard manner to create further coarse levels, as the anisotropic phenomena is no longer present in the single layer problem. The overall approach remains fully algebraic, with the minor exception that some additional information is needed to determine the extruded direction. Furthermore, this facilitates integration of the solver with a variety of different extruded mesh applications.
Tuminaro, Raymond S.; Perego, Mauro; Tezaur, Irina Kalashnikova; ...
2016-10-06
A multigrid method is proposed that combines ideas from matrix dependent multigrid for structured grids and algebraic multigrid for unstructured grids. It targets problems where a three-dimensional mesh can be viewed as an extrusion of a two-dimensional, unstructured mesh in a third dimension. Our motivation comes from the modeling of thin structures via finite elements and, more specifically, the modeling of ice sheets. Extruded meshes are relatively common for thin structures and often give rise to anisotropic problems when the thin direction mesh spacing is much smaller than the broad direction mesh spacing. Within our approach, the first few multigridmore » hierarchy levels are obtained by applying matrix dependent multigrid to semicoarsen in a structured thin direction fashion. After sufficient structured coarsening, the resulting mesh contains only a single layer corresponding to a two-dimensional, unstructured mesh. Algebraic multigrid can then be employed in a standard manner to create further coarse levels, as the anisotropic phenomena is no longer present in the single layer problem. The overall approach remains fully algebraic, with the minor exception that some additional information is needed to determine the extruded direction. Furthermore, this facilitates integration of the solver with a variety of different extruded mesh applications.« less
Two approaches to the model drug immobilization into conjugated polymer matrix.
Krukiewicz, Katarzyna; Stokfisz, Anna; Zak, Jerzy K
2015-09-01
The purpose of this study is to develop biocompatible and conducting coating being carrier of biologically active compounds with the potential use in neuroprosthetics. Conducting polypyrrole matrix has been used to immobilize and release model drugs, quercetin and ciprofloxacin. Two routes of immobilization are described: drugs have been incorporated in the polymer matrix in the course of the electropolymerization process or after polymerization, in the course of polymer oxidation. Using UV/Vis spectroscopic detection we demonstrate that both immobilization approaches display different drug-loading efficiencies. In the case of ciprofloxacin, drug incorporation following synthesis is a more efficient immobilization approach (final drug concentration: 43.3 (±9.5) μM/cm(2)), while for quercetin the highest loading is accomplished by drug incorporation during synthesis (final drug concentration: 29.1 (±5.9) μM/cm(2)). The process of drug incorporation results in the variation of surface morphology with respect to the method of immobilization as well as the choice of drug. The results prove that electrochemical methods are efficient procedures for making multifunctional polymer matrices which might be perspective bioactive coatings for implantable neuroprosthetic devices. Copyright © 2015 Elsevier B.V. All rights reserved.
Tuminaro, Raymond S.; Perego, Mauro; Tezaur, Irina Kalashnikova; Salinger, Andrew G.; Price, Stephen
2016-10-06
A multigrid method is proposed that combines ideas from matrix dependent multigrid for structured grids and algebraic multigrid for unstructured grids. It targets problems where a three-dimensional mesh can be viewed as an extrusion of a two-dimensional, unstructured mesh in a third dimension. Our motivation comes from the modeling of thin structures via finite elements and, more specifically, the modeling of ice sheets. Extruded meshes are relatively common for thin structures and often give rise to anisotropic problems when the thin direction mesh spacing is much smaller than the broad direction mesh spacing. Within our approach, the first few multigrid hierarchy levels are obtained by applying matrix dependent multigrid to semicoarsen in a structured thin direction fashion. After sufficient structured coarsening, the resulting mesh contains only a single layer corresponding to a two-dimensional, unstructured mesh. Algebraic multigrid can then be employed in a standard manner to create further coarse levels, as the anisotropic phenomena is no longer present in the single layer problem. The overall approach remains fully algebraic, with the minor exception that some additional information is needed to determine the extruded direction. Furthermore, this facilitates integration of the solver with a variety of different extruded mesh applications.
Gong, Yu; Andrews, Lester
2011-11-14
Reactions of laser-ablated thorium and uranium atoms with dimethyl ether were investigated using matrix isolation infrared spectroscopy. Four types of reaction products for both uranium and thorium were identified using deuterium substituted samples as well as density functional frequency and energy calculations. Ground state uranium and thorium atoms react with dimethyl ether spontaneously to give the M(CH(3)OCH(3)) complexes (M = Th, U) on annealing, which are predicted to have C(2v) symmetry with triplet (Th) and quintet (U) ground states. Subsequent visible irradiation produces the divalent CH(3)OThCH(3) and CH(3)OUCH(3) insertion products with singlet and quintet states lowest in energy. Further UV irradiation induces isomerization of the CH(3)OMCH(3) molecules to the (CH(3))(2)MO isomers with M=O double bonds and pyramidal structures. In the presence of another dimethyl ether reagent, evidence for (CH(3)O)(2)M(CH(3))(2) molecules is also produced upon UV irradiation.
NASA Astrophysics Data System (ADS)
Bartkiewicz, Karol; Beran, Jiří; Lemr, Karel; Norek, Michał; Miranowicz, Adam
2015-02-01
We describe a direct method to determine the negativity of an arbitrary two-qubit state in experiments. The method is derived by analyzing the relation between the purity, negativity, and a universal entanglement witness for two-qubit entanglement. We show how the negativity of a two-qubit state can be calculated from just three experimentally accessible moments of the partially transposed density matrix of a two-photon state. Moreover, we show that the negativity can be given as a function of only six invariants, which are linear combinations of nine invariants from the complete set of 21 fundamental and independent two-qubit invariants. We analyze the relation between these moments and the concurrence for some classes of two-qubit states (including the X states, as well as pure states affected by the amplitude-damping and phase-damping channels). We also discuss the possibility of using the universal entanglement witness as an entanglement measure for various classes of two-qubit states. Moreover, we analyze how noise affects the estimation of entanglement via this witness.
Transfer-matrix study of a hard-square lattice gas with two kinds of particles and density anomaly.
Oliveira, Tiago J; Stilck, Jürgen F
2015-09-01
Using transfer matrix and finite-size scaling methods, we study the thermodynamic behavior of a lattice gas with two kinds of particles on the square lattice. Only excluded volume interactions are considered, so that the model is athermal. Large particles exclude the site they occupy and its four first neighbors, while small particles exclude only their site. Two thermodynamic phases are found: a disordered phase where large particles occupy both sublattices with the same probability and an ordered phase where one of the two sublattices is preferentially occupied by them. The transition between these phases is continuous at small concentrations of the small particles and discontinuous at larger concentrations, both transitions are separated by a tricritical point. Estimates of the central charge suggest that the critical line is in the Ising universality class, while the tricritical point has tricritical Ising (Blume-Emery-Griffiths) exponents. The isobaric curves of the total density as functions of the fugacity of small or large particles display a minimum in the disordered phase.
Differential cross sections and spin density matrix elements for γp → φp from CLAS
NASA Astrophysics Data System (ADS)
Dey, Biplab; Meyer, Curtis A.
2011-10-01
Preliminary differential cross-sections and the ρMM'0 spin density matrix elements (SDME) for the reaction γρ → φp for both charged- (φ → K+K-) and neutral-mode (φ → KL0KS0) topologies obtained from CLAS are presented. Our kinematic coverage is from near production threshold (√s ˜1.97 GeV) to (√s = 2.84 GeV), with a wide coverage in the production angle. As seen in previous LEPS results, the differential cross-sections show a localized "bump" between (√s ˜2 and 2.2 GeV that is not expected from a simple Pomeron exchange picture. Comparisons between the charged- and neutral-mode results and possible effects from the K+Λ(1520) channel are discussed. Our SDME results confirm the well-known deviations from t-channel helicity conservation (TCHC) for Pomeron exchange, but s-channel helicity conservation (SCHC) is also seen to be broken.
