Plato: A localised orbital based density functional theory code

NASA Astrophysics Data System (ADS)

Kenny, S. D.; Horsfield, A. P.

2009-12-01

The Plato package allows both orthogonal and non-orthogonal tight-binding as well as density functional theory (DFT) calculations to be performed within a single framework. The package also provides extensive tools for analysing the results of simulations as well as a number of tools for creating input files. The code is based upon the ideas first discussed in Sankey and Niklewski (1989) [1] with extensions to allow high-quality DFT calculations to be performed. DFT calculations can utilise either the local density approximation or the generalised gradient approximation. Basis sets from minimal basis through to ones containing multiple radial functions per angular momenta and polarisation functions can be used. Illustrations of how the package has been employed are given along with instructions for its utilisation. Program summaryProgram title: Plato Catalogue identifier: AEFC_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFC_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 219 974 No. of bytes in distributed program, including test data, etc.: 1 821 493 Distribution format: tar.gz Programming language: C/MPI and PERL Computer: Apple Macintosh, PC, Unix machines Operating system: Unix, Linux and Mac OS X Has the code been vectorised or parallelised?: Yes, up to 256 processors tested RAM: Up to 2 Gbytes per processor Classification: 7.3 External routines: LAPACK, BLAS and optionally ScaLAPACK, BLACS, PBLAS, FFTW Nature of problem: Density functional theory study of electronic structure and total energies of molecules, crystals and surfaces. Solution method: Localised orbital based density functional theory. Restrictions: Tight-binding and density functional theory only, no exact exchange. Unusual features: Both atom centred and uniform meshes available. Can deal with arbitrary angular momenta for orbitals, whilst still retaining Slater-Koster tables for accuracy. Running time: Test cases will run in a few minutes, large calculations may run for several days.

Use of the rVV10 Nonlocal Correlation Functional in the B97M-V Density Functional: Defining B97M-rV and Related Functionals [On the Use of the rVV10 Nonlocal Correlation Functional in the B97M-V Density Functional: Defining B97M-rV and Related Functionals

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

Mardirossian, Narbe; Ruiz Pestana, Luis; Womack, James C.

The VV10 and rVV10 nonlocal correlation functionals are consistently implemented and assessed, with the goal of determining if the rVV10 nonlocal correlation functional can replace the VV10 nonlocal correlation functional in the recently developed B97M-V density functional, to give the B97M-rV density functional. Along the way, four density functionals are simultaneously tested: VV10, rVV10, B97M-V, and B97M-rV. An initial assessment is carried out across the S22 data set, and the short-range damping variable, b, is varied for all four density functionals in order to determine the sensitivity of the functionals to the empirical parameter. The results of this test indicatemore » that a value of b = 6 (fortuitously the same as that in B97M-V) is suitable for B97M-rV. The functionals are then compared across an extensive database of interaction energies, and it is demonstrated that B97M-rV either matches or outperforms B97M-V for all of the tests considered. Finally, the optimization of b across the S22 data set is extended to two range-separated hybrid density functionals, ωB97X-V and ωB97M-V, and a value of b = 6.2 is recommended for both ωB97X-rV and ωB97M-rV.« less

Use of the rVV10 Nonlocal Correlation Functional in the B97M-V Density Functional: Defining B97M-rV and Related Functionals [On the Use of the rVV10 Nonlocal Correlation Functional in the B97M-V Density Functional: Defining B97M-rV and Related Functionals

DOE PAGES

Mardirossian, Narbe; Ruiz Pestana, Luis; Womack, James C.; ...

2016-12-06

The VV10 and rVV10 nonlocal correlation functionals are consistently implemented and assessed, with the goal of determining if the rVV10 nonlocal correlation functional can replace the VV10 nonlocal correlation functional in the recently developed B97M-V density functional, to give the B97M-rV density functional. Along the way, four density functionals are simultaneously tested: VV10, rVV10, B97M-V, and B97M-rV. An initial assessment is carried out across the S22 data set, and the short-range damping variable, b, is varied for all four density functionals in order to determine the sensitivity of the functionals to the empirical parameter. The results of this test indicatemore » that a value of b = 6 (fortuitously the same as that in B97M-V) is suitable for B97M-rV. The functionals are then compared across an extensive database of interaction energies, and it is demonstrated that B97M-rV either matches or outperforms B97M-V for all of the tests considered. Finally, the optimization of b across the S22 data set is extended to two range-separated hybrid density functionals, ωB97X-V and ωB97M-V, and a value of b = 6.2 is recommended for both ωB97X-rV and ωB97M-rV.« less

Note: The performance of new density functionals for a recent blind test of non-covalent interactions

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

Mardirossian, Narbe; Head-Gordon, Martin

Benchmark datasets of non-covalent interactions are essential for assessing the performance of density functionals and other quantum chemistry approaches. In a recent blind test, Taylor et al. benchmarked 14 methods on a new dataset consisting of 10 dimer potential energy curves calculated using coupled cluster with singles, doubles, and perturbative triples (CCSD(T)) at the complete basis set (CBS) limit (80 data points in total). Finally, the dataset is particularly interesting because compressed, near-equilibrium, and stretched regions of the potential energy surface are extensively sampled.

Note: The performance of new density functionals for a recent blind test of non-covalent interactions

DOE PAGES

Mardirossian, Narbe; Head-Gordon, Martin

2016-11-09

Benchmark datasets of non-covalent interactions are essential for assessing the performance of density functionals and other quantum chemistry approaches. In a recent blind test, Taylor et al. benchmarked 14 methods on a new dataset consisting of 10 dimer potential energy curves calculated using coupled cluster with singles, doubles, and perturbative triples (CCSD(T)) at the complete basis set (CBS) limit (80 data points in total). Finally, the dataset is particularly interesting because compressed, near-equilibrium, and stretched regions of the potential energy surface are extensively sampled.

Dynamic kinetic energy potential for orbital-free density functional theory.

PubMed

Neuhauser, Daniel; Pistinner, Shlomo; Coomar, Arunima; Zhang, Xu; Lu, Gang

2011-04-14

A dynamic kinetic energy potential (DKEP) is developed for time-dependent orbital-free (TDOF) density function theory applications. This potential is constructed to affect only the dynamical (ω ≠ 0) response of an orbital-free electronic system. It aims at making the orbital-free simulation respond in the same way as that of a noninteracting homogenous electron gas (HEG), as required by a correct kinetic energy, therefore enabling extension of the success of orbital-free density functional theory in the static case (e.g., for embedding and description of processes in bulk materials) to dynamic processes. The potential is constructed by expansions of terms, each of which necessitates only simple time evolution (concurrent with the TDOF evolution) and a spatial convolution at each time-step. With 14 such terms a good fit is obtained to the response of the HEG at a large range of frequencies, wavevectors, and densities. The method is demonstrated for simple jellium spheres, approximating Na(9)(+) and Na(65)(+) clusters. It is applicable both to small and large (even ultralarge) excitations and the results converge (i.e., do not blow up) as a function of time. An extension to iterative frequency-resolved extraction is briefly outlined, as well as possibly numerically simpler expansions. The approach could also be extended to fit, instead of the HEG susceptibility, either an experimental susceptibility or a theoretically derived one for a non-HEG system. The DKEP potential should be a powerful tool for embedding a dynamical system described by a more accurate method (such as time-dependent density functional theory, TDDFT) in a large background described by TDOF with a DKEP potential. The type of expansions used and envisioned should be useful for other approaches, such as memory functionals in TDDFT. Finally, an appendix details the formal connection between TDOF and TDDFT.

Conjugate-gradient optimization method for orbital-free density functional calculations.

PubMed

Jiang, Hong; Yang, Weitao

2004-08-01

Orbital-free density functional theory as an extension of traditional Thomas-Fermi theory has attracted a lot of interest in the past decade because of developments in both more accurate kinetic energy functionals and highly efficient numerical methodology. In this paper, we developed a conjugate-gradient method for the numerical solution of spin-dependent extended Thomas-Fermi equation by incorporating techniques previously used in Kohn-Sham calculations. The key ingredient of the method is an approximate line-search scheme and a collective treatment of two spin densities in the case of spin-dependent extended Thomas-Fermi problem. Test calculations for a quartic two-dimensional quantum dot system and a three-dimensional sodium cluster Na216 with a local pseudopotential demonstrate that the method is accurate and efficient. (c) 2004 American Institute of Physics.

Modeling of nanoscale liquid mixture transport by density functional hydrodynamics

NASA Astrophysics Data System (ADS)

Dinariev, Oleg Yu.; Evseev, Nikolay V.

2017-06-01

Modeling of multiphase compositional hydrodynamics at nanoscale is performed by means of density functional hydrodynamics (DFH). DFH is the method based on density functional theory and continuum mechanics. This method has been developed by the authors over 20 years and used for modeling in various multiphase hydrodynamic applications. In this paper, DFH was further extended to encompass phenomena inherent in liquids at nanoscale. The new DFH extension is based on the introduction of external potentials for chemical components. These potentials are localized in the vicinity of solid surfaces and take account of the van der Waals forces. A set of numerical examples, including disjoining pressure, film precursors, anomalous rheology, liquid in contact with heterogeneous surface, capillary condensation, and forward and reverse osmosis, is presented to demonstrate modeling capabilities.

Modeling L2,3-Edge X-ray Absorption Spectroscopy with Real-Time Exact Two-Component Relativistic Time-Dependent Density Functional Theory.

PubMed

Kasper, Joseph M; Lestrange, Patrick J; Stetina, Torin F; Li, Xiaosong

2018-04-10

X-ray absorption spectroscopy is a powerful technique to probe local electronic and nuclear structure. There has been extensive theoretical work modeling K-edge spectra from first principles. However, modeling L-edge spectra directly with density functional theory poses a unique challenge requiring further study. Spin-orbit coupling must be included in the model, and a noncollinear density functional theory is required. Using the real-time exact two-component method, we are able to variationally include one-electron spin-orbit coupling terms when calculating the absorption spectrum. The abilities of different basis sets and density functionals to model spectra for both closed- and open-shell systems are investigated using SiCl 4 and three transition metal complexes, TiCl 4 , CrO 2 Cl 2 , and [FeCl 6 ] 3- . Although we are working in the real-time framework, individual molecular orbital transitions can still be recovered by projecting the density onto the ground state molecular orbital space and separating contributions to the time evolving dipole moment.

Multiphase aluminum equations of state via density functional theory

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

Sjostrom, Travis; Crockett, Scott; Rudin, Sven

2016-10-03

We have performed density functional theory (DFT) based calculations for aluminum in extreme conditions of both pressure and temperature, up to five times compressed ambient density, and over 1 000 000 K in temperature. In order to cover such a domain, DFT methods including phonon calculations, quantum molecular dynamics, and orbital-free DFT are employed. Our results are then used to construct a SESAME equation of state for the aluminum 1100 alloy, encompassing the fcc, hcp, and bcc solid phases as well as the liquid regime. We also provide extensive comparison with experiment, and based on this we also provide amore » slightly modified equation of state for the aluminum 6061 alloy.« less

Current Density Functional Theory Using Meta-Generalized Gradient Exchange-Correlation Functionals.

PubMed

Furness, James W; Verbeke, Joachim; Tellgren, Erik I; Stopkowicz, Stella; Ekström, Ulf; Helgaker, Trygve; Teale, Andrew M

2015-09-08

We present the self-consistent implementation of current-dependent (hybrid) meta-generalized gradient approximation (mGGA) density functionals using London atomic orbitals. A previously proposed generalized kinetic energy density is utilized to implement mGGAs in the framework of Kohn-Sham current density functional theory (KS-CDFT). A unique feature of the nonperturbative implementation of these functionals is the ability to seamlessly explore a wide range of magnetic fields up to 1 au (∼235 kT) in strength. CDFT functionals based on the TPSS and B98 forms are investigated, and their performance is assessed by comparison with accurate coupled-cluster singles, doubles, and perturbative triples (CCSD(T)) data. In the weak field regime, magnetic properties such as magnetizabilities and nuclear magnetic resonance shielding constants show modest but systematic improvements over generalized gradient approximations (GGA). However, in the strong field regime, the mGGA-based forms lead to a significantly improved description of the recently proposed perpendicular paramagnetic bonding mechanism, comparing well with CCSD(T) data. In contrast to functionals based on the vorticity, these forms are found to be numerically stable, and their accuracy at high field suggests that the extension of mGGAs to CDFT via the generalized kinetic energy density should provide a useful starting point for further development of CDFT approximations.

Electrostatics of DNA-Functionalized Nanoparticles

NASA Astrophysics Data System (ADS)

Hoffmann, Kyle; Krishnamoorthy, Kurinji; Kewalramani, Sumit; Bedzyk, Michael; Olvera de La Cruz, Monica

DNA-functionalized nanoparticles have applications in directed self-assembly and targeted cellular delivery of therapeutic proteins. In order to design specific systems, it is necessary to understand their self-assembly properties, of which the long-range electrostatic interactions are a critical component. We iteratively solved equations derived from classical density functional theory in order to predict the distribution of ions around DNA-functionalized Cg Catalase. We then compared estimates of the resonant intensity to those from SAXS measurements to estimate key features of DNA-functionalized proteins, such as the size of the region linking the protein and DNA and the extension of the single-stranded DNA. Using classical density functional theory and coarse-grained simulations, we are able to predict and understand these fundamental properties in order to rationally design new biomaterials.

Evaluation of atmospheric density models and preliminary functional specifications for the Langley Atmospheric Information Retrieval System (LAIRS)

NASA Technical Reports Server (NTRS)

Lee, T.; Boland, D. F., Jr.

1980-01-01

This document presents the results of an extensive survey and comparative evaluation of current atmosphere and wind models for inclusion in the Langley Atmospheric Information Retrieval System (LAIRS). It includes recommended models for use in LAIRS, estimated accuracies for the recommended models, and functional specifications for the development of LAIRS.

Extension of the Kohn-Sham formulation of density functional theory to finite temperature

NASA Astrophysics Data System (ADS)

Gonis, A.; Däne, M.

2018-05-01

Based on Mermin's extension of the Hohenberg and Kohn theorems to non-zero temperature, the Kohn-Sham formulation of density functional theory (KS-DFT) is generalized to finite temperature. We show that present formulations are inconsistent with Mermin's functional containing expressions, in particular describing the Coulomb energy, that defy derivation and are even in violation of rules of logical inference. More; current methodology is in violation of fundamental laws of both quantum and classical mechanics. Based on this feature, we demonstrate the impossibility of extending the KS formalism to finite temperature through the self-consistent solutions of the single-particle Schrödinger equation of T > 0. Guided by the form of Mermin's functional that depends on the eigenstates of a Hamiltonian, determined at T = 0, we base our extension of KS-DFT on the determination of the excited states of a non-interacting system at the zero of temperature. The resulting formulation is consistent with that of Mermin constructing the free energy at T > 0 in terms of the excited states of a non-interacting Hamiltonian (system) that, within the KS formalism, are described by Slater determinants. To determine the excited states at T = 0 use is made of the extension of the Hohenberg and Kohn theorems to excited states presented in previous work applied here to a non-interacting collection of replicas of a non-interacting N-particle system, whose ground state density is taken to match that of K non-interacting replicas of an interacting N-particle system at T = 0 . The formalism allows for an ever denser population of the excitation spectrum of a Hamiltonian, within the KS approximation. The form of the auxiliary potential, (Kohn-Sham potential), is formally identical to that in the ground state formalism with the contribution of the Coulomb energy provided by the derivative of the Coulomb energy in all excited states taken into account. Once the excited states are determined, the minimum of the free energy within the KS formalism follows immediately in the form of Mermin's functional, but with the exact excited states in that functional represented by Slater determinants obtained through self-consistency conditions at the zero of temperature. It is emphasized that, in departure from all existing formulations, no self-consistency conditions are implemented at finite T; as we show, in fact, such formulations are rigorously blocked.

Three-particle correlation functions of quasi-two-dimensional one-component and binary colloid suspensions.

PubMed

Ho, Hau My; Lin, Binhua; Rice, Stuart A

2006-11-14

We report the results of experimental determinations of the triplet correlation functions of quasi-two-dimensional one-component and binary colloid suspensions in which the colloid-colloid interaction is short ranged. The suspensions studied range in density from modestly dilute to solid. The triplet correlation function of the one-component colloid system reveals extensive ordering deep in the liquid phase. At the same density the ordering of the larger diameter component in a binary colloid system is greatly diminished by a very small amount of the smaller diameter component. The possible utilization of information contained in the triplet correlation function in the theory of melting of a quasi-two-dimensional system is briefly discussed.

Dynamical density functional theory for arbitrary-shape colloidal fluids including inertia and hydrodynamic interactions

NASA Astrophysics Data System (ADS)

Duran-Olivencia, Miguel A.; Goddard, Ben; Kalliadasis, Serafim

2015-11-01

Over the last few decades the classical density-functional theory (DFT) and its dynamic extensions (DDFTs) have become a remarkably powerful tool in the study of colloidal fluids. Recently there has been extensive research to generalise all previous DDFTs finally yielding a general DDFT equation (for spherical particles) which takes into account both inertia and hydrodynamic interactions (HI) which strongly influence non-equilibrium properties. The present work will be devoted to a further generalisation of such a framework to systems of anisotropic particles. To this end, the kinetic equation for the Brownian particle distribution function is derived starting from the Liouville equation and making use of Zwanzig's projection-operator techniques. By averaging over all but one particle, a DDFT equation is finally obtained with some similarities to that for spherical colloids. However, there is now an inevitable translational-rotational coupling which affects the diffusivity of asymmetric particles. Lastly, in the overdamped (high friction) limit the theory is notably simplified leading to a DDFT equation which agrees with previous derivations. We acknowledge financial support from European Research Council via Advanced Grant No. 247031.

The Surface Density Distribution in the Solar Nebula

NASA Technical Reports Server (NTRS)

Davis, Sanford S.

2004-01-01

The commonly used minimum mass power law representation of the pre-solar nebula is reanalyzed using a new cumulative-mass-model. This model predicts a smoother surface density approximation compared with methods based on direct computation of surface density. The density is quantified using two independent analytical formulations. First, a best-fit transcendental function is applied directly to the basic planetary data. Next a solution to the time-dependent disk evolution equation is parametrically adapted to the solar nebula data. The latter model is shown to be a good approximation to the finite-size early Solar Nebula, and by extension to other extra solar protoplanetary disks.

Molecular density functional theory of water describing hydrophobicity at short and long length scales

NASA Astrophysics Data System (ADS)

Jeanmairet, Guillaume; Levesque, Maximilien; Borgis, Daniel

2013-10-01

We present an extension of our recently introduced molecular density functional theory of water [G. Jeanmairet et al., J. Phys. Chem. Lett. 4, 619 (2013)] to the solvation of hydrophobic solutes of various sizes, going from angstroms to nanometers. The theory is based on the quadratic expansion of the excess free energy in terms of two classical density fields: the particle density and the multipolar polarization density. Its implementation requires as input a molecular model of water and three measurable bulk properties, namely, the structure factor and the k-dependent longitudinal and transverse dielectric susceptibilities. The fine three-dimensional water structure around small hydrophobic molecules is found to be well reproduced. In contrast, the computed solvation free-energies appear overestimated and do not exhibit the correct qualitative behavior when the hydrophobic solute is grown in size. These shortcomings are corrected, in the spirit of the Lum-Chandler-Weeks theory, by complementing the functional with a truncated hard-sphere functional acting beyond quadratic order in density, and making the resulting functional compatible with the Van-der-Waals theory of liquid-vapor coexistence at long range. Compared to available molecular simulations, the approach yields reasonable solvation structure and free energy of hard or soft spheres of increasing size, with a correct qualitative transition from a volume-driven to a surface-driven regime at the nanometer scale.

Calf muscle density is independently associated with physical function in overweight and obese older adults.

PubMed

Scott, David; Shore-Lorenti, Catherine; McMillan, Lachlan B; Mesinovic, Jakub; Clark, Ross A; Hayes, Alan; Sanders, Kerrie M; Duque, Gustavo; Ebeling, Peter R

2018-03-01

To determine whether associations of calf muscle density with physical function are independent of other determinants of functional decline in overweight and obese older adults. This was a secondary analysis of a cross-sectional study of 85 community-dwelling overweight and obese adults (mean±SD age 62.8±7.9 years; BMI 32.3±6.1 kg/m2; 58% women). Peripheral quantitative computed tomography assessed mid-calf muscle density (66% tibial length) and dual-energy X-ray absorptiometry determined visceral fat area. Fasting glucose, Homeostatic Model Assessment of Insulin Resistance (HOMA-IR) and C-reactive protein (CRP) were analysed. Physical function assessments included hand grip and knee extension strength, balance path length (computerised posturography), stair climb test, Short Physical Performance Battery (SPPB) and self-reported falls efficacy (Modified Falls Efficacy Scale; M-FES). Visceral fat area, not muscle density, was independently associated with CRP and fasting glucose (B=0.025; 95% CI 0.009-0.042 and B=0.009; 0.001-0.017, respectively). Nevertheless, higher muscle density was independently associated with lower path length and stair climb time, and higher SPPB and M-FES scores (all P⟨0.05). Visceral fat area, fasting glucose and CRP did not mediate these associations. Higher calf muscle density predicts better physical function in overweight and obese older adults independent of insulin resistance, visceral adiposity or inflammation.

Derivation of the RPA (Random Phase Approximation) Equation of ATDDFT (Adiabatic Time Dependent Density Functional Ground State Response Theory) from an Excited State Variational Approach Based on the Ground State Functional.

PubMed

Ziegler, Tom; Krykunov, Mykhaylo; Autschbach, Jochen

2014-09-09

The random phase approximation (RPA) equation of adiabatic time dependent density functional ground state response theory (ATDDFT) has been used extensively in studies of excited states. It extracts information about excited states from frequency dependent ground state response properties and avoids, thus, in an elegant way, direct Kohn-Sham calculations on excited states in accordance with the status of DFT as a ground state theory. Thus, excitation energies can be found as resonance poles of frequency dependent ground state polarizability from the eigenvalues of the RPA equation. ATDDFT is approximate in that it makes use of a frequency independent energy kernel derived from the ground state functional. It is shown in this study that one can derive the RPA equation of ATDDFT from a purely variational approach in which stationary states above the ground state are located using our constricted variational DFT (CV-DFT) method and the ground state functional. Thus, locating stationary states above the ground state due to one-electron excitations with a ground state functional is completely equivalent to solving the RPA equation of TDDFT employing the same functional. The present study is an extension of a previous work in which we demonstrated the equivalence between ATDDFT and CV-DFT within the Tamm-Dancoff approximation.

Local density approximation in site-occupation embedding theory

NASA Astrophysics Data System (ADS)

Senjean, Bruno; Tsuchiizu, Masahisa; Robert, Vincent; Fromager, Emmanuel

2017-01-01

Site-occupation embedding theory (SOET) is a density functional theory (DFT)-based method which aims at modelling strongly correlated electrons. It is in principle exact and applicable to model and quantum chemical Hamiltonians. The theory is presented here for the Hubbard Hamiltonian. In contrast to conventional DFT approaches, the site (or orbital) occupations are deduced in SOET from a partially interacting system consisting of one (or more) impurity site(s) and non-interacting bath sites. The correlation energy of the bath is then treated implicitly by means of a site-occupation functional. In this work, we propose a simple impurity-occupation functional approximation based on the two-level (2L) Hubbard model which is referred to as two-level impurity local density approximation (2L-ILDA). Results obtained on a prototypical uniform eight-site Hubbard ring are promising. The extension of the method to larger systems and more sophisticated model Hamiltonians is currently in progress.

Nonequilibrium phase transitions of sheared colloidal microphases: Results from dynamical density functional theory

NASA Astrophysics Data System (ADS)

Stopper, Daniel; Roth, Roland

2018-06-01

By means of classical density functional theory and its dynamical extension, we consider a colloidal fluid with spherically symmetric competing interactions, which are well known to exhibit a rich bulk phase behavior. This includes complex three-dimensional periodically ordered cluster phases such as lamellae, two-dimensional hexagonally packed cylinders, gyroid structures, or spherical micelles. While the bulk phase behavior has been studied extensively in earlier work, in this paper we focus on such structures confined between planar repulsive walls under shear flow. For sufficiently high shear rates, we observe that microphase separation can become fully suppressed. For lower shear rates, however, we find that, e.g., the gyroid structure undergoes a kinetic phase transition to a hexagonally packed cylindrical phase, which is found experimentally and theoretically in amphiphilic block copolymer systems. As such, besides the known similarities between the latter and colloidal systems regarding the equilibrium phase behavior, our work reveals further intriguing nonequilibrium relations between copolymer melts and colloidal fluids with competing interactions.

Orbital-free extension to Kohn-Sham density functional theory equation of state calculations: Application to silicon dioxide

DOE PAGES

Sjostrom, Travis; Crockett, Scott

2015-09-02

The liquid regime equation of state of silicon dioxide SiO 2 is calculated via quantum molecular dynamics in the density range of 5 to 15 g/cc and with temperatures from 0.5 to 100 eV, including the α-quartz and stishovite phase Hugoniot curves. Below 8 eV calculations are based on Kohn-Sham density functional theory (DFT), and above 8 eV a new orbital-free DFT formulation, presented here, based on matching Kohn-Sham DFT calculations is employed. Recent experimental shock data are found to be in very good agreement with the current results. Finally both experimental and simulation data are used in constructing amore » new liquid regime equation of state table for SiO 2.« less

Spacing distribution functions for the one-dimensional point-island model with irreversible attachment

NASA Astrophysics Data System (ADS)

González, Diego Luis; Pimpinelli, Alberto; Einstein, T. L.

2011-07-01

We study the configurational structure of the point-island model for epitaxial growth in one dimension. In particular, we calculate the island gap and capture zone distributions. Our model is based on an approximate description of nucleation inside the gaps. Nucleation is described by the joint probability density pnXY(x,y), which represents the probability density to have nucleation at position x within a gap of size y. Our proposed functional form for pnXY(x,y) describes excellently the statistical behavior of the system. We compare our analytical model with extensive numerical simulations. Our model retains the most relevant physical properties of the system.

Slowly rotating homogeneous masses revisited

NASA Astrophysics Data System (ADS)

Reina, Borja

2016-02-01

Hartle's model for slowly rotating stars has been extensively used to compute equilibrium configurations of slowly rotating stars to second order in perturbation theory in general relativity, given a barotropic equation of state. A recent study based on the modern theory of perturbed matchings concludes that the functions in the (first and second order) perturbation tensors can always be taken as continuous at the surface of the star, except for the second-order function m0. This function presents a jump at the surface of the star proportional to the discontinuity of the energy density there. This concerns only a particular outcome of the model: the change in mass δM. In this paper, the amended change in mass is calculated for the case of constant density stars.

Dynamic density functional theory with hydrodynamic interactions: theoretical development and application in the study of phase separation in gas-liquid systems.

PubMed

Kikkinides, E S; Monson, P A

2015-03-07

Building on recent developments in dynamic density functional theory, we have developed a version of the theory that includes hydrodynamic interactions. This is achieved by combining the continuity and momentum equations eliminating velocity fields, so the resulting model equation contains only terms related to the fluid density and its time and spatial derivatives. The new model satisfies simultaneously continuity and momentum equations under the assumptions of constant dynamic or kinematic viscosity and small velocities and/or density gradients. We present applications of the theory to spinodal decomposition of subcritical temperatures for one-dimensional and three-dimensional density perturbations for both a van der Waals fluid and for a lattice gas model in mean field theory. In the latter case, the theory provides a hydrodynamic extension to the recently studied dynamic mean field theory. We find that the theory correctly describes the transition from diffusive phase separation at short times to hydrodynamic behaviour at long times.

Dynamic density functional theory with hydrodynamic interactions: Theoretical development and application in the study of phase separation in gas-liquid systems

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

Kikkinides, E. S.; Monson, P. A.

Building on recent developments in dynamic density functional theory, we have developed a version of the theory that includes hydrodynamic interactions. This is achieved by combining the continuity and momentum equations eliminating velocity fields, so the resulting model equation contains only terms related to the fluid density and its time and spatial derivatives. The new model satisfies simultaneously continuity and momentum equations under the assumptions of constant dynamic or kinematic viscosity and small velocities and/or density gradients. We present applications of the theory to spinodal decomposition of subcritical temperatures for one-dimensional and three-dimensional density perturbations for both a van dermore » Waals fluid and for a lattice gas model in mean field theory. In the latter case, the theory provides a hydrodynamic extension to the recently studied dynamic mean field theory. We find that the theory correctly describes the transition from diffusive phase separation at short times to hydrodynamic behaviour at long times.« less

Using cryoEM Reconstruction and Phase Extension to Determine Crystal Structure of Bacteriophage $${\\Phi}$$6 Major Capsid Protein

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

Nemecek, Daniel; Plevka, Pavel; Boura, Evzen

2013-11-29

Bacteriophagemore » $${\\Phi}$$6 is a double-stranded RNA virus that has been extensively studied as a model organism. In this paper we describe structure determination of $${\\Phi}$$6 major capsid protein P1. The protein crystallized in base centered orthorhombic space group C2221. Matthews’s coefficient indicated that the crystals contain from four to seven P1 subunits in the crystallographic asymmetric unit. The self-rotation function had shown presence of fivefold axes of non-crystallographic symmetry in the crystals. Thus, electron density map corresponding to a P1 pentamer was excised from a previously determined cryoEM reconstruction of the $${\\Phi}$$6 procapsid at 7 Å resolution and used as a model for molecular replacement. The phases for reflections at higher than 7 Å resolution were obtained by phase extension employing the fivefold non-crystallographic symmetry present in the crystal. Lastly, the averaged 3.6 Å-resolution electron density map was of sufficient quality to allow model building.« less

Room-temperature d0 ferromagnetism in carbon-doped Y2O3 for spintronic applications: A density functional theory study

NASA Astrophysics Data System (ADS)

Chakraborty, Brahmananda; Nandi, Prithwish K.; Kawazoe, Yoshiyuki; Ramaniah, Lavanya M.

2018-05-01

Through density functional theory simulations with the generalized gradient approximation, confirmed by the more sophisticated hybrid functional, we predict the triggering of d0 ferromagnetism in C doped Y2O3 at a hole density of 3.36 ×1021c m-3 (one order less than the critical hole density of ZnO) having magnetic moment of 2.0 μB per defect with ferromagnetic coupling large enough to promote room-temperature ferromagnetism. The persistence of ferromagnetism at room temperature is established through computation of the Curie temperature by the mean field approximation and ab initio molecular dynamics simulations. The induced magnetic moment is mainly contributed by the 2 p orbital of the impurity C and the 2 p orbital of O and we quantitatively and extensively demonstrate through the analysis of density of states and ferromagnetic coupling that the Stoner criterion is satisfied to activate room-temperature ferromagnetism. As the system is stable at room temperature, C doped Y2O3 has feasible defect formation energy and ferromagnetism survives for the choice of hybrid exchange functional, and at room temperature we strongly believe that C doped Y2O3 can be tailored as a room-temperature diluted magnetic semiconductor for spintronic applications.

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

PubMed

Jana, Subrata; Samal, Prasanjit

2017-06-29

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

Extension of the Kohn-Sham formulation of density functional theory to finite temperature

DOE PAGES

Gonis, A.; Dane, M.

2017-12-20

Based on Mermin's extension of the Hohenberg and Kohn theorems to non-zero temperature, the Kohn-Sham formulation of density functional theory (KS-DFT) is generalized to finite temperature. Here, we show that present formulations are inconsistent with Mermin's functional containing expressions, in particular describing the Coulomb energy, that defy derivation and are even in violation of rules of logical inference. More; current methodology is in violation of fundamental laws of both quantum and classical mechanics. Based on this feature, we demonstrate the impossibility of extending the KS formalism to finite temperature through the self-consistent solutions of the single-particle Schrödinger equation of T>0.more » Guided by the form of Mermin's functional that depends on the eigenstates of a Hamiltonian, determined at T>0 we base our extension of KS-DFT on the determination of the excited states of a non-interacting system at the zero of temperature. The resulting formulation is consistent with that of Mermin constructing the free energy at T>0 in terms of the excited states of a non-interacting Hamiltonian (system) that, within the KS formalism, are described by Slater determinants. To determine the excited states at T=0 use is made of the extension of the Hohenberg and Kohn theorems to excited states presented in previous work applied here to a non-interacting collection of replicas of a non-interacting N-particle system, whose ground state density is taken to match that of K non-interacting replicas of an interacting N-particle system at T>0. The formalism allows for an ever denser population of the excitation spectrum of a Hamiltonian, within the KS approximation. The form of the auxiliary potential, (Kohn-Sham potential), is formally identical to that in the ground state formalism with the contribution of the Coulomb energy provided by the derivative of the Coulomb energy in all excited states taken into account. Once the excited states are determined, the minimum of the free energy within the KS formalism follows immediately in the form of Mermin's functional, but with the exact excited states in that functional represented by Slater determinants obtained through self-consistency conditions at the zero of temperature. Lastly, it is emphasized that, in departure from all existing formulations, no self-consistency conditions are implemented at finite T; as we show, in fact, such formulations are rigorously blocked.« less

Extension of the Kohn-Sham formulation of density functional theory to finite temperature

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

Gonis, A.; Dane, M.

Based on Mermin's extension of the Hohenberg and Kohn theorems to non-zero temperature, the Kohn-Sham formulation of density functional theory (KS-DFT) is generalized to finite temperature. Here, we show that present formulations are inconsistent with Mermin's functional containing expressions, in particular describing the Coulomb energy, that defy derivation and are even in violation of rules of logical inference. More; current methodology is in violation of fundamental laws of both quantum and classical mechanics. Based on this feature, we demonstrate the impossibility of extending the KS formalism to finite temperature through the self-consistent solutions of the single-particle Schrödinger equation of T>0.more » Guided by the form of Mermin's functional that depends on the eigenstates of a Hamiltonian, determined at T>0 we base our extension of KS-DFT on the determination of the excited states of a non-interacting system at the zero of temperature. The resulting formulation is consistent with that of Mermin constructing the free energy at T>0 in terms of the excited states of a non-interacting Hamiltonian (system) that, within the KS formalism, are described by Slater determinants. To determine the excited states at T=0 use is made of the extension of the Hohenberg and Kohn theorems to excited states presented in previous work applied here to a non-interacting collection of replicas of a non-interacting N-particle system, whose ground state density is taken to match that of K non-interacting replicas of an interacting N-particle system at T>0. The formalism allows for an ever denser population of the excitation spectrum of a Hamiltonian, within the KS approximation. The form of the auxiliary potential, (Kohn-Sham potential), is formally identical to that in the ground state formalism with the contribution of the Coulomb energy provided by the derivative of the Coulomb energy in all excited states taken into account. Once the excited states are determined, the minimum of the free energy within the KS formalism follows immediately in the form of Mermin's functional, but with the exact excited states in that functional represented by Slater determinants obtained through self-consistency conditions at the zero of temperature. Lastly, it is emphasized that, in departure from all existing formulations, no self-consistency conditions are implemented at finite T; as we show, in fact, such formulations are rigorously blocked.« less

Electronic structure calculation by nonlinear optimization: Application to metals

NASA Astrophysics Data System (ADS)

Benedek, R.; Min, B. I.; Woodward, C.; Garner, J.

1988-04-01

There is considerable interest in the development of novel algorithms for the calculation of electronic structure (e.g., at the level of the local-density approximation of density-functional theory). In this paper we consider a first-order equation-of-motion method. Two methods of solution are described, one proposed by Williams and Soler, and the other base on a Born-Dyson series expansion. The extension of the approach to metallic systems is outlined and preliminary numerical calculations for Zintl-phase NaTl are presented.

Periodicity in the autocorrelation function as a mechanism for regularly occurring zero crossings or extreme values of a Gaussian process.

PubMed

Wilson, Lorna R M; Hopcraft, Keith I

2017-12-01

The problem of zero crossings is of great historical prevalence and promises extensive application. The challenge is to establish precisely how the autocorrelation function or power spectrum of a one-dimensional continuous random process determines the density function of the intervals between the zero crossings of that process. This paper investigates the case where periodicities are incorporated into the autocorrelation function of a smooth process. Numerical simulations, and statistics about the number of crossings in a fixed interval, reveal that in this case the zero crossings segue between a random and deterministic point process depending on the relative time scales of the periodic and nonperiodic components of the autocorrelation function. By considering the Laplace transform of the density function, we show that incorporating correlation between successive intervals is essential to obtaining accurate results for the interval variance. The same method enables prediction of the density function tail in some regions, and we suggest approaches for extending this to cover all regions. In an ever-more complex world, the potential applications for this scale of regularity in a random process are far reaching and powerful.

Periodicity in the autocorrelation function as a mechanism for regularly occurring zero crossings or extreme values of a Gaussian process

NASA Astrophysics Data System (ADS)

Wilson, Lorna R. M.; Hopcraft, Keith I.

2017-12-01

The problem of zero crossings is of great historical prevalence and promises extensive application. The challenge is to establish precisely how the autocorrelation function or power spectrum of a one-dimensional continuous random process determines the density function of the intervals between the zero crossings of that process. This paper investigates the case where periodicities are incorporated into the autocorrelation function of a smooth process. Numerical simulations, and statistics about the number of crossings in a fixed interval, reveal that in this case the zero crossings segue between a random and deterministic point process depending on the relative time scales of the periodic and nonperiodic components of the autocorrelation function. By considering the Laplace transform of the density function, we show that incorporating correlation between successive intervals is essential to obtaining accurate results for the interval variance. The same method enables prediction of the density function tail in some regions, and we suggest approaches for extending this to cover all regions. In an ever-more complex world, the potential applications for this scale of regularity in a random process are far reaching and powerful.