Transfer-matrix study of a hard-square lattice gas with two kinds of particles and density anomaly
NASA Astrophysics Data System (ADS)
Oliveira, Tiago J.; Stilck, Jürgen F.
2015-09-01
Using transfer matrix and finite-size scaling methods, we study the thermodynamic behavior of a lattice gas with two kinds of particles on the square lattice. Only excluded volume interactions are considered, so that the model is athermal. Large particles exclude the site they occupy and its four first neighbors, while small particles exclude only their site. Two thermodynamic phases are found: a disordered phase where large particles occupy both sublattices with the same probability and an ordered phase where one of the two sublattices is preferentially occupied by them. The transition between these phases is continuous at small concentrations of the small particles and discontinuous at larger concentrations, both transitions are separated by a tricritical point. Estimates of the central charge suggest that the critical line is in the Ising universality class, while the tricritical point has tricritical Ising (Blume-Emery-Griffiths) exponents. The isobaric curves of the total density as functions of the fugacity of small or large particles display a minimum in the disordered phase.
Xia, Xianping; Tang, Ying; Xie, Changsheng; Wang, Yun; Cai, Shuizhou; Zhu, Changhong
2011-07-01
As a novel copper-containing intrauterine device (IUD), the prospective life-span of the copper/low-density-polyethylene (Cu/LDPE) nanocomposite IUD is very important for the future clinical use and should be given in advance. Here a novel approach, cupric ions accelerated release in diluted nitric acid solution and cupric ions concentration release in various volume of simulated uterine solution (SUS), is reported to verify the type of cupric ions release model of the cylindrical matrix-type nanocomposite IUD, and to obtain the minimal cupric ions release rate that need to ensure contraceptive efficacy and the thickness of copper particles exhausted layer of the cylindrical matrix-type nanocomposite IUD within two difficult immersion durations in experimental volume of SUS, respectively. Using these results, the prospective life-span of the cylindrical matrix-type nanocomposite IUD can be obtained. For instance, the prospective life-span of the novel γ-shape nanocomposite IUD with 25 wt% of copper nanoparticles and 2 mm of diameter and a total weight of 285 mg can be given in advance and it is about 5 years in the future clinical use.
Bottom-up and top-down solid-state NMR approaches for bacterial biofilm matrix composition
NASA Astrophysics Data System (ADS)
Cegelski, Lynette
2015-04-01
The genomics and proteomics revolutions have been enormously successful in providing crucial "parts lists" for biological systems. Yet, formidable challenges exist in generating complete descriptions of how the parts function and assemble into macromolecular complexes and whole-cell assemblies. Bacterial biofilms are complex multicellular bacterial communities protected by a slime-like extracellular matrix that confers protection to environmental stress and enhances resistance to antibiotics and host defenses. As a non-crystalline, insoluble, heterogeneous assembly, the biofilm extracellular matrix poses a challenge to compositional analysis by conventional methods. In this perspective, bottom-up and top-down solid-state NMR approaches are described for defining chemical composition in complex macrosystems. The "sum-of-the-parts" bottom-up approach was introduced to examine the amyloid-integrated biofilms formed by Escherichia coli and permitted the first determination of the composition of the intact extracellular matrix from a bacterial biofilm. An alternative top-down approach was developed to define composition in Vibrio cholerae biofilms and relied on an extensive panel of NMR measurements to tease out specific carbon pools from a single sample of the intact extracellular matrix. These two approaches are widely applicable to other heterogeneous assemblies. For bacterial biofilms, quantitative parameters of matrix composition are needed to understand how biofilms are assembled, to improve the development of biofilm inhibitors, and to dissect inhibitor modes of action. Solid-state NMR approaches will also be invaluable in obtaining parameters of matrix architecture.
2007-03-01
matrix element scaling were determined through the use of a training set of light atoms and molecules consisting of H2, He, Li, Be, B, C, N, O, F, Ne...as electron velocities near the nucleus become appreciable fractions of the speed of light . Electron or- bitals having high densities near the nucleus...contraction. However, the inner s- and p- orbitals nearest the nucleus experience the most contraction (108). In light -element molecules, this orbital
Shaping the Future Landscape: Catchment Systems Engineering and the Decision Support Matrix Approach
NASA Astrophysics Data System (ADS)
Hewett, Caspar; Quinn, Paul; Wilkinson, Mark; Wainwright, John
2017-04-01
Land degradation is widely recognised as one of the great environmental challenges facing humanity today, much of which is directly associated with human activity. The negative impacts of climate change and of the way in which we have engineered the landscape through, for example, agriculture intensification and deforestation, need to be addressed. However, the answer is not a simple matter of doing the opposite of current practice. Nor is non-intervention a viable option. There is a need to bring together approaches from the natural and social sciences both to understand the issues and to act to solve real problems. We propose combining a Catchment Systems Engineering (CSE) approach that builds on existing approaches such as Natural Water Retention Measures, Green infrastructure and Nature-Based Solutions with a multi-scale framework for decision support that has been successfully applied to diffuse pollution and flood risk management. The CSE philosophy follows that of Earth Systems Engineering and Management, which aims to engineer and manage complex coupled human-natural systems in a highly integrated, rational manner. CSE is multi-disciplinary, and necessarily involves a wide range of subject areas including anthropology, engineering, environmental science, ethics and philosophy. It offers a rational approach which accepts the fact that we need to engineer and act to improve the functioning of the existing catchment entity on which we rely. The decision support framework proposed draws on physical and mathematical modelling; Participatory Action Research; and demonstration sites at which practical interventions are implemented. It is predicated on the need to work with stakeholders to co-produce knowledge that leads to proactive interventions to reverse the land degradation we observe today while sustaining the agriculture humanity needs. The philosophy behind CSE and examples of where it has been applied successfully are presented. The Decision Support Matrix
A practical approach to lake water density from electrical conductivity and temperature
NASA Astrophysics Data System (ADS)
Moreira, Santiago; Schultze, Martin; Rahn, Karsten; Boehrer, Bertram
2016-07-01
Density calculations are essential to study stratification, circulation patterns, internal wave formation and other aspects of hydrodynamics in lakes and reservoirs. Currently, the most common procedure is the use of CTD (conductivity, temperature and depth) profilers and the conversion of measurements of temperature and electrical conductivity into density. In limnic waters, such approaches are of limited accuracy if they do not consider lake-specific composition of solutes, as we show. A new approach is presented to correlate density and electrical conductivity, using only two specific coefficients based on the composition of solutes. First, it is necessary to evaluate the lake-specific coefficients connecting electrical conductivity with density. Once these coefficients have been obtained, density can easily be calculated based on CTD data. The new method has been tested against measured values and the most common equations used in the calculation of density in limnic and ocean conditions. The results show that our new approach can reproduce the density contribution of solutes with a relative error of less than 10 % in lake waters from very low to very high concentrations as well as in lakes of very particular water chemistry, which is better than all commonly implemented density calculations in lakes. Finally, a web link is provided for downloading the corresponding density calculator.