Applications of Density Functional Theory in Soft Condensed Matter

NASA Astrophysics Data System (ADS)

Löwen, Hartmut

Applications of classical density functional theory (DFT) to soft matter systems like colloids, liquid crystals and polymer solutions are discussed with a focus on the freezing transition and on nonequilibrium Brownian dynamics. First, after a brief reminder of equilibrium density functional theory, DFT is applied to the freezing transition of liquids into crystalline lattices. In particular, spherical particles with radially symmetric pair potentials will be treated (like hard spheres, the classical one-component plasma or Gaussian-core particles). Second, the DFT will be generalized towards Brownian dynamics in order to tackle nonequilibrium problems. After a general introduction to Brownian dynamics using the complementary Smoluchowski and Langevin pictures appropriate for the dynamics of colloidal suspensions, the dynamical density functional theory (DDFT) will be derived from the Smoluchowski equation. This will be done first for spherical particles (e.g. hard spheres or Gaussian-cores) without hydrodynamic interactions. Then we show how to incorporate hydrodynamic interactions between the colloidal particles into the DDFT framework and compare to Brownian dynamics computer simulations. Third orientational degrees of freedom (rod-like particles) will be considered as well. In the latter case, the stability of intermediate liquid crystalline phases (isotropic, nematic, smectic-A, plastic crystals etc) can be predicted. Finally, the corresponding dynamical extension of density functional theory towards orientational degrees of freedom is proposed and the collective behaviour of "active" (self-propelled) Brownian particles is briefly discussed.

Nuclear structure and dynamics with density functional theory

NASA Astrophysics Data System (ADS)

Stetcu, Ionel

2015-10-01

Even in the absence of ab initio methods capable of tackling heavy nuclei without restrictions, one can obtain an ab initio description of ground-state properties by means of the density functional theory (DFT), and its extension to superfluid systems in its local variant, the superfluid local density approximation (SLDA). Information about the properties of excited states can be obtained in the same framework by using an extension to the time-dependent (TD) phenomena. Unlike other approaches in which the nuclear structure information is used as a separate input into reaction models, the TD approach treats on the same footing the nuclear structure and dynamics, and is well suited to provide more reliable description for a large number of processes involving heavy nuclei, from the nuclear response to electroweak probes, to nuclear reactions, such as neutron-induced reactions, or nuclear fusion and fission. Such processes, sometimes part of integrated nuclear systems, have important applications in astrophysics, energy production, global security, etc. In this talk, I will present the simulation of a simple reaction, that is the Coulomb excitation of a 238U nucleus, and discuss the application of the TD-DFT formalism to the description of induced fission. I gratefully acknowledge partial support of the U.S. Department of Energy through an Early Career Award of the LANL/LDRD Program.

Geometric model from microscopic theory for nuclear absorption

NASA Technical Reports Server (NTRS)

John, Sarah; Townsend, Lawrence W.; Wilson, John W.; Tripathi, Ram K.

1993-01-01

A parameter-free geometric model for nuclear absorption is derived herein from microscopic theory. The expression for the absorption cross section in the eikonal approximation, taken in integral form, is separated into a geometric contribution that is described by an energy-dependent effective radius and two surface terms that cancel in an asymptotic series expansion. For collisions of light nuclei, an expression for the effective radius is derived from harmonic oscillator nuclear density functions. A direct extension to heavy nuclei with Woods-Saxon densities is made by identifying the equivalent half-density radius for the harmonic oscillator functions. Coulomb corrections are incorporated, and a simplified geometric form of the Bradt-Peters type is obtained. Results spanning the energy range from 1 MeV/nucleon to 1 GeV/nucleon are presented. Good agreement with experimental results is obtained.

Geometric model for nuclear absorption from microscopic theory

NASA Technical Reports Server (NTRS)

John, S.; Townsend, L. W.; Wilson, J. W.; Tripathi, R. K.

1993-01-01

A parameter-free geometric model for nuclear absorption is derived from microscopic theory. The expression for the absorption cross section in the eikonal approximation taken in integral form is separated into a geometric contribution, described by an energy-dependent effective radius, and two surface terms which are shown to cancel in an asymptotic series expansion. For collisions of light nuclei, an expression for the effective radius is derived using harmonic-oscillator nuclear density functions. A direct extension to heavy nuclei with Woods-Saxon densities is made by identifying the equivalent half density radius for the harmonic-oscillator functions. Coulomb corrections are incorporated and a simplified geometric form of the Bradt-Peters type obtained. Results spanning the energy range of 1 MeV/nucleon to 1 GeV/nucleon are presented. Good agreement with experimental results are obtained.

Extending the accuracy of the SNAP interatomic potential form

NASA Astrophysics Data System (ADS)

Wood, Mitchell A.; Thompson, Aidan P.

2018-06-01

The Spectral Neighbor Analysis Potential (SNAP) is a classical interatomic potential that expresses the energy of each atom as a linear function of selected bispectrum components of the neighbor atoms. An extension of the SNAP form is proposed that includes quadratic terms in the bispectrum components. The extension is shown to provide a large increase in accuracy relative to the linear form, while incurring only a modest increase in computational cost. The mathematical structure of the quadratic SNAP form is similar to the embedded atom method (EAM), with the SNAP bispectrum components serving as counterparts to the two-body density functions in EAM. The effectiveness of the new form is demonstrated using an extensive set of training data for tantalum structures. Similar to artificial neural network potentials, the quadratic SNAP form requires substantially more training data in order to prevent overfitting. The quality of this new potential form is measured through a robust cross-validation analysis.

A density functional theory investigation on amantadine drug interaction with pristine and B, Al, Si, Ga, Ge doped C60 fullerenes

NASA Astrophysics Data System (ADS)

Parlak, Cemal; Alver, Özgür

2017-06-01

Amantadine is a well-known drug for its treatment effect on Parkinson's disease and influenza infection or hepatitis. Heteroatom doped fullerenes have been extensively examined for their possible usage in sensor technology and medical applications as drug delivery vehicles. In this research, pristine and B, Al, Si, Ga, Ge doped C60 fullerenes and their interaction with amantadine drug molecule were investigated based on the density functional theory calculations. Findings suggest that doped C60 fullerenes might be used to detect the presence of amantadine and they might be used as drug delivery vehicles because of their moderately high adsorption energies with amantadine.

Theory after experiment on sensing mechanism of a newly developed sensor molecule: Converging or diverging?

NASA Astrophysics Data System (ADS)

Paul, Suvendu; Karar, Monaj; Das, Biswajit; Mallick, Arabinda; Majumdar, Tapas

2017-12-01

Fluoride ion sensing mechanism of 3,3‧-bis(indolyl)-4-chlorophenylmethane has been analyzed with density functional and time-dependent density functional theories. Extensive theoretical calculations on molecular geometry & energy, charge distribution, orbital energies & electronic distribution, minima on potential energy surface confirmed strong hydrogen bonded sensor-anion complex with incomplete proton transfer in S0. In S1, strong hydrogen bonding extended towards complete ESDPT. The distinct and single minima on the PES of the sensor-anion complex for both ground and first singlet excited states confirmed the concerted proton transfer mechanism. Present study well reproduced the experimental spectroscopic data and provided ESDPT as probable fluoride sensing mechanism.

An improved exceedance theory for combined random stresses

NASA Technical Reports Server (NTRS)

Lester, H. C.

1974-01-01

An extension is presented of Rice's classic solution for the exceedances of a constant level by a single random process to its counterpart for an n-dimensional vector process. An interaction boundary, analogous to the constant level considered by Rice for the one-dimensional case, is assumed in the form of a hypersurface. The theory for the numbers of boundary exceedances is developed by using a joint statistical approach which fully accounts for all cross-correlation effects. An exact expression is derived for the n-dimensional exceedance density function, which is valid for an arbitrary interaction boundary. For application to biaxial states of combined random stress, the general theory is reduced to the two-dimensional case. An elliptical stress interaction boundary is assumed and the exact expression for the density function is presented. The equations are expressed in a format which facilitates calculating the exceedances by numerically evaluating a line integral. The behavior of the density function for the two-dimensional case is briefly discussed.

Density matrix embedding in an antisymmetrized geminal power bath

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

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

2015-07-14

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

Global and critical test of the perturbation density-functional theory based on extensive simulation of Lennard-Jones fluid near an interface and in confined systems.

PubMed

Zhou, Shiqi; Jamnik, Andrej

2005-09-22

The structure of a Lennard-Jones (LJ) fluid subjected to diverse external fields maintaining the equilibrium with the bulk LJ fluid is studied on the basis of the third-order+second-order perturbation density-functional approximation (DFA). The chosen density and potential parameters for the bulk fluid correspond to the conditions situated at "dangerous" regions of the phase diagram, i.e., near the critical temperature or close to the gas-liquid coexistence curve. The accuracy of DFA predictions is tested against the results of a grand canonical ensemble Monte Carlo simulation. It is found that the DFA theory presented in this work performs successfully for the nonuniform LJ fluid only on the condition of high accuracy of the required bulk second-order direct correlation function. The present report further indicates that the proposed perturbation DFA is efficient and suitable for both supercritical and subcritical temperatures.

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

Vidmer, Alexandre, E-mail: alexandre@vidmer.com; Sclauzero, Gabriele; Pasquarello, Alfredo

The infrared absorption spectra of jennite, tobermorite 14 Å, anomalous tobermorite 11 Å, and normal tobermorite 11 Å are simulated within a density-functional-theory scheme. The atomic coordinates and the cell parameters are optimized resulting in structures which agree with previous studies. The vibrational frequencies and modes are obtained for each mineral. The vibrational density of states is analyzed through extensive projections on silicon tetrahedra, oxygen atoms, OH groups, and water molecules. The coupling with the electric field is achieved through the use of density functional perturbation theory, which yields Born effective charges and dielectric constants. The simulated absorption spectra reproducemore » well the experimental spectra, thereby allowing for a detailed interpretation of the spectral features in terms of the underlying vibrational modes. In the far-infrared part of the absorption spectra, the interplay between Ca and Si related vibrations leads to differences which are sensitive to the calcium/silicon ratio of the mineral.« less

Electronic structure and electron-phonon interaction in hexagonal yttrium by density functional calculations

NASA Astrophysics Data System (ADS)

Singh, Prabhakar P.

2007-03-01

To understand the pressure-induced changes in the electronic structure and the electron-phonon interaction in yttrium, we have studied hexagonal-close-packed (hcp) yttrium, stable at ambient pressure, and double hexagonal-close-packed (dhcp) yttrium, stable up to around 44GPa , using density-functional-based methods. Our results show that as one goes from hcp yttrium to dhcp yttrium, there are (i) a substantial charge transfer from s→d with extensive modifications of the d band and a sizable reduction in the density of states at the Fermi energy, (ii) a substantial stiffening of phonon modes with the electron-phonon coupling covering the entire frequency range, and (iii) an increase in the electron-phonon coupling constant λ from 0.55 to 1.24, leading to a change in the superconducting transition temperature Tc from 0.3to15.3K for μ*=0.2 .

Self-consistent DFT +U method for real-space time-dependent density functional theory calculations

NASA Astrophysics Data System (ADS)

Tancogne-Dejean, Nicolas; Oliveira, Micael J. T.; Rubio, Angel

2017-12-01

We implemented various DFT+U schemes, including the Agapito, Curtarolo, and Buongiorno Nardelli functional (ACBN0) self-consistent density-functional version of the DFT +U method [Phys. Rev. X 5, 011006 (2015), 10.1103/PhysRevX.5.011006] within the massively parallel real-space time-dependent density functional theory (TDDFT) code octopus. We further extended the method to the case of the calculation of response functions with real-time TDDFT+U and to the description of noncollinear spin systems. The implementation is tested by investigating the ground-state and optical properties of various transition-metal oxides, bulk topological insulators, and molecules. Our results are found to be in good agreement with previously published results for both the electronic band structure and structural properties. The self-consistent calculated values of U and J are also in good agreement with the values commonly used in the literature. We found that the time-dependent extension of the self-consistent DFT+U method yields improved optical properties when compared to the empirical TDDFT+U scheme. This work thus opens a different theoretical framework to address the nonequilibrium properties of correlated systems.

A supercritical density of fast Na+ channels ensures rapid propagation of action potentials in GABAergic interneuron axons

PubMed Central

Hu, Hua; Jonas, Peter

2014-01-01

Fast-spiking, parvalbumin-expressing GABAergic interneurons/basket cells (BCs) play a key role in feedforward and feedback inhibition, gamma oscillations, and complex information processing. For these functions, fast propagation of action potentials (APs) from the soma to the presynaptic terminals is important. However, the functional properties of interneuron axons remain elusive. Here, we examined interneuron axons by confocally targeted subcellular patch-clamp recording in rat hippocampal slices. APs were initiated in the proximal axon ~20 μm from the soma, and propagated to the distal axon with high reliability and speed. Subcellular mapping revealed a stepwise increase of Na+ conductance density from the soma to the proximal axon, followed by a further gradual increase in the distal axon. Active cable modeling and experiments with partial channel block indicated that low axonal Na+ conductance density was sufficient for reliability, but high Na+ density was necessary for both speed of propagation and fast-spiking AP phenotype. Our results suggest that a supercritical density of Na+ channels compensates for the morphological properties of interneuron axons (small segmental diameter, extensive branching, and high bouton density), ensuring fast AP propagation and high-frequency repetitive firing. PMID:24657965

Density Functional Methods for Shock Physics and High Energy Density Science

NASA Astrophysics Data System (ADS)

Desjarlais, Michael

2017-06-01

Molecular dynamics with density functional theory has emerged over the last two decades as a powerful and accurate framework for calculating thermodynamic and transport properties with broad application to dynamic compression, high energy density science, and warm dense matter. These calculations have been extensively validated against shock and ramp wave experiments, are a principal component of high-fidelity equation of state generation, and are having wide-ranging impacts on inertial confinement fusion, planetary science, and shock physics research. In addition to thermodynamic properties, phase boundaries, and the equation of state, one also has access to electrical conductivity, thermal conductivity, and lower energy optical properties. Importantly, all these properties are obtained within the same theoretical framework and are manifestly consistent. In this talk I will give a brief history and overview of molecular dynamics with density functional theory and its use in calculating a wide variety of thermodynamic and transport properties for materials ranging from ambient to extreme conditions and with comparisons to experimental data. I will also discuss some of the limitations and difficulties, as well as active research areas. Sandia is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Phase diagram as a function of temperature and magnetic field for magnetic semiconductors

NASA Astrophysics Data System (ADS)

González, I.; Castro, J.; Baldomir, D.

2002-10-01

Using an extension of the Nagaev model of phase separation [E. L. Nagaev and A. I. Podel'shchikov, Sov. Phys. JETP, 71, 1108 (1990)] we calculate the phase diagram for degenerate antiferromagnetic semiconductors in the T-H plane for different current carrier densities. Both wide-band semiconductors and double-exchange materials are investigated.

The luminosity function for the CfA redshift survey slices

NASA Technical Reports Server (NTRS)

De Lapparent, Valerie; Geller, Margaret J.; Huchra, John P.

1989-01-01

The luminosity function for two complete slices of the extension of the CfA redshift survey is calculated. The nonparametric technique of Lynden-Bell (1971) and Turner (1979) is used to determine the shape for the luminosity function of the 12 deg slice of the redshift survey. The amplitude of the luminosity function is determined, taking large-scale inhomogeneities into account. The effects of the Malmquist bias on a magnitude-limited redshift survey are examined, showing that the random errors in the magnitudes for the 12 deg slice affect both the determination of the luminosity function and the spatial density constrast of large scale structures.

Topside Electron Density Representations for Middle and High Latitudes: A Topside Parameterization for E-CHAIM Based On the NeQuick

NASA Astrophysics Data System (ADS)

Themens, David R.; Jayachandran, P. T.; Bilitza, Dieter; Erickson, Philip J.; Häggström, Ingemar; Lyashenko, Mykhaylo V.; Reid, Benjamin; Varney, Roger H.; Pustovalova, Ljubov

2018-02-01

In this study, we present a topside model representation to be used by the Empirical Canadian High Arctic Ionospheric Model (E-CHAIM). In the process of this, we also present a comprehensive evaluation of the NeQuick's, and by extension the International Reference Ionosphere's, topside electron density model for middle and high latitudes in the Northern Hemisphere. Using data gathered from all available incoherent scatter radars, topside sounders, and Global Navigation Satellite System Radio Occultation satellites, we show that the current NeQuick parameterization suboptimally represents the shape of the topside electron density profile at these latitudes and performs poorly in the representation of seasonal and solar cycle variations of the topside scale thickness. Despite this, the simple, one variable, NeQuick model is a powerful tool for modeling the topside ionosphere. By refitting the parameters that define the maximum topside scale thickness and the rate of increase of the scale height within the NeQuick topside model function, r and g, respectively, and refitting the model's parameterization of the scale height at the F region peak, H0, we find considerable improvement in the NeQuick's ability to represent the topside shape and behavior. Building on these results, we present a new topside model extension of the E-CHAIM based on the revised NeQuick function. Overall, root-mean-square errors in topside electron density are improved over the traditional International Reference Ionosphere/NeQuick topside by 31% for a new NeQuick parameterization and by 36% for a newly proposed topside for E-CHAIM.

Long-term supratentorial brain structure and cognitive function following cerebellar tumour resections in childhood.

PubMed

Moberget, T; Andersson, S; Lundar, T; Due-Tønnessen, B J; Heldal, A; Endestad, T; Westlye, L T

2015-03-01

The cerebellum is connected to extensive regions of the cerebrum, and cognitive deficits following cerebellar lesions may thus be related to disrupted cerebello-cerebral connectivity. Moreover, early cerebellar lesions could affect distal brain development, effectively inducing long-term changes in brain structure and cognitive function. Here, we characterize supratentorial brain structure and cognitive function in 20 adult patients treated for cerebellar tumours in childhood (mean age at surgery: 7.1 years) and 26 matched controls. Relative to controls, patients showed reduced cognitive function and increased grey matter density in bilateral cingulum, left orbitofrontal cortex and the left hippocampus. Within the patient group, increased grey matter density in these regions was associated with decreased performance on tests of processing speed and executive function. Further, diffusion tensor imaging revealed widespread alterations in white matter microstructure in patients. While current ventricle volume (an index of previous hydrocephalus severity it patients) was associated with grey matter density and white matter microstructure in patients, this could only partially account for the observed group differences in brain structure and cognitive function. In conclusion, our results show distal effects of cerebellar lesions on cerebral integrity and wiring, likely caused by a combination of neurodegenerative processes and perturbed neurodevelopment. Copyright © 2015 Elsevier Ltd. All rights reserved.

Natural occupation numbers in two-electron quantum rings.

PubMed

Tognetti, Vincent; Loos, Pierre-François

2016-02-07

Natural orbitals (NOs) are central constituents for evaluating correlation energies through efficient approximations. Here, we report the closed-form expression of the NOs of two-electron quantum rings, which are prototypical finite-extension systems and new starting points for the development of exchange-correlation functionals in density functional theory. We also show that the natural occupation numbers for these two-electron paradigms are in general non-vanishing and follow the same power law decay as atomic and molecular two-electron systems.

Of pacemakers and statistics: the actuarial method extended.

PubMed

Dussel, J; Wolbarst, A B; Scott-Millar, R N; Obel, I W

1980-01-01

Pacemakers cease functioning because of either natural battery exhaustion (nbe) or component failure (cf). A study of four series of pacemakers shows that a simple extension of the actuarial method, so as to incorporate Normal statistics, makes possible a quantitative differentiation between the two modes of failure. This involves the separation of the overall failure probability density function PDF(t) into constituent parts pdfnbe(t) and pdfcf(t). The approach should allow a meaningful comparison of the characteristics of different pacemaker types.

Natural occupation numbers in two-electron quantum rings

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

Tognetti, Vincent, E-mail: vincent.tognetti@univ-rouen.fr; Loos, Pierre-François

2016-02-07

Natural orbitals (NOs) are central constituents for evaluating correlation energies through efficient approximations. Here, we report the closed-form expression of the NOs of two-electron quantum rings, which are prototypical finite-extension systems and new starting points for the development of exchange-correlation functionals in density functional theory. We also show that the natural occupation numbers for these two-electron paradigms are in general non-vanishing and follow the same power law decay as atomic and molecular two-electron systems.

One-shot K-region-selective annulative π-extension for nanographene synthesis and functionalization.

PubMed

Ozaki, Kyohei; Kawasumi, Katsuaki; Shibata, Mari; Ito, Hideto; Itami, Kenichiro

2015-02-16

The optoelectronic nature of two-dimensional sheets of sp(2)-hydridized carbons (for example, graphenes and nanographenes) can be dramatically altered and tuned by altering the degree of π-extension, shape, width and edge topology. Among various approaches to synthesize nanographenes with atom-by-atom precision, one-shot annulative π-extension (APEX) reactions of polycyclic aromatic hydrocarbons hold significant potential not only to achieve a 'growth from template' synthesis of nanographenes, but also to fine-tune the properties of nanographenes. Here we describe one-shot APEX reactions that occur at the K-region (convex armchair edge) of polycyclic aromatic hydrocarbons by the Pd(CH3CN)4(SbF6)2/o-chloranil catalytic system with silicon-bridged aromatics as π-extending agents. Density functional theory calculations suggest that the complete K-region selectivity stems from the olefinic (decreased aromatic) character of the K-region. The protocol is applicable to multiple APEX and sequential APEX reactions, to construct various nanographene structures in a rapid and programmable manner.

One-shot K-region-selective annulative π-extension for nanographene synthesis and functionalization

NASA Astrophysics Data System (ADS)

Ozaki, Kyohei; Kawasumi, Katsuaki; Shibata, Mari; Ito, Hideto; Itami, Kenichiro

2015-02-01

The optoelectronic nature of two-dimensional sheets of sp2-hydridized carbons (for example, graphenes and nanographenes) can be dramatically altered and tuned by altering the degree of π-extension, shape, width and edge topology. Among various approaches to synthesize nanographenes with atom-by-atom precision, one-shot annulative π-extension (APEX) reactions of polycyclic aromatic hydrocarbons hold significant potential not only to achieve a ‘growth from template’ synthesis of nanographenes, but also to fine-tune the properties of nanographenes. Here we describe one-shot APEX reactions that occur at the K-region (convex armchair edge) of polycyclic aromatic hydrocarbons by the Pd(CH3CN)4(SbF6)2/o-chloranil catalytic system with silicon-bridged aromatics as π-extending agents. Density functional theory calculations suggest that the complete K-region selectivity stems from the olefinic (decreased aromatic) character of the K-region. The protocol is applicable to multiple APEX and sequential APEX reactions, to construct various nanographene structures in a rapid and programmable manner.

Coarse-grained density functional theories for metallic alloys: Generalized coherent-potential approximations and charge-excess functional theory

NASA Astrophysics Data System (ADS)

Bruno, Ezio; Mammano, Francesco; Fiorino, Antonino; Morabito, Emanuela V.

2008-04-01

The class of the generalized coherent-potential approximations (GCPAs) to the density functional theory (DFT) is introduced within the multiple scattering theory formalism with the aim of dealing with ordered or disordered metallic alloys. All GCPA theories are based on a common ansatz for the kinetic part of the Hohenberg-Kohn functional and each theory of the class is specified by an external model concerning the potential reconstruction. Most existing DFT implementations of CPA-based theories belong to the GCPA class. The analysis of the formal properties of the density functional defined by GCPA theories shows that it consists of marginally coupled local contributions. Furthermore, it is shown that the GCPA functional does not depend on the details of the charge density and that it can be exactly rewritten as a function of the appropriate charge multipole moments to be associated with each lattice site. A general procedure based on the integration of the qV laws is described that allows for the explicit construction of the same function. The coarse-grained nature of the GCPA density functional implies a great deal of computational advantages and is connected with the O(N) scalability of GCPA algorithms. Moreover, it is shown that a convenient truncated series expansion of the GCPA functional leads to the charge-excess functional (CEF) theory [E. Bruno , Phys. Rev. Lett. 91, 166401 (2003)], which here is offered in a generalized version that includes multipolar interactions. CEF and the GCPA numerical results are compared with status of art linearized augmented plane wave (LAPW) full-potential density functional calculations for 62 bcc- and fcc-based ordered CuZn alloys, in all the range of concentrations. Two facts clearly emerge from these extensive tests. In the first place, the discrepancies between GCPA and CEF results are always within the numerical accuracy of the calculations, both for the site charges and the total energies. In the second place, the GCPA (or the CEF) is able to very carefully reproduce the LAPW site charges and a good agreement is obtained also about the total energies.

Many-Body Theory of Pyrochlore Iridates and Related Materials

NASA Astrophysics Data System (ADS)

Wang, Runzhi

In this thesis we focus on two problems. First we propose a numerical method for generating optimized Wannier functions with desired properties. Second we perform the state of the art density functional plus dynamical mean-field calculations in pyrochlore iridates, to investigate the physics induced by the cooperation of spin-orbit coupling and electron correlation. We begin with the introduction for maximally localized Wannier functions and other related extensions. Then we describe the current research in the field of spin-orbit coupling and its interplay with correlation effects, followed by a brief introduction of the `hot' materials of iridates. Before the end of the introduction, we discuss the numerical methods employed in our work, including the density functional theory; dynamical mean-field theory and its combination with the exact diagonalization impurity solver. Then we propose our approach for constructing an optimized set of Wannier functions, which is a generalization of the functionality of the classic maximal localization method put forward by Marzari and Vanderbilt. Our work is motivated by the requirement of the effective description of the local subspace of the Hamiltonian by the beyond density functional theory methods. In extensions of density functional theory such as dynamical mean-field theory, one may want highly accurate description of particular local orbitals, including correct centers and symmetries; while the basis for the remaining degrees of freedom is unimportant. Therefore, we develop the selectively localized Wannier function approach which allows for a greater localization in the selected subset of Wannier functions and at the same time allows us to fix the centers and ensure the point symmetries. Applications in real materials are presented to demonstrate the power of our approach. Next we move to the investigation of pyrochlore iridates, focussing on the metal-insulator transition and material dependence in these compounds. We perform combined density functional plus dynamical mean-field calculations in Lu2Ir2O7, Y2Ir2O 7, Eu2Ir2O7, with spin-orbit coupling included and both single-site and cluster approximations appiled. A broad range of Weyl metal is predicted as the intervening phase in the metal-insulator transition. By comparing to experiments, we find that the single-site approximation fails to predict the gap values and substantial difference between the Y and Eu-compound, demonstrating the inadequacy of this approximation and indicating the key role played by the intersite effects. Finally, we provide a more accurate description of the vicinity of the metal-insulator and topological transitions implied by density functional plus cluster dynamical mean-field calculations of pyrochlore iridates. We find definitive evidence of the Weyl semimetal phase, the electronic structure of which can be approximately described as ``Weyl rings" with an extremely flat dispersion of one of the Weyl bands. This Weyl semimetal phase is further investigated by the k • p analysis fitting to the numerical results. We find that this unusual structure leads to interesting behavior in the optical conductivity including a Hall effect in the interband component, and to an enhanced susceptibility.

Search for the First-Order Liquid-to-Liquid Phase Transition in Low-Temperature Confined Water by Neutron Scattering

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

Chen, Sow-Hsin; Wang, Zhe; Kolesnikov, Alexander I

2013-01-01

It has been conjectured that a 1st order liquid-to-liquid (L-L) phase transition (LLPT) between high density liquid (HDL) and low density liquid (LDL) in supercooled water may exist, as a thermodynamic extension to the liquid phase of the 1st order transition established between the two bulk solid phases of amorphous ice, the high density amorphous ice (HDA) and the low density amorphous ice (LDA). In this paper, we first recall our previous attempts to establish the existence of the 1st order L-L phase transition through the use of two neutron scattering techniques: a constant Q elastic diffraction study of isobaricmore » temperature scan of the D2O density, namely, the equation of state (EOS) measurements. A pronounced density hysteresis phenomenon in the temperature scan of the density above P = 1500 bar is observed which gives a plausible evidence of crossing the 1st order L-L phase transition line above this pressure; an incoherent quasi-elastic scattering measurements of temperature-dependence of the alpha-relaxation time of H2O at a series of pressures, namely, the study of the Fragile-to-Strong dynamic crossover (FSC) phenomenon as a function of pressure which we interpreted as the results of crossing the Widom line in the one-phase region. In this new experiment, we used incoherent inelastic neutron scattering (INS) to measure the density of states (DOS) of H atoms in H2O molecules in confined water as function of temperature and pressure, through which we may be able to follow the emergence of the LDL and HDL phases at supercooled temperature and high pressures. We here report for the first time the differences of librational and translational DOSs between the hypothetical HDL and LDL phases, which are similar to the corresponding differences between the well-established HDA and LDA ices. This is plausible evidence that the HDL and LDL phases are the thermodynamic extensions of the corresponding amorphous solid water HDA and LDA ices.« less

Search for the first-order liquid-to-liquid phase transition in low-temperature confined water by neutron scattering

NASA Astrophysics Data System (ADS)

Chen, Sow-Hsin; Wang, Zhe; Kolesnikov, Alexander I.; Zhang, Yang; Liu, Kao-Hsiang

2013-02-01

It has been conjectured that a 1st order liquid-to-liquid (L-L) phase transition (LLPT) between high density liquid (HDL) and low density liquid (LDL) in supercooled water may exist, as a thermodynamic extension to the liquid phase of the 1st order transition established between the two bulk solid phases of amorphous ice, the high density amorphous ice (HDA) and the low density amorphous ice (LDA). In this paper, we first recall our previous attempts to establish the existence of the 1st order L-L phase transition through the use of two neutron scattering techniques: a constant Q elastic diffraction study of isobaric temperature scan of the D2O density, namely, the equation of state (EOS) measurements. A pronounced density hysteresis phenomenon in the temperature scan of the density above P = 1500 bar is observed which gives a plausible evidence of crossing the 1st order L-L phase transition line above this pressure; an incoherent quasi-elastic scattering measurements of temperature-dependence of the α-relaxation time of H2O at a series of pressures, namely, the study of the Fragile-to-Strong dynamic crossover (FSC) phenomenon as a function of pressure which we interpreted as the results of crossing the Widom line in the one-phase region. In this new experiment, we used incoherent inelastic neutron scattering (INS) to measure the density of states (DOS) of H atoms in H2O molecules in confined water as function of temperature and pressure, through which we may be able to follow the emergence of the LDL and HDL phases at supercooled temperature and high pressures. We here report for the first time the differences of librational and translational DOSs between the hypothetical HDL and LDL phases, which are similar to the corresponding differences between the well-established HDA and LDA ices. This is plausible evidence that the HDL and LDL phases are the thermodynamic extensions of the corresponding amorphous solid water HDA and LDA ices.

Time-dependent density-functional theory with optimized effective potential and self-interaction correction and derivative discontinuity for the treatment of double ionization of He and Be atoms in intense laser fields

NASA Astrophysics Data System (ADS)

Heslar, John; Telnov, Dmitry A.; Chu, Shih-I.

2013-05-01

We present a self-interaction-free time-dependent density-functional theory (TDDFT) for the treatment of double-ionization processes of many-electron systems. The method is based on the extension of the Krieger-Li-Iafrate (KLI) treatment of the optimized effective potential (OEP) theory and the incorporation of an explicit self-interaction correction (SIC) term. In the framework of the time-dependent density functional theory, we have performed three-dimensional (3D) calculations of double ionization of He and Be atoms by intense near-infrared laser fields. We make use of the exchange-correlation potential with the integer discontinuity which improves the description of the double-ionization process. We found that a proper description of the double ionization requires the TDDFT exchange-correlation potential with the discontinuity with respect to the variation of the total particle number (TPN). The results for the intensity-dependent rates of double ionization of He and Be atoms are presented.

Force Field Accelerated Density Functional Theory Molecular Dynamics for Simulation of Reactive Systems at Extreme Conditions

NASA Astrophysics Data System (ADS)

Lindsey, Rebecca; Goldman, Nir; Fried, Laurence

2017-06-01

Atomistic modeling of chemistry at extreme conditions remains a challenge, despite continuing advances in computing resources and simulation tools. While first principles methods provide a powerful predictive tool, the time and length scales associated with chemistry at extreme conditions (ns and μm, respectively) largely preclude extension of such models to molecular dynamics. In this work, we develop a simulation approach that retains the accuracy of density functional theory (DFT) while decreasing computational effort by several orders of magnitude. We generate n-body descriptions for atomic interactions by mapping forces arising from short density functional theory (DFT) trajectories on to simple Chebyshev polynomial series. We examine the importance of including greater than 2-body interactions, model transferability to different state points, and discuss approaches to ensure smooth and reasonable model shape outside of the distance domain sampled by the DFT training set. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

Force Field Accelerated Density Functional Theory Molecular Dynamics for Simulation of Reactive Systems at Extreme Conditions

NASA Astrophysics Data System (ADS)

Lindsey, Rebecca; Goldman, Nir; Fried, Laurence

Understanding chemistry at extreme conditions is crucial in fields including geochemistry, astrobiology, and alternative energy. First principles methods can provide valuable microscopic insights into such systems while circumventing the risks of physical experiments, however the time and length scales associated with chemistry at extreme conditions (ns and μm, respectively) largely preclude extension of such models to molecular dynamics. In this work, we develop a simulation approach that retains the accuracy of density functional theory (DFT) while decreasing computational effort by several orders of magnitude. We generate n-body descriptions for atomic interactions by mapping forces arising from short density functional theory (DFT) trajectories on to simple Chebyshev polynomial series. We examine the importance of including greater than 2-body interactions, model transferability to different state points, and discuss approaches to ensure smooth and reasonable model shape outside of the distance domain sampled by the DFT training set. This work performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

Mapping surface charge density of lipid bilayers by quantitative surface conductivity microscopy

PubMed Central

Klausen, Lasse Hyldgaard; Fuhs, Thomas; Dong, Mingdong

2016-01-01

Local surface charge density of lipid membranes influences membrane–protein interactions leading to distinct functions in all living cells, and it is a vital parameter in understanding membrane-binding mechanisms, liposome design and drug delivery. Despite the significance, no method has so far been capable of mapping surface charge densities under physiologically relevant conditions. Here, we use a scanning nanopipette setup (scanning ion-conductance microscope) combined with a novel algorithm to investigate the surface conductivity near supported lipid bilayers, and we present a new approach, quantitative surface conductivity microscopy (QSCM), capable of mapping surface charge density with high-quantitative precision and nanoscale resolution. The method is validated through an extensive theoretical analysis of the ionic current at the nanopipette tip, and we demonstrate the capacity of QSCM by mapping the surface charge density of model cationic, anionic and zwitterionic lipids with results accurately matching theoretical values. PMID:27561322

Mapping surface charge density of lipid bilayers by quantitative surface conductivity microscopy

NASA Astrophysics Data System (ADS)

Klausen, Lasse Hyldgaard; Fuhs, Thomas; Dong, Mingdong

2016-08-01

Local surface charge density of lipid membranes influences membrane-protein interactions leading to distinct functions in all living cells, and it is a vital parameter in understanding membrane-binding mechanisms, liposome design and drug delivery. Despite the significance, no method has so far been capable of mapping surface charge densities under physiologically relevant conditions. Here, we use a scanning nanopipette setup (scanning ion-conductance microscope) combined with a novel algorithm to investigate the surface conductivity near supported lipid bilayers, and we present a new approach, quantitative surface conductivity microscopy (QSCM), capable of mapping surface charge density with high-quantitative precision and nanoscale resolution. The method is validated through an extensive theoretical analysis of the ionic current at the nanopipette tip, and we demonstrate the capacity of QSCM by mapping the surface charge density of model cationic, anionic and zwitterionic lipids with results accurately matching theoretical values.

Mapping surface charge density of lipid bilayers by quantitative surface conductivity microscopy.

PubMed

Klausen, Lasse Hyldgaard; Fuhs, Thomas; Dong, Mingdong

2016-08-26

Local surface charge density of lipid membranes influences membrane-protein interactions leading to distinct functions in all living cells, and it is a vital parameter in understanding membrane-binding mechanisms, liposome design and drug delivery. Despite the significance, no method has so far been capable of mapping surface charge densities under physiologically relevant conditions. Here, we use a scanning nanopipette setup (scanning ion-conductance microscope) combined with a novel algorithm to investigate the surface conductivity near supported lipid bilayers, and we present a new approach, quantitative surface conductivity microscopy (QSCM), capable of mapping surface charge density with high-quantitative precision and nanoscale resolution. The method is validated through an extensive theoretical analysis of the ionic current at the nanopipette tip, and we demonstrate the capacity of QSCM by mapping the surface charge density of model cationic, anionic and zwitterionic lipids with results accurately matching theoretical values.

Numerical investigation of deep-crust behavior under lithospheric extension

NASA Astrophysics Data System (ADS)

Korchinski, Megan; Rey, Patrice F.; Mondy, Luke; Teyssier, Christian; Whitney, Donna L.

2018-02-01

What are the conditions under which lithospheric extension drives exhumation of the deep orogenic crust during the formation of gneiss domes? The mechanical link between extension of shallow crust and flow of deep crust is investigated using two-dimensional numerical experiments of lithospheric extension in which the crust is 60 km thick and the deep-crust viscosity and density parameter space is explored. Results indicate that the style of extension of the shallow crust and the path, magnitude, and rate of flow of deep crust are dynamically linked through the deep-crust viscosity, with density playing an important role in experiments with a high-viscosity deep crust. Three main groups of domes are defined based on their mechanisms of exhumation across the viscosity-density parameter space. In the first group (low-viscosity, low-density deep crust), domes develop by lateral and upward flow of the deep crust at km m.y-1 velocity rates (i.e. rate of experiment boundary extension). In this case, extension in the shallow crust is localized on a single interface, and the deep crust traverses the entire thickness of the crust to the Earth's near-surface in 5 m.y. This high exhuming power relies on the dynamic feedback between the flow of deep crust and the localization of extension in the shallow crust. The second group (intermediate-viscosity, low-density deep crust) has less exhuming power because the stronger deep crust flows less readily and instead accommodates more uniform extension, which imparts distributed extension to the shallow crust. The third group represents the upper limits of viscosity and density for the deep crust; in this case the low buoyancy of the deep crust results in localized thinning of the crust with large upward motion of the Moho and lithosphere-asthenosphere boundary. These numerical experiments test the exhuming power of the deep crust in the formation of extensional gneiss domes.