Xu, Zhengbin; Ozcelikkale, Altug; Kim, Young L; Han, Bumsoo
2013-02-01
Quality and functionality of engineered tissues are closely related to the microstructures and integrity of their extracellular matrix (ECM). However, currently available methods for characterizing ECM structures are often labor-intensive, destructive, and limited to a small fraction of the total area. These methods are also inappropriate for assessing temporal variations in ECM structures. In this study, to overcome these limitations and challenges, we propose an elastic light scattering approach to spatiotemporally assess ECM microstructures in a relatively large area in a nondestructive manner. To demonstrate its feasibility, we analyze spectroscopic imaging data obtained from acellular collagen scaffolds and dermal equivalents as model ECM structures. For spatial characterization, acellular scaffolds are examined after a freeze/thaw process mimicking a cryopreservation procedure to quantify freezing-induced structural changes in the collagen matrix. We further analyze spatial and temporal changes in ECM structures during cell-driven compaction in dermal equivalents. The results show that spectral dependence of light elastically backscattered from engineered tissue is sensitively associated with alterations in ECM microstructures. In particular, a spectral decay rate over the wavelength can serve as an indicator for the pore size changes in ECM structures, which are at nanometer scale. A decrease in the spectral decay rate suggests enlarged pore sizes of ECM structures. The combination of this approach with a whole-field imaging platform further allows visualization of spatial heterogeneity of EMC microstructures in engineered tissues. This demonstrates the feasibility of the proposed method that nano- and micrometer scale alteration of the ECM structure can be detected and visualized at a whole-field level. Thus, we envision that this spectroscopic imaging approach could potentially serve as an effective characterization tool to nondestructively, accurately
NASA Astrophysics Data System (ADS)
Xu, Hao; Shakeshaft, Robin
2011-01-01
We develop an R-matrix approach to treating collision processes which explicitly takes into account, by means of a simple energy-dependent analytic function, the out-of-phase oscillations of the incident and scattered standing waves in the interior region. Thereby we avoid the use of the Bloch operator. In place of the Bloch operator the incident wave provides the source term in an inhomogeneous equation for the scattered wave. We take those subchannels not treated exactly into account via the optical potential, which is generally non-Hermitian due to dissipation at the boundary. The optical potential is constructed on a real analytic basis using a resolvent that satisfies outgoing-wave boundary conditions. The use of an analytic basis together with the direct determination of the K matrix, rather than the R matrix, at the boundary (this is done by matching the interior wave function to the nearly exact analytic solution beyond the boundary) makes the method particularly well suited to the treatment of ultracold collisions. We have tested our method by applying it to one-photon single-ionization of (He1s2) accompanied by excitation to He+(2s) or He+(2p) for photon energies above the complete breakup threshold, where the optical potential is non-Hermitian. Excellent agreement with experiment is obtained for the cross sections for photoionization to both He+(n=1) and to He+(n=2). The 2s-to-2p branching ratio is strongly influenced by both the optical potential and, at photon energies less than a few tens of eV above the breakup threshold, the nonadiabatic dipole mixing of the 2s and 2p states.
Lev, S M; Gasparich, G; Choi, F; King, L; Moore, J; Zimmerman, S
2011-09-30
Methods for the detection and characterization of airborne biological warfare agents, such as bacteria, using their DNA or organic composition are fairly well developed. This approach is useful for identifying the type of bacterial strain once the organism has been isolated from the matrix sampled (e.g., dust particles) and can identify genetically related organisms, which might be helpful during a forensic investigation. However, this genetic signature will not reveal information related to the methods used to grow and weaponize the organism. Bacteria will take on an inorganic signature that is related to their growth and processing history. Therefore, the ability to characterize the inorganic fingerprint of a biological particle has the potential to detect the presence of a bio-agent and expand the forensic tools available to those investigating the origin of biological weapons. This investigation builds on previous work documenting the usefulness of the inorganic fingerprint and evaluates the limits of detection in the presence of background dust. Based on ICP-MS measurements and mixing models of digested mixtures of laboratory cultured Bacillus subtilis (anthrax stimulant) and NIST Standard Reference Material 2709 (dust stimulant), the inorganic fingerprint method is capable of detecting toxicologically relevant levels of a bio-warfare agent in the presence of a complex background matrix. Copyright © 2011 Elsevier B.V. All rights reserved.
Global financial indices and twitter sentiment: A random matrix theory approach
NASA Astrophysics Data System (ADS)
García, A.
2016-11-01
We use Random Matrix Theory (RMT) approach to analyze the correlation matrix structure of a collection of public tweets and the corresponding return time series associated to 20 global financial indices along 7 trading months of 2014. In order to quantify the collection of tweets, we constructed daily polarity time series from public tweets via sentiment analysis. The results from RMT analysis support the fact of the existence of true correlations between financial indices, polarities, and the mixture of them. Moreover, we found a good agreement between the temporal behavior of the extreme eigenvalues of both empirical data, and similar results were found when computing the inverse participation ratio, which provides an evidence about the emergence of common factors in global financial information whether we use the return or polarity data as a source. In addition, we found a very strong presumption that polarity Granger causes returns of an Indonesian index for a long range of lag trading days, whereas for Israel, South Korea, Australia, and Japan, the predictive information of returns is also presented but with less presumption. Our results suggest that incorporating polarity as a financial indicator may open up new insights to understand the collective and even individual behavior of global financial indices.
Electron Collisional Excitation Rates for OI USING the B-Spline R-Matrix Approach
NASA Technical Reports Server (NTRS)
Zatsarinny, O.; Tayal, S. S.
2003-01-01
The B-spline R-matrix approach has been used to calculate electron collisional excitation strengths and rates for transitions between the 3P, 1D, and 1S states of ground configuration and from these states to the states of the excited 2s(sup 2)2p(sup 3)ns (n = 3-5), 2s(sup 2)2p(sup 3)np (n = 3-4), 2s(sup 2)2p(sup 3)nd (n = 3-4), 2s(sup 2)2p(sup 3)4f, and 2s2p(sup 5) configurations. The nonorthogonal orbitals are used for an accurate description of both the target wave functions and the R-matrix basis functions. The thermally averaged collision strengths are obtained from the collision strengths by integrating over a Maxwellian velocity distribution of electron energies, and these are tabulated over a temperature range from 1000 to 60,000 K. The parametric functions of scaled energy have also been obtained to represent collision strengths over a wide energy range or thermally averaged collision strengths at any desired temperature.
Current-induced forces in mesoscopic systems: A scattering-matrix approach.
Bode, Niels; Kusminskiy, Silvia Viola; Egger, Reinhold; von Oppen, Felix
2012-01-01
Nanoelectromechanical systems are characterized by an intimate connection between electronic and mechanical degrees of freedom. Due to the nanoscopic scale, current flowing through the system noticeably impacts upons the vibrational dynamics of the device, complementing the effect of the vibrational modes on the electronic dynamics. We employ the scattering-matrix approach to quantum transport in order to develop a unified theory of nanoelectromechanical systems out of equilibrium. For a slow mechanical mode the current can be obtained from the Landauer-Büttiker formula in the strictly adiabatic limit. The leading correction to the adiabatic limit reduces to Brouwer's formula for the current of a quantum pump in the absence of a bias voltage. The principal results of the present paper are the scattering-matrix expressions for the current-induced forces acting on the mechanical degrees of freedom. These forces control the Langevin dynamics of the mechanical modes. Specifically, we derive expressions for the (typically nonconservative) mean force, for the (possibly negative) damping force, an effective "Lorentz" force that exists even for time-reversal-invariant systems, and the fluctuating Langevin force originating from Nyquist and shot noise of the current flow. We apply our general formalism to several simple models that illustrate the peculiar nature of the current-induced forces. Specifically, we find that in out-of-equilibrium situations the current-induced forces can destabilize the mechanical vibrations and cause limit-cycle dynamics.
Scattering matrix approach to the dissociative recombination of HCO+ and N2H+.
Fonseca dos Santos, S; Douguet, N; Kokoouline, V; Orel, A E
2014-04-28
We present a theoretical study of the indirect dissociative recombination of linear polyatomic ions at low collisional energies. The approach is based on the computation of the scattering matrix just above the ionization threshold and enables the explicit determination of all diabatic electronic couplings responsible for dissociative recombination. In addition, we use the multi-channel quantum-defect theory to demonstrate the precision of the scattering matrix by reproducing accurately ab initio Rydberg state energies of the neutral molecule. We consider the molecular ions N2H(+) and HCO(+) as benchmark systems of astrophysical interest and improve former theoretical studies, which had repeatedly produced smaller cross sections than experimentally measured. Specifically, we demonstrate the crucial role of the previously overlooked stretching modes for linear polyatomic ions with large permanent dipole moment. The theoretical cross sections for both ions agree well with experimental data over a wide energy range. Finally, we consider the potential role of the HOC(+) isomer in the experimental cross sections of HCO(+) at energies below 10 meV.
Electron Collisional Excitation Rates for OI USING the B-Spline R-Matrix Approach
NASA Technical Reports Server (NTRS)
Zatsarinny, O.; Tayal, S. S.
2003-01-01
The B-spline R-matrix approach has been used to calculate electron collisional excitation strengths and rates for transitions between the 3P, 1D, and 1S states of ground configuration and from these states to the states of the excited 2s(sup 2)2p(sup 3)ns (n = 3-5), 2s(sup 2)2p(sup 3)np (n = 3-4), 2s(sup 2)2p(sup 3)nd (n = 3-4), 2s(sup 2)2p(sup 3)4f, and 2s2p(sup 5) configurations. The nonorthogonal orbitals are used for an accurate description of both the target wave functions and the R-matrix basis functions. The thermally averaged collision strengths are obtained from the collision strengths by integrating over a Maxwellian velocity distribution of electron energies, and these are tabulated over a temperature range from 1000 to 60,000 K. The parametric functions of scaled energy have also been obtained to represent collision strengths over a wide energy range or thermally averaged collision strengths at any desired temperature.
van Grootel, Leonie; van Wesel, Floryt; O'Mara-Eves, Alison; Thomas, James; Hox, Joop; Boeije, Hennie
2017-09-01
This study describes an approach for the use of a specific type of qualitative evidence synthesis in the matrix approach, a mixed studies reviewing method. The matrix approach compares quantitative and qualitative data on the review level by juxtaposing concrete recommendations from the qualitative evidence synthesis against interventions in primary quantitative studies. However, types of qualitative evidence syntheses that are associated with theory building generate theoretical models instead of recommendations. Therefore, the output from these types of qualitative evidence syntheses cannot directly be used for the matrix approach but requires transformation. This approach allows for the transformation of these types of output. The approach enables the inference of moderation effects instead of direct effects from the theoretical model developed in a qualitative evidence synthesis. Recommendations for practice are formulated on the basis of interactional relations inferred from the qualitative evidence synthesis. In doing so, we apply the realist perspective to model variables from the qualitative evidence synthesis according to the context-mechanism-outcome configuration. A worked example shows that it is possible to identify recommendations from a theory-building qualitative evidence synthesis using the realist perspective. We created subsets of the interventions from primary quantitative studies based on whether they matched the recommendations or not and compared the weighted mean effect sizes of the subsets. The comparison shows a slight difference in effect sizes between the groups of studies. The study concludes that the approach enhances the applicability of the matrix approach. Copyright © 2017 John Wiley & Sons, Ltd.
NASA Astrophysics Data System (ADS)
Sharma, Sandeep
2015-01-01
We extend our previous work [S. Sharma and G. K.-L. Chan, J. Chem. Phys. 136, 124121 (2012)], which described a spin-adapted (SU(2) symmetry) density matrix renormalization group algorithm, to additionally utilize general non-Abelian point group symmetries. A key strength of the present formulation is that the requisite tensor operators are not hard-coded for each symmetry group, but are instead generated on the fly using the appropriate Clebsch-Gordan coefficients. This allows our single implementation to easily enable (or disable) any non-Abelian point group symmetry (including SU(2) spin symmetry). We use our implementation to compute the ground state potential energy curve of the C2 dimer in the cc-pVQZ basis set (with a frozen-core), corresponding to a Hilbert space dimension of 1012 many-body states. While our calculated energy lies within the 0.3 mEh error bound of previous initiator full configuration interaction quantum Monte Carlo and correlation energy extrapolation by intrinsic scaling calculations, our estimated residual error is only 0.01 mEh, much more accurate than these previous estimates. Due to the additional efficiency afforded by the algorithm, the excitation energies (Te) of eight lowest lying excited states: a3Πu, b 3 Σg - , A1Πu, c 3 Σu + , B1Δg, B ' 1 Σg + , d3Πg, and C1Πg are calculated, which agree with experimentally derived values to better than 0.06 eV. In addition, we also compute the potential energy curves of twelve states: the three lowest levels for each of the irreducible representations 1 Σg + , 1 Σu + , 1 Σg - , and 1 Σu - , to an estimated accuracy of 0.1 mEh of the exact result in this basis.
The role of extracellular matrix in glioma invasion: a cellular Potts model approach.
Rubenstein, Brenda M; Kaufman, Laura J
2008-12-15
In this work, a cellular Potts model based on the differential adhesion hypothesis is employed to analyze the relative importance of select cell-cell and cell-extracellular matrix (ECM) contacts in glioma invasion. To perform these simulations, three types of cells and two ECM components are included. The inclusion of explicit ECM with an inhomogeneous fibrous component and a homogeneously dispersed afibrous component allows exploration of the importance of relative energies of cell-cell and cell-ECM contacts in a variety of environments relevant to in vitro and in vivo experimental investigations of glioma invasion. Simulations performed here focus chiefly on reproducing findings of in vitro experiments on glioma spheroids embedded in collagen I gels. For a given range and set ordering of energies associated with key cell-cell and cell-ECM interactions, our model qualitatively reproduces the dispersed glioma invasion patterns found for most glioma cell lines embedded as spheroids in collagen I gels of moderate concentration. In our model, we find that invasion is maximized at intermediate collagen concentrations, as occurs experimentally. This effect is seen more strongly in model gels composed of short collagen fibers than in those composed of long fibers, which retain significant connectivity even at low density. Additional simulations in aligned model matrices further elucidate how matrix structure dictates invasive patterns. Finally, simulations that allow invading cells to both dissolve and deposit ECM components demonstrate how Q-Potts models may be elaborated to allow active cell alteration of their surroundings. The model employed here provides a quantitative framework with which to bound the relative values of cell-cell and cell-ECM interactions and investigate how varying the magnitude and type of these interactions, as well as ECM structure, could potentially curtail glioma invasion.
NASA Astrophysics Data System (ADS)
Caballero, B.; García-Martín, A.; Cuevas, J. C.
2012-06-01
We present here a generalization of the scattering-matrix approach for the description of the propagation of electromagnetic waves in nanostructured magneto-optical systems. Our formalism allows us to describe all the key magneto-optical effects in any configuration in periodically patterned multilayer structures. The method can also be applied to describe periodic multilayer systems comprising materials with any type of optical anisotropy. We illustrate the method with the analysis of a recent experiment in which the transverse magneto-optical Kerr effect was measured in an Fe film with a periodic array of subwavelength circular holes. We show, in agreement with the experiments, that the excitation of surface plasmon polaritons in this system leads to a resonant enhancement of the transverse magneto-optical Kerr effect.