Communication: Density functional theory embedding with the orthogonality constrained basis set expansion procedure

NASA Astrophysics Data System (ADS)

Culpitt, Tanner; Brorsen, Kurt R.; Hammes-Schiffer, Sharon

2017-06-01

Density functional theory (DFT) embedding approaches have generated considerable interest in the field of computational chemistry because they enable calculations on larger systems by treating subsystems at different levels of theory. To circumvent the calculation of the non-additive kinetic potential, various projector methods have been developed to ensure the orthogonality of molecular orbitals between subsystems. Herein the orthogonality constrained basis set expansion (OCBSE) procedure is implemented to enforce this subsystem orbital orthogonality without requiring a level shifting parameter. This scheme is a simple alternative to existing parameter-free projector-based schemes, such as the Huzinaga equation. The main advantage of the OCBSE procedure is that excellent convergence behavior is attained for DFT-in-DFT embedding without freezing any of the subsystem densities. For the three chemical systems studied, the level of accuracy is comparable to or higher than that obtained with the Huzinaga scheme with frozen subsystem densities. Allowing both the high-level and low-level DFT densities to respond to each other during DFT-in-DFT embedding calculations provides more flexibility and renders this approach more generally applicable to chemical systems. It could also be useful for future extensions to embedding approaches combining wavefunction theories and DFT.

Theory of disordered Heisenberg ferromagnets

NASA Technical Reports Server (NTRS)

Stubbs, R. M.

1973-01-01

A Green's function technique is used to calculate the magnetic properties of Heisenberg ferromagnets in which the exchange interactions deviate randomly in strength from the mean interaction. Systems of sc, bcc, and fcc topologies and of general spin values are treated. Disorder produces marked effects in the density of spin wave states, in the form of enhancement of the low-energy density and extension of the energy band to higher values. The spontaneous magnetization and the Curie temperature decrease with increasing disorder. The effects of disorder are shown to be more pronounced in the ferromagnetic than in the paramagnetic phase.

The phonon-coupling model for Skyrme forces

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

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

2016-11-15

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

Experimental study of the valence band of Bi 2 Se 3

DOE PAGES

Gao, Yi-Bin; He, Bin; Parker, David; ...

2014-09-26

The valence band of Bi 2Se 3 is investigated with Shubnikov - de Haas measurements, galvanomagnetic and thermoelectric transport. At low hole concentration, the hole Fermi surface is closed and box-like, but at higher concentrations it develops tube-like extensions that are open. The experimentally determined density-of-states effective mass is lighter than density-functional theory calculations predict; while we cannot give a definitive explanation for this, we suspect that the theory may lack sufficient precision to compute room-temperature transport properties, such as the Seebeck coefficient, in solids in which there are Van der Waals interlayer bonds.

What Density Functional Theory could do for Quantum Information

NASA Astrophysics Data System (ADS)

Mattsson, Ann

2015-03-01

The Hohenberg-Kohn theorem of Density Functional Theory (DFT), and extensions thereof, tells us that all properties of a system of electrons can be determined through their density, which uniquely determines the many-body wave-function. Given access to the appropriate, universal, functionals of the density we would, in theory, be able to determine all observables of any electronic system, without explicit reference to the wave-function. On the other hand, the wave-function is at the core of Quantum Information (QI), with the wave-function of a set of qubits being the central computational resource in a quantum computer. While there is seemingly little overlap between DFT and QI, reliance upon observables form a key connection. Though the time-evolution of the wave-function and associated phase information is fundamental to quantum computation, the initial and final states of a quantum computer are characterized by observables of the system. While observables can be extracted directly from a system's wave-function, DFT tells us that we may be able to intuit a method for extracting them from its density. In this talk, I will review the fundamentals of DFT and how these principles connect to the world of QI. This will range from DFT's utility in the engineering of physical qubits, to the possibility of using it to efficiently (but approximately) simulate Hamiltonians at the logical level. The apparent paradox of describing algorithms based on the quantum mechanical many-body wave-function with a DFT-like theory based on observables will remain a focus throughout. The ultimate goal of this talk is to initiate a dialog about what DFT could do for QI, in theory and in practice. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Advanced capabilities for materials modelling with Quantum ESPRESSO

NASA Astrophysics Data System (ADS)

Giannozzi, P.; Andreussi, O.; Brumme, T.; Bunau, O.; Buongiorno Nardelli, M.; Calandra, M.; Car, R.; Cavazzoni, C.; Ceresoli, D.; Cococcioni, M.; Colonna, N.; Carnimeo, I.; Dal Corso, A.; de Gironcoli, S.; Delugas, P.; DiStasio, R. A., Jr.; Ferretti, A.; Floris, A.; Fratesi, G.; Fugallo, G.; Gebauer, R.; Gerstmann, U.; Giustino, F.; Gorni, T.; Jia, J.; Kawamura, M.; Ko, H.-Y.; Kokalj, A.; Küçükbenli, E.; Lazzeri, M.; Marsili, M.; Marzari, N.; Mauri, F.; Nguyen, N. L.; Nguyen, H.-V.; Otero-de-la-Roza, A.; Paulatto, L.; Poncé, S.; Rocca, D.; Sabatini, R.; Santra, B.; Schlipf, M.; Seitsonen, A. P.; Smogunov, A.; Timrov, I.; Thonhauser, T.; Umari, P.; Vast, N.; Wu, X.; Baroni, S.

2017-11-01

Quantum EXPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the-art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudopotential and projector-augmented-wave approaches. Quantum EXPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement their ideas. In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software.

Advanced capabilities for materials modelling with Quantum ESPRESSO.

PubMed

Giannozzi, P; Andreussi, O; Brumme, T; Bunau, O; Buongiorno Nardelli, M; Calandra, M; Car, R; Cavazzoni, C; Ceresoli, D; Cococcioni, M; Colonna, N; Carnimeo, I; Dal Corso, A; de Gironcoli, S; Delugas, P; DiStasio, R A; Ferretti, A; Floris, A; Fratesi, G; Fugallo, G; Gebauer, R; Gerstmann, U; Giustino, F; Gorni, T; Jia, J; Kawamura, M; Ko, H-Y; Kokalj, A; Küçükbenli, E; Lazzeri, M; Marsili, M; Marzari, N; Mauri, F; Nguyen, N L; Nguyen, H-V; Otero-de-la-Roza, A; Paulatto, L; Poncé, S; Rocca, D; Sabatini, R; Santra, B; Schlipf, M; Seitsonen, A P; Smogunov, A; Timrov, I; Thonhauser, T; Umari, P; Vast, N; Wu, X; Baroni, S

2017-10-24

Quantum EXPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the-art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudopotential and projector-augmented-wave approaches. Quantum EXPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement their ideas. In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software.

Advanced capabilities for materials modelling with Quantum ESPRESSO.

PubMed

Andreussi, Oliviero; Brumme, Thomas; Bunau, Oana; Buongiorno Nardelli, Marco; Calandra, Matteo; Car, Roberto; Cavazzoni, Carlo; Ceresoli, Davide; Cococcioni, Matteo; Colonna, Nicola; Carnimeo, Ivan; Dal Corso, Andrea; de Gironcoli, Stefano; Delugas, Pietro; DiStasio, Robert; Ferretti, Andrea; Floris, Andrea; Fratesi, Guido; Fugallo, Giorgia; Gebauer, Ralph; Gerstmann, Uwe; Giustino, Feliciano; Gorni, Tommaso; Jia, Junteng; Kawamura, Mitsuaki; Ko, Hsin-Yu; Kokalj, Anton; Küçükbenli, Emine; Lazzeri, Michele; Marsili, Margherita; Marzari, Nicola; Mauri, Francesco; Nguyen, Ngoc Linh; Nguyen, Huy-Viet; Otero-de-la-Roza, Alberto; Paulatto, Lorenzo; Poncé, Samuel; Giannozzi, Paolo; Rocca, Dario; Sabatini, Riccardo; Santra, Biswajit; Schlipf, Martin; Seitsonen, Ari Paavo; Smogunov, Alexander; Timrov, Iurii; Thonhauser, Timo; Umari, Paolo; Vast, Nathalie; Wu, Xifan; Baroni, Stefano

2017-09-27

Quantum ESPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudo-potential and projector-augmented-wave approaches. Quantum ESPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement theirs ideas. In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software. © 2017 IOP Publishing Ltd.

Superconductivity in 2D and nearly 2D: A Conserving Description

NASA Astrophysics Data System (ADS)

Deisz, John; Hess, Daryl; Serene, Joe

1998-03-01

In a previous work,(J.J. Deisz, D.W. Hess, and J.W. Serene, Phys. Rev. Lett., to appear.) we used a 2D Hubbard model with an attractive interaction to explicitly show that a superconducting state in the fluctuation exchange approximation (FEA) could be detected from self-consistent calculations of the internal energy and free energy as a function of a threaded flux. The FEA is a conserving approximation beyond mean field theory that includes the exchange of Cooper pair, density, and spin fluctuations. Here, we present extensions of our previous calculations and show a phase diagram as a function of interaction strength and density. We discuss the nature of the FEA phase transition in 2D and focus on how it changes with increasing coupling between planes.

A mutation that eliminates bundle sheath extensions reduces leaf hydraulic conductance, stomatal conductance and assimilation rates in tomato (Solanum lycopersicum).

PubMed

Zsögön, Agustin; Negrini, Ana Clarissa Alves; Peres, Lázaro Eustáquio Pereira; Nguyen, Hoa Thi; Ball, Marilyn C

2015-01-01

Bundle sheath extensions (BSEs) are key features of leaf structure whose distribution differs among species and ecosystems. The genetic control of BSE development is unknown, so BSE physiological function has not yet been studied through mutant analysis. We screened a population of ethyl methanesulfonate (EMS)-induced mutants in the genetic background of the tomato (Solanum lycopersicum) model Micro-Tom and found a mutant lacking BSEs. The leaf phenotype of the mutant strongly resembled the tomato mutant obscuravenosa (obv). We confirmed that obv lacks BSEs and that it is not allelic to our induced mutant, which we named obv-2. Leaves lacking BSEs had lower leaf hydraulic conductance and operated with lower stomatal conductance and correspondingly lower assimilation rates than wild-type leaves. This lower level of function occurred despite similarities in vein density, midvein vessel diameter and number, stomatal density, and leaf area between wild-type and mutant leaves, the implication being that the lack of BSEs hindered water dispersal within mutant leaves. Our results comparing near-isogenic lines within a single species confirm the hypothesised role of BSEs in leaf hydraulic function. They further pave the way for a genetic model-based analysis of a common leaf structure with deep ecological consequences. © 2014 The Authors New Phytologist © 2014 New Phytologist Trust.

A space-based climatology of diurnal MLT tidal winds, temperatures and densities from UARS wind measurements

NASA Astrophysics Data System (ADS)

Svoboda, Aaron A.; Forbes, Jeffrey M.; Miyahara, Saburo

2005-11-01

A self-consistent global tidal climatology, useful for comparing and interpreting radar observations from different locations around the globe, is created from space-based Upper Atmosphere Research Satellite (UARS) horizontal wind measurements. The climatology created includes tidal structures for horizontal winds, temperature and relative density, and is constructed by fitting local (in latitude and height) UARS wind data at 95 km to a set of basis functions called Hough mode extensions (HMEs). These basis functions are numerically computed modifications to Hough modes and are globally self-consistent in wind, temperature, and density. We first demonstrate this self-consistency with a proxy data set from the Kyushu University General Circulation Model, and then use a linear weighted superposition of the HMEs obtained from monthly fits to the UARS data to extrapolate the global, multi-variable tidal structure. A brief explanation of the HMEs’ origin is provided as well as information about a public website that has been set up to make the full extrapolated data sets available.

Synthesis of generalized surface plasmon beams

NASA Astrophysics Data System (ADS)

Martinez-Niconoff, G.; Munoz-Lopez, J.; Martinez-Vara, P.

2009-08-01

Surface plasmon modes can be considered as the analogous to plane waves for homogeneous media. The extension to partially coherent surface plasmon beams is obtained by means of the incoherent superposition of the interference between surface plasmon modes whose profile is controlled associating a probability density function to the structural parameters implicit in their representation. We show computational simulations for cosine, Bessel, gaussian and dark hollow surface plasmon beams.

Addendum to strangeness production and color deconfinement

NASA Astrophysics Data System (ADS)

Castorina, P.; Plumari, S.; Satz, H.

Recent extensive data from the beam energy scan of the STAR collaboration at BNL-RHIC provide the basis for a detailed update for the universal behavior of the strangeness suppression factor γs as function of the initial entropy density as proposed in our recent paper (P. Castorina, S Plumari and H. Satz, Int. J. Mod. Phys. E 26 (2017) 1750081, arXiv:1709.02706 [nucl-th]).

Chaotic attractors and physical measures for some density dependent Leslie population models

NASA Astrophysics Data System (ADS)

Ugarcovici, Ilie; Weiss, Howard

2007-12-01

Following ecologists' discoveries, mathematicians have begun studying extensions of the ubiquitous age structured Leslie population model that allow some survival probabilities and/or fertility rates to depend on population densities. These nonlinear extensions commonly exhibit very complicated dynamics: through computer studies, some authors have discovered robust Hénon-like strange attractors in several families. Population biologists and demographers frequently wish to average a function over many generations and conclude that the average is independent of the initial population distribution. This type of 'ergodicity' seems to be a fundamental tenet in population biology. In this paper we develop the first rigorous ergodic theoretic framework for density dependent Leslie population models. We study two generation models with Ricker and Hassell (recruitment type) fertility terms. We prove that for some parameter regions these models admit a chaotic (ergodic) attractor which supports a unique physical probability measure. This physical measure, having full Lebesgue measure basin, satisfies in the strongest possible sense the population biologist's requirement for ergodicity in their population models. We use the celebrated work of Wang and Young 2001 Commun. Math. Phys. 218 1-97, and our results are the first applications of their method to biology, ecology or demography.

First-principles Theory of Inelastic Transport and Local Heating in Atomic Gold Wires

NASA Astrophysics Data System (ADS)

Frederiksen, Thomas; Paulsson, Magnus; Brandbyge, Mads; Jauho, Antti-Pekka

2007-04-01

We present theoretical calculations of the inelastic transport properties in atomic gold wires. Our method is based on a combination of density functional theory and non-equilibrium Green's functions. The vibrational spectra for extensive series of wire geometries have been calculated using SIESTA, and the corresponding effects in the conductance are analyzed. In particular, we focus on the heating of the active vibrational modes. By a detailed comparison with experiments we are able to estimate an order of magnitude for the external damping of the active vibrations.

Binary collision approximations for the memory function for density fluctuations in equilibrium atomic liquids

NASA Astrophysics Data System (ADS)

Noah, Joyce E.

Time correlation functions of density fluctuations of liquids at equilibrium can be used to relate the microscopic dynamics of a liquid to its macroscopic transport properties. Time correlation functions are especially useful since they can be generated in a variety of ways, from scattering experiments to computer simulation to analytic theory. The kinetic theory of fluctuations in equilibrium liquids is an analytic theory for calculating correlation functions using memory functions. In this work, we use a diagrammatic formulation of the kinetic theory to develop a series of binary collision approximations for the collisional part of the memory function. We define binary collisions as collisions between two distinct density fluctuations whose identities are fixed during the duration of a collsion. R approximations are for the short time part of the memory function, and build upon the work of Ranganathan and Andersen. These approximations have purely repulsive interactions between the fluctuations. The second type of approximation, RA approximations, is for the longer time part of the memory function, where the density fluctuations now interact via repulsive and attractive forces. Although RA approximations are a natural extension of R approximations, they permit two density fluctuations to become trapped in the wells of the interaction potential, leading to long-lived oscillatory behavior, which is unphysical. Therefore we consider S approximations which describe binary particles which experience the random effect of the surroundings while interacting via repulsive or repulsive and attractive interactions. For each of these approximations for the memory function we numerically solve the kinetic equation to generate correlation functions. These results are compared to molecular dynamics results for the correlation functions. Comparing the successes and failures of the different approximations, we conclude that R approximations give more accurate intermediate and long time results while RA and S approximations do particularly well at predicting the short time behavior. Lastly, we also develop a series of non-graphically derived approximations and use an optimization procedure to determine the underlying memory function from the simulation data. These approaches provide valuable information about the memory function that will be used in the development of future kinetic theories.

Do muscle mass, muscle density, strength, and physical function similarly influence risk of hospitalization in older adults?

PubMed

Cawthon, Peggy Mannen; Fox, Kathleen M; Gandra, Shravanthi R; Delmonico, Matthew J; Chiou, Chiun-Fang; Anthony, Mary S; Sewall, Ase; Goodpaster, Bret; Satterfield, Suzanne; Cummings, Steven R; Harris, Tamara B

2009-08-01

To examine the association between strength, function, lean mass, muscle density, and risk of hospitalization. Prospective cohort study. Two U.S. clinical centers. Adults aged 70 to 80 (N=3,011) from the Health, Aging and Body Composition Study. Measurements were of grip strength, knee extension strength, lean mass, walking speed, and chair stand pace. Thigh computed tomography scans assessed muscle area and density (a proxy for muscle fat infiltration). Hospitalizations were confirmed by local review of medical records. Negative binomial regression models estimated incident rate ratios (IRRs) of hospitalization for race- and sex-specific quartiles of each muscle and function parameter separately. Multivariate models adjusted for age, body mass index, health status, and coexisting medical conditions. During an average 4.7 years of follow-up, 1,678 (55.7%) participants experienced one or more hospitalizations. Participants in the lowest quartile of muscle density were more likely to be subsequently hospitalized (multivariate IRR=1.47, 95% confidence interval (CI)=1.24-1.73) than those in the highest quartile. Similarly, participants with the weakest grip strength were at greater risk of hospitalization (multivariate IRR=1.52, 95% CI=1.30-1.78, Q1 vs. Q4). Comparable results were seen for knee strength, walking pace, and chair stands pace. Lean mass and muscle area were not associated with risk of hospitalization. Weak strength, poor function, and low muscle density, but not muscle size or lean mass, were associated with greater risk of hospitalization. Interventions to reduce the disease burden associated with sarcopenia should focus on increasing muscle strength and improving physical function rather than simply increasing lean mass.

Importance of van der Waals interaction on structural, vibrational, and thermodynamic properties of NaCl

NASA Astrophysics Data System (ADS)

Marcondes, Michel L.; Wentzcovitch, Renata M.; Assali, Lucy V. C.

2018-05-01

Thermal equations of state (EOS) are essential in several scientific domains. However, experimental determination of EOS parameters may be limited at extreme conditions, therefore, ab initio calculations have become an important method to obtain them. Density functional theory (DFT) and its extensions with various degrees of approximations for the exchange and correlation (XC) energy is the method of choice, but large errors in the EOS parameters are still common. The alkali halides have been problematic from the onset of this field and the quest for appropriate DFT functionals for such ionic and relatively weakly bonded systems has remained an active topic of research. Here we use DFT + van der Waals functionals to calculate vibrational properties, thermal EOS, thermodynamic properties, and the B1 to B2 phase boundary of NaCl with high precision. Our results reveal a remarkable improvement over the performance of standard local density approximation and generalized gradient approximation functionals for all these properties and phase transition boundary, as well as great sensitivity of anharmonic effects on the choice of XC functional.

Detailed Wave Function Analysis for Multireference Methods: Implementation in the Molcas Program Package and Applications to Tetracene.

PubMed

Plasser, Felix; Mewes, Stefanie A; Dreuw, Andreas; González, Leticia

2017-11-14

High-level multireference computations on electronically excited and charged states of tetracene are performed, and the results are analyzed using an extensive wave function analysis toolbox that has been newly implemented in the Molcas program package. Aside from verifying the strong effect of dynamic correlation, this study reveals an unexpected critical influence of the atomic orbital basis set. It is shown that different polarized double-ζ basis sets produce significantly different results for energies, densities, and overall wave functions, with the best performance obtained for the atomic natural orbital (ANO) basis set by Pierloot et al. Strikingly, the ANO basis set not only reproduces the energies but also performs exceptionally well in terms of describing the diffuseness of the different states and of their attachment/detachment densities. This study, thus, not only underlines the fact that diffuse basis functions are needed for an accurate description of the electronic wave functions but also shows that, at least for the present example, it is enough to include them implicitly in the contraction scheme.

IRI STORM validation over Europe

NASA Astrophysics Data System (ADS)

Haralambous, Haris; Vryonides, Photos; Demetrescu, Crişan; Dobrică, Venera; Maris, Georgeta; Ionescu, Diana

2014-05-01

The International Reference Ionosphere (IRI) model includes an empirical Storm-Time Ionospheric Correction Model (STORM) extension to account for storm-time changes of the F layer peak electron density (NmF2) during increased geomagnetic activity. This model extension is driven by past history values of the geomagnetic index ap (The magnetic index applied is the integral of ap over the previous 33 hours with a weighting function deduced from physically based modeling) and it adjusts the quiet-time F layer peak electron density (NmF2) to account for storm-time changes in the ionosphere. In this investigation manually scaled hourly values of NmF2 measured during the main and recovery phases of selected storms for the maximum solar activity period of the current solar cycle are compared with the predicted IRI-2012 NmF2 over European ionospheric stations using the STORM model option. Based on the comparison a subsequent performance evaluation of the STORM option during this period is quantified.

Dynamics of entanglement in expanding quantum fields

NASA Astrophysics Data System (ADS)

Berges, Jürgen; Floerchinger, Stefan; Venugopalan, Raju

2018-04-01

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

Truncated Calogero-Sutherland models

NASA Astrophysics Data System (ADS)

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

2017-05-01

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

Spacing distribution functions for 1D point island model with irreversible attachment

NASA Astrophysics Data System (ADS)

Gonzalez, Diego; Einstein, Theodore; Pimpinelli, Alberto

2011-03-01

We study the configurational structure of the point island model for epitaxial growth in one dimension. In particular, we calculate the island gap and capture zone distributions. Our model is based on an approximate description of nucleation inside the gaps. Nucleation is described by the joint probability density p xy n (x,y), which represents the probability density to have nucleation at position x within a gap of size y. Our proposed functional form for p xy n (x,y) describes excellently the statistical behavior of the system. We compare our analytical model with extensive numerical simulations. Our model retains the most relevant physical properties of the system. This work was supported by the NSF-MRSEC at the University of Maryland, Grant No. DMR 05-20471, with ancillary support from the Center for Nanophysics and Advanced Materials (CNAM).

Optimal Base Station Density of Dense Network: From the Viewpoint of Interference and Load.

PubMed

Feng, Jianyuan; Feng, Zhiyong

2017-09-11

Network densification is attracting increasing attention recently due to its ability to improve network capacity by spatial reuse and relieve congestion by offloading. However, excessive densification and aggressive offloading can also cause the degradation of network performance due to problems of interference and load. In this paper, with consideration of load issues, we study the optimal base station density that maximizes the throughput of the network. The expected link rate and the utilization ratio of the contention-based channel are derived as the functions of base station density using the Poisson Point Process (PPP) and Markov Chain. They reveal the rules of deployment. Based on these results, we obtain the throughput of the network and indicate the optimal deployment density under different network conditions. Extensive simulations are conducted to validate our analysis and show the substantial performance gain obtained by the proposed deployment scheme. These results can provide guidance for the network densification.

Extended analytical solutions for effective elastic moduli of cracked porous media

NASA Astrophysics Data System (ADS)

Nguyen, Sy-Tuan; To, Quy Dong; Vu, Minh Ngoc

2017-05-01

Extended solutions are derived, on the basis of the micromechanical methods, for the effective elastic moduli of porous media containing stiff pores and both open and closed cracks. Analytical formulas of the overall bulk and shear moduli are obtained as functions of the elastic moduli of the solid skeleton, porosity and the densities of open and closed cracks families. We show that the obtained results are extensions of the classical widely used Walsh's (JGR, 1965) and Budiansky-O‧Connell's (JGR, 1974) solutions. Parametric sensitivity analysis clarifies the impact of the model parameters on the effective elastic properties. An inverse analysis, using sonic and density data, is considered to quantify the density of both open and closed cracks. It is observed that the density of closed cracks depends strongly on stress condition while the dependence of open cracks on the confining stress is negligible.

Testing critical point universality along the λ-line

NASA Astrophysics Data System (ADS)

Nissen, J. A.; Swanson, D. R.; Geng, Z. K.; Dohm, V.; Israelsson, U. E.; DiPirro, M. J.; Lipa, J. A.

1998-02-01

We are currently building a prototype for a new test of critical-point universality at the lambda transition in 4He, which is to be performed in microgravity conditions. The flight experiment will measure the second-sound velocity as a function of temperature at pressures from 1 to 30 bars in the region close to the lambda line. The critical exponents and other parameters characterizing the behavior of the superfluid density will be determined from the measurements. The microgravity measurements will be quite extensive, probably taking 30 days to complete. In addition to the superfluid density, some measurements of the specific heat will be made using the low-g simulator at the Jet Propulsion Laboratory. The results of the superfluid density and specific heat measurements will be used to compare the asymptotic exponents and other universal aspects of the superfluid density with the theoretical predictions currently established by renormalization group techniques.

Theoretical study of the hyperfine parameters of OH

NASA Technical Reports Server (NTRS)

Chong, Delano P.; Langhoff, Stephen R.; Bauschlicher, Charles W., Jr.

1991-01-01

In the present study of the hyperfine parameters of O-17H as a function of the one- and n-particle spaces, all of the parameters except oxygen's spin density, b sub F(O), are sufficiently easily tractable to allow concentration on the computational requirements for accurate determination of b sub F(O). Full configuration-interaction (FCI) calculations in six Gaussian basis sets yield unambiguous results for (1) the effect of uncontracting the O s and p basis sets; (2) that of adding diffuse s and p functions; and (3) that of adding polarization functions to O. The size-extensive modified coupled-pair functional method yields b sub F values which are in fair agreement with FCI results.

Extended polarization in 3rd order SCC-DFTB from chemical potential equilization

PubMed Central

Kaminski, Steve; Giese, Timothy J.; Gaus, Michael; York, Darrin M.; Elstner, Marcus

2012-01-01

In this work we augment the approximate density functional method SCC-DFTB (DFTB3) with the chemical potential equilization (CPE) approach in order to improve the performance for molecular electronic polarizabilities. The CPE method, originally implemented for NDDO type methods by Giese and York, has been shown to emend minimal basis methods wrt response properties significantly, and has been applied to SCC-DFTB recently. CPE allows to overcome this inherent limitation of minimal basis methods by supplying an additional response density. The systematic underestimation is thereby corrected quantitatively without the need to extend the atomic orbital basis, i.e. without increasing the overall computational cost significantly. Especially the dependency of polarizability as a function of molecular charge state was significantly improved from the CPE extension of DFTB3. The empirical parameters introduced by the CPE approach were optimized for 172 organic molecules in order to match the results from density functional methods (DFT) methods using large basis sets. However, the first order derivatives of molecular polarizabilities, as e.g. required to compute Raman activities, are not improved by the current CPE implementation, i.e. Raman spectra are not improved. PMID:22894819

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

PubMed Central

Smith, Lachlan J; Fazzalari, Nicola L

2006-01-01

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

An experimental test of plant canopy reflectance models on cotton

NASA Technical Reports Server (NTRS)

Lemaster, E. W.

1974-01-01

Extensive data on the plant parameters necessary to evaluate any model are presented for a cotton crop. The variation of the bidirectional reflectance function with observer altitude, observer azimuth, and sun altitude angle is presented for a high density cotton crop having leaf index of 19. A comparison with the quantitative behavior obtained from the Suits model is accomplished in the wavelength region from 400 nm to 1050 nm.

Mild Oxidation Promotes and Advanced Oxidation Impairs Remodeling of Human High-Density Lipoprotein in vitro

PubMed Central

Gao, Xuan; Jayaraman, Shobini; Gursky, Olga

2008-01-01

SUMMARY High-density lipoproteins (HDL) prevent atherosclerosis by removing cholesterol from macrophages and by exerting anti-oxidant and anti-inflammatory effects. Oxidation is thought to impair HDL functions, yet certain oxidative modifications may be advantageous; thus, mild oxidation reportedly enhances cell cholesterol uptake by HDL whereas extensive oxidation impairs it. To elucidate the underlying energetic and structural basis, we analyzed the effects of copper and hypochlorite (that preferentially oxidize lipids and proteins, respectively) on thermal stability of plasma spherical HDL. Circular dichroism, light scattering, calorimetry, gel electrophoresis and electron microscopy showed that mild oxidation destabilizes HDL and accelerates protein dissociation and lipoprotein fusion, while extensive oxidation inhibits these reactions; this inhibition correlates with massive protein cross-linking and lipolysis. We propose that mild oxidation lowers kinetic barriers for HDL remodeling due to diminished apolipoprotein affinity for lipids resulting from oxidation of methionine and aromatic residues in apolipoproteins A-I and A-II followed by protein cross-linking into dimers and/or trimers. In contrast, advanced oxidation inhibits protein dissociation and HDL fusion due to lipid re-distribution from core to surface upon lipolysis and to massive protein cross-linking. Our results help reconcile the apparent controversy in the studies of oxidized HDL and suggest that mild oxidation may benefit HDL functions. PMID:18190928

Nonparametric Density Estimation Based on Self-Organizing Incremental Neural Network for Large Noisy Data.

PubMed

Nakamura, Yoshihiro; Hasegawa, Osamu

2017-01-01

With the ongoing development and expansion of communication networks and sensors, massive amounts of data are continuously generated in real time from real environments. Beforehand, prediction of a distribution underlying such data is difficult; furthermore, the data include substantial amounts of noise. These factors make it difficult to estimate probability densities. To handle these issues and massive amounts of data, we propose a nonparametric density estimator that rapidly learns data online and has high robustness. Our approach is an extension of both kernel density estimation (KDE) and a self-organizing incremental neural network (SOINN); therefore, we call our approach KDESOINN. An SOINN provides a clustering method that learns about the given data as networks of prototype of data; more specifically, an SOINN can learn the distribution underlying the given data. Using this information, KDESOINN estimates the probability density function. The results of our experiments show that KDESOINN outperforms or achieves performance comparable to the current state-of-the-art approaches in terms of robustness, learning time, and accuracy.

The Minimum-Mass Surface Density of the Solar Nebula using the Disk Evolution Equation

NASA Technical Reports Server (NTRS)

Davis, Sanford S.

2005-01-01

The Hayashi minimum-mass power law representation of the pre-solar nebula (Hayashi 1981, Prog. Theo. Phys.70,35) is revisited using analytic solutions of the disk evolution equation. A new cumulative-planetary-mass-model (an integrated form of the surface density) is shown to predict a smoother surface density compared with methods based on direct estimates of surface density from planetary data. First, a best-fit transcendental function is applied directly to the cumulative planetary mass data with the surface density obtained by direct differentiation. Next a solution to the time-dependent disk evolution equation is parametrically adapted to the planetary data. The latter model indicates a decay rate of r -1/2 in the inner disk followed by a rapid decay which results in a sharper outer boundary than predicted by the minimum mass model. The model is shown to be a good approximation to the finite-size early Solar Nebula and by extension to extra solar protoplanetary disks.

Statistics of Smoothed Cosmic Fields in Perturbation Theory. I. Formulation and Useful Formulae in Second-Order Perturbation Theory

NASA Astrophysics Data System (ADS)

Matsubara, Takahiko

2003-02-01

We formulate a general method for perturbative evaluations of statistics of smoothed cosmic fields and provide useful formulae for application of the perturbation theory to various statistics. This formalism is an extensive generalization of the method used by Matsubara, who derived a weakly nonlinear formula of the genus statistic in a three-dimensional density field. After describing the general method, we apply the formalism to a series of statistics, including genus statistics, level-crossing statistics, Minkowski functionals, and a density extrema statistic, regardless of the dimensions in which each statistic is defined. The relation between the Minkowski functionals and other geometrical statistics is clarified. These statistics can be applied to several cosmic fields, including three-dimensional density field, three-dimensional velocity field, two-dimensional projected density field, and so forth. The results are detailed for second-order theory of the formalism. The effect of the bias is discussed. The statistics of smoothed cosmic fields as functions of rescaled threshold by volume fraction are discussed in the framework of second-order perturbation theory. In CDM-like models, their functional deviations from linear predictions plotted against the rescaled threshold are generally much smaller than that plotted against the direct threshold. There is still a slight meatball shift against rescaled threshold, which is characterized by asymmetry in depths of troughs in the genus curve. A theory-motivated asymmetry factor in the genus curve is proposed.

Modeling solvation effects in real-space and real-time within density functional approaches

NASA Astrophysics Data System (ADS)

Delgado, Alain; Corni, Stefano; Pittalis, Stefano; Rozzi, Carlo Andrea

2015-10-01

The Polarizable Continuum Model (PCM) can be used in conjunction with Density Functional Theory (DFT) and its time-dependent extension (TDDFT) to simulate the electronic and optical properties of molecules and nanoparticles immersed in a dielectric environment, typically liquid solvents. In this contribution, we develop a methodology to account for solvation effects in real-space (and real-time) (TD)DFT calculations. The boundary elements method is used to calculate the solvent reaction potential in terms of the apparent charges that spread over the van der Waals solute surface. In a real-space representation, this potential may exhibit a Coulomb singularity at grid points that are close to the cavity surface. We propose a simple approach to regularize such singularity by using a set of spherical Gaussian functions to distribute the apparent charges. We have implemented the proposed method in the Octopus code and present results for the solvation free energies and solvatochromic shifts for a representative set of organic molecules in water.

Modeling solvation effects in real-space and real-time within density functional approaches

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

Delgado, Alain; Centro de Aplicaciones Tecnológicas y Desarrollo Nuclear, Calle 30 # 502, 11300 La Habana; Corni, Stefano

2015-10-14

The Polarizable Continuum Model (PCM) can be used in conjunction with Density Functional Theory (DFT) and its time-dependent extension (TDDFT) to simulate the electronic and optical properties of molecules and nanoparticles immersed in a dielectric environment, typically liquid solvents. In this contribution, we develop a methodology to account for solvation effects in real-space (and real-time) (TD)DFT calculations. The boundary elements method is used to calculate the solvent reaction potential in terms of the apparent charges that spread over the van der Waals solute surface. In a real-space representation, this potential may exhibit a Coulomb singularity at grid points that aremore » close to the cavity surface. We propose a simple approach to regularize such singularity by using a set of spherical Gaussian functions to distribute the apparent charges. We have implemented the proposed method in the OCTOPUS code and present results for the solvation free energies and solvatochromic shifts for a representative set of organic molecules in water.« less

The emergence of different tail exponents in the distributions of firm size variables

NASA Astrophysics Data System (ADS)

Ishikawa, Atushi; Fujimoto, Shouji; Watanabe, Tsutomu; Mizuno, Takayuki

2013-05-01

We discuss a mechanism through which inversion symmetry (i.e., invariance of a joint probability density function under the exchange of variables) and Gibrat’s law generate power-law distributions with different tail exponents. Using a dataset of firm size variables, that is, tangible fixed assets K, the number of workers L, and sales Y, we confirm that these variables have power-law tails with different exponents, and that inversion symmetry and Gibrat’s law hold. Based on these findings, we argue that there exists a plane in the three dimensional space (logK,logL,logY), with respect to which the joint probability density function for the three variables is invariant under the exchange of variables. We provide empirical evidence suggesting that this plane fits the data well, and argue that the plane can be interpreted as the Cobb-Douglas production function, which has been extensively used in various areas of economics since it was first introduced almost a century ago.

Finite temperature behavior of the CPT-even and parity-even electrodynamics of the standard model extension

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

Casana, Rodolfo; Ferreira, Manoel M. Jr; Rodrigues, Josberg S.

2009-10-15

In this work, we examine the finite temperature properties of the CPT-even and Lorentz-invariance-violating (LIV) electrodynamics of the standard model extension, represented by the term W{sub {alpha}}{sub {nu}}{sub {rho}}{sub {phi}}F{sup {alpha}}{sup {nu}}F{sup {rho}}{sup {phi}}. We begin analyzing the Hamiltonian structure following the Dirac's procedure for constrained systems and construct a well-defined and gauge invariant partition function in the functional integral formalism. Next, we specialize for the nonbirefringent coefficients of the tensor W{sub {alpha}}{sub {nu}}{sub {rho}}{sub {phi}}. In the sequel, the partition function is explicitly carried out for the parity-even sector of the tensor W{sub {alpha}}{sub {nu}}{sub {rho}}{sub {phi}}. The modifiedmore » partition function is a power of the Maxwell's partition function. It is observed that the LIV coefficients induce an anisotropy in the black body angular energy density distribution. The Planck's radiation law, however, retains its frequency dependence and the Stefan-Boltzmann law keeps the usual form, except for a change in the Stefan-Boltzmann constant by a factor containing the LIV contributions.« less

Extension of the master sintering curve for constant heating rate modeling

NASA Astrophysics Data System (ADS)

McCoy, Tammy Michelle

The purpose of this work is to extend the functionality of the Master Sintering Curve (MSC) such that it can be used as a practical tool for predicting sintering schemes that combine both a constant heating rate and an isothermal hold. Rather than just being able to predict a final density for the object of interest, the extension to the MSC will actually be able to model a sintering run from start to finish. Because the Johnson model does not incorporate this capability, the work presented is an extension of what has already been shown in literature to be a valuable resource in many sintering situations. A predicted sintering curve that incorporates a combination of constant heating rate and an isothermal hold is more indicative of what is found in real-life sintering operations. This research offers the possibility of predicting the sintering schedule for a material, thereby having advanced information about the extent of sintering, the time schedule for sintering, and the sintering temperature with a high degree of accuracy and repeatability. The research conducted in this thesis focuses on the development of a working model for predicting the sintering schedules of several stabilized zirconia powders having the compositions YSZ (HSY8), 10Sc1CeSZ, 10Sc1YSZ, and 11ScSZ1A. The compositions of the four powders are first verified using x-ray diffraction (XRD) and the particle size and surface area are verified using a particle size analyzer and BET analysis, respectively. The sintering studies were conducted on powder compacts using a double pushrod dilatometer. Density measurements are obtained both geometrically and using the Archimedes method. Each of the four powders is pressed into ¼" diameter pellets using a manual press with no additives, such as a binder or lubricant. Using a double push-rod dilatometer, shrinkage data for the pellets is obtained over several different heating rates. The shrinkage data is then converted to reflect the change in relative density of the pellets based on the green density and the theoretical density of each of the compositions. The Master Sintering Curve (MSC) model is then utilized to generate data that can be utilized to predict the final density of the respective powder over a range of heating rates. The Elton Master Sintering Curve Extension (EMSCE) is developed to extend the functionality of the MSC tool. The parameters generated from the original MSC are used in tandem with the solution to the closed integral, theta ≡ 1cTo T1Texp -QRT dT, over a set range of temperatures. The EMSCE is used to generate a set of sintering curves having both constant heating rate and isothermal hold portions. The EMSCE extends the usefulness of the MSC by allowing this generation of a complete sintering schedule rather than just being able to predict the final relative density of a given material. The EMSCE is verified by generating a set of curves having both constant heating rate and an isothermal hold for the heat-treatment. The modeled curves are verified experimentally and a comparison of the model and experimental results are given for a selected composition. Porosity within the final product can hinder the product from sintering to full density. It is shown that some of the compositions studied did not sinter to full density because of the presence of large porosity that could not be eliminated in a reasonable amount of time. A statistical analysis of the volume fraction of porosity is completed to show the significance of the presence in the final product. The reason this is relevant to the MSC is that the model does not take into account the presence of porosity and assumes that the samples sinter to full density. When this does not happen, the model actually under-predicts the final density of the material.

Effects of season on ecological processes in extensive earthen tilapia ponds in Southeastern Brazil.

PubMed

Favaro, E G P; Sipaúba-Tavares, L H; Milstein, A

2015-11-01

In Southeastern Brazil tilapia culture is conducted in extensive and semi-intensive flow-through earthen ponds, being water availability and flow management different in the rainy and dry seasons. In this region lettuce wastes are a potential cheap input for tilapia culture. This study examined the ecological processes developing during the rainy and dry seasons in three extensive flow-through earthen tilapia ponds fertilized with lettuce wastes. Water quality, plankton and sediment parameters were sampled monthly during a year. Factor analysis was used to identify the ecological processes occurring within the ponds and to construct a conceptual graphic model of the pond ecosystem functioning during the rainy and dry seasons. Processes related to nitrogen cycling presented differences between both seasons while processes related to phosphorus cycling did not. Ecological differences among ponds were due to effects of wind protection by surrounding vegetation, organic loading entering, tilapia density and its grazing pressure on zooplankton. Differences in tilapia growth among ponds were related to stocking density and ecological process affecting tilapia food availability and intraspecific competition. Lettuce wastes addition into the ponds did not produce negative effects, thus this practice may be considered a disposal option and a low-cost input source for tilapia, at least at the amounts applied in this study.

The distribution of density in supersonic turbulence

NASA Astrophysics Data System (ADS)

Squire, Jonathan; Hopkins, Philip F.

2017-11-01

We propose a model for the statistics of the mass density in supersonic turbulence, which plays a crucial role in star formation and the physics of the interstellar medium (ISM). The model is derived by considering the density to be arranged as a collection of strong shocks of width ˜ M^{-2}, where M is the turbulent Mach number. With two physically motivated parameters, the model predicts all density statistics for M>1 turbulence: the density probability distribution and its intermittency (deviation from lognormality), the density variance-Mach number relation, power spectra and structure functions. For the proposed model parameters, reasonable agreement is seen between model predictions and numerical simulations, albeit within the large uncertainties associated with current simulation results. More generally, the model could provide a useful framework for more detailed analysis of future simulations and observational data. Due to the simple physical motivations for the model in terms of shocks, it is straightforward to generalize to more complex physical processes, which will be helpful in future more detailed applications to the ISM. We see good qualitative agreement between such extensions and recent simulations of non-isothermal turbulence.

Density Functional Theory Investigations of D-A-D' Structural Molecules as Donor Materials in Organic Solar Cell.

PubMed

Chen, Junxian; Liu, Qingyu; Li, Hao; Zhao, Zhigang; Lu, Zhiyun; Huang, Yan; Xu, Dingguo

2018-01-01

Squaraine core based small molecules in bulk heterojunction organic solar cells have received extensive attentions due to their distinguished photochemical properties in far red and infrared domain. In this paper, combining theoretical simulations and experimental syntheses and characterizations, three major factors (fill factor, short circuit and open-cirvuit voltage) have been carried out together to achieve improvement of power conversion efficiencies of solar cells. As model material systems with D-A-D' framework, two asymmetric squaraines (CNSQ and CCSQ-Tol) as donor materials in bulk heterojunction organic solar cell were synthesized and characterized. Intensive density functional theory computations were applied to identify some direct connections between three factors and corresponding molecular structural properties. It then helps us to predict one new molecule of CCSQ'-Ox that matches all the requirements to improve the power conversion efficiency.

Quantifying Ab Initio Equation of State Errors for Hydrogen-Helium Mixtures

NASA Astrophysics Data System (ADS)

Clay, Raymond; Morales, Miguel

2017-06-01

In order to produce predictive models of Jovian planets, an accurate equation of state for hydrogen-helium mixtures is needed over pressure and temperature ranges spanning multiple orders of magnitude. While extensive theoretical work has been done in this area, previous controversies regarding the equation of state of pure hydrogen have demonstrated exceptional sensitivity to approximations commonly employed in ab initio calculations. To this end, we present the results of our quantum Monte Carlo based benchmarking studies for several major classes of density functionals. Additionally, we expand upon our published results by considering the impact that ionic finite size effects and density functional errors translate to errors in the equation of state. Sandia National Laboratories is a multi-mission laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Simulating Valence-to-Core X-ray Emission Spectroscopy of Transition Metal Complexes with Time-Dependent Density Functional Theory.

PubMed

Zhang, Yu; Mukamel, Shaul; Khalil, Munira; Govind, Niranjan

2015-12-08

Valence-to-core (VtC) X-ray emission spectroscopy (XES) has emerged as a powerful technique for the structural characterization of complex organometallic compounds in realistic environments. Since the spectrum represents electronic transitions from the ligand molecular orbitals to the core holes of the metal centers, the approach is more chemically sensitive to the metal-ligand bonding character compared with conventional X-ray absorption techniques. In this paper we study how linear-response time-dependent density functional theory (LR-TDDFT) can be harnessed to simulate K-edge VtC X-ray emission spectra reliably. LR-TDDFT allows one to go beyond the single-particle picture that has been extensively used to simulate VtC-XES. We consider seven low- and high-spin model complexes involving chromium, manganese, and iron transition metal centers. Our results are in good agreement with experiment.

Weighted-density functionals for cavity formation and dispersion energies in continuum solvation models

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

Sundararaman, Ravishankar; Gunceler, Deniz; Arias, T. A.

2014-10-07

Continuum solvation models enable efficient first principles calculations of chemical reactions in solution, but require extensive parametrization and fitting for each solvent and class of solute systems. Here, we examine the assumptions of continuum solvation models in detail and replace empirical terms with physical models in order to construct a minimally-empirical solvation model. Specifically, we derive solvent radii from the nonlocal dielectric response of the solvent from ab initio calculations, construct a closed-form and parameter-free weighted-density approximation for the free energy of the cavity formation, and employ a pair-potential approximation for the dispersion energy. We show that the resulting modelmore » with a single solvent-independent parameter: the electron density threshold (n c), and a single solvent-dependent parameter: the dispersion scale factor (s 6), reproduces solvation energies of organic molecules in water, chloroform, and carbon tetrachloride with RMS errors of 1.1, 0.6 and 0.5 kcal/mol, respectively. We additionally show that fitting the solvent-dependent s 6 parameter to the solvation energy of a single non-polar molecule does not substantially increase these errors. Parametrization of this model for other solvents, therefore, requires minimal effort and is possible without extensive databases of experimental solvation free energies.« less

Weighted-density functionals for cavity formation and dispersion energies in continuum solvation models

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

Sundararaman, Ravishankar; Gunceler, Deniz; Arias, T. A.

2014-10-07

Continuum solvation models enable efficient first principles calculations of chemical reactions in solution, but require extensive parametrization and fitting for each solvent and class of solute systems. Here, we examine the assumptions of continuum solvation models in detail and replace empirical terms with physical models in order to construct a minimally-empirical solvation model. Specifically, we derive solvent radii from the nonlocal dielectric response of the solvent from ab initio calculations, construct a closed-form and parameter-free weighted-density approximation for the free energy of the cavity formation, and employ a pair-potential approximation for the dispersion energy. We show that the resulting modelmore » with a single solvent-independent parameter: the electron density threshold (n{sub c}), and a single solvent-dependent parameter: the dispersion scale factor (s{sub 6}), reproduces solvation energies of organic molecules in water, chloroform, and carbon tetrachloride with RMS errors of 1.1, 0.6 and 0.5 kcal/mol, respectively. We additionally show that fitting the solvent-dependent s{sub 6} parameter to the solvation energy of a single non-polar molecule does not substantially increase these errors. Parametrization of this model for other solvents, therefore, requires minimal effort and is possible without extensive databases of experimental solvation free energies.« less

Nonparametric probability density estimation by optimization theoretic techniques

NASA Technical Reports Server (NTRS)

Scott, D. W.

1976-01-01

Two nonparametric probability density estimators are considered. The first is the kernel estimator. The problem of choosing the kernel scaling factor based solely on a random sample is addressed. An interactive mode is discussed and an algorithm proposed to choose the scaling factor automatically. The second nonparametric probability estimate uses penalty function techniques with the maximum likelihood criterion. A discrete maximum penalized likelihood estimator is proposed and is shown to be consistent in the mean square error. A numerical implementation technique for the discrete solution is discussed and examples displayed. An extensive simulation study compares the integrated mean square error of the discrete and kernel estimators. The robustness of the discrete estimator is demonstrated graphically.

Radiative lifetimes and cooling functions for astrophysically important molecules

NASA Astrophysics Data System (ADS)

Tennyson, Jonathan; Hulme, Kelsey; Naim, Omree K.; Yurchenko, Sergei N.

2016-02-01

Extensive line lists generated as part of the ExoMol project are used to compute lifetimes for individual rotational, rovibrational and rovibronic excited states, and temperature-dependent cooling functions by summing over all dipole-allowed transitions for the states concerned. Results are presented for SiO, CaH, AlO, ScH, H2O and methane. The results for CH4 are particularly unusual with four excited states with no dipole-allowed decay route and several others, where these decays lead to exceptionally long lifetimes. These lifetime data should be useful in models of masers and estimates of critical densities, and can provide a link with laboratory measurements. Cooling functions are important in stellar and planet formation.

Well behaved anisotropic compact star models in general relativity

NASA Astrophysics Data System (ADS)

Jasim, M. K.; Maurya, S. K.; Gupta, Y. K.; Dayanandan, B.

2016-11-01

Anisotropic compact star models have been constructed by assuming a particular form of a metric function e^{λ}. We solved the Einstein field equations for determining the metric function e^{ν}. For this purpose we have assumed a physically valid expression of radial pressure (pr). The obtained anisotropic compact star model is representing the realistic compact objects such as PSR 1937 +21. We have done an extensive study about physical parameters for anisotropic models and found that these parameters are well behaved throughout inside the star. Along with these we have also determined the equation of state for compact star which gives the radial pressure is purely the function of density i.e. pr=f(ρ).

Performance of Density Functional Theory Procedures for the Calculation of Proton-Exchange Barriers: Unusual Behavior of M06-Type Functionals.

PubMed

Chan, Bun; Gilbert, Andrew T B; Gill, Peter M W; Radom, Leo

2014-09-09

We have examined the performance of a variety of density functional theory procedures for the calculation of complexation energies and proton-exchange barriers, with a focus on the Minnesota-class of functionals that are generally highly robust and generally show good accuracy. A curious observation is that M05-type and M06-type methods show an atypical decrease in calculated barriers with increasing proportion of Hartree-Fock exchange. To obtain a clearer picture of the performance of the underlying components of M05-type and M06-type functionals, we have investigated the combination of MPW-type and PBE-type exchange and B95-type and PBE-type correlation procedures. We find that, for the extensive E3 test set, the general performance of the various hybrid-DFT procedures improves in the following order: PBE1-B95 → PBE1-PBE → MPW1-PBE → PW6-B95. As M05-type and M06-type procedures are related to PBE1-B95, it would be of interest to formulate and examine the general performance of an alternative Minnesota DFT method related to PW6-B95.

The structure, energetics, and nature of the chemical bonding of phenylthiol adsorbed on the Au(111) surface: implications for density-functional calculations of molecular-electronic conduction.

PubMed

Bilić, Ante; Reimers, Jeffrey R; Hush, Noel S

2005-03-01

The adsorption of phenylthiol on the Au(111) surface is modeled using Perdew and Wang density-functional calculations. Both direct molecular physisorption and dissociative chemisorption via S-H bond cleavage are considered as well as dimerization to form disulfides. For the major observed product, the chemisorbed thiol, an extensive potential-energy surface is produced as a function of both the azimuthal orientation of the adsorbate and the linear translation of the adsorbate through the key fcc, hcp, bridge, and top binding sites. Key structures are characterized, the lowest-energy one being a broad minimum of tilted orientation ranging from the bridge structure halfway towards the fcc one. The vertically oriented threefold binding sites, often assumed to dominate molecular electronics measurements, are identified as transition states at low coverage but become favored in dense monolayers. A similar surface is also produced for chemisorption of phenylthiol on Ag(111); this displays significant qualitative differences, consistent with the qualitatively different observed structures for thiol chemisorption on Ag and Au. Full contours of the minimum potential energy as a function of sulfur translation over the crystal face are described, from which the barrier to diffusion is deduced to be 5.8 kcal mol(-1), indicating that the potential-energy surface has low corrugation. The calculated bond lengths, adsorbate charge and spin density, and the density of electronic states all indicate that, at all sulfur locations, the adsorbate can be regarded as a thiyl species that forms a net single covalent bond to the surface of strength 31 kcal mol(-1). No detectable thiolate character is predicted, however, contrary to experimental results for alkyl thiols that indicate up to 20%-30% thiolate involvement. This effect is attributed to the asymptotic-potential error of all modern density functionals that becomes manifest through a 3-4 eV error in the lineup of the adsorbate and substrate bands. Significant implications are described for density-functional calculations of through-molecule electron transport in molecular electronics.

Tsallis non-extensive statistics and solar wind plasma complexity

NASA Astrophysics Data System (ADS)

Pavlos, G. P.; Iliopoulos, A. C.; Zastenker, G. N.; Zelenyi, L. M.; Karakatsanis, L. P.; Riazantseva, M. O.; Xenakis, M. N.; Pavlos, E. G.

2015-03-01

This article presents novel results revealing non-equilibrium phase transition processes in the solar wind plasma during a strong shock event, which took place on 26th September 2011. Solar wind plasma is a typical case of stochastic spatiotemporal distribution of physical state variables such as force fields (B → , E →) and matter fields (particle and current densities or bulk plasma distributions). This study shows clearly the non-extensive and non-Gaussian character of the solar wind plasma and the existence of multi-scale strong correlations from the microscopic to the macroscopic level. It also underlines the inefficiency of classical magneto-hydro-dynamic (MHD) or plasma statistical theories, based on the classical central limit theorem (CLT), to explain the complexity of the solar wind dynamics, since these theories include smooth and differentiable spatial-temporal functions (MHD theory) or Gaussian statistics (Boltzmann-Maxwell statistical mechanics). On the contrary, the results of this study indicate the presence of non-Gaussian non-extensive statistics with heavy tails probability distribution functions, which are related to the q-extension of CLT. Finally, the results of this study can be understood in the framework of modern theoretical concepts such as non-extensive statistical mechanics (Tsallis, 2009), fractal topology (Zelenyi and Milovanov, 2004), turbulence theory (Frisch, 1996), strange dynamics (Zaslavsky, 2002), percolation theory (Milovanov, 1997), anomalous diffusion theory and anomalous transport theory (Milovanov, 2001), fractional dynamics (Tarasov, 2013) and non-equilibrium phase transition theory (Chang, 1992).

RipleyGUI: software for analyzing spatial patterns in 3D cell distributions

PubMed Central

Hansson, Kristin; Jafari-Mamaghani, Mehrdad; Krieger, Patrik

2013-01-01

The true revolution in the age of digital neuroanatomy is the ability to extensively quantify anatomical structures and thus investigate structure-function relationships in great detail. To facilitate the quantification of neuronal cell patterns we have developed RipleyGUI, a MATLAB-based software that can be used to detect patterns in the 3D distribution of cells. RipleyGUI uses Ripley's K-function to analyze spatial distributions. In addition the software contains statistical tools to determine quantitative statistical differences, and tools for spatial transformations that are useful for analyzing non-stationary point patterns. The software has a graphical user interface making it easy to use without programming experience, and an extensive user manual explaining the basic concepts underlying the different statistical tools used to analyze spatial point patterns. The described analysis tool can be used for determining the spatial organization of neurons that is important for a detailed study of structure-function relationships. For example, neocortex that can be subdivided into six layers based on cell density and cell types can also be analyzed in terms of organizational principles distinguishing the layers. PMID:23658544

An improved numerical method for the kernel density functional estimation of disperse flow

NASA Astrophysics Data System (ADS)

Smith, Timothy; Ranjan, Reetesh; Pantano, Carlos

2014-11-01

We present an improved numerical method to solve the transport equation for the one-point particle density function (pdf), which can be used to model disperse flows. The transport equation, a hyperbolic partial differential equation (PDE) with a source term, is derived from the Lagrangian equations for a dilute particle system by treating position and velocity as state-space variables. The method approximates the pdf by a discrete mixture of kernel density functions (KDFs) with space and time varying parameters and performs a global Rayleigh-Ritz like least-square minimization on the state-space of velocity. Such an approximation leads to a hyperbolic system of PDEs for the KDF parameters that cannot be written completely in conservation form. This system is solved using a numerical method that is path-consistent, according to the theory of non-conservative hyperbolic equations. The resulting formulation is a Roe-like update that utilizes the local eigensystem information of the linearized system of PDEs. We will present the formulation of the base method, its higher-order extension and further regularization to demonstrate that the method can predict statistics of disperse flows in an accurate, consistent and efficient manner. This project was funded by NSF Project NSF-DMS 1318161.

Property control of graphene aerogels by in situ growth of silicone polymer

NASA Astrophysics Data System (ADS)

Zhou, Shuai; Zhou, Xiang; Hao, Gazi; Jiang, Wei; Wang, Tianhe

2018-05-01

Modulation of the density (from 3.5 to 64 mg cm-3), hydrophobicity and oil-uptake capability of graphene aerogels in extensive ranges were achieved by reacting (3-Mercaptopropyl)trimethoxysilane (MPS) with graphene oxide solutions under heating. The reaction allowed a characteristic silicone substructure to be formed on graphene and joint the graphene layers firmly together. With the increase of MPS concentrations (≤ca. 0.2 vol%), the nano silicone polymer grown on graphene functioned as a "linker" and "spacer", leading to a substantial decrease of the aerogel density. Because of the formation of silicone polymer and the characteristic nano-micro substructures on the backbones of graphene aerogels, the graphene aerogels exhibited a high hydrophobicity with the water contact angle consistently exceeding 142 degrees. Functionalized graphene aerogels with a density of 3.5 mg cm-3 were conveniently fabricated that displayed an extraordinary oil absorption capacity, 182 times for lubricating oil and 143 times for n-hexane of its own weight. Furthermore, the aerogels maintained their ultra-high absorption capability even after 20 absorption-distillation cycles, due to structural integrity held by the strong interfacial adhesion between graphene sheets and polymer chains of aerogels. This study offers a promising graphene aerogels and also provides a strategy for fabricating extra low dense functional materials.

A minimal model for the structural energetics of VO2

NASA Astrophysics Data System (ADS)

Kim, Chanul; Marianetti, Chris; The Marianetti Group Team

Resolving the structural, magnetic, and electronic structure of VO2 from the first-principles of quantum mechanics is still a forefront problem despite decades of attention. Hybrid functionals have been shown to qualitatively ruin the structural energetics. While density functional theory (DFT) combined with cluster extensions of dynamical mean-field theory (DMFT) have demonstrated promising results in terms of the electronic properties, structural phase stability has not yet been addressed. In order to capture the basic physics of the structural transition, we propose a minimal model of VO2 based on the one dimensional Peierls-Hubbard model and parameterize this based on DFT calculations of VO2. The total energy versus dimerization in the minimal mode is then solved numerically exactly using density matrix renormalization group (DMRG) and compared to the Hartree-Fock solution. We demonstrate that the Hartree-Fock solution exhibits the same pathologies as DFT+U, and spin density functional theory for that matter, while the DMRG solution is consistent with experimental observation. Our results demonstrate the critical role of non-locality in the total energy, and this will need to be accounted for to obtain a complete description of VO2 from first-principles. The authors acknowledge support from FAME, one of six centers of STARnet, a Semiconductor Research Corporation program sponsored by MARCO and DARPA.

Modeling of Materials for Energy Storage: A Challenge for Density Functional Theory

NASA Astrophysics Data System (ADS)

Kaltak, Merzuk; Fernandez-Serra, Marivi; Hybertsen, Mark S.

Hollandite α-MnO2 is a promising material for rechargeable batteries and is studied extensively in the community because of its interesting tunnel structure and the corresponding large capacity for lithium as well as sodium ions. However, the presence of partially reduced Mn ions due to doping with Ag or during lithiation makes hollandite a challenging system for density functional theory and the conventionally employed PBE+U method. A naive attempt to model the ternary system LixAgyMnO2 with density functionals, similar to those employed for the case y = 0 , fails and predicts a strong monoclinic distortion of the experimentally observed tetragonal unit cell for Ag2Mn8O16. Structure and binding energies are compared with experimental data and show the importance of van der Waals interactions as well as the necessity for an accurate description of the cooperative Jan-Teller effects for silver hollandite AgyMnO2. Based on these observations a ternary phase diagram is calculated allowing to predict the physical and chemical properties of LixAgyMnO2, such as stable stoichiometries, open circuit voltages, the formation of Ag metal and the structural change during lithiation. Department of Energy (DOE) under award #DE-SC0012673.

Information carriers and (reading them through) information theory in quantum chemistry.

PubMed

Geerlings, Paul; Borgoo, Alex

2011-01-21

This Perspective discusses the reduction of the electronic wave function via the second-order reduced density matrix to the electron density ρ(r), which is the key ingredient in density functional theory (DFT) as a basic carrier of information. Simplifying further, the 1-normalized density function turns out to contain essentially the same information as ρ(r) and is even of preferred use as an information carrier when discussing the periodic properties along Mendeleev's table where essentially the valence electrons are at stake. The Kullback-Leibler information deficiency turns out to be the most interesting choice to obtain information on the differences in ρ(r) or σ(r) between two systems. To put it otherwise: when looking for the construction of a functional F(AB) = F[ζ(A)(r),ζ(B)(r)] for extracting differences in information from an information carrier ζ(r) (i.e. ρ(r), σ(r)) for two systems A and B the Kullback-Leibler information measure ΔS is a particularly adequate choice. Examples are given, varying from atoms, to molecules and molecular interactions. Quantum similarity of atoms indicates that the shape function based KL information deficiency is the most appropriate tool to retrieve periodicity in the Periodic Table. The dissimilarity of enantiomers for which different information measures are presented at global and local (i.e. molecular and atomic) level leads to an extension of Mezey's holographic density theorem and shows numerical evidence that in a chiral molecule the whole molecule is pervaded by chirality. Finally Kullback-Leibler information profiles are discussed for intra- and intermolecular proton transfer reactions and a simple S(N)2 reaction indicating that the theoretical information profile can be used as a companion to the energy based Hammond postulate to discuss the early or late transition state character of a reaction. All in all this Perspective's answer is positive to the question of whether an even simpler carrier of information than the electron density function ρ(r) can be envisaged: the shape function, integrating to 1 by construction fulfils this role. On the other hand obtaining the information (or information difference) contained in one (or two) systems from ρ(r) or σ(r) can be most efficiently done by using information theory, the Kulback-Leibler information deficiency being at the moment (one of) the most advisable functionals.

The spatial distribution of fixed mutations within genes coding for proteins

NASA Technical Reports Server (NTRS)

Holmquist, R.; Goodman, M.; Conroy, T.; Czelusniak, J.

1983-01-01

An examination has been conducted of the extensive amino acid sequence data now available for five protein families - the alpha crystallin A chain, myoglobin, alpha and beta hemoglobin, and the cytochromes c - with the goal of estimating the true spatial distribution of base substitutions within genes that code for proteins. In every case the commonly used Poisson density failed to even approximate the experimental pattern of base substitution. For the 87 species of beta hemoglobin examined, for example, the probability that the observed results were from a Poisson process was the minuscule 10 to the -44th. Analogous results were obtained for the other functional families. All the data were reasonably, but not perfectly, described by the negative binomial density. In particular, most of the data were described by one of the very simple limiting forms of this density, the geometric density. The implications of this for evolutionary inference are discussed. It is evident that most estimates of total base substitutions between genes are badly in need of revision.

Transgenerational Effects Alter Plant Defense and Resistance in Nature

PubMed Central

Colicchio, Jack

2017-01-01

Trichomes, or leaf hairs, are epidermal extensions that take a variety of forms and perform many functions in plants, including herbivore defense. In this study, I document genetically determined variation, within-generation plasticity, and a direct role of trichomes in herbivore defense for Mimulus guttatus. After establishing the relationship between trichomes and herbivory, I test for transgenerational effects of wounding on trichome density and herbivore resistance. Patterns of inter-annual variation in herbivore density and the high cost of plant defense makes plant-herbivore interactions a system in which transgenerational phenotypic plasticity (TPP) is apt to evolve. Here, I demonstrate that parental damage alters offspring trichome density and herbivore resistance in nature. Moreover, this response varies between populations. This is among the first studies to demonstrate that TPP contributes to variation in nature, and also suggests that selection can modify TPP in response to local conditions. PMID:28102915

Nonlinear dynamics of the cellular-automaton ``game of Life''

NASA Astrophysics Data System (ADS)

Garcia, J. B. C.; Gomes, M. A. F.; Jyh, T. I.; Ren, T. I.; Sales, T. R. M.

1993-11-01

A statistical analysis of the ``game of Life'' due to Conway [Berlekamp, Conway, and Guy, Winning Ways for Your Mathematical Plays (Academic, New York, 1982), Vol. 2] is reported. The results are based on extensive computer simulations starting with uncorrelated distributions of live sites at t=0. The number n(s,t) of clusters of s live sites at time t, the mean cluster size s¯(t), and the diversity of sizes among other statistical functions are obtained. The dependence of the statistical functions with the initial density of live sites is examined. Several scaling relations as well as static and dynamic critical exponents are found.

Charge plasma technique based dopingless accumulation mode junctionless cylindrical surrounding gate MOSFET: analog performance improvement

NASA Astrophysics Data System (ADS)

Trivedi, Nitin; Kumar, Manoj; Haldar, Subhasis; Deswal, S. S.; Gupta, Mridula; Gupta, R. S.

2017-09-01

A charge plasma technique based dopingless (DL) accumulation mode (AM) junctionless (JL) cylindrical surrounding gate (CSG) MOSFET has been proposed and extensively investigated. Proposed device has no physical junction at source to channel and channel to drain interface. The complete silicon pillar has been considered as undoped. The high free electron density or induced N+ region is designed by keeping the work function of source/drain metal contacts lower than the work function of undoped silicon. Thus, its fabrication complexity is drastically reduced by curbing the requirement of high temperature doping techniques. The electrical/analog characteristics for the proposed device has been extensively investigated using the numerical simulation and are compared with conventional junctionless cylindrical surrounding gate (JL-CSG) MOSFET with identical dimensions. For the numerical simulation purpose ATLAS-3D device simulator is used. The results show that the proposed device is more short channel immune to conventional JL-CSG MOSFET and suitable for faster switching applications due to higher I ON/ I OFF ratio.

Increasing the applicability of density functional theory. IV. Consequences of ionization-potential improved exchange-correlation potentials.

PubMed

Verma, Prakash; Bartlett, Rodney J

2014-05-14

This paper's objective is to create a "consistent" mean-field based Kohn-Sham (KS) density functional theory (DFT) meaning the functional should not only provide good total energy properties, but also the corresponding KS eigenvalues should be accurate approximations to the vertical ionization potentials (VIPs) of the molecule, as the latter condition attests to the viability of the exchange-correlation potential (VXC). None of the prominently used DFT approaches show these properties: the optimized effective potential VXC based ab initio dft does. A local, range-separated hybrid potential cam-QTP-00 is introduced as the basis for a "consistent" KS DFT approach. The computed VIPs as the negative of KS eigenvalue have a mean absolute error of 0.8 eV for an extensive set of molecule's electron ionizations, including the core. Barrier heights, equilibrium geometries, and magnetic properties obtained from the potential are in good agreement with experiment. A similar accuracy with less computational efforts can be achieved by using a non-variational global hybrid variant of the QTP-00 approach.

Analyzing the substitution effect on the CoMFA results within the framework of density functional theory (DFT).

PubMed

Morales-Bayuelo, Alejandro

2016-07-01

Though QSAR was originally developed in the context of physical organic chemistry, it has been applied very extensively to chemicals (drugs) which act on biological systems, in this idea one of the most important QSAR methods is the 3D QSAR model. However, due to the complexity of understanding the results it is necessary to postulate new methodologies to highlight their physical-chemical meaning. In this sense, this work postulates new insights to understand the CoMFA results using molecular quantum similarity and chemical reactivity descriptors within the framework of density functional theory. To obtain these insights a simple theoretical scheme involving quantum similarity (overlap, coulomb operators, their euclidean distances) and chemical reactivity descriptors such as chemical potential (μ), hardness (ɳ), softness (S), electrophilicity (ω), and the Fukui functions, was used to understand the substitution effect. In this sense, this methodology can be applied to analyze the biological activity and the stabilization process in the non-covalent interactions on a particular molecular set taking a reference compound.

Nanosecond Enhancements of the Atmospheric Electron Density by Extensive Air Showers

NASA Astrophysics Data System (ADS)

Rutjes, C.; Camporeale, E.; Ebert, U.; Buitink, S.; Scholten, O.; Trinh, G. T. N.; Witteveen, J.

2015-12-01

As is well known a sufficient density of free electrons and strong electric fields are the basic requirements to start any electrical discharge. In the context of thunderstorm discharges it has become clear that in addition droplets and or ice particles are required to enhance the electric field to values above breakdown. In our recent study [1] we have shown that these three ingredients have to interplay to allow for lightning inception, triggered by an extensive air shower event. The extensive air showers are a very stochastic natural phenomenon, creating highly coherent sub-nanosecond enhancements of the atmospheric electron density. Predicting these electron density enhancements accurately one has to take the uncertainty of the input variables into account. For this study we use the initial energy, inclination and altitude of first interaction, which will influence the evolution of the shower significantly. To this end, we use the stochastic collocation method, [2] to post-process our detailed Monte Carlo extensive air shower simulations, done with the CORSIKA [3] software package, which provides an efficient and elegant way to determine the distribution of the atmospheric electron density enhancements. [1] Dubinova, A., Rutjes, C., Ebert, E., Buitink, S., Scholten, O., and Trinh, G. T. N. "Prediction of Lightning Inception by Large Ice Particles and Extensive Air Showers." PRL 115 015002 (2015)[2] G.J.A. Loeven, J.A.S. Witteveen, H. Bijl, Probabilistic collocation: an efficient nonintrusive approach for arbitrarily distributed parametric uncertainties, 45th AIAA Aerospace Sciences Meeting, Reno, Nevada, 2007, AIAA-2007-317[3] Heck, Dieter, et al. CORSIKA: A Monte Carlo code to simulate extensive air showers. No. FZKA-6019. 1998.

AN EMPIRICAL FORMULA FOR THE DISTRIBUTION FUNCTION OF A THIN EXPONENTIAL DISC

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

Sharma, Sanjib; Bland-Hawthorn, Joss

2013-08-20

An empirical formula for a Shu distribution function that reproduces a thin disc with exponential surface density to good accuracy is presented. The formula has two free parameters that specify the functional form of the velocity dispersion. Conventionally, this requires the use of an iterative algorithm to produce the correct solution, which is computationally taxing for applications like Markov Chain Monte Carlo model fitting. The formula has been shown to work for flat, rising, and falling rotation curves. Application of this methodology to one of the Dehnen distribution functions is also shown. Finally, an extension of this formula to reproducemore » velocity dispersion profiles that are an exponential function of radius is also presented. Our empirical formula should greatly aid the efficient comparison of disc models with large stellar surveys or N-body simulations.« less

Many-body effects in electron liquids with Rashba spin-orbit coupling

NASA Astrophysics Data System (ADS)

Simion, George E.

The main topic of the present thesis is represented by the many-body effects which characterize the physical behavior of an electron liquid in various realizations. We begin by studying the problem of the response of an otherwise homogeneous electron liquid to the potential of an impurity embedded in its bulk. The most dramatic consequence of this perturbation is the existence of so called Friedel density oscillations. We present calculations of their amplitude valid in two as well as in three dimensions. The second problem we will discuss is that of the correlation effects in a three dimensional electron liquid in the metallic density regime. A number of quasiparticle properties are evaluated: the electron self-energy, the quasiparticle effective mass and the renormalization constant. We also present an analysis of the effective Lande g-factor as well as the compressibility. The effects of the Coulomb interactions beyond the random phase approximation have been treated by means of an approach based on the many-body local field factors theory and by utilizing the latest numerical results of Quantum Monte Carlo numerical simulations. The final chapter includes the results of our extensive work on various aspects regarding the two dimensional Fermi liquid in the presence of linear Rashba spin-orbit coupling. By using a number of many-body techniques, we have studied the interplay between spin-orbit coupling and electron-electron interaction. After proving an extension to the famous Overhauser Hartree-Fock instability theorem, a considerable amount of work will be presented on the problem of the density and spin response functions. For the study of the spin response, we will present the results of extensive numerical calculations based on the time dependent mean field theory approach.

Hydrodynamic model for conductivity in graphene.

PubMed

Mendoza, M; Herrmann, H J; Succi, S

2013-01-01

Based on the recently developed picture of an electronic ideal relativistic fluid at the Dirac point, we present an analytical model for the conductivity in graphene that is able to describe the linear dependence on the carrier density and the existence of a minimum conductivity. The model treats impurities as submerged rigid obstacles, forming a disordered medium through which graphene electrons flow, in close analogy with classical fluid dynamics. To describe the minimum conductivity, we take into account the additional carrier density induced by the impurities in the sample. The model, which predicts the conductivity as a function of the impurity fraction of the sample, is supported by extensive simulations for different values of ε, the dimensionless strength of the electric field, and provides excellent agreement with experimental data.

Estimating canopy bulk density and canopy base height for conifer stands in the interior Western United States using the Forest Vegetation Simulator Fire and Fuels Extension.

Treesearch

Seth Ex; Frederick Smith; Tara Keyser; Stephanie Rebain

2017-01-01

The Forest Vegetation Simulator Fire and Fuels Extension (FFE-FVS) is often used to estimate canopy bulk density (CBD) and canopy base height (CBH), which are key indicators of crown fire hazard for conifer stands in the Western United States. Estimated CBD from FFE-FVS is calculated as the maximum 4 m running mean bulk density of predefined 0.3 m thick canopy layers (...

An Extension of the Krieger-Li-Iafrate Approximation to the Optimized-Effective-Potential Method

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

Wilson, B.G.

1999-11-11

The Krieger-Li-Iafrate approximation can be expressed as the zeroth order result of an unstable iterative method for solving the integral equation form of the optimized-effective-potential method. By pre-conditioning the iterate a first order correction can be obtained which recovers the bulk of quantal oscillations missing in the zeroth order approximation. A comparison of calculated total energies are given with Krieger-Li-Iafrate, Local Density Functional, and Hyper-Hartree-Fock results for non-relativistic atoms and ions.

The Center for Astrophysics Redshift Survey - Recent results

NASA Technical Reports Server (NTRS)

Geller, Margaret J.; Huchra, John P.

1989-01-01

Six strips of the CfA redshift survey extension are now complete. The data continue to support a picture in which galaxies are on thin sheets which nearly surround vast low-density voids. The largest structures are comparable with the extent of the survey. Voids like the one in Bootes are a common feature of the large-scale distribution of galaxies. The issue of fair samples of the galaxy distribution is discussed, examining statistical measures of the galaxy distribution including the two-point correlation functions.

Understanding the Relativistic Generalization of Density Functional Theory (DFT) and Completing it in Practice

NASA Astrophysics Data System (ADS)

Bagayoko, Diola

In 2014, 50 years following the introduction of density functional theory (DFT), a rigorous understanding of it was published [AIP Advances, 4, 127104 (2014)]. This understanding included necessary steps ab initio electronic structure calculations have to take if their results are to possess the full physical content of DFT. These steps guarantee the fulfillment of conditions of validity of DFT; not surprisingly, they have led to accurate descriptions of several dozens of semiconductors, from first principle, without invoking derivative discontinuity or self-interaction correction. This presentation shows the mathematically and physically rigorous understanding of the relativistic extension of DFT by Rajagopal and Callaway {Phys. Rev. B 7, 1912 (1973)]. As in the non-relativistic case, the attainment of the absolute minima of the occupied energies is a necessary condition for the corresponding current density to be that of the ground state of the system and for computational results to agree with corresponding, experimental ones. Acknowledgments:This work was funded in part by the US National Science Foundation [NSF, Award Nos. EPS-1003897, NSF (2010-2015)-RII-SUBR, and HRD-1002541], the US Department of Energy, National Nuclear Security Administration (NNSA, Award No. DE-NA0002630), LaSPACE, and LONI-SUBR.