A transfer matrix approach to vibration localization in mistuned blade assemblies
NASA Technical Reports Server (NTRS)
Ottarson, Gisli; Pierre, Chritophe
1993-01-01
A study of mode localization in mistuned bladed disks is performed using transfer matrices. The transfer matrix approach yields the free response of a general, mono-coupled, perfectly cyclic assembly in closed form. A mistuned structure is represented by random transfer matrices, and the expansion of these matrices in terms of the small mistuning parameter leads to the definition of a measure of sensitivity to mistuning. An approximation of the localization factor, the spatially averaged rate of exponential attenuation per blade-disk sector, is obtained through perturbation techniques in the limits of high and low sensitivity. The methodology is applied to a common model of a bladed disk and the results verified by Monte Carlo simulations. The easily calculated sensitivity measure may prove to be a valuable design tool due to its system-independent quantification of mistuning effects such as mode localization.
Lapchuk, Anatoliy; Prygun, Olexandr; Fu, Minglei; Le, Zichun; Xiong, Qiyuan; Kryuchyn, Andriy
2017-06-26
We present the first general theoretical description of speckle suppression efficiency based on an active diffractive optical element (DOE). The approach is based on spectral analysis of diffracted beams and a coherent matrix. Analytical formulae are obtained for the dispersion of speckle suppression efficiency using different DOE structures and different DOE activation methods. We show that a one-sided 2D DOE structure has smaller speckle suppression range than a two-sided 1D DOE structure. Both DOE structures have sufficient speckle suppression range to suppress low-order speckles in the entire visible range, but only the two-sided 1D DOE can suppress higher-order speckles. We also show that a linear shift 2D DOE in a laser projector with a large numerical aperture has higher effective speckle suppression efficiency than the method using switching or step-wise shift DOE structures. The generalized theoretical models elucidate the mechanism and practical realization of speckle suppression.
Vibration localization in mono- and bi-coupled bladed disks - A transfer matrix approach
NASA Technical Reports Server (NTRS)
Ottarsson, Gisli; Pierre, Christophe
1993-01-01
A transfer matrix approach to the analysis of the dynamics of mistuned bladed disks is presented. The study focuses on mono-coupled systems, in which each blade is coupled to its two neighboring blades, and bi-coupled systems, where each blade is coupled to its four nearest neighbors. Transfer matrices yield the free dynamics, both the characteristic free wave and the normal modes - in closed form for the tuned assemblies. Mistuned assemblies are represented by random transfer matrices and an examination of the effect of mistuning on harmonic wave propagation yields the localization factor - the average rate of spatial wave amplitude decay per blade - in the mono-coupled assembly. Based on a comparison of the wave propagation characteristics of the mono- and bi-coupled assemblies, important conclusions are drawn about the effect of the additional coupling coordinate on the sensitivity to mistuning and the strength of mode localization predicted by a mono-coupled analysis.
Scaling laws for the largest Lyapunov exponent in long-range systems: A random matrix approach.
Anteneodo, Celia; Vallejos, Raúl O
2002-01-01
We investigate the laws that rule the behavior of the largest Lyapunov exponent (LLE) in many particle systems with long-range interactions. We consider as a representative system the so-called Hamiltonian alpha-XY model where the adjustable parameter alpha controls the range of the interactions of N ferromagnetic spins in a lattice of dimension d. In previous work the dependence of the LLE with the system size N, for sufficiently high energies, was established through numerical simulations. In the thermodynamic limit, the LLE becomes constant for alpha>d whereas it decays as an inverse power law of N for alpha
NASA Technical Reports Server (NTRS)
Cramer, Nick; Swei, Sean Shan-Min; Cheung, Kenny; Teodorescu, Mircea
2015-01-01
This paper presents a modeling and control of aerostructure developed by lattice-based cellular materials/components. The proposed aerostructure concept leverages a building block strategy for lattice-based components which provide great adaptability to varying ight scenarios, the needs of which are essential for in- ight wing shaping control. A decentralized structural control design is proposed that utilizes discrete-time lumped mass transfer matrix method (DT-LM-TMM). The objective is to develop an e ective reduced order model through DT-LM-TMM that can be used to design a decentralized controller for the structural control of a wing. The proposed approach developed in this paper shows that, as far as the performance of overall structural system is concerned, the reduced order model can be as e ective as the full order model in designing an optimal stabilizing controller.
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.
A formulation of a matrix sparsity approach for the quantum ordered search algorithm
NASA Astrophysics Data System (ADS)
Parmar, Jupinder; Rahman, Saarim; Thiara, Jaskaran
One specific subset of quantum algorithms is Grovers Ordered Search Problem (OSP), the quantum counterpart of the classical binary search algorithm, which utilizes oracle functions to produce a specified value within an ordered database. Classically, the optimal algorithm is known to have a log2N complexity; however, Grovers algorithm has been found to have an optimal complexity between the lower bound of ((lnN-1)/π≈0.221log2N) and the upper bound of 0.433log2N. We sought to lower the known upper bound of the OSP. With Farhi et al. MITCTP 2815 (1999), arXiv:quant-ph/9901059], we see that the OSP can be resolved into a translational invariant algorithm to create quantum query algorithm restraints. With these restraints, one can find Laurent polynomials for various k — queries — and N — database sizes — thus finding larger recursive sets to solve the OSP and effectively reducing the upper bound. These polynomials are found to be convex functions, allowing one to make use of convex optimization to find an improvement on the known bounds. According to Childs et al. [Phys. Rev. A 75 (2007) 032335], semidefinite programming, a subset of convex optimization, can solve the particular problem represented by the constraints. We were able to implement a program abiding to their formulation of a semidefinite program (SDP), leading us to find that it takes an immense amount of storage and time to compute. To combat this setback, we then formulated an approach to improve results of the SDP using matrix sparsity. Through the development of this approach, along with an implementation of a rudimentary solver, we demonstrate how matrix sparsity reduces the amount of time and storage required to compute the SDP — overall ensuring further improvements will likely be made to reach the theorized lower bound.
NASA Astrophysics Data System (ADS)
Wagner, Daniel Robert
Linear matrix inequalities and convex optimization techniques have become popular tools to solve nontrivial problems in the field of adaptive control. Specifically, the stability of adaptive control laws in the presence of actuator dynamics remains as an important open control problem. In this thesis, we present a linear matrix inequalities-based hedging approach and evaluate it for model reference adaptive control of an uncertain dynamical system in the presence of actuator dynamics. The ideal reference dynamics are modified such that the hedging approach allows the correct adaptation without being hindered by the presence of actuator dynamics. The hedging approach is first generalized such that two cases are considered where the actuator output and control effectiveness are known and unknown. We then show the stability of the closed-loop dynamical system using Lyapunov based stability analysis tools and propose a linear matrix inequality-based framework for the computation of the minimum allowable actuator bandwidth limits such that the closed-loop dynamical system remains stable. The results of the linear matrix inequality-based heading approach are then generalized to multiactuator systems with a new linear matrix inequality condition. The minimum actuator bandwidth solutions for closed-loop system stability are theoretically guaranteed to exist in a convex set with a partially convex constraint and then solved numerically using an algorithm in the case where there are multiple actuators. Finally, the efficacy of the results contained in this thesis are demonstrated using several illustrative numerical examples.
Transition-density-fragment interaction approach for exciton-coupled circular dichroism spectra
NASA Astrophysics Data System (ADS)
Fujimoto, Kazuhiro J.