Evidence of the non-extensive character of Earth's ambient noise.

NASA Astrophysics Data System (ADS)

Koutalonis, Ioannis; Vallianatos, Filippos

2017-04-01

Investigation of dynamical features of ambient seismic noise is one of the important scientific and practical research challenges. In the same time there isgrowing interest concerning an approach to study Earth Physics based on thescience of complex systems and non extensive statistical mechanics which is a generalization of Boltzmann-Gibbs statistical physics (Vallianatos et al., 2016).This seems to be a promising framework for studying complex systems exhibitingphenomena such as, long-range interactions, and memory effects. Inthis work we use non-extensive statistical mechanics and signal analysis methodsto explore the nature of ambient noise as measured in the stations of the HSNC in South Aegean (Chatzopoulos et al., 2016). In the present work we analyzed the de-trended increments time series of ambient seismic noise X(t), in time windows of 20 minutes to 10 seconds within "calm time zones" where the human-induced noise presents a minimum. Following the non extensive statistical physics approach, the probability distribution function of the increments of ambient noise is investigated. Analyzing the probability density function (PDF)p(X), normalized to zero mean and unit varianceresults that the fluctuations of Earth's ambient noise follows a q-Gaussian distribution asdefined in the frame of non-extensive statisticalmechanics indicated the possible existence of memory effects in Earth's ambient noise. References: F. Vallianatos, G. Papadakis, G. Michas, Generalized statistical mechanics approaches to earthquakes and tectonics. Proc. R. Soc. A, 472, 20160497, 2016. G. Chatzopoulos, I.Papadopoulos, F.Vallianatos, The Hellenic Seismological Network of Crete (HSNC): Validation and results of the 2013 aftershock,Advances in Geosciences, 41, 65-72, 2016.

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

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

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

2011-02-15

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

Applications of quantum entropy to statistics

NASA Astrophysics Data System (ADS)

Silver, R. N.; Martz, H. F.

This paper develops two generalizations of the maximum entropy (ME) principle. First, Shannon classical entropy is replaced by von Neumann quantum entropy to yield a broader class of information divergences (or penalty functions) for statistics applications. Negative relative quantum entropy enforces convexity, positivity, non-local extensivity and prior correlations such as smoothness. This enables the extension of ME methods from their traditional domain of ill-posed in-verse problems to new applications such as non-parametric density estimation. Second, given a choice of information divergence, a combination of ME and Bayes rule is used to assign both prior and posterior probabilities. Hyperparameters are interpreted as Lagrange multipliers enforcing constraints. Conservation principles are proposed to act statistical regularization and other hyperparameters, such as conservation of information and smoothness. ME provides an alternative to hierarchical Bayes methods.

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

PubMed

Hoy, Erik P; Mazziotti, David A

2015-08-14

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

Gauge-invariant screening masses and static quark free energies in Nf=2 +1 QCD at nonzero baryon density

NASA Astrophysics Data System (ADS)

Andreoli, Michele; Bonati, Claudio; D'Elia, Massimo; Mesiti, Michele; Negro, Francesco; Rucci, Andrea; Sanfilippo, Francesco

2018-03-01

We discuss the extension of gauge-invariant electric and magnetic screening masses in the quark-gluon plasma to the case of a finite baryon density, defining them in terms of a matrix of Polyakov loop correlators. We present lattice results for Nf=2 +1 QCD with physical quark masses, obtained using the imaginary chemical potential approach, which indicate that the screening masses increase as a function of μB. A separate analysis is carried out for the theoretically interesting case μB/T =3 i π , where charge conjugation is not explicitly broken and the usual definition of the screening masses can be used for temperatures below the Roberge-Weiss transition. Finally, we investigate the dependence of the static quark free energy on the baryon chemical potential, showing that it is a decreasing function of μB, which displays a peculiar behavior as the pseudocritical transition temperature at μB=0 is approached.

Simulating pump-probe photoelectron and absorption spectroscopy on the attosecond timescale with time-dependent density functional theory.

PubMed

De Giovannini, Umberto; Brunetto, Gustavo; Castro, Alberto; Walkenhorst, Jessica; Rubio, Angel

2013-05-10

Molecular absorption and photoelectron spectra can be efficiently predicted with real-time time-dependent density functional theory. We show herein how these techniques can be easily extended to study time-resolved pump-probe experiments, in which a system response (absorption or electron emission) to a probe pulse is measured in an excited state. This simulation tool helps with the interpretation of fast-evolving attosecond time-resolved spectroscopic experiments, in which electronic motion must be followed at its natural timescale. We show how the extra degrees of freedom (pump-pulse duration, intensity, frequency, and time delay), which are absent in a conventional steady-state experiment, provide additional information about electronic structure and dynamics that improve characterization of a system. As an extension of this approach, time-dependent 2D spectroscopy can also be simulated, in principle, for large-scale structures and extended systems. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Near-infrared spectrometry allows fast and extensive predictions of functional traits from dry leaves and branches.

PubMed

Costa, Flávia R C; Lang, Carla; Almeida, Danilo R A; Castilho, Carolina V; Poorter, Lourens

2018-05-16

The linking of individual functional traits to ecosystem processes is the basis for making generalizations in ecology, but the measurement of individual values is laborious and time consuming, preventing large-scale trait mapping. Also, in hyper-diverse systems, errors occur because identification is difficult, and species level values ignore intra-specific variation. To allow extensive trait mapping at the individual level, we evaluated the potential of Fourrier-Transformed Near Infra-Red Spectrometry (FT-NIR) to adequately describe 14 traits that are key for plant carbon, water, and nutrient balance. FT-NIR absorption spectra (1,000-2,500 nm) were obtained from dry leaves and branches of 1,324 trees of 432 species from a hyper-diverse Amazonian forest. FT-NIR spectra were related to measured traits for the same plants using partial least squares regressions. A further 80 plants were collected from a different site to evaluate model applicability across sites. Relative prediction error (RMSE rel ) was calculated as the percentage of the trait value range represented by the final model RMSE. The key traits used in most functional trait studies; specific leaf area, leaf dry matter content, wood density and wood dry matter content can be well predicted by the model (R 2  = 0.69-0.78, RMSE rel  = 9-11%), while leaf density, xylem proportion, bark density and bark dry matter content can be moderately well predicted (R 2  = 0.53-0.61, RMSE rel  = 14-17%). Community-weighted means of all traits were well estimated with NIR, as did the shape of the frequency distribution of the community values for the above key traits. The model developed at the core site provided good estimations of the key traits of a different site. An evaluation of the sampling effort indicated that 400 or less individuals may be sufficient for establishing a good local model. We conclude that FT-NIR is an easy, fast and cheap method for the large-scale estimation of individual plant traits that was previously impossible. The ability to use dry intact leaves and branches unlocks the potential for using herbarium material to estimate functional traits; thus advancing our knowledge of community and ecosystem functioning from local to global scales. © 2018 by the Ecological Society of America.

Extending the accuracy of the SNAP interatomic potential form

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

Wood, Mitchell A.; Thompson, Aidan P.

The Spectral Neighbor Analysis Potential (SNAP) is a classical interatomic potential that expresses the energy of each atom as a linear function of selected bispectrum components of the neighbor atoms. An extension of the SNAP form is proposed that includes quadratic terms in the bispectrum components. The extension is shown to provide a large increase in accuracy relative to the linear form, while incurring only a modest increase in computational cost. The mathematical structure of the quadratic SNAP form is similar to the embedded atom method (EAM), with the SNAP bispectrum components serving as counterparts to the two-body density functionsmore » in EAM. It is also argued that the quadratic SNAP form is a special case of an artificial neural network (ANN). The effectiveness of the new form is demonstrated using an extensive set of training data for tantalum structures. Similarly to ANN potentials, the quadratic SNAP form requires substantially more training data in order to prevent overfitting, as measured by cross-validation analysis.« less

Extending the accuracy of the SNAP interatomic potential form

DOE PAGES

Wood, Mitchell A.; Thompson, Aidan P.

2018-03-28

The Spectral Neighbor Analysis Potential (SNAP) is a classical interatomic potential that expresses the energy of each atom as a linear function of selected bispectrum components of the neighbor atoms. An extension of the SNAP form is proposed that includes quadratic terms in the bispectrum components. The extension is shown to provide a large increase in accuracy relative to the linear form, while incurring only a modest increase in computational cost. The mathematical structure of the quadratic SNAP form is similar to the embedded atom method (EAM), with the SNAP bispectrum components serving as counterparts to the two-body density functionsmore » in EAM. It is also argued that the quadratic SNAP form is a special case of an artificial neural network (ANN). The effectiveness of the new form is demonstrated using an extensive set of training data for tantalum structures. Similarly to ANN potentials, the quadratic SNAP form requires substantially more training data in order to prevent overfitting, as measured by cross-validation analysis.« less

Thermal density functional theory, ensemble density functional theory, and potential functional theory for warm dense matter

NASA Astrophysics Data System (ADS)

Pribram-Jones, Aurora

Warm dense matter (WDM) is a high energy phase between solids and plasmas, with characteristics of both. It is present in the centers of giant planets, within the earth's core, and on the path to ignition of inertial confinement fusion. The high temperatures and pressures of warm dense matter lead to complications in its simulation, as both classical and quantum effects must be included. One of the most successful simulation methods is density functional theory-molecular dynamics (DFT-MD). Despite great success in a diverse array of applications, DFT-MD remains computationally expensive and it neglects the explicit temperature dependence of electron-electron interactions known to exist within exact DFT. Finite-temperature density functional theory (FT DFT) is an extension of the wildly successful ground-state DFT formalism via thermal ensembles, broadening its quantum mechanical treatment of electrons to include systems at non-zero temperatures. Exact mathematical conditions have been used to predict the behavior of approximations in limiting conditions and to connect FT DFT to the ground-state theory. An introduction to FT DFT is given within the context of ensemble DFT and the larger field of DFT is discussed for context. Ensemble DFT is used to describe ensembles of ground-state and excited systems. Exact conditions in ensemble DFT and the performance of approximations depend on ensemble weights. Using an inversion method, exact Kohn-Sham ensemble potentials are found and compared to approximations. The symmetry eigenstate Hartree-exchange approximation is in good agreement with exact calculations because of its inclusion of an ensemble derivative discontinuity. Since ensemble weights in FT DFT are temperature-dependent Fermi weights, this insight may help develop approximations well-suited to both ground-state and FT DFT. A novel, highly efficient approach to free energy calculations, finite-temperature potential functional theory, is derived, which has the potential to transform the simulation of warm dense matter. As a semiclassical method, it connects the normally disparate regimes of cold condensed matter physics and hot plasma physics. This orbital-free approach captures the smooth classical density envelope and quantum density oscillations that are both crucial to accurate modeling of materials where temperature and pressure effects are influential.

Improving Density Functional Tight Binding Predictions of Free Energy Surfaces for Slow Chemical Reactions in Solution

NASA Astrophysics Data System (ADS)

Kroonblawd, Matthew; Goldman, Nir

2017-06-01

First principles molecular dynamics using highly accurate density functional theory (DFT) is a common tool for predicting chemistry, but the accessible time and space scales are often orders of magnitude beyond the resolution of experiments. Semi-empirical methods such as density functional tight binding (DFTB) offer up to a thousand-fold reduction in required CPU hours and can approach experimental scales. However, standard DFTB parameter sets lack good transferability and calibration for a particular system is usually necessary. Force matching the pairwise repulsive energy term in DFTB to short DFT trajectories can improve the former's accuracy for reactions that are fast relative to DFT simulation times (<10 ps), but the effects on slow reactions and the free energy surface are not well-known. We present a force matching approach to improve the chemical accuracy of DFTB. Accelerated sampling techniques are combined with path collective variables to generate the reference DFT data set and validate fitted DFTB potentials. Accuracy of force-matched DFTB free energy surfaces is assessed for slow peptide-forming reactions by direct comparison to DFT for particular paths. Extensions to model prebiotic chemistry under shock conditions are discussed. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

Improving density functional tight binding predictions of free energy surfaces for peptide condensation reactions in solution

NASA Astrophysics Data System (ADS)

Kroonblawd, Matthew; Goldman, Nir

First principles molecular dynamics using highly accurate density functional theory (DFT) is a common tool for predicting chemistry, but the accessible time and space scales are often orders of magnitude beyond the resolution of experiments. Semi-empirical methods such as density functional tight binding (DFTB) offer up to a thousand-fold reduction in required CPU hours and can approach experimental scales. However, standard DFTB parameter sets lack good transferability and calibration for a particular system is usually necessary. Force matching the pairwise repulsive energy term in DFTB to short DFT trajectories can improve the former's accuracy for chemistry that is fast relative to DFT simulation times (<10 ps), but the effects on slow chemistry and the free energy surface are not well-known. We present a force matching approach to increase the accuracy of DFTB predictions for free energy surfaces. Accelerated sampling techniques are combined with path collective variables to generate the reference DFT data set and validate fitted DFTB potentials without a priori knowledge of transition states. Accuracy of force-matched DFTB free energy surfaces is assessed for slow peptide-forming reactions by direct comparison to DFT results for particular paths. Extensions to model prebiotic chemistry under shock conditions are discussed. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

Density functional theory: Foundations reviewed

NASA Astrophysics Data System (ADS)

Kryachko, Eugene S.; Ludeña, Eduardo V.

2014-11-01

Guided by the above motto (quotation), we review a broad range of issues lying at the foundations of Density Functional Theory, DFT, a theory which is currently omnipresent in our everyday computational study of atoms and molecules, solids and nano-materials, and which lies at the heart of modern many-body computational technologies. The key goal is to demonstrate that there are definitely the ways to improve DFT. We start by considering DFT in the larger context provided by reduced density matrix theory (RDMT) and natural orbital functional theory (NOFT), and examine the implications that N-representability conditions on the second-order reduced density matrix (2-RDM) have not only on RDMT and NOFT but, also, by extension, on the functionals of DFT. This examination is timely in view of the fact that necessary and sufficient N-representability conditions on the 2-RDM have recently been attained. In the second place, we review some problems appearing in the original formulation of the first Hohenberg-Kohn theorem which is still a subject of some controversy. In this vein we recall Lieb's comment on this proof and the extension to this proof given by Pino et al. (2009), and in this context examine the conditions that must be met in order that the one-to-one correspondence between ground-state densities and external potentials remains valid for finite subspaces (namely, the subspaces where all Kohn-Sham solutions are obtained in practical applications). We also consider the issue of whether the Kohn-Sham equations can be derived from basic principles or whether they are postulated. We examine this problem in relation to ab initio DFT. The possibility of postulating arbitrary Kohn-Sham-type equations, where the effective potential is by definition some arbitrary mixture of local and non-local terms, is discussed. We also deal with the issue of whether there exists a universal functional, or whether one should advocate instead the construction of problem-geared functionals. These problems are discussed by making reference to ab initio DFT as well as to the local-scaling-transformation version of DFT, LS-DFT. In addition, we examine the question of the accuracy of approximate exchange-correlation functionals in the light of their non-observance of the variational principle. Why do approximate functionals yield reasonable (and accurate) descriptions of many molecular and condensed matter properties? Are the conditions imposed on exchange and correlation functionals sufficiently adequate to produce accurate semi-empirical functionals? In this respect, we consider the question of whether the results reflect a true approach to chemical accuracy or are just the outcome of a virtuoso-like performance which cannot be systematically improved. We discuss the issue of the accuracy of the contemporary DFT results by contrasting them to those obtained by the alternative RDMT and NOFT. We discuss the possibility of improving DFT functionals by applying in a systematic way the N-representability conditions on the 2-RDM. In this respect, we emphasize the possibility of constructing 2-matrices in the context of the local scaling transformation version of DFT to which the N-representability condition of RDM theory may be applied. We end up our revision of HKS-DFT by considering some of the problems related to spin symmetry and discuss some current issues dealing with a proper treatment of open-shell systems. We are particularly concerned, as in the rest of this paper, mostly with foundational issues arising in the construction of functionals. We dedicate the whole Section 4 to the local-scaling transformation version of density functional theory, LS-DFT. The reason is that in this theory some of the fundamental problems that appear in HKS-DFT, have been solved. For example, in LS-DFT the functionals are, in principle, designed to fulfill v- and N-representability conditions from the outset. This is possible because LS-DFT is based on density transformation (local-scaling of coordinates proceeds through density transformation) and so, because these functionals are constructed from prototype N-particle wavefunctions, the ensuing density functionals already have built-in N-representability conditions. This theory is presented in great detail with the purpose of illustrating an alternative way to HKS-DFT which could be used to improve the construction of HKS-DFT functionals. Let us clearly indicate, however, that although appealing from a theoretical point of view, the actual application of LS-DFT to large systems has not taken place mostly because of technical difficulties. Thus, our aim in introducing this theory is to foster a better understanding of its foundations with the hope that it may promote a cross-hybridization with the already existing approaches. Also, to complete our previous discussion on symmetry, in particular, spin-symmetry, we discuss this issue from the perspective of LS-DFT. Finally, in Section 6, we discuss dispersion molecular forces emphasizing their relevance to DFT approaches.

Fundamental measure theory for the inhomogeneous hard-sphere system based on Santos' consistent free energy.

PubMed

Hansen-Goos, Hendrik; Mortazavifar, Mostafa; Oettel, Martin; Roth, Roland

2015-05-01

Based on Santos' general solution for the scaled-particle differential equation [Phys. Rev. E 86, 040102(R) (2012)], we construct a free-energy functional for the hard-sphere system. The functional is obtained by a suitable generalization and extension of the set of scaled-particle variables using the weighted densities from Rosenfeld's fundamental measure theory for the hard-sphere mixture [Phys. Rev. Lett. 63, 980 (1989)]. While our general result applies to the hard-sphere mixture, we specify remaining degrees of freedom by requiring the functional to comply with known properties of the pure hard-sphere system. Both for mixtures and pure systems, the functional can be systematically extended following the lines of our derivation. We test the resulting functionals regarding their behavior upon dimensional reduction of the fluid as well as their ability to accurately describe the hard-sphere crystal and the liquid-solid transition.

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

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

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

2015-12-07

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

The role of plasma chemistry on functional silicon nitride film properties deposited at low-temperature by mixing two frequency powers using PECVD.

PubMed

Sahu, B B; Yin, Y Y; Tsutsumi, T; Hori, M; Han, Jeon G

2016-05-14

Control of the plasma densities and energies of the principal plasma species is crucial to induce modification of the plasma reactivity, chemistry, and film properties. This work presents a systematic and integrated approach to the low-temperature deposition of hydrogenated amorphous silicon nitride films looking into optimization and control of the plasma processes. Radiofrequency (RF) and ultrahigh frequency (UHF) power are combined to enhance significantly the nitrogen plasma and atomic-radical density to enforce their effect on film properties. This study presents an extensive investigation of the influence of combining radiofrequency (RF) and ultrahigh frequency (UHF) power as a power ratio (PR = RF : UHF), ranging from 4 : 0 to 0 : 4, on the compositional, structural, and optical properties of the synthesized films. The data reveal that DF power with a characteristic bi-Maxwellian electron energy distribution function (EEDF) is effectively useful for enhancing the ionization and dissociation of neutrals, which in turn helps in enabling high rate deposition with better film properties than that of SF operations. Utilizing DF PECVD, a wide-bandgap of ∼3.5 eV with strong photoluminescence features can be achieved only by using a high-density plasma and high nitrogen atom density at room temperature. The present work also proposes the suitability of the DF PECVD approach for industrial applications.

Toward chemical accuracy in the description of ion-water interactions through many-body representations. Alkali-water dimer potential energy surfaces

NASA Astrophysics Data System (ADS)

Riera, Marc; Mardirossian, Narbe; Bajaj, Pushp; Götz, Andreas W.; Paesani, Francesco

2017-10-01

This study presents the extension of the MB-nrg (Many-Body energy) theoretical/computational framework of transferable potential energy functions (PEFs) for molecular simulations of alkali metal ion-water systems. The MB-nrg PEFs are built upon the many-body expansion of the total energy and include the explicit treatment of one-body, two-body, and three-body interactions, with all higher-order contributions described by classical induction. This study focuses on the MB-nrg two-body terms describing the full-dimensional potential energy surfaces of the M+(H2O) dimers, where M+ = Li+, Na+, K+, Rb+, and Cs+. The MB-nrg PEFs are derived entirely from "first principles" calculations carried out at the explicitly correlated coupled-cluster level including single, double, and perturbative triple excitations [CCSD(T)-F12b] for Li+ and Na+ and at the CCSD(T) level for K+, Rb+, and Cs+. The accuracy of the MB-nrg PEFs is systematically assessed through an extensive analysis of interaction energies, structures, and harmonic frequencies for all five M+(H2O) dimers. In all cases, the MB-nrg PEFs are shown to be superior to both polarizable force fields and ab initio models based on density functional theory. As previously demonstrated for halide-water dimers, the MB-nrg PEFs achieve higher accuracy by correctly describing short-range quantum-mechanical effects associated with electron density overlap as well as long-range electrostatic many-body interactions.

Interplay between self-assembled structure of bone morphogenetic protein-2 (BMP-2) and osteoblast functions in three-dimensional titanium alloy scaffolds: Stimulation of osteogenic activity.

PubMed

Nune, K C; Kumar, A; Murr, L E; Misra, R D K

2016-02-01

Three-dimensional cellular scaffolds are receiving significant attention in bone tissue engineering to treat segmental bone defects. However, there are indications of lack of significant osteoinductive ability of three-dimensional cellular scaffolds. In this regard, the objective of the study is to elucidate the interplay between bone morphogenetic protein (BMP-2) and osteoblast functions on 3D mesh structures with different porosities and pore size that were fabricated by electron beam melting. Self-assembled dendritic microstructure with interconnected cellular-type morphology of BMP-2 on 3D scaffolds stimulated osteoblast functions including adhesion, proliferation, and mineralization, with prominent effect on 2-mm mesh. Furthermore, immunofluorescence studies demonstrated higher density and viability of osteoblasts on lower porosity mesh structure (2 mm) as compared to 3- and 4-mm mesh structures. Enhanced filopodia cellular extensions with extensive cell spreading was observed on BMP-2 treated mesh structures, a behavior that is attributed to the unique self-assembled structure of BMP-2 that effectively communicates with the cells. The study underscores the potential of BMP-2 in imparting osteoinductive capability to the 3D printed scaffolds. © 2015 Wiley Periodicals, Inc.

Impact-parameter dependence of the energy loss of fast molecular clusters in hydrogen

NASA Astrophysics Data System (ADS)

Fadanelli, R. C.; Grande, P. L.; Schiwietz, G.

2008-03-01

The electronic energy loss of molecular clusters as a function of impact parameter is far less understood than atomic energy losses. For instance, there are no analytical expressions for the energy loss as a function of impact parameter for cluster ions. In this work, we describe two procedures to evaluate the combined energy loss of molecules: Ab initio calculations within the semiclassical approximation and the coupled-channels method using atomic orbitals; and simplified models for the electronic cluster energy loss as a function of the impact parameter, namely the molecular perturbative convolution approximation (MPCA, an extension of the corresponding atomic model PCA) and the molecular unitary convolution approximation (MUCA, a molecular extension of the previous unitary convolution approximation UCA). In this work, an improved ansatz for MPCA is proposed, extending its validity for very compact clusters. For the simplified models, the physical inputs are the oscillators strengths of the target atoms and the target-electron density. The results from these models applied to an atomic hydrogen target yield remarkable agreement with their corresponding ab initio counterparts for different angles between cluster axis and velocity direction at specific energies of 150 and 300 keV/u.

Complete Mie-Gruneisen Equation of State

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

Menikoff, Ralph

2012-06-28

The Mie-Gruneisen equation of state (EOS) is frequently used in hydro simulations to model solids at high pressure (up to a few Mb). It is an incomplete EOS characterized by a Gruneisen coefficient, {Lambda} = -V({partial_derivative}{sub e}P){sub V}, that is a function of only V. Expressions are derived for isentropes and isotherms. This enables the extension to a complete EOS. Thermodynamic consistency requires that the specific heat is a function of a single scaled temperature. A complete extension is uniquely determined by the temperature dependence of the specific heat at a fixed reference density. In addition we show that ifmore » the domain of the EOS extends to T = 0 and the specific heat vanishes on the zero isotherm then {Lambda} a function of only V is equivalent to a specific heat with a single temperature scale. If the EOS domain does not include the zero isotherm, then a specific heat with a single temperature scale leads to a generalization of the Mie-Gruneisen EOS in which the pressure is linear in both the specific energy and the temperature. Such an EOS has previously been used to model liquid nitromethane.« less

Many-body Green’s function theory for electron-phonon interactions: The Kadanoff-Baym approach to spectral properties of the Holstein dimer

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

Säkkinen, Niko; Peng, Yang; Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin-Dahlem

2015-12-21

We present a Kadanoff-Baym formalism to study time-dependent phenomena for systems of interacting electrons and phonons in the framework of many-body perturbation theory. The formalism takes correctly into account effects of the initial preparation of an equilibrium state and allows for an explicit time-dependence of both the electronic and phononic degrees of freedom. The method is applied to investigate the charge neutral and non-neutral excitation spectra of a homogeneous, two-site, two-electron Holstein model. This is an extension of a previous study of the ground state properties in the Hartree (H), partially self-consistent Born (Gd) and fully self-consistent Born (GD) approximationsmore » published in Säkkinen et al. [J. Chem. Phys. 143, 234101 (2015)]. Here, the homogeneous ground state solution is shown to become unstable for a sufficiently strong interaction while a symmetry-broken ground state solution is shown to be stable in the Hartree approximation. Signatures of this instability are observed for the partially self-consistent Born approximation but are not found for the fully self-consistent Born approximation. By understanding the stability properties, we are able to study the linear response regime by calculating the density-density response function by time-propagation. This amounts to a solution of the Bethe-Salpeter equation with a sophisticated kernel. The results indicate that none of the approximations is able to describe the response function during or beyond the bipolaronic crossover for the parameters investigated. Overall, we provide an extensive discussion on when the approximations are valid and how they fail to describe the studied exact properties of the chosen model system.« less

Associations between bone mineral density, grip strength, and lead body burden in older men.

PubMed

Khalil, Naila; Faulkner, Kimberly A; Greenspan, Susan L; Cauley, Jane A

2014-01-01

To study the association between blood lead concentration (BPb) and bone mineral density (BMD), physical function, and cognitive function in noninstitutionalized community-dwelling older men. Cross-sectional study. University of Pittsburgh clinic, Pittsburgh, Pennsylvania. Non-Hispanic Caucasian men aged 65 and older (N = 445) recruited as a subset of a prospective cohort for the Osteoporotic Fractures in Men Study. BPb was measured in 2007/08. From 2007 to 2009, BMD (g/cm(2)) was measured using dual-energy X-ray absorptiometry. At the same time, physical performance was measured using five tests: grip strength, leg extension power, walking speed, narrow-walk pace, and chair stands. Cognitive performance was assessed using the modified Mini-Mental State Examination and the Trail-Making Test Part B. Participants were categorized into quartiles of BPb. Multivariate regression analysis was used to evaluate the independent relationship between BPb, BMD, and cognitive and physical function. Mean BPb ± standard deviation was 2.25 ± 1.20 μg/dL (median 2 μg/dL, range 1-10 μg/dL). In multivariate-adjusted models, men in higher BPb quartiles had lower BMD at femoral neck and total hip (P-trend < .001 for both). Men with higher BPb had lower age-adjusted score for grip strength (P-trend < .001), although this association was not significant in multivariate-adjusted models (P-trend < .15). BPb was not associated with lumbar spine BMD, cognition, leg extension power, walking speed, narrow-walk pace, or chair stands. Environmental lead exposure may adversely affect bone health in older men. These findings support consideration of environmental exposure in age-associated bone fragility. © 2013, Copyright the Authors Journal compilation © 2013, The American Geriatrics Society.

The competition of particle-vibration coupling and tensor interaction in spherical nuclei

NASA Astrophysics Data System (ADS)

Afanasjev, Anatoli; Litvinova, Elena

2014-09-01

The search for missing terms in the energy density functionals (EDF) is one of the leading directions in the development of nuclear density functional theory (DFT). Tensor force is one of possible candidates. However, despite extensive studies the questions about its effective strength and unambiguous signals still remain open. One of the main experimental benchmarks for the studies of tensor interaction is provided by the data on the single-particle states in the N = 82 and Z = 50 isotopes. The energy splittings of the proton h11 / 2 and g7 / 2 states in the Z = 50 isotopes and neutron 1i13 / 2 and 1h9 / 2 states in the N = 82 isotones are used in the definition of tensor force in the Skyrme DFT. However, in experiment these states are not ``mean-field'' states because of coupling with vibrations. Employing relativistic particle-vibration coupling (PVC) model we show that many features of these splittings can be reproduced when PVC is taken into account. This suggests the competition of PVC and tensor interaction and that tensor interaction should be weaker as compared with previous estimates. The search for missing terms in the energy density functionals (EDF) is one of the leading directions in the development of nuclear density functional theory (DFT). Tensor force is one of possible candidates. However, despite extensive studies the questions about its effective strength and unambiguous signals still remain open. One of the main experimental benchmarks for the studies of tensor interaction is provided by the data on the single-particle states in the N = 82 and Z = 50 isotopes. The energy splittings of the proton h11 / 2 and g7 / 2 states in the Z = 50 isotopes and neutron 1i13 / 2 and 1h9 / 2 states in the N = 82 isotones are used in the definition of tensor force in the Skyrme DFT. However, in experiment these states are not ``mean-field'' states because of coupling with vibrations. Employing relativistic particle-vibration coupling (PVC) model we show that many features of these splittings can be reproduced when PVC is taken into account. This suggests the competition of PVC and tensor interaction and that tensor interaction should be weaker as compared with previous estimates. This work has been supported by the U.S. Department of Energy under the Grant DE-FG02-07ER41459 and National Science Foundation Award PHY-1204486.

A simulation study on few parameters of Cherenkov photons in extensive air showers of different primaries incident at various zenith angles over a high altitude observation level

NASA Astrophysics Data System (ADS)

Das, G. S.; Hazarika, P.; Goswami, U. D.

2018-07-01

We have studied the distribution patterns of lateral density, arrival time and angular position of Cherenkov photons generated in Extensive Air Showers (EASs) initiated by γ-ray, proton and iron primaries incident with various energies and at various zenith angles. This study is the extension of our earlier work [1] to cover a wide energy range of ground based γ-ray astronomy with a wide range of zenith angles (≤40°) of primary particles, as well as the extension to study the angular distribution patterns of Cherenkov photons in EASs. This type of study is important for distinguishing the γ-ray initiated showers from the hadronic showers in the ground based γ-ray astronomy, where Atmospheric Cherenkov Technique (ACT) is being used. Importantly, such study gives an insight on the nature of γ-ray and hadronic showers in general. In this work, the CORSIKA 6.990 simulation code is used for generation of EASs. Similarly to the case of Ref. [1], this study also revealed that, the lateral density and arrival time distributions of Cherenkov photons vary almost in accordance with the functions: ρch(r) =ρ0e-βr and tch(r) =t0eΓ/rλ respectively by taking different values of the parameters of functions for the type, energy and zenith angle of the primary particle. The distribution of Cherenkov photon's angular positions with respect to shower axis shows distinctive features depending on the primary type, its energy and the zenith angle. As a whole this distribution pattern for the iron primary is noticeably different from those for γ-ray and proton primaries. The value of the angular position at which the maximum number of Cherenkov photons are concentrated, increases with increase in energy of vertically incident primary, but for inclined primary it lies within a small value (≤1°) for almost all energies and primary types. No significant difference in the results obtained by using the high energy hadronic interaction models, viz., QGSJETII and EPOS has been observed.

Spatio-temporal analysis of aftershock sequences in terms of Non Extensive Statistical Physics.

NASA Astrophysics Data System (ADS)

Chochlaki, Kalliopi; Vallianatos, Filippos

2017-04-01

Earth's seismicity is considered as an extremely complicated process where long-range interactions and fracturing exist (Vallianatos et al., 2016). For this reason, in order to analyze it, we use an innovative methodological approach, introduced by Tsallis (Tsallis, 1988; 2009), named Non Extensive Statistical Physics. This approach introduce a generalization of the Boltzmann-Gibbs statistical mechanics and it is based on the definition of Tsallis entropy Sq, which maximized leads the the so-called q-exponential function that expresses the probability distribution function that maximizes the Sq. In the present work, we utilize the concept of Non Extensive Statistical Physics in order to analyze the spatiotemporal properties of several aftershock series. Marekova (Marekova, 2014) suggested that the probability densities of the inter-event distances between successive aftershocks follow a beta distribution. Using the same data set we analyze the inter-event distance distribution of several aftershocks sequences in different geographic regions by calculating non extensive parameters that determine the behavior of the system and by fitting the q-exponential function, which expresses the degree of non-extentivity of the investigated system. Furthermore, the inter-event times distribution of the aftershocks as well as the frequency-magnitude distribution has been analyzed. The results supports the applicability of Non Extensive Statistical Physics ideas in aftershock sequences where a strong correlation exists along with memory effects. References C. Tsallis, Possible generalization of Boltzmann-Gibbs statistics, J. Stat. Phys. 52 (1988) 479-487. doi:10.1007/BF01016429 C. Tsallis, Introduction to nonextensive statistical mechanics: Approaching a complex world, 2009. doi:10.1007/978-0-387-85359-8. E. Marekova, Analysis of the spatial distribution between successive earthquakes in aftershocks series, Annals of Geophysics, 57, 5, doi:10.4401/ag-6556, 2014 F. Vallianatos, G. Papadakis, G. Michas, Generalized statistical mechanics approaches to earthquakes and tectonics. Proc. R. Soc. A, 472, 20160497, 2016.

Multiple model cardinalized probability hypothesis density filter

NASA Astrophysics Data System (ADS)

Georgescu, Ramona; Willett, Peter

2011-09-01

The Probability Hypothesis Density (PHD) filter propagates the first-moment approximation to the multi-target Bayesian posterior distribution while the Cardinalized PHD (CPHD) filter propagates both the posterior likelihood of (an unlabeled) target state and the posterior probability mass function of the number of targets. Extensions of the PHD filter to the multiple model (MM) framework have been published and were implemented either with a Sequential Monte Carlo or a Gaussian Mixture approach. In this work, we introduce the multiple model version of the more elaborate CPHD filter. We present the derivation of the prediction and update steps of the MMCPHD particularized for the case of two target motion models and proceed to show that in the case of a single model, the new MMCPHD equations reduce to the original CPHD equations.

Phase transition and monopole densities in a nearest neighbor two-dimensional spin ice model

NASA Astrophysics Data System (ADS)

Morais, C. W.; de Freitas, D. N.; Mota, A. L.; Bastone, E. C.

2017-12-01

In this work, we show that, due to the alternating orientation of the spins in the ground state of the artificial square spin ice, the influence of a set of spins at a certain distance of a reference spin decreases faster than the expected result for the long range dipolar interaction, justifying the use of the nearest neighbor two-dimensional square spin ice model as an effective model. Using an extension of the model presented in Y. L. Xie et al., Sci. Rep. 5, 15875 (2015), considering the influence of the eight nearest neighbors of each spin on the lattice, we analyze the thermodynamics of the model and study the dependence of monopoles and string densities as a function of the temperature.

Modelling of the Thermo-Physical and Physical Properties for Solidification of Al-Alloys

NASA Astrophysics Data System (ADS)

Saunders, N.; Li, X.; Miodownik, A. P.; Schillé, J.-P.

The thermo-physical and physical properties of the liquid and solid phases are critical components in casting simulations. Such properties include the fraction solid transformed, enthalpy release, thermal conductivity, volume and density, all as a function of temperature. Due to the difficulty in experimentally determining such properties at solidification temperatures, little information exists for multi-component alloys. As part of the development of a new computer program for modelling of materials properties (JMatPro) extensive work has been carried out on the development of sound, physically based models for these properties. Wide ranging results will presented for Al-based alloys, which will include more detailed information concerning the density change of the liquid that intrinsically occurs during solidification due to its change in composition.

Hydrodynamic Model for Conductivity in Graphene

PubMed Central

Mendoza, M.; Herrmann, H. J.; Succi, S.

2013-01-01

Based on the recently developed picture of an electronic ideal relativistic fluid at the Dirac point, we present an analytical model for the conductivity in graphene that is able to describe the linear dependence on the carrier density and the existence of a minimum conductivity. The model treats impurities as submerged rigid obstacles, forming a disordered medium through which graphene electrons flow, in close analogy with classical fluid dynamics. To describe the minimum conductivity, we take into account the additional carrier density induced by the impurities in the sample. The model, which predicts the conductivity as a function of the impurity fraction of the sample, is supported by extensive simulations for different values of ε, the dimensionless strength of the electric field, and provides excellent agreement with experimental data. PMID:23316277

Self-consistent predictor/corrector algorithms for stable and efficient integration of the time-dependent Kohn-Sham equation

NASA Astrophysics Data System (ADS)

Zhu, Ying; Herbert, John M.

2018-01-01

The "real time" formulation of time-dependent density functional theory (TDDFT) involves integration of the time-dependent Kohn-Sham (TDKS) equation in order to describe the time evolution of the electron density following a perturbation. This approach, which is complementary to the more traditional linear-response formulation of TDDFT, is more efficient for computation of broad-band spectra (including core-excited states) and for systems where the density of states is large. Integration of the TDKS equation is complicated by the time-dependent nature of the effective Hamiltonian, and we introduce several predictor/corrector algorithms to propagate the density matrix, one of which can be viewed as a self-consistent extension of the widely used modified-midpoint algorithm. The predictor/corrector algorithms facilitate larger time steps and are shown to be more efficient despite requiring more than one Fock build per time step, and furthermore can be used to detect a divergent simulation on-the-fly, which can then be halted or else the time step modified.