2010-09-01
A transition-density-fragment interaction (TDFI) method for exciton-coupled circular dichroism (ECCD) spectra is proposed. The TDFI method was previously developed for excitation-energy transfer, which led to the successful estimation of the electronic coupling energy between donor and accepter molecules in xanthorhodopsin [K. J. Fujimoto and S. Hayashi, J. Am. Chem. Soc. 131, 14152 (2009)]. In the present study, the TDFI scheme is extended to the ECCD spectral calculation based on the matrix method and is applied to a dimerized retinal (all-trans N-retinylidene-L-alanine Schiff base) chromophore. Compared with the dipole-dipole and transition charge from ESP methods, TDFI has a much improved description of the electronic coupling. In addition, the matrix method combined with TDFI can reduce the computational costs compared with the full quantum-mechanical calculation. These advantages of the present method make it possible to accurately evaluate the CD Cotton effects observed in experiment.
NASA Astrophysics Data System (ADS)
Manthe, Uwe; Ellerbrock, Roman
2016-05-01
A new approach for the quantum-state resolved analysis of polyatomic reactions is introduced. Based on the singular value decomposition of the S-matrix, energy-dependent natural reaction channels and natural reaction probabilities are defined. It is shown that the natural reaction probabilities are equal to the eigenvalues of the reaction probability operator [U. Manthe and W. H. Miller, J. Chem. Phys. 99, 3411 (1993)]. Consequently, the natural reaction channels can be interpreted as uniquely defined pathways through the transition state of the reaction. The analysis can efficiently be combined with reactive scattering calculations based on the propagation of thermal flux eigenstates. In contrast to a decomposition based straightforwardly on thermal flux eigenstates, it does not depend on the choice of the dividing surface separating reactants from products. The new approach is illustrated studying a prototypical example, the H + CH4 → H2 + CH3 reaction. The natural reaction probabilities and the contributions of the different vibrational states of the methyl product to the natural reaction channels are calculated and discussed. The relation between the thermal flux eigenstates and the natural reaction channels is studied in detail.
Manthe, Uwe; Ellerbrock, Roman
2016-05-28
A new approach for the quantum-state resolved analysis of polyatomic reactions is introduced. Based on the singular value decomposition of the S-matrix, energy-dependent natural reaction channels and natural reaction probabilities are defined. It is shown that the natural reaction probabilities are equal to the eigenvalues of the reaction probability operator [U. Manthe and W. H. Miller, J. Chem. Phys. 99, 3411 (1993)]. Consequently, the natural reaction channels can be interpreted as uniquely defined pathways through the transition state of the reaction. The analysis can efficiently be combined with reactive scattering calculations based on the propagation of thermal flux eigenstates. In contrast to a decomposition based straightforwardly on thermal flux eigenstates, it does not depend on the choice of the dividing surface separating reactants from products. The new approach is illustrated studying a prototypical example, the H + CH4 → H2 + CH3 reaction. The natural reaction probabilities and the contributions of the different vibrational states of the methyl product to the natural reaction channels are calculated and discussed. The relation between the thermal flux eigenstates and the natural reaction channels is studied in detail.
Mueller matrix approach for probing multifractality in the underlying anisotropic connective tissue
NASA Astrophysics Data System (ADS)
Das, Nandan Kumar; Dey, Rajib; Ghosh, Nirmalya
2016-09-01
Spatial variation of refractive index (RI) in connective tissues exhibits multifractality, which encodes useful morphological and ultrastructural information about the disease. We present a spectral Mueller matrix (MM)-based approach in combination with multifractal detrended fluctuation analysis (MFDFA) to exclusively pick out the signature of the underlying connective tissue multifractality through the superficial epithelium layer. The method is based on inverse analysis on selected spectral scattering MM elements encoding the birefringence information on the anisotropic connective tissue. The light scattering spectra corresponding to the birefringence carrying MM elements are then subjected to the Born approximation-based Fourier domain preprocessing to extract ultrastructural RI fluctuations of anisotropic tissue. The extracted RI fluctuations are subsequently analyzed via MFDFA to yield the multifractal tissue parameters. The approach was experimentally validated on a simple tissue model comprising of TiO2 as scatterers of the superficial isotropic layer and rat tail collagen as an underlying anisotropic layer. Finally, the method enabled probing of precancer-related subtle alterations in underlying connective tissue ultrastructural multifractality from intact tissues.
NASA Astrophysics Data System (ADS)
Müller, Silvia; Brockmann, Jan Martin; Schuh, Wolf-Dieter
2015-04-01
final product is accomplished. In conclusion, the developed integrated approach allows for estimating the dynamic topography and its inverse covariance matrix on arbitrary grids in space and time. The inverse covariance matrix contains the appropriate weights for model-data misfits in least-squares ocean model inversions. The focus of this study is on the North Atlantic Ocean. We will present the conceptual design and dynamic topography estimates based on time variable data from seven satellite altimeter missions (Jason-1, Jason-2, Topex/Poseidon, Envisat, ERS-2, GFO, Cryosat2) in combination with the latest GOCE gravity field model and in-situ data from the Argo floats and near-surface drifting buoys.
A novel approach to antibiofilm susceptibility testing using a thermo-reversible matrix.
Taylor, B J; Marsh, L L; Nosworthy, J O; Williams, D W
2016-02-01
Biofilm microorganisms are known to have a much higher tolerance to antimicrobials compared to their planktonic equivalents. Therefore, traditional antimicrobial susceptibility testing may not extrapolate to clinical treatment of infections of biofilm origin, and as a result, there is a need to not only develop antimicrobials with antibiofilm activity, but also suitable in vitro testing methods for their evaluation. In this study, we report on a novel method of antibiofilm testing using a thermo-reversible matrix (poloxamer 407), coupled with live/dead staining of bacteria cultured from the matrix. Pseudomonas aeruginosa (NCIMB 8626) was cultured in medium containing poloxamer 407 at 37°C for 24 hours to generate biofilms. The preparation was cooled to liquefy the poloxamer and allow recovery of the biofilm cells, which were then stained with SYTO9 to determine viability following exposure to four antimicrobials: polyhexanide, octenadine dihydrochloride, povidone-iodine and silver carbonate. Over an 8-minute time period, fluorescence levels were spectrophotometrically measured and compared with bacterial controls, cultured in the absence of poloxamer and without antimicrobial. Untreated cells showed no reduction in viability over this period. Importantly, planktonic cells were more susceptible to test agents compared with those of a 'biofilm' phenotype cultured in poloxamer. Antibiofilm activity was evident for all of the test agents, with highest relative activity seen with octenadine dihydrochloride. In summary, a novel and relatively rapid approach to screen compounds for antibiofilm activity has been described. The method uses standard laboratory equipment and can be readily adapted to test a wide range of microorganisms and other antibiofilm compounds. This research was, in part, supported by Advanced Medical Solutions in the form of a Knowledge Transfer Project. Mr J. Nosworthy was employed by Advanced Medical Solutions. There are no other conflicts of
Bone Mineral 31P and Matrix-Bound Water Densities Measured by Solid-State 1H and 31P MRI
Seifert, Alan C.; Li, Cheng; Rajapakse, Chamith S.; Bashoor- Zadeh, Mahdieh; Bhagat, Yusuf A.; Wright, Alexander C.; Zemel, Babette S.; Zavaliangos, Antonios; Wehrli, Felix W.