The stationary non-equilibrium plasma of cosmic-ray electrons and positrons

NASA Astrophysics Data System (ADS)

Tomaschitz, Roman

2016-06-01

The statistical properties of the two-component plasma of cosmic-ray electrons and positrons measured by the AMS-02 experiment on the International Space Station and the HESS array of imaging atmospheric Cherenkov telescopes are analyzed. Stationary non-equilibrium distributions defining the relativistic electron-positron plasma are derived semi-empirically by performing spectral fits to the flux data and reconstructing the spectral number densities of the electronic and positronic components in phase space. These distributions are relativistic power-law densities with exponential cutoff, admitting an extensive entropy variable and converging to the Maxwell-Boltzmann or Fermi-Dirac distributions in the non-relativistic limit. Cosmic-ray electrons and positrons constitute a classical (low-density high-temperature) plasma due to the low fugacity in the quantized partition function. The positron fraction is assembled from the flux densities inferred from least-squares fits to the electron and positron spectra and is subjected to test by comparing with the AMS-02 flux ratio measured in the GeV interval. The calculated positron fraction extends to TeV energies, predicting a broad spectral peak at about 1 TeV followed by exponential decay.

Quadratic canonical transformation theory and higher order density matrices.

PubMed

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

2009-03-28

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

Molecular design and property prediction of high density polynitro[3.3.3]-propellane-derivatized frameworks as potential high explosives.

PubMed

Zhang, Qinghua; Zhang, Jiaheng; Qi, Xiujuan; Shreeve, Jean'ne M

2014-11-13

Research in energetic materials is now heavily focused on the design and synthesis of novel insensitive high explosives (IHEs) for specialized applications. As an effective and time-saving tool for screening potential explosive structures, computer simulation has been widely used for the prediction of detonation properties of energetic molecules with relatively high precision. In this work, a series of new polynitrotetraoxopentaaza[3.3.3]-propellane molecules with tricyclic structures were designed. Their properties as potential high explosives including density, heats of formation, detonation properties, impact sensitivity, etc., have been extensively evaluated using volume-based thermodynamic calculations and density functional theory (DFT).These new energetic molecules exhibit high densities of >1.82 g cm(-3), in which 1 gives the highest density of 2.04 g cm(-3). Moreover, most new materials show good detonation properties and acceptable impact sensitivities, in which 5 displays much higher detonation velocity (9482 m s(-1)) and pressure (43.9 GPa) than HMX and has a h50 value of 11 cm. These results are expected to facilitate the experimental synthesis of new-generation nitramine-based high explosives.

States of phage T3/T7 capsids: buoyant density centrifugation and cryo-EM.

PubMed

Serwer, Philip; Wright, Elena T; Demeler, Borries; Jiang, Wen

2018-04-01

Mature double-stranded DNA bacteriophages have capsids with symmetrical shells that typically resist disruption, as they must to survive in the wild. However, flexibility and associated dynamism assist function. We describe biochemistry-oriented procedures used to find previously obscure flexibility for capsids of the related phages, T3 and T7. The primary procedures are hydration-based buoyant density ultracentrifugation and purified particle-based cryo-electron microscopy (cryo-EM). We review the buoyant density centrifugation in detail. The mature, stable T3/T7 capsid is a shell flexibility-derived conversion product of an initially assembled procapsid (capsid I). During DNA packaging, capsid I expands and loses a scaffolding protein to form capsid II. The following are observations made with capsid II. (1) The in vivo DNA packaging of wild type T3 generates capsid II that has a slight (1.4%), cryo-EM-detected hyper-expansion relative to the mature phage capsid. (2) DNA packaging in some altered conditions generates more extensive hyper-expansion of capsid II, initially detected by hydration-based preparative buoyant density centrifugation in Nycodenz density gradients. (3) Capsid contraction sometimes occurs, e.g., during quantized leakage of DNA from mature T3 capsids without a tail.

Transcallosal Projections Require Glycoprotein M6-Dependent Neurite Growth and Guidance.

PubMed

Mita, Sakura; de Monasterio-Schrader, Patricia; Fünfschilling, Ursula; Kawasaki, Takahiko; Mizuno, Hidenobu; Iwasato, Takuji; Nave, Klaus-Armin; Werner, Hauke B; Hirata, Tatsumi

2015-11-01

The function of mature neurons critically relies on the developmental outgrowth and projection of their cellular processes. It has long been postulated that the neuronal glycoproteins M6a and M6b are involved in axon growth because these four-transmembrane domain-proteins of the proteolipid protein family are highly enriched on growth cones, but in vivo evidence has been lacking. Here, we report that the function of M6 proteins is required for normal axonal extension and guidance in vivo. In mice lacking both M6a and M6b, a severe hypoplasia of axon tracts was manifested. Most strikingly, the corpus callosum was reduced in thickness despite normal densities of cortical projection neurons. In single neuron tracing, many axons appeared shorter and disorganized in the double-mutant cortex, and some of them were even misdirected laterally toward the subcortex. Probst bundles were not observed. Upon culturing, double-mutant cortical and cerebellar neurons displayed impaired neurite outgrowth, indicating a cell-intrinsic function of M6 proteins. A rescue experiment showed that the intracellular loop of M6a is essential for the support of neurite extension. We propose that M6 proteins are required for proper extension and guidance of callosal axons that follow one of the most complex trajectories in the mammalian nervous system. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Genotype by environment interaction for plant density response in maize

USDA-ARS?s Scientific Manuscript database

Increased adaptation to high plant density has been an important factor in improvements in grain yield in maize. Despite extensive public literature on variation in plant density response among maize varieties, almost no public information is available on environmental effects on plant density respo...

Testing time-dependent density functional theory with depopulated molecular orbitals for predicting electronic excitation energies of valence, Rydberg, and charge-transfer states and potential energies near a conical intersection

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

Li, Shaohong L.; Truhlar, Donald G., E-mail: truhlar@umn.edu

2014-09-14

Kohn-Sham (KS) time-dependent density functional theory (TDDFT) with most exchange-correlation functionals is well known to systematically underestimate the excitation energies of Rydberg and charge-transfer excited states of atomic and molecular systems. To improve the description of Rydberg states within the KS TDDFT framework, Gaiduk et al. [Phys. Rev. Lett. 108, 253005 (2012)] proposed a scheme that may be called HOMO depopulation. In this study, we tested this scheme on an extensive dataset of valence and Rydberg excitation energies of various atoms, ions, and molecules. It is also tested on a charge-transfer excitation of NH{sub 3}-F{sub 2} and on the potentialmore » energy curves of NH{sub 3} near a conical intersection. We found that the method can indeed significantly improve the accuracy of predicted Rydberg excitation energies while preserving reasonable accuracy for valence excitation energies. However, it does not appear to improve the description of charge-transfer excitations that are severely underestimated by standard KS TDDFT with conventional exchange-correlation functionals, nor does it perform appreciably better than standard TDDFT for the calculation of potential energy surfaces.« less

Probability Density Functions of Observed Rainfall in Montana

NASA Technical Reports Server (NTRS)

Larsen, Scott D.; Johnson, L. Ronald; Smith, Paul L.

1995-01-01

The question of whether a rain rate probability density function (PDF) can vary uniformly between precipitation events is examined. Image analysis on large samples of radar echoes is possible because of advances in technology. The data provided by such an analysis easily allow development of radar reflectivity factors (and by extension rain rate) distribution. Finding a PDF becomes a matter of finding a function that describes the curve approximating the resulting distributions. Ideally, one PDF would exist for all cases; or many PDF's that have the same functional form with only systematic variations in parameters (such as size or shape) exist. Satisfying either of theses cases will, validate the theoretical basis of the Area Time Integral (ATI). Using the method of moments and Elderton's curve selection criteria, the Pearson Type 1 equation was identified as a potential fit for 89 percent of the observed distributions. Further analysis indicates that the Type 1 curve does approximate the shape of the distributions but quantitatively does not produce a great fit. Using the method of moments and Elderton's curve selection criteria, the Pearson Type 1 equation was identified as a potential fit for 89% of the observed distributions. Further analysis indicates that the Type 1 curve does approximate the shape of the distributions but quantitatively does not produce a great fit.

Media effects in modulating the conformational equilibrium of a model compound for tumor necrosis factor converting enzyme inhibition

NASA Astrophysics Data System (ADS)

Banchelli, Martina; Guardiani, Carlo; Sandberg, Robert B.; Menichetti, Stefano; Procacci, Piero; Caminati, Gabriella

2015-07-01

Small-molecule inhibitors of Tumor Necrosis Factor α Converting Enzyme (TACE) are a promising therapeutic tool for Rheumatoid Arthritis, Multiple Sclerosis and other autoimmune diseases. Here we report on an extensive chemical-physical analysis of the media effects in modulating the conformational landscape of MBET306, the common scaffold and a synthetic precursor of a family of recently discovered tartrate-based TACE inhibitors. The structural features of this molecule with potential pharmaceutical applications have been disclosed by interpreting extensive photophysical measurements in various solvents with the aid of enhanced sampling molecular dynamics simulations and time dependent density functional calculations. Using a combination of experimental and computational techniques, the paper provides a general protocol for studying the structure in solution of molecular systems characterized by the existence of conformational metastable states.

Application of multivariate Gaussian detection theory to known non-Gaussian probability density functions

NASA Astrophysics Data System (ADS)

Schwartz, Craig R.; Thelen, Brian J.; Kenton, Arthur C.

1995-06-01

A statistical parametric multispectral sensor performance model was developed by ERIM to support mine field detection studies, multispectral sensor design/performance trade-off studies, and target detection algorithm development. The model assumes target detection algorithms and their performance models which are based on data assumed to obey multivariate Gaussian probability distribution functions (PDFs). The applicability of these algorithms and performance models can be generalized to data having non-Gaussian PDFs through the use of transforms which convert non-Gaussian data to Gaussian (or near-Gaussian) data. An example of one such transform is the Box-Cox power law transform. In practice, such a transform can be applied to non-Gaussian data prior to the introduction of a detection algorithm that is formally based on the assumption of multivariate Gaussian data. This paper presents an extension of these techniques to the case where the joint multivariate probability density function of the non-Gaussian input data is known, and where the joint estimate of the multivariate Gaussian statistics, under the Box-Cox transform, is desired. The jointly estimated multivariate Gaussian statistics can then be used to predict the performance of a target detection algorithm which has an associated Gaussian performance model.

Electrostatics-mediated α-chymotrypsin inhibition by functionalized single-walled carbon nanotubes.

PubMed

Zhao, Daohui; Zhou, Jian

2017-01-04

The α-chymotrypsin (α-ChT) enzyme is extensively used for studying nanomaterial-induced enzymatic activity inhibition. A recent experimental study reported that carboxylized carbon nanotubes (CNTs) played an important role in regulating the α-ChT activity. In this study, parallel tempering Monte Carlo and molecular dynamics simulations were combined to elucidate the interactions between α-ChT and CNTs in relation to the CNT functional group density. The simulation results indicate that the adsorption and the driving force of α-ChT on different CNTs are contingent on the carboxyl density. Meanwhile, minor secondary structural changes are observed in adsorption processes. It is revealed that α-ChT interacts with pristine CNTs through hydrophobic forces and exhibits a non-competitive characteristic with the active site facing towards the solution; while it binds to carboxylized CNTs with the active pocket through a dominant electrostatic association, which causes enzymatic activity inhibition in a competitive-like mode. These findings are in line with experimental results, and well interpret the activity inhibition of α-ChT at the molecular level. Moreover, this study would shed light on the detailed mechanism of specific recognition and regulation of α-ChT by other functionalized nanomaterials.

Ginzburg-Landau theory for the solid-liquid interface of bcc elements. II - Application to the classical one-component plasma, the Wigner crystal, and He-4

NASA Technical Reports Server (NTRS)

Zeng, X. C.; Stroud, D.

1989-01-01

The previously developed Ginzburg-Landau theory for calculating the crystal-melt interfacial tension of bcc elements to treat the classical one-component plasma (OCP), the charged fermion system, and the Bose crystal. For the OCP, a direct application of the theory of Shih et al. (1987) yields for the surface tension 0.0012(Z-squared e-squared/a-cubed), where Ze is the ionic charge and a is the radius of the ionic sphere. Bose crystal-melt interface is treated by a quantum extension of the classical density-functional theory, using the Feynman formalism to estimate the relevant correlation functions. The theory is applied to the metastable He-4 solid-superfluid interface at T = 0, with a resulting surface tension of 0.085 erg/sq cm, in reasonable agreement with the value extrapolated from the measured surface tension of the bcc solid in the range 1.46-1.76 K. These results suggest that the density-functional approach is a satisfactory mean-field theory for estimating the equilibrium properties of liquid-solid interfaces, given knowledge of the uniform phases.

Performances of 250 Amp-hr lithium/thionyl chloride cells

NASA Technical Reports Server (NTRS)

Goualard, Jacques

1991-01-01

A 250 Ah lithium thionyl chloride battery is being developed for a booster rocket engine. Extensive cell testing is running to evaluate functional and safety performances. Some results are presented. The lithium/thionyl chloride batteries were selected for their high energy density (low weight) as compared to other sources. The temperature of a lower weight item will be more sensitive to variations of internal and external heat fluxes than a heavier one. The use of high energy density L/TC batteries is subjected to stringent thermal environments to have benefit of energy density and to stay safe in any conditions. The battery thermal environment and discharge rate have to be adjusted to obtain the right temperature range at cell level, to have the maximum performances. Voltage and capacity are very sensitive to temperature. This temperature is the cell internal actual temperature during discharge. This temperature is directed by external thermal environment and by cell internal heat dissipation, i.e., cell actual voltage.

Higher-order ionospheric error at Arecibo, Millstone, and Jicamarca

NASA Astrophysics Data System (ADS)

Matteo, N. A.; Morton, Y. T.

2010-12-01

The ionosphere is a dominant source of Global Positioning System receiver range measurement error. Although dual-frequency receivers can eliminate the first-order ionospheric error, most second- and third-order errors remain in the range measurements. Higher-order ionospheric error is a function of both electron density distribution and the magnetic field vector along the GPS signal propagation path. This paper expands previous efforts by combining incoherent scatter radar (ISR) electron density measurements, the International Reference Ionosphere model, exponential decay extensions of electron densities, the International Geomagnetic Reference Field, and total electron content maps to compute higher-order error at ISRs in Arecibo, Puerto Rico; Jicamarca, Peru; and Millstone Hill, Massachusetts. Diurnal patterns, dependency on signal direction, seasonal variation, and geomagnetic activity dependency are analyzed. Higher-order error is largest at Arecibo with code phase maxima circa 7 cm for low-elevation southern signals. The maximum variation of the error over all angles of arrival is circa 8 cm.

Individual Colorimetric Observer Model

PubMed Central

Asano, Yuta; Fairchild, Mark D.; Blondé, Laurent

2016-01-01

This study proposes a vision model for individual colorimetric observers. The proposed model can be beneficial in many color-critical applications such as color grading and soft proofing to assess ranges of color matches instead of a single average match. We extended the CIE 2006 physiological observer by adding eight additional physiological parameters to model individual color-normal observers. These eight parameters control lens pigment density, macular pigment density, optical densities of L-, M-, and S-cone photopigments, and λmax shifts of L-, M-, and S-cone photopigments. By identifying the variability of each physiological parameter, the model can simulate color matching functions among color-normal populations using Monte Carlo simulation. The variabilities of the eight parameters were identified through two steps. In the first step, extensive reviews of past studies were performed for each of the eight physiological parameters. In the second step, the obtained variabilities were scaled to fit a color matching dataset. The model was validated using three different datasets: traditional color matching, applied color matching, and Rayleigh matches. PMID:26862905

Coordination characteristics of uranyl BBP complexes: Insights from an electronic structure analysis

DOE PAGES

Pemmaraju, Chaitanya Das; Copping, Roy; Smiles, Danil E.; ...

2017-03-21

Here, organic ligand complexes of lanthanide/actinide ions have been studied extensively for applications in nuclear fuel storage and recycling. Several complexes of 2,6-bis(2-benzimidazyl)pyridine (H2BBP) featuring the uranyl moiety have been reported recently, and the present study investigates the coordination characteristics of these complexes using density functional theory-based electronic structure analysis. In particular, with the aid of several computational models, the nonplanar equatorial coordination about uranyl, observed in some of the compounds, is studied and its origin traced to steric effects.

Quadratic integrand double-hybrid made spin-component-scaled

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

Brémond, Éric, E-mail: eric.bremond@iit.it; Savarese, Marika; Sancho-García, Juan C.

2016-03-28

We propose two analytical expressions aiming to rationalize the spin-component-scaled (SCS) and spin-opposite-scaled (SOS) schemes for double-hybrid exchange-correlation density-functionals. Their performances are extensively tested within the framework of the nonempirical quadratic integrand double-hybrid (QIDH) model on energetic properties included into the very large GMTKN30 benchmark database, and on structural properties of semirigid medium-sized organic compounds. The SOS variant is revealed as a less computationally demanding alternative to reach the accuracy of the original QIDH model without losing any theoretical background.

Theory of earthquakes interevent times applied to financial markets

NASA Astrophysics Data System (ADS)

Jagielski, Maciej; Kutner, Ryszard; Sornette, Didier

2017-10-01

We analyze the probability density function (PDF) of waiting times between financial loss exceedances. The empirical PDFs are fitted with the self-excited Hawkes conditional Poisson process with a long power law memory kernel. The Hawkes process is the simplest extension of the Poisson process that takes into account how past events influence the occurrence of future events. By analyzing the empirical data for 15 different financial assets, we show that the formalism of the Hawkes process used for earthquakes can successfully model the PDF of interevent times between successive market losses.

Density functional theory for the description of spherical non-associating monomers in confined media using the SAFT-VR equation of state and weighted density approximations.

PubMed

Malheiro, Carine; Mendiboure, Bruno; Plantier, Frédéric; Blas, Felipe J; Miqueu, Christelle

2014-04-07

As a first step of an ongoing study of thermodynamic properties and adsorption of complex fluids in confined media, we present a new theoretical description for spherical monomers using the Statistical Associating Fluid Theory for potential of Variable Range (SAFT-VR) and a Non-Local Density Functional Theory (NLDFT) with Weighted Density Approximations (WDA). The well-known Modified Fundamental Measure Theory is used to describe the inhomogeneous hard-sphere contribution as a reference for the monomer and two WDA approaches are developed for the dispersive terms from the high-temperature Barker and Henderson perturbation expansion. The first approach extends the dispersive contributions using the scalar and vector weighted densities introduced in the Fundamental Measure Theory (FMT) and the second one uses a coarse-grained (CG) approach with a unique weighted density. To test the accuracy of this new NLDFT/SAFT-VR coupling, the two versions of the theoretical model are compared with Grand Canonical Monte Carlo (GCMC) molecular simulations using the same molecular model. Only the version with the "CG" approach for the dispersive terms provides results in excellent agreement with GCMC calculations in a wide range of conditions while the "FMT" extension version gives a good representation solely at low pressures. Hence, the "CG" version of the theoretical model is used to reproduce methane adsorption isotherms in a Carbon Molecular Sieve and compared with experimental data after a characterization of the material. The whole results show an excellent agreement between modeling and experiments. Thus, through a complete and consistent comparison both with molecular simulations and with experimental data, the NLDFT/SAFT-VR theory has been validated for the description of monomers.

Electronic Structure and Transport in Solids from First Principles

NASA Astrophysics Data System (ADS)

Mustafa, Jamal Ibrahim

The focus of this dissertation is the determination of the electronic structure and trans- port properties of solids. We first review some of the theory and computational methodology used in the calculation of electronic structure and materials properties. Throughout the dissertation, we make extensive use of state-of-the-art software packages that implement density functional theory, density functional perturbation theory, and the GW approximation, in addition to specialized methods for interpolating matrix elements for extremely accurate results. The first application of the computational framework introduced is the determination of band offsets in semiconductor heterojunctions using a theory of quantum dipoles at the interface. This method is applied to the case of heterojunction formed between a new metastable phase of silicon, with a rhombohedral structure, and cubic silicon. Next, we introduce a novel method for the construction of localized Wannier functions, which we have named the optimized projection functions method (OPFM). We illustrate the method on a variety of systems and find that it can reliably construct localized Wannier functions with minimal user intervention. We further develop the OPFM to investigate a class of materials called topological insulators, which are insulating in the bulk but have conductive surface states. These properties are a result of a nontrivial topology in their band structure, which has interesting effects on the character of the Wannier functions. In the last sections of the main text, the noble metals are studied in great detail, including their electronic properties and carrier dynamics. In particular, we investigate, the Fermi surface properties of the noble metals, specifically electron-phonon scattering lifetimes, and subsequently the transport properties determined by carriers on the Fermi surface. To achieve this, a novel sampling technique is developed, with wide applicability to transport calculations. Additionally, the generation and transport of hot carriers is studied extensively. The distribution of hot carriers generated from the decay of plasmons is explored over a range of energy, and the transport properties, particularly the lifetimes and mean-free-paths, of the hot carriers are determined. Lastly, appendices detailing the implementation of the algorithms developed in the work is presented, along with a useful derivation of the electron-plasmon matrix elements.

Modification of dendritic development.

PubMed

Feria-Velasco, Alfredo; del Angel, Alma Rosa; Gonzalez-Burgos, Ignacio

2002-01-01

Since 1890 Ramón y Cajal strongly defended the theory that dendrites and their processes and spines had a function of not just nutrient transport to the cell body, but they had an important conductive role in neural impulse transmission. He extensively discussed and supported this theory in the Volume 1 of his extraordinary book Textura del Sistema Nervioso del Hombre y de los Vertebrados. Also, Don Santiago significantly contributed to a detailed description of the various neural components of the hippocampus and cerebral cortex during development. Extensive investigation has been done in the last Century related to the functional role of these complex brain regions, and their association with learning, memory and some limbic functions. Likewise, the organization and expression of neuropsychological qualities such as memory, exploratory behavior and spatial orientation, among others, depend on the integrity and adequate functional activity of the cerebral cortex and hippocampus. It is known that brain serotonin synthesis and release depend directly and proportionally on the availability of its precursor, tryptophan (TRY). By using a chronic TRY restriction model in rats, we studied their place learning ability in correlation with the dendritic spine density of pyramidal neurons in field CA1 of the hippocampus during postnatal development. We have also reported alterations in the maturation pattern of the ability for spontaneous alternation and task performance evaluating short-term memory, as well as adverse effects on the density of dendritic spines of hippocampal CA1 field pyramidal neurons and on the dendritic arborization and the number of dendritic spines of pyramidal neurons from the third layer of the prefrontal cortex using the same model of TRY restriction. The findings obtained in these studies employing a modified Golgi method, can be interpreted as a trans-synaptic plastic response due to understimulation of serotoninergic receptors located in the hippocampal Ammon's horn and, particularly, on the CA1 field pyramidal neurons, as well as on afferences to the hippocampus which needs to be further investigated.

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

Lin, Jiusheng; van den Bedem, Henry; Brunger, Axel T.

Calmodulin (CaM) is the primary calcium signaling protein in eukaryotes and has been extensively studied using various biophysical techniques. Prior crystal structures have noted the presence of ambiguous electron density in both hydrophobic binding pockets of Ca 2+-CaM, but no assignment of these features has been made. In addition, Ca 2+-CaM samples many conformational substates in the crystal and accurately modeling the full range of this functionally important disorder is challenging. In order to characterize these features in a minimally biased manner, a 1.0 Å resolution single-wavelength anomalous diffraction data set was measured for selenomethionine-substituted Ca 2+-CaM. Density-modified electron-density mapsmore » enabled the accurate assignment of Ca 2+-CaM main-chain and side-chain disorder. These experimental maps also substantiate complex disorder models that were automatically built using low-contour features of model-phased electron density. Furthermore, experimental electron-density maps reveal that 2-methyl-2,4-pentanediol (MPD) is present in the C-terminal domain, mediates a lattice contact between N-terminal domains and may occupy the N-terminal binding pocket. The majority of the crystal structures of target-free Ca 2+-CaM have been derived from crystals grown using MPD as a precipitant, and thus MPD is likely to be bound in functionally critical regions of Ca 2+-CaM in most of these structures. The adventitious binding of MPD helps to explain differences between the Ca 2+-CaM crystal and solution structures and is likely to favor more open conformations of the EF-hands in the crystal.« less

Effects of wildlife forestry on abundance of breeding birds in bottomland hardwood forests of Louisiana

USGS Publications Warehouse

Norris, Jennifer L.; Chamberlain, Michael J.; Twedt, Daniel J.

2009-01-01

Effects of silvicultural activities on birds are of increasing interest because of documented national declines in breeding bird populations for some species and the potential that these declines are in part due to changes in forest habitat. Silviculturally induced disturbances have been advocated as a means to achieve suitable forest conditions for priority wildlife species in bottomland hardwood forests. We evaluated how silvicultural activities on conservation lands in bottomland hardwood forests of Louisiana, USA, influenced species-specific densities of breeding birds. Our data were from independent studies, which used standardized point-count surveys for breeding birds in 124 bottomland hardwood forest stands on 12 management areas. We used Program DISTANCE 5.0, Release 2.0 (Thomas et al. 2006) to estimate density for 43 species with > 50 detections. For 36 of those species we compared density estimates among harvest regimes (individual selection, group selection, extensive harvest, and no harvest). We observed 10 species with similar densities in those harvest regimes compared with densities in stands not harvested. However, we observed 10 species that were negatively impacted by harvest with greater densities in stands not harvested, 9 species with greater densities in individual selection stands, 4 species with greater densities in group selection stands, and 4 species with greater densities in stands receiving an extensive harvest (e.g., > 40% canopy removal). Differences in intensity of harvest influenced densities of breeding birds. Moreover, community-wide avian conservation values of stands subjected to individual and group selection, and stands not harvested, were similar to each other and greater than that of stands subjected to extensive harvest that removed > 40% canopy cover. These results have implications for managers estimating breeding bird populations, in addition to predicting changes in bird communities as a result of prescribed and future forest management practices.

Tartarus: A relativistic Green's function quantum average atom code

DOE PAGES

Gill, Nathanael Matthew; Starrett, Charles Edward

2017-06-28

A relativistic Green’s Function quantum average atom model is implemented in the Tartarus code for the calculation of equation of state data in dense plasmas. We first present the relativistic extension of the quantum Green’s Function average atom model described by Starrett [1]. The Green’s Function approach addresses the numerical challenges arising from resonances in the continuum density of states without the need for resonance tracking algorithms or adaptive meshes, though there are still numerical challenges inherent to this algorithm. We discuss how these challenges are addressed in the Tartarus algorithm. The outputs of the calculation are shown in comparisonmore » to PIMC/DFT-MD simulations of the Principal Shock Hugoniot in Silicon. Finally, we also present the calculation of the Hugoniot for Silver coming from both the relativistic and nonrelativistic modes of the Tartarus code.« less

Tartarus: A relativistic Green's function quantum average atom code

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

Gill, Nathanael Matthew; Starrett, Charles Edward

A relativistic Green’s Function quantum average atom model is implemented in the Tartarus code for the calculation of equation of state data in dense plasmas. We first present the relativistic extension of the quantum Green’s Function average atom model described by Starrett [1]. The Green’s Function approach addresses the numerical challenges arising from resonances in the continuum density of states without the need for resonance tracking algorithms or adaptive meshes, though there are still numerical challenges inherent to this algorithm. We discuss how these challenges are addressed in the Tartarus algorithm. The outputs of the calculation are shown in comparisonmore » to PIMC/DFT-MD simulations of the Principal Shock Hugoniot in Silicon. Finally, we also present the calculation of the Hugoniot for Silver coming from both the relativistic and nonrelativistic modes of the Tartarus code.« less

Power-law partition and entropy production of high-energy cosmic rays: Knee-ankle structure of the all-particle spectrum

NASA Astrophysics Data System (ADS)

Tomaschitz, Roman

2013-10-01

A statistical description of the all-particle cosmic-ray spectrum is given in the 10^{14}\\ \\text{eV} to 10^{20}\\ \\text{eV} interval. The high-energy cosmic-ray flux is modeled as an ultra-relativistic multi-component plasma, whose components constitute a mixture of nearly ideal but nonthermal gases of low density and high temperature. Each plasma component is described by an ultra-relativistic power-law density manifested as spectral peak in the wideband fit. The “knee” and “ankle” features of the high- and ultra-high-energy spectrum turn out to be the global and local extrema of the double-logarithmic E3-scaled flux representation in which the spectral fit is performed. The all-particle spectrum is covered by recent data sets from several air shower arrays, and can be modeled as three-component plasma in the indicated energy range extending over six decades. The temperature, specific number density, internal energy and entropy of each plasma component are extracted from the partial fluxes in the broadband fit. The grand partition function and the extensive entropy functional of a non-equilibrated gas mixture with power-law components are derived in phase space by ensemble averaging.

Ab initio density-functional calculations in materials science: from quasicrystals over microporous catalysts to spintronics.

PubMed

Hafner, Jürgen

2010-09-29

During the last 20 years computer simulations based on a quantum-mechanical description of the interactions between electrons and atomic nuclei have developed an increasingly important impact on materials science, not only in promoting a deeper understanding of the fundamental physical phenomena, but also enabling the computer-assisted design of materials for future technologies. The backbone of atomic-scale computational materials science is density-functional theory (DFT) which allows us to cast the intractable complexity of electron-electron interactions into the form of an effective single-particle equation determined by the exchange-correlation functional. Progress in DFT-based calculations of the properties of materials and of simulations of processes in materials depends on: (1) the development of improved exchange-correlation functionals and advanced post-DFT methods and their implementation in highly efficient computer codes, (2) the development of methods allowing us to bridge the gaps in the temperature, pressure, time and length scales between the ab initio calculations and real-world experiments and (3) the extension of the functionality of these codes, permitting us to treat additional properties and new processes. In this paper we discuss the current status of techniques for performing quantum-based simulations on materials and present some illustrative examples of applications to complex quasiperiodic alloys, cluster-support interactions in microporous acid catalysts and magnetic nanostructures.

Grid-Based Projector Augmented Wave (GPAW) Implementation of Quantum Mechanics/Molecular Mechanics (QM/MM) Electrostatic Embedding and Application to a Solvated Diplatinum Complex.

PubMed

Dohn, A O; Jónsson, E Ö; Levi, G; Mortensen, J J; Lopez-Acevedo, O; Thygesen, K S; Jacobsen, K W; Ulstrup, J; Henriksen, N E; Møller, K B; Jónsson, H

2017-12-12

A multiscale density functional theory-quantum mechanics/molecular mechanics (DFT-QM/MM) scheme is presented, based on an efficient electrostatic coupling between the electronic density obtained from a grid-based projector augmented wave (GPAW) implementation of density functional theory and a classical potential energy function. The scheme is implemented in a general fashion and can be used with various choices for the descriptions of the QM or MM regions. Tests on H 2 O clusters, ranging from dimer to decamer show that no systematic energy errors are introduced by the coupling that exceeds the differences in the QM and MM descriptions. Over 1 ns of liquid water, Born-Oppenheimer QM/MM molecular dynamics (MD) are sampled combining 10 parallel simulations, showing consistent liquid water structure over the QM/MM border. The method is applied in extensive parallel MD simulations of an aqueous solution of the diplatinum [Pt 2 (P 2 O 5 H 2 ) 4 ] 4- complex (PtPOP), spanning a total time period of roughly half a nanosecond. An average Pt-Pt distance deviating only 0.01 Å from experimental results, and a ground-state Pt-Pt oscillation frequency deviating by <2% from experimental results were obtained. The simulations highlight a remarkable harmonicity of the Pt-Pt oscillation, while also showing clear signs of Pt-H hydrogen bonding and directional coordination of water molecules along the Pt-Pt axis of the complex.

Ion distribution in quaternary-ammonium-functionalized aromatic polymers: effects on the ionic clustering and conductivity of anion-exchange membranes.

PubMed

Weiber, E Annika; Jannasch, Patric

2014-09-01

A series of copoly(arylene ether sulfone)s that have precisely two, three, or four quaternary ammonium (QA) groups clustered directly on single phenylene rings along the backbone are studied as anion-exchange membranes. The copolymers are synthesized by condensation polymerizations that involve either di-, tri-, or tetramethylhydroquinone followed by virtually complete benzylic bromination using N-bromosuccinimide and quaternization with trimethylamine. This synthetic strategy allows excellent control and systematic variation of the local density and distribution of QA groups along the backbone. Small-angle X-ray scattering of these copolymers shows extensive ionic clustering, promoted by an increasing density of QA on the single phenylene rings. At an ion-exchange capacity (IEC) of 2.1 meq g(-1), the water uptake decreases with the increasing local density of QA groups. Moreover, at moderate IECs at 20 °C, the Br(-) conductivity of the densely functionalized copolymers is higher than a corresponding randomly functionalized polymer, despite the significantly higher water uptake of the latter. Thus, the location of multiple cations on single aromatic rings in the polymers facilitates the formation of a distinct percolating hydrophilic phase domain with a high ionic concentration to promote efficient anion transport, despite probable limitations by reduced ion dissociation. These findings imply a viable strategy to improve the performance of alkaline membrane fuel cells. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Application of CORSIKA Simulation Code to Study Lateral and Longitudinal Distribution of Fluorescence Light in Cosmic Ray Extensive Air Showers

NASA Astrophysics Data System (ADS)

Bagheri, Zahra; Davoudifar, Pantea; Rastegarzadeh, Gohar; Shayan, Milad

2017-03-01

In this paper, we used CORSIKA code to understand the characteristics of cosmic ray induced showers at extremely high energy as a function of energy, detector distance to shower axis, number, and density of secondary charged particles and the nature particle producing the shower. Based on the standard properties of the atmosphere, lateral and longitudinal development of the shower for photons and electrons has been investigated. Fluorescent light has been collected by the detector for protons, helium, oxygen, silicon, calcium and iron primary cosmic rays in different energies. So we have obtained a number of electrons per unit area, distance to the shower axis, shape function of particles density, percentage of fluorescent light, lateral distribution of energy dissipated in the atmosphere and visual field angle of detector as well as size of the shower image. We have also shown that location of highest percentage of fluorescence light is directly proportional to atomic number of elements. Also we have shown when the distance from shower axis increases and the shape function of particles density decreases severely. At the first stages of development, shower axis distance from detector is high and visual field angle is small; then with shower moving toward the Earth, angle increases. Overall, in higher energies, the fluorescent light method has more efficiency. The paper provides standard calibration lines for high energy showers which can be used to determine the nature of the particles.

Unraveling hadron structure with generalized parton distributions

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

Andrei Belitsky; Anatoly Radyushkin

2004-10-01

The recently introduced generalized parton distributions have emerged as a universal tool to describe hadrons in terms of quark and gluonic degrees of freedom. They combine the features of form factors, parton densities and distribution amplitudes - the functions used for a long time in studies of hadronic structure. Generalized parton distributions are analogous to the phase-space Wigner quasi-probability function of non-relativistic quantum mechanics which encodes full information on a quantum-mechanical system. We give an extensive review of main achievements in the development of this formalism. We discuss physical interpretation and basic properties of generalized parton distributions, their modeling andmore » QCD evolution in the leading and next-to-leading orders. We describe how these functions enter a wide class of exclusive reactions, such as electro- and photo-production of photons, lepton pairs, or mesons.« less

Singlet Orbital Ordering in Bilayer Sr_{3}Cr_{2}O_{7}.

PubMed

Jeanneau, Justin; Toulemonde, Pierre; Remenyi, Gyorgy; Sulpice, André; Colin, Claire; Nassif, Vivian; Suard, Emmanuelle; Salas Colera, Eduardo; Castro, Germán R; Gay, Frederic; Urdaniz, Corina; Weht, Ruben; Fevrier, Clement; Ralko, Arnaud; Lacroix, Claudine; Aligia, Armando A; Núñez-Regueiro, Manuel

2017-05-19

We perform an extensive study of Sr_{3}Cr_{2}O_{7}, the n=2 member of the Ruddlesden-Popper Sr_{n+1}Cr_{n}O_{3n+1} system. An antiferromagnetic ordering is clearly visible in the magnetization and the specific heat, which yields a huge transition entropy, Rln(6). By neutron diffraction as a function of temperature we have determined the antiferromagnetic structure that coincides with the one obtained from density functional theory calculations. It is accompanied by anomalous asymmetric distortions of the CrO_{6} octahedra. Strong coupling and Lanczos calculations on a derived Kugel-Khomskii Hamiltonian yield a simultaneous orbital and moment ordering. Our results favor an exotic ordered phase of orbital singlets not originated by frustration.

Development and validation of a high density SNP genotyping array for Atlantic salmon (Salmo salar).

PubMed

Houston, Ross D; Taggart, John B; Cézard, Timothé; Bekaert, Michaël; Lowe, Natalie R; Downing, Alison; Talbot, Richard; Bishop, Stephen C; Archibald, Alan L; Bron, James E; Penman, David J; Davassi, Alessandro; Brew, Fiona; Tinch, Alan E; Gharbi, Karim; Hamilton, Alastair

2014-02-06

Dense single nucleotide polymorphism (SNP) genotyping arrays provide extensive information on polymorphic variation across the genome of species of interest. Such information can be used in studies of the genetic architecture of quantitative traits and to improve the accuracy of selection in breeding programs. In Atlantic salmon (Salmo salar), these goals are currently hampered by the lack of a high-density SNP genotyping platform. Therefore, the aim of the study was to develop and test a dense Atlantic salmon SNP array. SNP discovery was performed using extensive deep sequencing of Reduced Representation (RR-Seq), Restriction site-Associated DNA (RAD-Seq) and mRNA (RNA-Seq) libraries derived from farmed and wild Atlantic salmon samples (n = 283) resulting in the discovery of > 400 K putative SNPs. An Affymetrix Axiom® myDesign Custom Array was created and tested on samples of animals of wild and farmed origin (n = 96) revealing a total of 132,033 polymorphic SNPs with high call rate, good cluster separation on the array and stable Mendelian inheritance in our sample. At least 38% of these SNPs are from transcribed genomic regions and therefore more likely to include functional variants. Linkage analysis utilising the lack of male recombination in salmonids allowed the mapping of 40,214 SNPs distributed across all 29 pairs of chromosomes, highlighting the extensive genome-wide coverage of the SNPs. An identity-by-state clustering analysis revealed that the array can clearly distinguish between fish of different origins, within and between farmed and wild populations. Finally, Y-chromosome-specific probes included on the array provide an accurate molecular genetic test for sex. This manuscript describes the first high-density SNP genotyping array for Atlantic salmon. This array will be publicly available and is likely to be used as a platform for high-resolution genetics research into traits of evolutionary and economic importance in salmonids and in aquaculture breeding programs via genomic selection.

Development and validation of a high density SNP genotyping array for Atlantic salmon (Salmo salar)

PubMed Central

2014-01-01

Background Dense single nucleotide polymorphism (SNP) genotyping arrays provide extensive information on polymorphic variation across the genome of species of interest. Such information can be used in studies of the genetic architecture of quantitative traits and to improve the accuracy of selection in breeding programs. In Atlantic salmon (Salmo salar), these goals are currently hampered by the lack of a high-density SNP genotyping platform. Therefore, the aim of the study was to develop and test a dense Atlantic salmon SNP array. Results SNP discovery was performed using extensive deep sequencing of Reduced Representation (RR-Seq), Restriction site-Associated DNA (RAD-Seq) and mRNA (RNA-Seq) libraries derived from farmed and wild Atlantic salmon samples (n = 283) resulting in the discovery of > 400 K putative SNPs. An Affymetrix Axiom® myDesign Custom Array was created and tested on samples of animals of wild and farmed origin (n = 96) revealing a total of 132,033 polymorphic SNPs with high call rate, good cluster separation on the array and stable Mendelian inheritance in our sample. At least 38% of these SNPs are from transcribed genomic regions and therefore more likely to include functional variants. Linkage analysis utilising the lack of male recombination in salmonids allowed the mapping of 40,214 SNPs distributed across all 29 pairs of chromosomes, highlighting the extensive genome-wide coverage of the SNPs. An identity-by-state clustering analysis revealed that the array can clearly distinguish between fish of different origins, within and between farmed and wild populations. Finally, Y-chromosome-specific probes included on the array provide an accurate molecular genetic test for sex. Conclusions This manuscript describes the first high-density SNP genotyping array for Atlantic salmon. This array will be publicly available and is likely to be used as a platform for high-resolution genetics research into traits of evolutionary and economic importance in salmonids and in aquaculture breeding programs via genomic selection. PMID:24524230

Optimization of self-catalyzed InAs Nanowires on flexible graphite for photovoltaic infrared photodetectors

PubMed Central

Anyebe, Ezekiel A.; Sandall, I.; Jin, Z. M.; Sanchez, Ana M.; Rajpalke, Mohana K.; Veal, Timothy D.; Cao, Y. C.; Li, H. D.; Harvey, R.; Zhuang, Q. D.

2017-01-01

The recent discovery of flexible graphene monolayers has triggered extensive research interest for the development of III-V/graphene functional hybrid heterostructures. In order to fully exploit their enormous potential in device applications, it is essential to optimize epitaxial growth for the precise control of nanowire geometry and density. Herein, we present a comprehensive growth study of InAs nanowires on graphitic substrates by molecular beam epitaxy. Vertically well-aligned and thin InAs nanowires with high yield were obtained in a narrow growth temperature window of 420–450 °C within a restricted domain of growth rate and V/III flux ratio. The graphitic substrates enable high nanowire growth rates, which is favourable for cost-effective device fabrication. A relatively low density of defects was observed. We have also demonstrated InAs-NWs/graphite heterojunction devices exhibiting rectifying behaviour. Room temperature photovoltaic response with a cut-off wavelength of 3.4 μm was demonstrated. This elucidates a promising route towards the monolithic integration of InAs nanowires with graphite for flexible and functional hybrid devices. PMID:28393845

Capillary wave Hamiltonian for the Landau-Ginzburg-Wilson density functional

NASA Astrophysics Data System (ADS)

Chacón, Enrique; Tarazona, Pedro

2016-06-01

We study the link between the density functional (DF) formalism and the capillary wave theory (CWT) for liquid surfaces, focused on the Landau-Ginzburg-Wilson (LGW) model, or square gradient DF expansion, with a symmetric double parabola free energy, which has been extensively used in theoretical studies of this problem. We show the equivalence between the non-local DF results of Parry and coworkers and the direct evaluation of the mean square fluctuations of the intrinsic surface, as is done in the intrinsic sampling method for computer simulations. The definition of effective wave-vector dependent surface tensions is reviewed and we obtain new proposals for the LGW model. The surface weight proposed by Blokhuis and the surface mode analysis proposed by Stecki provide consistent and optimal effective definitions for the extended CWT Hamiltonian associated to the DF model. A non-local, or coarse-grained, definition of the intrinsic surface provides the missing element to get the mesoscopic surface Hamiltonian from the molecular DF description, as had been proposed a long time ago by Dietrich and coworkers.

Statistics of initial density perturbations in heavy ion collisions and their fluid dynamic response

NASA Astrophysics Data System (ADS)

Floerchinger, Stefan; Wiedemann, Urs Achim

2014-08-01

An interesting opportunity to determine thermodynamic and transport properties in more detail is to identify generic statistical properties of initial density perturbations. Here we study event-by-event fluctuations in terms of correlation functions for two models that can be solved analytically. The first assumes Gaussian fluctuations around a distribution that is fixed by the collision geometry but leads to non-Gaussian features after averaging over the reaction plane orientation at non-zero impact parameter. In this context, we derive a three-parameter extension of the commonly used Bessel-Gaussian event-by-event distribution of harmonic flow coefficients. Secondly, we study a model of N independent point sources for which connected n-point correlation functions of initial perturbations scale like 1 /N n-1. This scaling is violated for non-central collisions in a way that can be characterized by its impact parameter dependence. We discuss to what extent these are generic properties that can be expected to hold for any model of initial conditions, and how this can improve the fluid dynamical analysis of heavy ion collisions.

A review of theoretical study of graphene chemical vapor deposition synthesis on metals: nucleation, growth, and the role of hydrogen and oxygen

NASA Astrophysics Data System (ADS)

Rezwan Habib, Mohammad; Liang, Tao; Yu, Xuegong; Pi, Xiaodong; Liu, Yingchun; Xu, Mingsheng

2018-03-01

Graphene has attracted intense research interest due to its extraordinary properties and great application potential. Various methods have been proposed for the synthesis of graphene, among which chemical vapor deposition has drawn a great deal of attention for synthesizing large-area and high-quality graphene. Theoretical understanding of the synthesis mechanism is crucial for optimizing the experimental design for desired graphene production. In this review, we discuss the three fundamental steps of graphene synthesis in details, i.e. (1) decomposition of carbon feedstocks and formation of various active carbon species, (2) nucleation, and (3) attachment and extension. We provide a complete scenario of graphene synthesis on metal surfaces at atomistic level by means of density functional theory, molecular dynamics (MD), Monte Carlo (MC) and their combination and interface with other simulation methods such as quantum mechanical molecular dynamics, density functional tight binding molecular dynamics, and combination of MD and MC. We also address the latest investigation of the influences of the hydrogen and oxygen on the synthesis and the quality of the synthesized graphene.

Nuclear Fission: from more phenomenology and adjusted parameters to more fundamental theory and increased predictive power

NASA Astrophysics Data System (ADS)

Bulgac, Aurel; Jin, Shi; Magierski, Piotr; Roche, Kenneth; Schunck, Nicolas; Stetcu, Ionel

2017-11-01

Two major recent developments in theory and computational resources created the favorable conditions for achieving a microscopic description of fission dynamics in classically allowed regions of the collective potential energy surface, almost eighty years after its discovery in 1939 by Hahn and Strassmann [1]. The first major development was in theory, the extension of the Time-Dependent Density Functional Theory (TDDFT) [2-5] to superfluid fermion systems [6]. The second development was in computing, the emergence of powerful enough supercomputers capable of solving the complex systems of equations describing the time evolution in three dimensions without any restrictions of hundreds of strongly interacting nucleons. Thus the conditions have been created to renounce phenomenological models and incomplete microscopic treatments with uncontrollable approximations and/or assumptions in the description of the complex dynamics of fission. Even though the available nuclear energy density functionals (NEDFs) are phenomenological still, their accuracy is improving steadily and the prospects of being able to perform calculations of the nuclear fission dynamics and to predict many properties of the fission fragments, otherwise not possible to extract from experiments.

Toward the Prediction of Water Exchange Rates in Magnetic Resonance Imaging Contrast Agents: A Density Functional Theory Study.

PubMed

Regueiro-Figueroa, Martín; Platas-Iglesias, Carlos

2015-06-18

We present a theoretical investigation of Gd-Owater bonds in different complexes relevant as contrast agents in magnetic resonance imaging (MRI). The analysis of the Ln-Owater distances, electron density (ρBCP), and electron localization function (ELF) at the bond critical points of [Ln(DOTA)(H2O)](-) and [Ln(DTPA-BMA)(H2O)] indicates that the strength of the Ln-Owater bonds follows the order DTPA-BMA > DOTA (M isomer) > DOTA (m isomer). The ELF values decrease along the 4f period as the Ln-Owater bonds get shorter, in line with the labile capping bond phenomenon. Extension of these calculations to other Gd(3+) complexes allowed us to correlate the experimentally observed water exchange rates and the calculated ρBCP and ELF values. The water exchange reaction becomes faster as the Gd-Owater bonds are weakened, which is reflected in longer bond distances and lower values of ρBCP and ELF. DKH2 calculations show that the two coordinated water molecules may also have significantly different (17)O hyperfine coupling constants (HFCCs).

Capillary wave Hamiltonian for the Landau-Ginzburg-Wilson density functional.

PubMed

Chacón, Enrique; Tarazona, Pedro

2016-06-22

We study the link between the density functional (DF) formalism and the capillary wave theory (CWT) for liquid surfaces, focused on the Landau-Ginzburg-Wilson (LGW) model, or square gradient DF expansion, with a symmetric double parabola free energy, which has been extensively used in theoretical studies of this problem. We show the equivalence between the non-local DF results of Parry and coworkers and the direct evaluation of the mean square fluctuations of the intrinsic surface, as is done in the intrinsic sampling method for computer simulations. The definition of effective wave-vector dependent surface tensions is reviewed and we obtain new proposals for the LGW model. The surface weight proposed by Blokhuis and the surface mode analysis proposed by Stecki provide consistent and optimal effective definitions for the extended CWT Hamiltonian associated to the DF model. A non-local, or coarse-grained, definition of the intrinsic surface provides the missing element to get the mesoscopic surface Hamiltonian from the molecular DF description, as had been proposed a long time ago by Dietrich and coworkers.

Note: Formation of the nematic splay-bend in two-dimensional systems of bow-shaped particles

NASA Astrophysics Data System (ADS)

Karbowniczek, Paweł

2018-04-01

Recently, Tavarone et al. (J. Chem. Phys. 143, 114505 (2015)) discussed phase behavior of zig-zag and bow-shaped particles composed of three needles. The authors presented very interesting results of extensive Monte Carlo simulations with periodic boundary conditions in the constant-NVT and the constant-NPT ensembles. In addition to isotropic, nematic, and smectic phases, they identified a modulated nematic, which is actually the nematic splay-bend phase ($N_{SB}$), long-anticipated for bent-core systems (Europhys. Lett. 56, 247 (2001)). They also described isotropic-nematic and nematic-smectic transitions using Density Functional Theory in mean-field approximation. The authors, however, did not provided a theoretical description of the $N_{SB}$. Here, we present a simple theory of a phase transition to the $N_{SB}$ phase to fill the gap. In our study, we use Onsager-type Density Functional Theory with perfect order approximation and Meyer parametrization of modulated structures. We present results for arbitrary ratios of the length of central and side segments and opening angles of bow-shaped particles.

Indirect Validation of Probe Speed Data on Arterial Corridors

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

Eshragh, Sepideh; Young, Stanley E.; Sharifi, Elham

This study aimed to estimate the accuracy of probe speed data on arterial corridors on the basis of roadway geometric attributes and functional classification. It was assumed that functional class (medium and low) along with other road characteristics (such as weighted average of the annual average daily traffic, average signal density, average access point density, and average speed) were available as correlation factors to estimate the accuracy of probe traffic data. This study tested these factors as predictors of the fidelity of probe traffic data by using the results of an extensive validation exercise. This study showed strong correlations betweenmore » these geometric attributes and the accuracy of probe data when they were assessed by using average absolute speed error. Linear models were regressed to existing data to estimate appropriate models for medium- and low-type arterial corridors. The proposed models for medium- and low-type arterials were validated further on the basis of the results of a slowdown analysis. These models can be used to predict the accuracy of probe data indirectly in medium and low types of arterial corridors.« less

Locating structures and evolution pathways of reconstructed rutile TiO2(011) using genetic algorithm aided density functional theory calculations.

PubMed

Ding, Pan; Gong, Xue-Qing

2016-05-01

Titanium dioxide (TiO2) is an important metal oxide that has been used in many different applications. TiO2 has also been widely employed as a model system to study basic processes and reactions in surface chemistry and heterogeneous catalysis. In this work, we investigated the (011) surface of rutile TiO2 by focusing on its reconstruction. Density functional theory calculations aided by a genetic algorithm based optimization scheme were performed to extensively sample the potential energy surfaces of reconstructed rutile TiO2 structures that obey (2 × 1) periodicity. A lot of stable surface configurations were located, including the global-minimum configuration that was proposed previously. The wide variety of surface structures determined through the calculations performed in this work provide insight into the relationship between the atomic configuration of a surface and its stability. More importantly, several analytical schemes were proposed and tested to gauge the differences and similarities among various surface structures, aiding the construction of the complete pathway for the reconstruction process.

Challenges in Wireless System Integration as Enablers for Indoor Context Aware Environments

PubMed Central

Aguirre, Erik

2017-01-01

The advent of fully interactive environments within Smart Cities and Smart Regions requires the use of multiple wireless systems. In the case of user-device interaction, which finds multiple applications such as Ambient Assisted Living, Intelligent Transportation Systems or Smart Grids, among others, large amount of transceivers are employed in order to achieve anytime, anyplace and any device connectivity. The resulting combination of heterogeneous wireless network exhibits fundamental limitations derived from Coverage/Capacity relations, as a function of required Quality of Service parameters, required bit rate, energy restrictions and adaptive modulation and coding schemes. In this context, inherent transceiver density poses challenges in overall system operation, given by multiple node operation which increases overall interference levels. In this work, a deterministic based analysis applied to variable density wireless sensor network operation within complex indoor scenarios is presented, as a function of topological node distribution. The extensive analysis derives interference characterizations, both for conventional transceivers as well as wearables, which provide relevant information in terms of individual node configuration as well as complete network layout. PMID:28704963

Complete Mie-Gruneisen Equation of State (update)

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

Menikoff, Ralph

2016-03-14

The Mie-Gruneisen equation of state (EOS) is frequently used in hydro simulations to model solids at high pressure (up to a few Mb). It is an incomplete EOS characterized by a Gr¨uneisen coefficient, = -V (@eP)V , that is a function of only V . Expressions are derived for isentropes and isotherms. This enables the extension to a complete EOS. Thermodynamic consistency requires that the specific heat is a function of a single scaled-temperature. A complete extension is uniquely determined by the temperature dependence of the specific heat at a fixed reference density. In addition we show that if themore » domain of the EOS extends to T = 0 and the specific heat vanishes on the zero isotherm then a function of only V is equivalent to a specific heat with a single temperature scale. If the EOS domain does not include the zero isotherm, then a specific heat with a single temperature scale leads to a generalization of the Mie-Gr¨uneisen EOS in which the pressure is linear in both the specific energy and the temperature. This corresponds to the limiting case of two temperature scales with one of the scales in the high temperature limit. Such an EOS has previously been used to model liquid nitromethane.« less

The UK10K project identifies rare variants in health and disease.

PubMed

Walter, Klaudia; Min, Josine L; Huang, Jie; Crooks, Lucy; Memari, Yasin; McCarthy, Shane; Perry, John R B; Xu, ChangJiang; Futema, Marta; Lawson, Daniel; Iotchkova, Valentina; Schiffels, Stephan; Hendricks, Audrey E; Danecek, Petr; Li, Rui; Floyd, James; Wain, Louise V; Barroso, Inês; Humphries, Steve E; Hurles, Matthew E; Zeggini, Eleftheria; Barrett, Jeffrey C; Plagnol, Vincent; Richards, J Brent; Greenwood, Celia M T; Timpson, Nicholas J; Durbin, Richard; Soranzo, Nicole

2015-10-01

The contribution of rare and low-frequency variants to human traits is largely unexplored. Here we describe insights from sequencing whole genomes (low read depth, 7×) or exomes (high read depth, 80×) of nearly 10,000 individuals from population-based and disease collections. In extensively phenotyped cohorts we characterize over 24 million novel sequence variants, generate a highly accurate imputation reference panel and identify novel alleles associated with levels of triglycerides (APOB), adiponectin (ADIPOQ) and low-density lipoprotein cholesterol (LDLR and RGAG1) from single-marker and rare variant aggregation tests. We describe population structure and functional annotation of rare and low-frequency variants, use the data to estimate the benefits of sequencing for association studies, and summarize lessons from disease-specific collections. Finally, we make available an extensive resource, including individual-level genetic and phenotypic data and web-based tools to facilitate the exploration of association results.

Full self-consistency in the Fermi-orbital self-interaction correction

NASA Astrophysics Data System (ADS)

Yang, Zeng-hui; Pederson, Mark R.; Perdew, John P.

2017-05-01

The Perdew-Zunger self-interaction correction cures many common problems associated with semilocal density functionals, but suffers from a size-extensivity problem when Kohn-Sham orbitals are used in the correction. Fermi-Löwdin-orbital self-interaction correction (FLOSIC) solves the size-extensivity problem, allowing its use in periodic systems and resulting in better accuracy in finite systems. Although the previously published FLOSIC algorithm Pederson et al., J. Chem. Phys. 140, 121103 (2014)., 10.1063/1.4869581 appears to work well in many cases, it is not fully self-consistent. This would be particularly problematic for systems where the occupied manifold is strongly changed by the correction. In this paper, we demonstrate a different algorithm for FLOSIC to achieve full self-consistency with only marginal increase of computational cost. The resulting total energies are found to be lower than previously reported non-self-consistent results.

Kullback-Leibler divergence measure of intermittency: Application to turbulence

NASA Astrophysics Data System (ADS)

Granero-Belinchón, Carlos; Roux, Stéphane G.; Garnier, Nicolas B.

2018-01-01

For generic systems exhibiting power law behaviors, and hence multiscale dependencies, we propose a simple tool to analyze multifractality and intermittency, after noticing that these concepts are directly related to the deformation of a probability density function from Gaussian at large scales to non-Gaussian at smaller scales. Our framework is based on information theory and uses Shannon entropy and Kullback-Leibler divergence. We provide an extensive application to three-dimensional fully developed turbulence, seen here as a paradigmatic complex system where intermittency was historically defined and the concepts of scale invariance and multifractality were extensively studied and benchmarked. We compute our quantity on experimental Eulerian velocity measurements, as well as on synthetic processes and phenomenological models of fluid turbulence. Our approach is very general and does not require any underlying model of the system, although it can probe the relevance of such a model.

Continental extension, magmatism and elevation; formal relations and rules of thumb

USGS Publications Warehouse

Lachenbruch, A.H.; Morgan, P.

1990-01-01

To investigate simplified relations between elevation and the extensional, magmatic and thermal processes that influence lithosphere buoyancy, we assume that the lithosphere floats on an asthenosphere of uniform density and has no flexural strength. A simple graph relating elevation to lithosphere density and thickness provides an overview of expectable conditions around the earth and a simple test for consistancy of continental and oceanic lithosphere models. The mass-balance relations yield simple general rules for estimating elevation changes caused by various tectonic, magmatic and thermal processes without referring to detailed models. The rules are general because they depend principally on buoyancy, which under our assumptions is specified by elevation, a known quantity; they do not generally require a knowledge of lithosphere thickness and density. The elevation of an extended terrain contains important information on its tectonic and magmatic history. In the Great Basin where Cenozoic extension is estimated to be 100%, the present high mean elevation ( ~ 1.75 km) probably requires substantial low-density magmatic contributions to the extending lithosphere. The elevation cannot be reasonably explained solely as the buoyant residue of a very high initial terrane, or of a lithosphere that was initially very thick and subsequently delaminated and heated. Even models with a high initial elevation typically call for 10 km or so of accumulated magmatic material of near-crustal density. To understand the evolution of the Great Basin, it is important to determine whether such intruded material is present; some could replenish the stretching crust by underplating and crustal intrusion and some might reside in the upper mantle. The elevation maintained or approached by an intruded extending lithosphere depends on the ratio B of how fast magma is supplied from the asthenosphere ( b km/Ma) to how fast the lithosphere spreads the magma out by extension (?? Ma-1). For a surface maintained 2 1 2km below sea level (e.g., an ocean ridge) B is about 5 km; for continental extension the ratio may be much greater. The frequent association of volcanism with continental extension, the high elevation (and buoyancy) of some appreciably extended terrains, and the oceanic spreading analog all suggest that magmatism may play an important role in continental extension. Better estimates of total extension and elevation change in extended regions can help to identify that role. ?? 1990.

Numerical Experiments on the Role of the Lower Crust in the Development of Extension-driven Gneiss Domes

NASA Astrophysics Data System (ADS)

Korchinski, M.; Rey, P. F.; Teyssier, C. P.; Mondy, L. S.; Whitney, D.

2016-12-01

Flow of orogenic crust is a critical geodynamic process in the chemical and physical evolution of continents. Deeply sourced rocks are transported to the near surface within gneiss domes, which are ubiquitous features in orogens and extensional regions. Exhumation of material within a gneiss dome can occur as the result of tectonic stresses, where material moves into space previously occupied by the shallow crust as the result of extension localized along a detachment system. Gravitationally driven flow may also contribute to exhumation. This research addresses how physical parameters (density, viscosity) of the deep crust (base of brittle crust to Moho) impact (1) the localization of extension in the shallow crust, and (2) the flow of deep crust by tectonic and non-tectonic stresses. We present 2D numerical experiments in which the density (2900-3100 kg m-3) and viscosity (1e19-1e21 Pa s) of the deep crust are systematically varied. Lateral and vertical transport of deep crustal rocks toward the gneiss dome occurs across the entire parameter space. A low viscosity deep crust yields localized extension in the upper crust and crustal-scale upward flow; this case produces the highest exhumation. A high viscosity deep crust results in distributed thinning of the upper crust, which suppresses upward mass transport. The density of the deep crust has only a second-order effect on the shallow crust extension regime. We capture the flow field generated after the cessation of extension to evaluate mass transport that is not driven by tectonic stresses. Upward transport of material within the gneiss dome is present across the entire parameter space. In the case of a low-viscosity deep crust, horizontal flow occurs adjacent to the dome above the Moho; this flow is an order of magnitude higher than that within the dome. Density variations do not drastically alter the flow field in the low viscosity lower crust. However, a high density and high viscosity deep crust results in boudinage of the whole crust, which generates significant upward flow from the buoyant asthenosphere.

Single-molecule analysis of the major glycopolymers of pathogenic and non-pathogenic yeast cells

NASA Astrophysics Data System (ADS)

El-Kirat-Chatel, Sofiane; Beaussart, Audrey; Alsteens, David; Sarazin, Aurore; Jouault, Thierry; Dufrêne, Yves F.

2013-05-01

Most microbes are coated with carbohydrates that show remarkable structural variability and play a crucial role in mediating microbial-host interactions. Understanding the functions of cell wall glycoconjugates requires detailed knowledge of their molecular organization, diversity and heterogeneity. Here we use atomic force microscopy (AFM) with tips bearing specific probes (lectins, antibodies) to analyze the major glycopolymers of pathogenic and non-pathogenic yeast cells at molecular resolution. We show that non-ubiquitous β-1,2-mannans are largely exposed on the surface of native cells from pathogenic Candida albicans and C. glabrata, the former species displaying the highest glycopolymer density and extensions. We also find that chitin, a major component of the inner layer of the yeast cell wall, is much more abundant in C. albicans. These differences in molecular properties, further supported by flow cytometry measurements, may play an important role in strengthening cell wall mechanics and immune interactions. This study demonstrates that single-molecule AFM, combined with immunological and fluorescence methods, is a powerful platform in fungal glycobiology for probing the density, distribution and extension of specific cell wall glycoconjugates. In nanomedicine, we anticipate that this new form of AFM-based nanoglycobiology will contribute to the development of sugar-based drugs, immunotherapeutics, vaccines and diagnostics.

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

Isler, R.C.; Colchin, R.J.; Wade, M.R.

Collapses of stored energy are typically observed in low-density ({anti n}{sub e} {approx} 10{sup 13} cm{sup {minus}3}) extensively gettered ATF plasmas when the electron density rises to the ECH cutoff point, and the central heating is supplied only by neutral- beam-injection (NBI). However, the decline of stored energy can be avoided if the density is raised rapidly to about 5 {times} 10{sup 13} cm{sup {minus}3}. Three mechanisms have been proposed to explain the collapses: (1) impurity radiation, (2) excitation of an electron instability driven by the neutral beams, or (3) poor coupling of the beam ions to the thermal plasmas.more » Detailed spectroscopic studies of plasma cleanliness as a function of the gettering procedure have shown that radiation is an unlikely candidate for initiating collapses, although it may become an important loss mechanism once the electron temperature has fallen to a low level. No specific electron instability has yet been identified with injection, but recent experimental and computational work indicates that losses by shinethrough and charge exchange strongly influence the evolution of low-density plasmas. This report discusses the beam particle losses, thermal ions, and the evolution of radiation profiles.« less

A molecular dynamics study of ambient and high pressure phases of silica: structure and enthalpy variation with molar volume.

PubMed

Rajappa, Chitra; Sringeri, S Bhuvaneshwari; Subramanian, Yashonath; Gopalakrishnan, J

2014-06-28

Extensive molecular dynamics studies of 13 different silica polymorphs are reported in the isothermal-isobaric ensemble with the Parrinello-Rahman variable shape simulation cell. The van Beest-Kramer-van Santen (BKS) potential is shown to predict lattice parameters for most phases within 2%-3% accuracy, as well as the relative stabilities of different polymorphs in agreement with experiment. Enthalpies of high-density polymorphs - CaCl2-type, α-PbO2-type, and pyrite-type - for which no experimental data are available as yet, are predicted here. Further, the calculated enthalpies exhibit two distinct regimes as a function of molar volume-for low and medium-density polymorphs, it is almost independent of volume, while for high-pressure phases a steep dependence is seen. A detailed analysis indicates that the increased short-range contributions to enthalpy in the high-density phases arise not only from an increased coordination number of silicon but also shorter Si-O bond lengths. Our results indicate that amorphous phases of silica exhibit better optimization of short-range interactions than crystalline phases at the same density while the magnitude of Coulombic contributions is lower in the amorphous phase.

A random-walk algorithm for modeling lithospheric density and the role of body forces in the evolution of the Midcontinent Rift

USGS Publications Warehouse

Levandowski, William Brower; Boyd, Oliver; Briggs, Richard; Gold, Ryan D.

2015-01-01

We test this algorithm on the Proterozoic Midcontinent Rift (MCR), north-central U.S. The MCR provides a challenge because it hosts a gravity high overlying low shear-wave velocity crust in a generally flat region. Our initial density estimates are derived from a seismic velocity/crustal thickness model based on joint inversion of surface-wave dispersion and receiver functions. By adjusting these estimates to reproduce gravity and topography, we generate a lithospheric-scale model that reveals dense middle crust and eclogitized lowermost crust within the rift. Mantle lithospheric density beneath the MCR is not anomalous, consistent with geochemical evidence that lithospheric mantle was not the primary source of rift-related magmas and suggesting that extension occurred in response to far-field stress rather than a hot mantle plume. Similarly, the subsequent inversion of normal faults resulted from changing far-field stress that exploited not only warm, recently faulted crust but also a gravitational potential energy low in the MCR. The success of this density modeling algorithm in the face of such apparently contradictory geophysical properties suggests that it may be applicable to a variety of tectonic and geodynamic problems. 

Production of a high-efficiency TILLING population through polyploidization.

PubMed

Tsai, Helen; Missirian, Victor; Ngo, Kathie J; Tran, Robert K; Chan, Simon R; Sundaresan, Venkatesan; Comai, Luca

2013-04-01

Targeting Induced Local Lesions in Genomes (TILLING) provides a nontransgenic method for reverse genetics that is widely applicable, even in species where other functional resources are missing or expensive to build. The efficiency of TILLING, however, is greatly facilitated by high mutation density. Species vary in the number of mutations induced by comparable mutagenic treatments, suggesting that genetic background may affect the response. Allopolyploid species have often yielded higher mutation density than diploids. To examine the effect of ploidy, we autotetraploidized the Arabidopsis (Arabidopsis thaliana) ecotype Columbia, whose diploid has been used for TILLING extensively, and mutagenized it with 50 mm ethylmethane sulfonate. While the same treatment sterilized diploid Columbia, the tetraploid M1 plants produced good seed. To determine the mutation density, we searched 528 individuals for induced mutations in 15 genes for which few or no knockout alleles were previously available. We constructed tridimensional pools from the genomic DNA of M2 plants, amplified target DNA, and subjected them to Illumina sequencing. The results were analyzed with an improved version of the mutation detection software CAMBa that accepts any pooling scheme. This small population provided a rich resource with approximately 25 mutations per queried 1.5-kb fragment, including on average four severe missense and 1.3 truncation mutations. The overall mutation density of 19.4 mutations Mb(-1) is 4 times that achieved in the corresponding diploid accession, indicating that genomic redundancy engenders tolerance to high mutation density. Polyploidization of diploids will allow the production of small populations, such as less than 2,000, that provide allelic series from knockout to mild loss of function for virtually all genes.

Theoretical investigation of structures and energetics of sodium adatom and its dimer on graphene: DFT study

NASA Astrophysics Data System (ADS)

Kaur, Gagandeep; Gupta, Shuchi; Rani, Pooja; Dharamvir, Keya

2015-11-01

Extensive ab initio calculations have been performed to study the energetics of a sodium (Na) atom and its dimer adsorbed on graphene using the SIESTA package Soler et al. (2002) [1] which works within a DFT(density functional theory)-GGA (generalized gradient approximation) pseudopotential framework. The adsorption energy, geometry, charge transfer, ionization potential and density of states (DOS), partial density states (PDOS) of adatom/dimer-graphene system have been calculated. After considering various sites for adsorption of Na on graphene, the center of a hexagonal ring of carbon atoms is found to be the preferred site of adsorption while the Na2 dimer prefers to rest parallel to the graphene sheet. We find insignificant energy differences among adsorption configurations involving different possible sites in parallel orientation, which implies high mobility of the dimer on the graphene sheet. We also notice only a slight distortion of the graphene sheet perpendicular to its plane upon adatom adsorption. However, some lateral displacements seen are more perceptible. Summary The adsorption energy, geometry, charge transfer, ionization potential and density of states (DOS) and PDOS of adatom/dimer-graphene system have been calculated using SIESTA package Soler et al. (2002) [1] which works within a DFT(density functional theory)-GGA (generalized gradient approximation) pseudopotential framework. Preferred site for adsorption of a sodium atom on graphene is the hollow site. For the Na dimer adsorption, we found that horizontal orientation is favored over the vertical one. From DOS plots, it is clear that graphene's states are nearly unaffected by the adsorption of Na adatom and Interaction between sodium and graphene is predominantly ionic

Stretchable and semitransparent conductive hybrid hydrogels for flexible supercapacitors.

PubMed

Hao, Guang-Ping; Hippauf, Felix; Oschatz, Martin; Wisser, Florian M; Leifert, Annika; Nickel, Winfried; Mohamed-Noriega, Nasser; Zheng, Zhikun; Kaskel, Stefan

2014-07-22

Conductive polymers showing stretchable and transparent properties have received extensive attention due to their enormous potential in flexible electronic devices. Here, we demonstrate a facile and smart strategy for the preparation of structurally stretchable, electrically conductive, and optically semitransparent polyaniline-containing hybrid hydrogel networks as electrode, which show high-performances in supercapacitor application. Remarkably, the stability can extend up to 35,000 cycles at a high current density of 8 A/g, because of the combined structural advantages in terms of flexible polymer chains, highly interconnected pores, and excellent contact between the host and guest functional polymer phase.

An operational modal analysis method in frequency and spatial domain

NASA Astrophysics Data System (ADS)

Wang, Tong; Zhang, Lingmi; Tamura, Yukio

2005-12-01

A frequency and spatial domain decomposition method (FSDD) for operational modal analysis (OMA) is presented in this paper, which is an extension of the complex mode indicator function (CMIF) method for experimental modal analysis (EMA). The theoretical background of the FSDD method is clarified. Singular value decomposition is adopted to separate the signal space from the noise space. Finally, an enhanced power spectrum density (PSD) is proposed to obtain more accurate modal parameters by curve fitting in the frequency domain. Moreover, a simulation case and an application case are used to validate this method.

Convection-driven tectonics on Venus

NASA Astrophysics Data System (ADS)

Phillips, R. J.

1990-02-01

An analysis is presented of convective stress coupling to an elastic lithosphere as applied to Venus. Theoretical solutions are introduced for the response of a mathematically thick elastic plate overlying a Newtonian viscous medium with an exponential depth dependence of viscosity, and a Green's function solution is obtained for the viscous flow driven by a harmonic density distribution at a specified depth. An elastic-plastic analysis is carried out for the deformation of a model Venus lithosphere. The results predict that dynamic uplift of Venusian topography must be accompanied by extensive brittle failure and viscous flow in the lithosphere.

Energy Dependence of Directed Flow over a Wide Range of Pseudorapidity in Au+Au Collisions at the BNL Relativistic Heavy Ion Collider

NASA Astrophysics Data System (ADS)

Back, B. B.; Baker, M. D.; Ballintijn, M.; Barton, D. S.; Betts, R. R.; Bickley, A. A.; Bindel, R.; Budzanowski, A.; Busza, W.; Carroll, A.; Chai, Z.; Decowski, M. P.; García, E.; Gburek, T.; George, N.; Gulbrandsen, K.; Gushue, S.; Halliwell, C.; Hamblen, J.; Hauer, M.; Heintzelman, G. A.; Henderson, C.; Hofman, D. J.; Hollis, R. S.; Hołyński, R.; Holzman, B.; Iordanova, A.; Johnson, E.; Kane, J. L.; Katzy, J.; Khan, N.; Kucewicz, W.; Kulinich, P.; Kuo, C. M.; Lin, W. T.; Manly, S.; McLeod, D.; Mignerey, A. C.; Nouicer, R.; Olszewski, A.; Pak, R.; Park, I. C.; Pernegger, H.; Reed, C.; Remsberg, L. P.; Reuter, M.; Roland, C.; Roland, G.; Rosenberg, L.; Sagerer, J.; Sarin, P.; Sawicki, P.; Seals, H.; Sedykh, I.; Skulski, W.; Smith, C. E.; Stankiewicz, M. A.; Steinberg, P.; Stephans, G. S. F.; Sukhanov, A.; Tang, J.-L.; Tonjes, M. B.; Trzupek, A.; Vale, C.; van Nieuwenhuizen, G. J.; Vaurynovich, S. S.; Verdier, R.; Veres, G. I.; Wenger, E.; Wolfs, F. L. H.; Wosiek, B.; Woźniak, K.; Wuosmaa, A. H.; Wysłouch, B.

2006-07-01

We report on measurements of directed flow as a function of pseudorapidity in Au+Au collisions at energies of sNN=19.6, 62.4, 130 and 200 GeV as measured by the PHOBOS detector at the BNL Relativistic Heavy Ion Collider. These results are particularly valuable because of the extensive, continuous pseudorapidity coverage of the PHOBOS detector. There is no significant indication of structure near midrapidity and the data surprisingly exhibit extended longitudinal scaling similar to that seen for elliptic flow and charged particle pseudorapidity density.

Scale matters

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

Margolin, L. G.

The applicability of Navier–Stokes equations is limited to near-equilibrium flows in which the gradients of density, velocity and energy are small. Here I propose an extension of the Chapman–Enskog approximation in which the velocity probability distribution function (PDF) is averaged in the coordinate phase space as well as the velocity phase space. I derive a PDF that depends on the gradients and represents a first-order generalization of local thermodynamic equilibrium. I then integrate this PDF to derive a hydrodynamic model. Finally, I discuss the properties of that model and its relation to the discrete equations of computational fluid dynamics.

Scale matters

DOE PAGES

Margolin, L. G.

2018-03-19

The applicability of Navier–Stokes equations is limited to near-equilibrium flows in which the gradients of density, velocity and energy are small. Here I propose an extension of the Chapman–Enskog approximation in which the velocity probability distribution function (PDF) is averaged in the coordinate phase space as well as the velocity phase space. I derive a PDF that depends on the gradients and represents a first-order generalization of local thermodynamic equilibrium. I then integrate this PDF to derive a hydrodynamic model. Finally, I discuss the properties of that model and its relation to the discrete equations of computational fluid dynamics.

Supramolecular network through Nsbnd H…O, Osbnd H…O and Csbnd H…O hydrogen bonding interaction and density functional theory studies of 4-methylanilinium-3-carboxy-4-hydroxybenzenesulphonate crystal

NASA Astrophysics Data System (ADS)

Rajkumar, M.; Muthuraja, P.; Dhandapani, M.; Chandramohan, A.