2014-01-01
Bone is a composite material consisting of mineral and hydrated collagen fractions. MRI of bone is challenging due to extremely short transverse relaxation times, but solid-state imaging sequences exist that can acquire the short-lived signal from bone tissue. Previous work to quantify bone density via MRI used powerful experimental scanners. This work seeks to establish the feasibility of MRI-based measurement on clinical scanners of bone mineral and collagen-bound water densities, the latter as a surrogate of matrix density, and to examine the associations of these parameters with porosity and donors’ age. Mineral and matrix-bound water images of reference phantoms and cortical bone from 16 human donors, ages 27-97 years, were acquired by zero-echo-time 31P and 1H MRI on whole body 7T and 3T scanners, respectively. Images were corrected for relaxation and RF inhomogeneity to obtain density maps. Cortical porosity was measured by micro-CT, and apparent mineral density by pQCT. MRI-derived densities were compared to x-ray-based measurements by least-squares regression. Mean bone mineral 31P density was 6.74±1.22 mol/L (corresponding to 1129±204 mg/cc mineral), and mean bound water 1H density was 31.3±4.2 mol/L (corresponding to 28.3±3.7 %v/v). Both 31P and bound water (BW) densities were correlated negatively with porosity (31P: R2 = 0.32, p < 0.005; BW: R2 = 0.63, p < 0.0005) and age (31P: R2 = 0.39, p < 0.05; BW: R2 = 0.70, p < 0.0001), and positively with pQCT density (31P: R2 = 0.46, p < 0.05; BW: R2 = 0.50, p < 0.005). In contrast, the bone mineralization ratio (expressed here as the ratio of 31P density to bound water density), which is proportional to true bone mineralization, was found to be uncorrelated with porosity, age, or pQCT density. This work establishes the feasibility of image-based quantification of bone mineral and bound water densities using clinical hardware. PMID:24846186
Sharma, Sandeep
2015-01-14
We extend our previous work [S. Sharma and G. K.-L. Chan, J. Chem. Phys. 136, 124121 (2012)], which described a spin-adapted (SU(2) symmetry) density matrix renormalization group algorithm, to additionally utilize general non-Abelian point group symmetries. A key strength of the present formulation is that the requisite tensor operators are not hard-coded for each symmetry group, but are instead generated on the fly using the appropriate Clebsch-Gordan coefficients. This allows our single implementation to easily enable (or disable) any non-Abelian point group symmetry (including SU(2) spin symmetry). We use our implementation to compute the ground state potential energy curve of the C{sub 2} dimer in the cc-pVQZ basis set (with a frozen-core), corresponding to a Hilbert space dimension of 10{sup 12} many-body states. While our calculated energy lies within the 0.3 mE{sub h} error bound of previous initiator full configuration interaction quantum Monte Carlo and correlation energy extrapolation by intrinsic scaling calculations, our estimated residual error is only 0.01 mE{sub h}, much more accurate than these previous estimates. Due to the additional efficiency afforded by the algorithm, the excitation energies (T{sub e}) of eight lowest lying excited states: a{sup 3}Π{sub u}, b{sup 3}Σ{sub g}{sup −}, A{sup 1}Π{sub u}, c{sup 3}Σ{sub u}{sup +}, B{sup 1}Δ{sub g}, B{sup ′1}Σ{sub g}{sup +}, d{sup 3}Π{sub g}, and C{sup 1}Π{sub g} are calculated, which agree with experimentally derived values to better than 0.06 eV. In addition, we also compute the potential energy curves of twelve states: the three lowest levels for each of the irreducible representations {sup 1}Σ{sub g}{sup +}, {sup 1}Σ{sub u}{sup +}, {sup 1}Σ{sub g}{sup −}, and {sup 1}Σ{sub u}{sup −}, to an estimated accuracy of 0.1 mE{sub h} of the exact result in this basis.
NASA Astrophysics Data System (ADS)
Schwerdtfeger, Christine A.; Mazziotti, David A.
2009-06-01
Quantum phase transitions in N-particle systems can be identified and characterized by the movement of the two-particle reduced density matrix (2-RDM) along the boundary of its N-representable convex set as a function of the Hamiltonian parameter controlling the phase transition [G. Gidofalvi and D. A. Mazziotti, Phys. Rev. A 74, 012501 (2006)]. For the one-dimensional transverse Ising model quantum phase transitions as well as their finite-lattice analogs are computed and characterized by the 2-RDM movement with respect to the transverse magnetic field strength g. The definition of a 2-RDM "speed" quantifies the movement of the 2-RDM per unit of g, which reaches its maximum at the critical point of the phase transition. For the infinite lattice the convex set of 2-RDMs and the 2-RDM speed are computed from the exact solution of the 2-RDM in the thermodynamic limit of infinite N [P. Pfeuty, Ann. Phys. 57, 79 (1970)]. For the finite lattices we compute the 2-RDM convex set and its speed by the variational 2-RDM method [D. A. Mazziotti, Phys. Rev. Lett. 93, 213001 (2004)] in which approximate ground-state 2-RDMs are calculated without N-particle wave functions by using constraints, known as N-representability conditions, to restrict the 2-RDMs to represent quantum system of N fermions. Advantages of the method include: (i) rigorous lower bounds on the ground-state energies, (ii) polynomial scaling of the calculation with N, and (iii) independence of the N-representability conditions from a reference wave function, which enables the modeling of multiple quantum phases. Comparing the 2-RDM convex sets for the finite- and infinite-site lattices reveals that the variational 2-RDM method accurately captures the shape of the convex set and the signature of the phase transition in the 2-RDM movement. From the 2-RDM all one- and two-particle expectation values (or order parameters) of the quantum Ising model can also be computed including the pair correlation function, which
Schwerdtfeger, Christine A; Mazziotti, David A
2009-06-14
Quantum phase transitions in N-particle systems can be identified and characterized by the movement of the two-particle reduced density matrix (2-RDM) along the boundary of its N-representable convex set as a function of the Hamiltonian parameter controlling the phase transition [G. Gidofalvi and D. A. Mazziotti, Phys. Rev. A 74, 012501 (2006)]. For the one-dimensional transverse Ising model quantum phase transitions as well as their finite-lattice analogs are computed and characterized by the 2-RDM movement with respect to the transverse magnetic field strength g. The definition of a 2-RDM "speed" quantifies the movement of the 2-RDM per unit of g, which reaches its maximum at the critical point of the phase transition. For the infinite lattice the convex set of 2-RDMs and the 2-RDM speed are computed from the exact solution of the 2-RDM in the thermodynamic limit of infinite N [P. Pfeuty, Ann. Phys. 57, 79 (1970)]. For the finite lattices we compute the 2-RDM convex set and its speed by the variational 2-RDM method [D. A. Mazziotti, Phys. Rev. Lett. 93, 213001 (2004)] in which approximate ground-state 2-RDMs are calculated without N-particle wave functions by using constraints, known as N-representability conditions, to restrict the 2-RDMs to represent quantum system of N fermions. Advantages of the method include: (i) rigorous lower bounds on the ground-state energies, (ii) polynomial scaling of the calculation with N, and (iii) independence of the N-representability conditions from a reference wave function, which enables the modeling of multiple quantum phases. Comparing the 2-RDM convex sets for the finite- and infinite-site lattices reveals that the variational 2-RDM method accurately captures the shape of the convex set and the signature of the phase transition in the 2-RDM movement. From the 2-RDM all one- and two-particle expectation values (or order parameters) of the quantum Ising model can also be computed including the pair correlation function, which
Structure of fluid mixtures near a solute: a density functional approach.
Patra, Chandra N
2014-09-14
The structure of fluid mixtures near a spherical solute is studied using a density functional approach and computer simulation. The input direct correlation function is obtained from integral equation theory with an accurate closure relation. The density and concentration profiles of binary as well as ternary hard-sphere mixtures near a large hard-spherical solute compare quite well with the computer simulation results over a wide range of parametric conditions.
Spectral densities for Frenkel exciton dynamics in molecular crystals: A TD-DFTB approach
NASA Astrophysics Data System (ADS)
Plötz, Per-Arno; Megow, Jörg; Niehaus, Thomas; Kühn, Oliver
2017-02-01
Effects of thermal fluctuations on the electronic excitation energies and intermonomeric Coulomb couplings are investigated for a perylene-tetracarboxylic-diimide crystal. To this end, time dependent density functional theory based tight binding (TD-DFTB) in the linear response formulation is used in combination with electronic ground state classical molecular dynamics. As a result, a parametrized Frenkel exciton Hamiltonian is obtained, with the effect of exciton-vibrational coupling being described by spectral densities. Employing dynamically defined normal modes, these spectral densities are analyzed in great detail, thus providing insight into the effect of specific intramolecular motions on excitation energies and Coulomb couplings. This distinguishes the present method from approaches using fixed transition densities. The efficiency by which intramolecular contributions to the spectral density can be calculated is a clear advantage of this method as compared with standard TD-DFT.
Spectral densities for Frenkel exciton dynamics in molecular crystals: A TD-DFTB approach.
Plötz, Per-Arno; Megow, Jörg; Niehaus, Thomas; Kühn, Oliver
2017-02-28
Effects of thermal fluctuations on the electronic excitation energies and intermonomeric Coulomb couplings are investigated for a perylene-tetracarboxylic-diimide crystal. To this end, time dependent density functional theory based tight binding (TD-DFTB) in the linear response formulation is used in combination with electronic ground state classical molecular dynamics. As a result, a parametrized Frenkel exciton Hamiltonian is obtained, with the effect of exciton-vibrational coupling being described by spectral densities. Employing dynamically defined normal modes, these spectral densities are analyzed in great detail, thus providing insight into the effect of specific intramolecular motions on excitation energies and Coulomb couplings. This distinguishes the present method from approaches using fixed transition densities. The efficiency by which intramolecular contributions to the spectral density can be calculated is a clear advantage of this method as compared with standard TD-DFT.
NASA Astrophysics Data System (ADS)
Shedge, Sapana V.; Pal, Sourav; Köster, Andreas M.
2011-07-01
Recently, two non-iterative approaches have been proposed to calculate response properties within density functional theory (DFT). These approaches are auxiliary density perturbation theory (ADPT) and the non-iterative approach to the coupled-perturbed Kohn-Sham (NIA-CPKS) method. Though both methods are non-iterative, they use different techniques to obtain the perturbed Kohn-Sham matrix. In this Letter, for the first time, both of these two independent methods have been used for the calculation of dipole-quadrupole polarizabilities. To validate these methods, three tetrahedral molecules viz., P4,CH4 and adamantane (C10H16) have been used as examples. The comparison with MP2 and CCSD proves the reliability of the methodology.
Sun, Jin; Song, Jian; Zhao, Yi; Liang, Wan-Zhen
2007-12-21
We solve the time-dependent density functional theory equation by propagating the reduced one-electron density matrix in real-time domain. The efficiency of several standard solvers such as the short-iterative Krylov-subspace propagator, the low-order Magnus integration method with the matrix polynomial (MP) or Chebyshev matrix polynomial (CMP) expansion of the evolution operator, and Runge-Kutta algorithm are assessed. Fast methods for summing MP and CMP are implemented to speed the calculation of the matrix exponential. It is found that the exponential propagators can tolerate large time step size and retain the computational accuracy whereas the Krylov-subspace algorithm is a little inferior for a larger time step size compared with the second-order Magnus integration method with the MP/CMP expansion of the evolution operator in both weak and intense fields. As an application, we calculate the absorption spectra of hydrogen-passivated silicon nanoparticles Si(29)H(x). The popular hybrid and generalized gradient approximation exchange-correlation functionals are applied. We find that the experimental spectra can be reproduced by using B3LYP and that the silicon particles with sizes of 1 nm and the optical excitations at 3.7, 4.0, and 4.6 eV may consist of 29 Si atoms surrounded by 24 hydrogen atoms.
Gudur, Madhu Sudhan Reddy; Hara, Wendy; Le, Quynh-Thu; Wang, Lei; Xing, Lei; Li, Ruijiang
2014-01-01
MRI significantly improves the accuracy and reliability of target delineation in radiation therapy for certain tumors due to its superior soft tissue contrast compared to CT. A treatment planning process with MRI as the sole imaging modality will eliminate systematic CT/MRI co-registration errors, reduce cost and radiation exposure, and simplify clinical workflow. However, MRI lacks the key electron density information necessary for accurate dose calculation and generating reference images for patient setup. The purpose of this work is to develop a unifying method to derive electron density from standard T1-weighted MRI. We propose to combine both intensity and geometry information into a unifying probabilistic Bayesian framework for electron density mapping. For each voxel, we compute two conditional probability density functions (PDFs) of electron density given its: (1) T1-weighted MRI intensity, and (2) geometry in a reference anatomy, obtained by deformable image registration between the MRI of the atlas and test patient. The two conditional PDFs containing intensity and geometry information are combined into a unifying posterior PDF, whose mean value corresponds to the optimal electron density value under the mean-square error criterion. We evaluated the algorithm's accuracy of electron density mapping and its ability to detect bone in the head for 8 patients, using an additional patient as the atlas or template. Mean absolute HU error between the estimated and true CT, as well as ROC's for bone detection (HU>200) were calculated. The performance was compared with a global intensity approach based on T1 and no density correction (set whole head to water). The proposed technique significantly reduced the errors in electron density estimation, with a mean absolute HU error of 126, compared with 139 for deformable registration (p=2×10-4), 283 for the intensity approach (p=2×10-6) and 282 without density correction (p=5×10-6). For 90% sensitivity in bone
NASA Astrophysics Data System (ADS)
Sudhan Reddy Gudur, Madhu; Hara, Wendy; Le, Quynh-Thu; Wang, Lei; Xing, Lei; Li, Ruijiang
2014-11-01
MRI significantly improves the accuracy and reliability of target delineation in radiation therapy for certain tumors due to its superior soft tissue contrast compared to CT. A treatment planning process with MRI as the sole imaging modality will eliminate systematic CT/MRI co-registration errors, reduce cost and radiation exposure, and simplify clinical workflow. However, MRI lacks the key electron density information necessary for accurate dose calculation and generating reference images for patient setup. The purpose of this work is to develop a unifying method to derive electron density from standard T1-weighted MRI. We propose to combine both intensity and geometry information into a unifying probabilistic Bayesian framework for electron density mapping. For each voxel, we compute two conditional probability density functions (PDFs) of electron density given its: (1) T1-weighted MRI intensity, and (2) geometry in a reference anatomy, obtained by deformable image registration between the MRI of the atlas and test patient. The two conditional PDFs containing intensity and geometry information are combined into a unifying posterior PDF, whose mean value corresponds to the optimal electron density value under the mean-square error criterion. We evaluated the algorithm’s accuracy of electron density mapping and its ability to detect bone in the head for eight patients, using an additional patient as the atlas or template. Mean absolute HU error between the estimated and true CT, as well as receiver operating characteristics for bone detection (HU > 200) were calculated. The performance was compared with a global intensity approach based on T1 and no density correction (set whole head to water). The proposed technique significantly reduced the errors in electron density estimation, with a mean absolute HU error of 126, compared with 139 for deformable registration (p = 2 × 10-4), 283 for the intensity approach (p = 2 × 10-6) and 282 without density