2018-02-01

By utilizing the hydrogen bonding strategy, 4-methylanilinium-3-hydroxy-4-corboxy-benzenesulphonate (4MABS), an organic proton transfer molecular salt was synthesized and single crystals of it were successfully grown by slow solvent evaporation solution growth technique at ambient temperature. The 1H and 13C NMR spectra were recorded to establish the molecular structure of the title salt. The single crystal XRD analysis reveals that the title salt crystallizes in monoclinic crystal system with centrosymmetric space group, P21/n. Further, the title salt involves extensive intermolecular Nsbnd H…O, Osbnd H…O and Csbnd H…O as well as intramolecular Osbnd H…O hydrogen bonding interactions to construct supramolecular architecture. All quantum chemical calculations were performed at the level of density functional theory (DFT) with B3LYP functional using 6-311G (d,p) basis atomic set. The photoluminescence spectrum was recorded to explore the emission property of the title crystal. The presence of the various vibrational modes and functional groups in the synthesized salt was confirmed by FT-IR studies. The thermal behaviour of title crystal was established employing TG/DTA analyses. The mechanical properties of the grown crystal were determined by Vicker's microhardness studies. Dielectric measurements were carried out on the grown crystal at a different temperature to evaluate electrical properties.

Reactant conversion in homogeneous turbulence: Mathematical modeling, computational validations and practical applications

NASA Technical Reports Server (NTRS)

Madnia, C. K.; Frankel, S. H.; Givi, P.

1992-01-01

Closed form analytical expressions are obtained for predicting the limited rate of reactant conversion in a binary reaction of the type F + rO yields (1 + r) Product in unpremixed homogeneous turbulence. These relations are obtained by means of a single point Probability Density Function (PDF) method based on the Amplitude Mapping Closure. It is demonstrated that with this model, the maximum rate of the reactants' decay can be conveniently expressed in terms of definite integrals of the Parabolic Cylinder Functions. For the cases with complete initial segregation, it is shown that the results agree very closely with those predicted by employing a Beta density of the first kind for an appropriately defined Shvab-Zeldovich scalar variable. With this assumption, the final results can also be expressed in terms of closed form analytical expressions which are based on the Incomplete Beta Functions. With both models, the dependence of the results on the stoichiometric coefficient and the equivalence ratio can be expressed in an explicit manner. For a stoichiometric mixture, the analytical results simplify significantly. In the mapping closure, these results are expressed in terms of simple trigonometric functions. For the Beta density model, they are in the form of Gamma Functions. In all the cases considered, the results are shown to agree well with data generated by Direct Numerical Simulations (DNS). Due to the simplicity of these expressions and because of nice mathematical features of the Parabolic Cylinder and the Incomplete Beta Functions, these models are recommended for estimating the limiting rate of reactant conversion in homogeneous reacting flows. These results also provide useful insights in assessing the extent of validity of turbulence closures in the modeling of unpremixed reacting flows. Some discussions are provided on the extension of the model for treating more complicated reacting systems including realistic kinetics schemes and multi-scalar mixing with finite rate chemical reactions in more complex configurations.

Background oriented schlieren in a density stratified fluid.

PubMed

Verso, Lilly; Liberzon, Alex

2015-10-01

Non-intrusive quantitative fluid density measurement methods are essential in the stratified flow experiments. Digital imaging leads to synthetic schlieren methods in which the variations of the index of refraction are reconstructed computationally. In this study, an extension to one of these methods, called background oriented schlieren, is proposed. The extension enables an accurate reconstruction of the density field in stratified liquid experiments. Typically, the experiments are performed by the light source, background pattern, and the camera positioned on the opposite sides of a transparent vessel. The multimedia imaging through air-glass-water-glass-air leads to an additional aberration that destroys the reconstruction. A two-step calibration and image remapping transform are the key components that correct the images through the stratified media and provide a non-intrusive full-field density measurements of transparent liquids.

New method to incorporate Type B uncertainty into least-squares procedures in radionuclide metrology.

PubMed

Han, Jubong; Lee, K B; Lee, Jong-Man; Park, Tae Soon; Oh, J S; Oh, Pil-Jei

2016-03-01

We discuss a new method to incorporate Type B uncertainty into least-squares procedures. The new method is based on an extension of the likelihood function from which a conventional least-squares function is derived. The extended likelihood function is the product of the original likelihood function with additional PDFs (Probability Density Functions) that characterize the Type B uncertainties. The PDFs are considered to describe one's incomplete knowledge on correction factors being called nuisance parameters. We use the extended likelihood function to make point and interval estimations of parameters in the basically same way as the least-squares function used in the conventional least-squares method is derived. Since the nuisance parameters are not of interest and should be prevented from appearing in the final result, we eliminate such nuisance parameters by using the profile likelihood. As an example, we present a case study for a linear regression analysis with a common component of Type B uncertainty. In this example we compare the analysis results obtained from using our procedure with those from conventional methods. Copyright © 2015. Published by Elsevier Ltd.

Crossover from incoherent to coherent phonon scattering in epitaxial oxide superlattices.

PubMed

Ravichandran, Jayakanth; Yadav, Ajay K; Cheaito, Ramez; Rossen, Pim B; Soukiassian, Arsen; Suresha, S J; Duda, John C; Foley, Brian M; Lee, Che-Hui; Zhu, Ye; Lichtenberger, Arthur W; Moore, Joel E; Muller, David A; Schlom, Darrell G; Hopkins, Patrick E; Majumdar, Arun; Ramesh, Ramamoorthy; Zurbuchen, Mark A

2014-02-01

Elementary particles such as electrons or photons are frequent subjects of wave-nature-driven investigations, unlike collective excitations such as phonons. The demonstration of wave-particle crossover, in terms of macroscopic properties, is crucial to the understanding and application of the wave behaviour of matter. We present an unambiguous demonstration of the theoretically predicted crossover from diffuse (particle-like) to specular (wave-like) phonon scattering in epitaxial oxide superlattices, manifested by a minimum in lattice thermal conductivity as a function of interface density. We do so by synthesizing superlattices of electrically insulating perovskite oxides and systematically varying the interface density, with unit-cell precision, using two different epitaxial-growth techniques. These observations open up opportunities for studies on the wave nature of phonons, particularly phonon interference effects, using oxide superlattices as model systems, with extensive applications in thermoelectrics and thermal management.

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

NASA Astrophysics Data System (ADS)

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

2013-06-01

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

A measurement and QCD analysis of the proton structure function F2 ( x, Q2) at HERA

NASA Astrophysics Data System (ADS)

Aid, S.; Andreev, V.; Andrieu, B.; Appuhn, R.-D.; Arpagaus, M.; Babaev, A.; Bähr, J.; Bán, J.; Ban, Y.; Baranov, P.; Barrelet, E.; Barschke, R.; Bartel, W.; Barth, M.; Bassler, U.; Beck, H. P.; Behrend, H.-J.; Belousov, A.; Berger, Ch.; Bernardi, G.; Bernet, R.; Bertrand-Coremans, G.; Besançoni, M.; Beyer, R.; Biddulph, P.; Bispham, P.; Bizot, J. C.; Blobel, V.; Borras, K.; Botterweck, F.; Boudry, V.; Braemer, A.; Braunschweig, W.; Brisson, V.; Bruncko, D.; Brune, C.; Buchholz, R.; Büngener, L.; BurgerF. W. Büsser, J.; Buniatian, A.; Burke, S.; Burton, M. J.; Buschhorn, G.; Campbell, A. J.; Carli, T.; Charles, F.; Charlet, M.; Clarke, D.; Clegg, A. B.; Clerbaux, B.; Cocks, S.; Contreras, J. G.; Cormack, C.; Coughlan, J. A.; Courau, A.; Cousinou, M.-C.; Cozzika, G.; Criegee, L.; Cussans, D. G.; Cvach, J.; Dagoret, S.; Dainton, J. B.; Dau, W. D.; Daum, K.; David, M.; Davis, C. L.; Delcourt, B.; De Roeck, A.; De Wolf, E. A.; Dirkmann, M.; Dixon, P.; Di Nezza, P.; Dlugosz, W.; Dollfus, C.; Dowell, J. D.; Dreis, H. B.; Droutskoi, A.; Düllmann, D.; Dünger, O.; Duhm, H.; Ebert, J.; Ebert, T. R.; Eckerlin, G.; Efremenko, V.; Egli, S.; Eichler, R.; Eisele, F.; Eisenhandler, E.; Ellison, R. J.; Elsen, E.; Erdmann, M.; Erdmann, W.; Evrard, E.; Fahr, A. B.; Favart, L.; Fedotov, A.; Feeken, D.; Felst, R.; Feltesse, J.; Ferencei, J.; Ferrarotto, F.; Flamm, K.; Fleischer, M.; Flieser, M.; Flügge, G.; Fomenko, A.; Fominykh, B.; Formánek, J.; Foster, J. M.; Franke, G.; Fretwurst, E.; Gabathuler, E.; Gabathuler, K.; Gaede, F.; Garvey, J.; Gayler, J.; Gebauer, M.; Gellrich, A.; Genzel, H.; Gerhards, R.; Glazov, A.; Goerlach, U.; Goerlich, L.; Gogitidze, N.; Goldberg, M.; Goldner, D.; Golec-Biernat, K.; Gonzalez-Pineiro, B.; Gorelov, I.; Grab, C.; Grässler, H.; Grässler, R.; Greenshaw, T.; Griffiths, R.; Grindhammer, G.; Gruber, A.; Gruber, C.; Haack, J.; Haidt, D.; Hajduk, L.; Hampel, M.; Haynes, W. J.; Heinzelmann, G.; Henderson, R. C. W.; Henschel, H.; Herynek, I.; Hess, M. F.; Hildesheim, W.; Hiller, K. H.; Hilton, C. D.; Hladký, J.; Hoeger, K. C.; Höppner, M.; Hoffmann, D.; Holtom, T.; Horisberger, R.; Hudgson, V. L.; Hütte, M.; Hufnagel, H.; Ibbotson, M.; Itterbeck, H.; Jacholkowska, A.; Jacobsson, C.; Jaffre, M.; Janoth, J.; Jansen, T.; Jönsson, L.; Johannsen, K.; Johnson, D. P.; Johnson, L.; Jung, H.; Kalmus, P. I. P.; Kander, M.; Kant, D.; Kaschowitz, R.; Kathage, U.; Katzy, J.; Kaufmann, H. H.; Kazarian, S.; Kenyon, I. R.; Kermiche, S.; Keuker, C.; Kiesling, C.; Klein, M.; Kleinwort, C.; Knies, G.; Köhler, T.; Köhne, J. H.; Kolanoski, H.; Kole, F.; Kolya, S. D.; Korbel, V.; Korn, M.; Kostka, P.; Kotelnikov, S. K.; Krämerkämper, T.; Krasny, M. W.; Krehbie, H.; Krücker, D.; Krüger, U.; Krüner-Marquis, U.; Küster, H.; Kuhlen, M.; Kurča, T.; Kurzhöfer, J.; Lacour, D.; Laforge, B.; Lander, R.; Landon, M. P. J.; Lange, W.; Langenegger, U.; Laporte, J.-F.; Lebedev, A.; Lehner, F.; Leverenz, C.; Levonian, S.; Ley, Ch.; Lindström, G.; Lindstroem, M.; Link, J.; Linsel, F.; Lipinski, J.; List, B.; Lobo, G.; Lohmander, H.; Lomas, J. W.; Lopez, G. C.; Lubimov, V.; Lüke, D.; Magnussen, N.; Malinovski, E.; Mani, S.; Maraček, R.; Marage, P.; Marks, J.; Marshall, R.; Martens, J.; Martin, G.; Martin, R.; Martyn, H.-U.; Martyniak, J.; Mavroidis, T.; Maxfield, S. J.; McMahon, S. J.; Mehta, A.; Meier, K.; Merz, T.; Meyer, A.; MeyerH. Meyer, A.; Meyer, J.; Meyer, P.-O.; Migliori, A.; Mikocki, S.; Milstead, D.; Moeck, J.; Moreau, F.; Morris, J. V.; Mroczko, E.; Müller, D.; Müller, G.; Müller, K.; Murín, P.; Nagovizin, V.; Nahnhauer, R.; Naroska, B.; Naumann, Th.; Newman, P. R.; Newton, D.; Neyret, D.; Nguyen, H. K.; Nicholls, T. C.; Niebergall, F.; Niebuhr, C.; Niedzballa, Ch.; Niggli, H.; Nisius, R.; Nowak, G.; Noyes, G. W.; Nyberg-Werther, M.; Oakden, M.; Oberlack, H.; Obrock, U.; Olsson, J. E.; Ozerov, D.; Palmen, P.; Panaro, E.; Panitch, A.; Pascaud, C.; Patel, G. D.; Pawletta, H.; Peppel, E.; Perez, E.; Phillips, J. P.; Pieuchot, A.; Pitzl, D.; Pope, G.; Prell, S.; Prosi, R.; Rabbertz, K.; Rädel, G.; Raupach, F.; Reimer, P.; Reinshagen, S.; Rick, H.; Riech, V.; Riedlberger, J.; Riepenhausen, F.; Riess, S.; Rizvi, E.; Robertson, S. M.; Robmann, P.; Roloff, H. E.; Roosen, R.; Rosenbauer, K.; Rostovtsev, A.; Rouse, F.; Royon, C.; Rüter, K.; Rusakov, S.; Rybicki, K.; Sahlmann, N.; Sankey, D. P. C.; Schacht, P.; Schiek, S.; Schleif, S.; Schleper, P.; von Schlippe, W.; Schmidt, D.; Schmidt, G.; Schöning, A.; Schröder, V.; Schuhmann, E.; Schwab, B.; Sefkow, F.; Seidel, M.; Sell, R.; Semenov, A.; Shekelyan, V.; Sheviakov, I.; Shtarkov, L. N.; Siegmon, G.; Siewert, U.; Sirois, Y.; Skillicorn, I. O.; Smirnov, P.; Smith, J. R.; Solochenko, V.; Soloviev, H.; Specka, A.; Spiekermann, J.; Spielman, S.; Spitzer, H.; Squinabl, F.; Starosta, R.; Steenbock, M.; Steffen, P.; Steinberg, R.; Steiner, H.; Stella, B.; Stellberger, A.; Stier, J.; Stiewe, J.; Stößlein, U.; Stolze, K.; Straumann, U.; Struczinski, W.; Sutton, J. P.; Tapprogge, S.; Taševský, M.; Tchernyshov, V.; Tchetchelnitski, S.; Theissen, J.; Thiebaux, C.; Thompson, G.; Truöl, P.; Turnau, J.; Tutas, J.; Uelkes, P.; Usik, A.; Valkár, S.; Valkárová, A.; Vallée, C.; Vandenplas, D.; Van Esch, P.; Van Mechelen, P.; Vazdik, Y.; Verrecchi, P.; Villet, G.; Wacker, K.; Wagener, A.; Wagener, M.; Walther, A.; Waugh, B.; Weber, G.; Weber, M.; Wegener, D.; Wegner, A.; Wengler, T.; Werner, M.; West, L. R.; Wilksen, T.; Willard, S.; Winde, M.; Winter, G.-G.; Wittek, C.; Wünsch, E.; Žáček, J.; Zarbock, D.; Zhang, Z.; Zhokin, A.; Zimmer, M.; Zomer, F.; Zsembery, J.; Zuber, K.; zurNedden, M.; Kaufmannxa, O.; H1 Collaboration

1996-02-01

A new measurement of the proton structure function F2 ( x, Q2) is reported for momentum transfers squared Q2 between ].5 GeV 2 and 5000 GeV 2 and for Bjorken x between 3 · 10 -5 and 0.32 using data collected by the HERA experiment H1 in 1994. The data represent an increase in statistics by a factor of ten with respect to the analysis of the 1993 data. Substantial extension of the kinematic range towards low Q2 and x has been achieved using dedicated data samples and events with initial state photon radiation. The structure function is found to increase significantly with decreasing x, even in the lowest accessible Q2 region. The data are well described by a Next to Leading Order QCD fit and the gluon density is extracted.

Multivariate η-μ fading distribution with arbitrary correlation model

NASA Astrophysics Data System (ADS)

Ghareeb, Ibrahim; Atiani, Amani

2018-03-01

An extensive analysis for the multivariate ? distribution with arbitrary correlation is presented, where novel analytical expressions for the multivariate probability density function, cumulative distribution function and moment generating function (MGF) of arbitrarily correlated and not necessarily identically distributed ? power random variables are derived. Also, this paper provides exact-form expression for the MGF of the instantaneous signal-to-noise ratio at the combiner output in a diversity reception system with maximal-ratio combining and post-detection equal-gain combining operating in slow frequency nonselective arbitrarily correlated not necessarily identically distributed ?-fading channels. The average bit error probability of differentially detected quadrature phase shift keying signals with post-detection diversity reception system over arbitrarily correlated and not necessarily identical fading parameters ?-fading channels is determined by using the MGF-based approach. The effect of fading correlation between diversity branches, fading severity parameters and diversity level is studied.

Extension and Density of Root Fillings and Post-operative Apical Radiolucencies in the Veterans Affairs Dental Longitudinal Study

PubMed Central

Zhong, Yan; Chasen, Joel; Yamanaka, Ryan; Garcia, Raul; Kaye, Elizabeth Krall; Kaufman, Jay S; Cai, Jianwen; Wilcosky, Tim; Trope, Martin; Caplan, Daniel J

2008-01-01

We evaluated the association between radiographically-assessed extension and density of root canal fillings and post-operative apical radiolucencies (AR) using data from 288 participants in the Veterans Affairs Dental Longitudinal Study. Study subjects were not VA patients; all received their medical and dental care in the private sector. Generalized Estimating Equations were used to account for multiple teeth within subjects and to control for covariates of interest. Defective root filling density was associated with increased odds of post-operative AR among teeth with no pre-operative AR (Odds Ratio=3.0, 95%CI=1.3–7.1), though pre-operative AR was the strongest risk factor for post-operative AR (Odds Ratio=29.2, 95%CI=13.6–63.0 among teeth with ideal density). Compared to well-extended root fillings, neither over- nor under-extended root fillings separately were related to post-operative AR, but when those two categories were collapsed into one “poorly-extended” category, poor extension was related to post-operative AR (Odds Ratio=1.8, 95%CI=1.1–3.2). PMID:18570982

Coastal habitats as surrogates for taxonomic, functional and trophic structures of benthic faunal communities.

PubMed

Törnroos, Anna; Nordström, Marie C; Bonsdorff, Erik

2013-01-01

Due to human impact, there is extensive degradation and loss of marine habitats, which calls for measures that incorporate taxonomic as well as functional and trophic aspects of biodiversity. Since such data is less easily quantifiable in nature, the use of habitats as surrogates or proxies for biodiversity is on the rise in marine conservation and management. However, there is a critical gap in knowledge of whether pre-defined habitat units adequately represent the functional and trophic structure of communities. We also lack comparisons of different measures of community structure in terms of both between- (β) and within-habitat (α) variability when accounting for species densities. Thus, we evaluated a priori defined coastal habitats as surrogates for traditional taxonomic, functional and trophic zoobenthic community structure. We focused on four habitats (bare sand, canopy-forming algae, seagrass above- and belowground), all easily delineated in nature and defined through classification systems. We analyzed uni- and multivariate data on species and trait diversity as well as stable isotope ratios of benthic macrofauna. A good fit between habitat types and taxonomic and functional structure was found, although habitats were more similar functionally. This was attributed to within-habitat heterogeneity so when habitat divisions matched the taxonomic structure, only bare sand was functionally distinct. The pre-defined habitats did not meet the variability of trophic structure, which also proved to differentiate on a smaller spatial scale. The quantification of trophic structure using species density only identified an epi- and an infaunal unit. To summarize the results we present a conceptual model illustrating the match between pre-defined habitat types and the taxonomic, functional and trophic community structure. Our results show the importance of including functional and trophic aspects more comprehensively in marine management and spatial planning.

Plasticity in skeletal characteristics of nursery-raised staghorn coral, Acropora cervicornis

USGS Publications Warehouse

Kuffner, Ilsa B.; Bartels, Erich; Stathakopoulos, Anastasios; Enochs, Ian C.; Kolodziej, Graham; Toth, Lauren; Manzello, Derek P.

2017-01-01

Staghorn coral, Acropora cervicornis, is a threatened species and the primary focus of western Atlantic reef restoration efforts to date. We compared linear extension, calcification rate, and skeletal density of nursery-raised A. cervicornis branches reared for 6 months either on blocks attached to substratum or hanging from PVC trees in the water column. We demonstrate that branches grown on the substratum had significantly higher skeletal density, measured using computerized tomography, and lower linear extension rates compared to water-column fragments. Calcification rates determined with buoyant weighing were not statistically different between the two grow-out methods, but did vary among coral genotypes. Whereas skeletal density and extension rates were plastic traits that depended on grow-out method, calcification rate was conserved. Our results show that the two rearing methods generate the same amount of calcium carbonate skeleton but produce colonies with different skeletal characteristics and suggest that there is genetically based variability in coral calcification performance.

Plasticity in skeletal characteristics of nursery-raised staghorn coral, Acropora cervicornis

NASA Astrophysics Data System (ADS)

Kuffner, Ilsa B.; Bartels, Erich; Stathakopoulos, Anastasios; Enochs, Ian C.; Kolodziej, G.; Toth, Lauren T.; Manzello, Derek P.

2017-09-01

Staghorn coral, Acropora cervicornis, is a threatened species and the primary focus of western Atlantic reef restoration efforts to date. We compared linear extension, calcification rate, and skeletal density of nursery-raised A. cervicornis branches reared for 6 months either on blocks attached to substratum or hanging from PVC trees in the water column. We demonstrate that branches grown on the substratum had significantly higher skeletal density, measured using computerized tomography, and lower linear extension rates compared to water-column fragments. Calcification rates determined with buoyant weighing were not statistically different between the two grow-out methods, but did vary among coral genotypes. Whereas skeletal density and extension rates were plastic traits that depended on grow-out method, calcification rate was conserved. Our results show that the two rearing methods generate the same amount of calcium carbonate skeleton but produce colonies with different skeletal characteristics and suggest that there is genetically based variability in coral calcification performance.

Elastic Behavior and Platelet Retraction in Low- and High-Density Fibrin Gels

PubMed Central

Wufsus, Adam R.; Rana, Kuldeepsinh; Brown, Andrea; Dorgan, John R.; Liberatore, Matthew W.; Neeves, Keith B.

2015-01-01

Fibrin is a biopolymer that gives thrombi the mechanical strength to withstand the forces imparted on them by blood flow. Importantly, fibrin is highly extensible, but strain hardens at low deformation rates. The density of fibrin in clots, especially arterial clots, is higher than that in gels made at plasma concentrations of fibrinogen (3–10 mg/mL), where most rheology studies have been conducted. Our objective in this study was to measure and characterize the elastic regimes of low (3–10 mg/mL) and high (30–100 mg/mL) density fibrin gels using shear and extensional rheology. Confocal microscopy of the gels shows that fiber density increases with fibrinogen concentration. At low strains, fibrin gels act as thermal networks independent of fibrinogen concentration. Within the low-strain regime, one can predict the mesh size of fibrin gels by the elastic modulus using semiflexible polymer theory. Significantly, this provides a link between gel mechanics and interstitial fluid flow. At moderate strains, we find that low-density fibrin gels act as nonaffine mechanical networks and transition to affine mechanical networks with increasing strains within the moderate regime, whereas high-density fibrin gels only act as affine mechanical networks. At high strains, the backbone of individual fibrin fibers stretches for all fibrin gels. Platelets can retract low-density gels by >80% of their initial volumes, but retraction is attenuated in high-density fibrin gels and with decreasing platelet density. Taken together, these results show that the nature of fibrin deformation is a strong function of fibrin fiber density, which has ramifications for the growth, embolization, and lysis of thrombi. PMID:25564864

Developing a tissue-engineered neural-electrical relay using encapsulated neuronal constructs on conducting polymer fibers.

PubMed

Cullen, D Kacy; R Patel, Ankur; Doorish, John F; Smith, Douglas H; Pfister, Bryan J

2008-12-01

Neural-electrical interface platforms are being developed to extracellularly monitor neuronal population activity. Polyaniline-based electrically conducting polymer fibers are attractive substrates for sustained functional interfaces with neurons due to their flexibility, tailored geometry and controlled electro-conductive properties. In this study, we addressed the neurobiological considerations of utilizing small diameter (<400 microm) fibers consisting of a blend of electrically conductive polyaniline and polypropylene (PA-PP) as the backbone of encapsulated tissue-engineered neural-electrical relays. We devised new approaches to promote survival, adhesion and neurite outgrowth of primary dorsal root ganglion neurons on PA-PP fibers. We attained a greater than ten-fold increase in the density of viable neurons on fiber surfaces to approximately 700 neurons mm(-2) by manipulating surrounding surface charges to bias settling neuronal suspensions toward fibers coated with cell-adhesive ligands. This stark increase in neuronal density resulted in robust neuritic extension and network formation directly along the fibers. Additionally, we encapsulated these neuronal networks on PA-PP fibers using agarose to form a protective barrier while potentially facilitating network stability. Following encapsulation, the neuronal networks maintained integrity, high viability (>85%) and intimate adhesion to PA-PP fibers. These efforts accomplished key prerequisites for the establishment of functional electrical interfaces with neuronal populations using small diameter PA-PP fibers-specifically, improved neurocompatibility, high-density neuronal adhesion and neuritic network development directly on fiber surfaces.

Revealing electronic open quantum systems with subsystem TDDFT

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

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

2016-03-28

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

Revealing electronic open quantum systems with subsystem TDDFT.

PubMed

Krishtal, Alisa; Pavanello, Michele

2016-03-28

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

Revealing electronic open quantum systems with subsystem TDDFT

NASA Astrophysics Data System (ADS)

Krishtal, Alisa; Pavanello, Michele

2016-03-01

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

The Thermal Equilibrium Solution of a Generic Bipolar Quantum Hydrodynamic Model

NASA Astrophysics Data System (ADS)

Unterreiter, Andreas

The thermal equilibrium state of a bipolar, isothermic quantum fluid confined to a bounded domain ,d = 1,2 or d = 3 is entirely described by the particle densities n, p, minimizing the energy where G1,2 are strictly convex real valued functions, . It is shown that this variational problem has a unique minimizer in and some regularity results are proven. The semi-classical limit is carried out recovering the minimizer of the limiting functional. The subsequent zero space charge limit leads to extensions of the classical boundary conditions. Due to the lack of regularity the asymptotics can not be settled on Sobolev embedding arguments. The limit is carried out by means of a compactness-by-convexity principle.

Potassium Binding Adjacent to Cationic Transition-Metal Fragments: Unusual Heterobimetallic Adducts of a Calix[4]arene-Based Thione Ligand.

PubMed

Patchett, Ruth; Knighton, Richard C; Mattock, James D; Vargas, Alfredo; Chaplin, Adrian B

2017-11-20

The synthesis of cationic rhodium and iridium complexes of a bis(imidazole-2-thione)-functionalized calix[4]arene ligand and their surprising capacity for potassium binding are described. In both cases, uptake of the alkali metal into the calix[4]arene cavity occurs despite adverse electrostatic interactions associated with close proximity to the transition-metal fragment [Rh + ···K + = 3.715(1) Å; Ir + ···K + = 3.690(1) Å]. The formation and constituent bonding of these unusual heterobimetallic adducts have been interrogated through extensive solution and solid-state characterization, examination of the host-guest chemistry of the ligand and its upper-rim unfunctionalized calix[4]arene analogue, and use of density functional theory based energy decomposition analysis.

Acoustics of marine sediment under compaction: binary grain-size model and viscoelastic extension of Biot's theory.

PubMed

Leurer, Klaus C; Brown, Colin

2008-04-01

This paper presents a model of acoustic wave propagation in unconsolidated marine sediment, including compaction, using a concept of a simplified sediment structure, modeled as a binary grain-size sphere pack. Compressional- and shear-wave velocities and attenuation follow from a combination of Biot's model, used as the general framework, and two viscoelastic extensions resulting in complex grain and frame moduli, respectively. An effective-grain model accounts for the viscoelasticity arising from local fluid flow in expandable clay minerals in clay-bearing sediments. A viscoelastic-contact model describes local fluid flow at the grain contacts. Porosity, density, and the structural Biot parameters (permeability, pore size, structure factor) as a function of pressure follow from the binary model, so that the remaining input parameters to the acoustic model consist solely of the mass fractions and the known mechanical properties of each constituent (e.g., carbonates, sand, clay, and expandable clay) of the sediment, effective pressure, or depth, and the environmental parameters (water depth, salinity, temperature). Velocity and attenuation as a function of pressure from the model are in good agreement with data on coarse- and fine-grained unconsolidated marine sediments.

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

Zhang, Miao; Du, Yonghui; Gao, Lili

A recent experimental study reported the successful synthesis of an orthorhombic FeB{sub 4} with a high hardness of 62(5) GPa [H. Gou et al., Phys. Rev. Lett. 111, 157002 (2013)], which has reignited extensive interests on whether transition-metal borides compounds will become superhard materials. However, it is contradicted with some theoretical studies suggesting transition-metal boron compounds are unlikely to become superhard materials. Here, we examined structural and electronic properties of FeB{sub 4} using density functional theory. The electronic calculations show the good metallicity and covalent Fe–B bonding. Meanwhile, we extensively investigated stress-strain relations of FeB{sub 4} under various tensile andmore » shear loading directions. The calculated weakest tensile and shear stresses are 40 GPa and 25 GPa, respectively. Further simulations (e.g., electron localization function and bond length along the weakest loading direction) on FeB{sub 4} show the weak Fe–B bonding is responsible for this low hardness. Moreover, these results are consistent with the value of Vickers hardness (11.7–32.3 GPa) by employing different empirical hardness models and below the superhardness threshold of 40 GPa. Our current results suggest FeB{sub 4} is a hard material and unlikely to become superhard (>40 GPa)« less

Impact crater densities on volcanoes and coronae on venus: implications for volcanic resurfacing.

PubMed

Namiki, N; Solomon, S C

1994-08-12

The density of impact craters on large volcanoes on Venus is half the average crater density for the planet. The crater density on some classes of coronae is not significantly different from the global average density, but coronae with extensive associated volcanic deposits have lower crater densities. These results are inconsistent with both single-age and steady-state models for global resurfacing and suggest that volcanoes and coronae with associated volcanism have been active on Venus over the last 500 million years.

Charge-balanced biphasic electrical stimulation inhibits neurite extension of spiral ganglion neurons.

PubMed

Shen, Na; Liang, Qiong; Liu, Yuehong; Lai, Bin; Li, Wen; Wang, Zhengmin; Li, Shufeng

2016-06-15

Intracochlear application of exogenous or transgenic neurotrophins, such as neurotrophin-3 (NT-3) and brain derived neurotrophic factor (BDNF), could promote the resprouting of spiral ganglion neuron (SGN) neurites in deafened animals. These resprouting neurites might reduce the gap between cochlear implant electrodes and their targeting SGNs, allowing for an improvement of spatial resolution of electrical stimulation. This study is to investigate the impact of electrical stimulation employed in CI on the extension of resprouting SGN neurites. We established an in vitro model including the devices delivering charge-balanced biphasic electrical stimulation, and spiral ganglion (SG) dissociated culture treated with BDNF and NT-3. After electrical stimulation with varying durations and intensities, we quantified neurite lengths and Schwann cell densities in SG cultures. Stimulations that were greater than 50μA or longer than 8h significantly decreased SG neurite length. Schwann cell density under 100μA electrical stimulation for 48h was significantly lower compared to that in non-stimulated group. These electrical stimulation-induced decreases of neurite extension and Schwann cell density were attenuated by various types of voltage-dependent calcium channel (VDCC) blockers, or completely prevented by their combination, cadmium or calcium-free medium. Our study suggested that charge-balanced biphasic electrical stimulation inhibited the extension of resprouting SGN neurites and decreased Schwann cell density in vitro. Calcium influx through multiple types of VDCCs was involved in the electrical stimulation-induced inhibition. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Size-density metrics, leaf area, and productivity in eastern white pine

Treesearch

J. C. Innes; M. J. Ducey; J. H. Gove; W. B. Leak; J. P. Barrett

2005-01-01

Size-density metrics are used extensively for silvicultural planning; however, they operate on biological assumptions that remain relatively untested. Using data from 12 even-aged stands of eastern white pine (Pinus strobus L.) growing in southern New Hampshire, we compared size-density metrics with stand productivity and its biological components,...

Optical Imaging and Radiometric Modeling and Simulation

NASA Technical Reports Server (NTRS)

Ha, Kong Q.; Fitzmaurice, Michael W.; Moiser, Gary E.; Howard, Joseph M.; Le, Chi M.

2010-01-01

OPTOOL software is a general-purpose optical systems analysis tool that was developed to offer a solution to problems associated with computational programs written for the James Webb Space Telescope optical system. It integrates existing routines into coherent processes, and provides a structure with reusable capabilities that allow additional processes to be quickly developed and integrated. It has an extensive graphical user interface, which makes the tool more intuitive and friendly. OPTOOL is implemented using MATLAB with a Fourier optics-based approach for point spread function (PSF) calculations. It features parametric and Monte Carlo simulation capabilities, and uses a direct integration calculation to permit high spatial sampling of the PSF. Exit pupil optical path difference (OPD) maps can be generated using combinations of Zernike polynomials or shaped power spectral densities. The graphical user interface allows rapid creation of arbitrary pupil geometries, and entry of all other modeling parameters to support basic imaging and radiometric analyses. OPTOOL provides the capability to generate wavefront-error (WFE) maps for arbitrary grid sizes. These maps are 2D arrays containing digital sampled versions of functions ranging from Zernike polynomials to combination of sinusoidal wave functions in 2D, to functions generated from a spatial frequency power spectral distribution (PSD). It also can generate optical transfer functions (OTFs), which are incorporated into the PSF calculation. The user can specify radiometrics for the target and sky background, and key performance parameters for the instrument s focal plane array (FPA). This radiometric and detector model setup is fairly extensive, and includes parameters such as zodiacal background, thermal emission noise, read noise, and dark current. The setup also includes target spectral energy distribution as a function of wavelength for polychromatic sources, detector pixel size, and the FPA s charge diffusion modulation transfer function (MTF).

Physicochemical properties and carbon density of alpine sod layer with their variation across habitat gradients in the Zoige Plateau

NASA Astrophysics Data System (ADS)

Peixi, Su; Zijuan, Zhou; Rui, Shi; tingting, Xie

2017-04-01

The alpine sod layer is a soft, tough and resistant to shifting surface soil layer under the formation of the natural vegetation in the plateau cold region, understanding its ecological function is a prerequisite to promote grass and animal husbandry production for recuperation and protection, and the active use of project construction. Based on the extensive investigation on the alpine vegetation of the Zoige Plateau in the Eastern Qinghai-Tibetan Plateau of China, set up moisture gradient community sample plots: swamp, degraded swamp, swampy meadow, wet meadow, dry meadow and degraded meadow, and the elevation gradient community sample plots: subalpine meadow, subalpine shrub meadow, alpine shrub meadow and alpine meadow were set up. The sod layer bulk density, soil particle composition and soil organic carbon (SOC) content of different types of community plots were analyzed and to compare its carbon sequestration capacity on the moisture and elevation gradients. The results showed that the average thickness of the sod layer was 30 cm, the bulk density of the swamp was the smallest, and the SOC content was above 300 g/kg. The bulk density of degraded meadow was the highest while its SOC content was decreased significantly. The SOC density of sod layer in different communities was between 10 and 24 kg C/m2, and decreased with the decreasing of soil water availability, and meadow degradation significantly decreased the soil organic carbon storage in sod layer. The sod layer SOC density of alpine shrub meadow was 15% higher than that of meadow on the altitudinal gradient. It was concluded that the mass water content threshold value for maintaining the sod layer stable is 30%. In the degraded succession of alpine vegetation from swamp to meadow, the bulk density and compactness of sod layer became larger, while the organic carbon content, carbon density and carbon storage decreased. The higher the gravel content of swamp, the more easily degraded, and the higher the sand content of the meadow, the more easily degraded. Shrub meadow had higher carbon sequestration capacity than that of meadow, but the productive function of shrub meadow was lower. Keeping the sustainable development of grassland productivity and maintaining the carbon sequestration ecological function, it is necessary to prevent the degradation of the sod layer, and restrain the succession from meadow to scrub meadow. Key Words: surface soil layer, soil organic carbon, carbon density, alpine vegetation, Zoige Plateau

Function-Space-Based Solution Scheme for the Size-Modified Poisson-Boltzmann Equation in Full-Potential DFT.

PubMed

Ringe, Stefan; Oberhofer, Harald; Hille, Christoph; Matera, Sebastian; Reuter, Karsten

2016-08-09

The size-modified Poisson-Boltzmann (MPB) equation is an efficient implicit solvation model which also captures electrolytic solvent effects. It combines an account of the dielectric solvent response with a mean-field description of solvated finite-sized ions. We present a general solution scheme for the MPB equation based on a fast function-space-oriented Newton method and a Green's function preconditioned iterative linear solver. In contrast to popular multigrid solvers, this approach allows us to fully exploit specialized integration grids and optimized integration schemes. We describe a corresponding numerically efficient implementation for the full-potential density-functional theory (DFT) code FHI-aims. We show that together with an additional Stern layer correction the DFT+MPB approach can describe the mean activity coefficient of a KCl aqueous solution over a wide range of concentrations. The high sensitivity of the calculated activity coefficient on the employed ionic parameters thereby suggests to use extensively tabulated experimental activity coefficients of salt solutions for a systematic parametrization protocol.

Gender-related differences in the apparent timing of skeletal density bands in the reef-building coral Siderastrea siderea

NASA Astrophysics Data System (ADS)

Carricart-Ganivet, J. P.; Vásquez-Bedoya, L. F.; Cabanillas-Terán, N.; Blanchon, P.

2013-09-01

Density banding in skeletons of reef-building corals is a valuable source of proxy environmental data. However, skeletal growth strategy has a significant impact on the apparent timing of density-band formation. Some corals employ a strategy where the tissue occupies previously formed skeleton during as the new band forms, which leads to differences between the actual and apparent band timing. To investigate this effect, we collected cores from female and male colonies of Siderastrea siderea and report tissue thicknesses and density-related growth parameters over a 17-yr interval. Correlating these results with monthly sea surface temperature (SST) shows that maximum skeletal density in the female coincides with low winter SSTs, whereas in the male, it coincides with high summer SSTs. Furthermore, maximum skeletal densities in the female coincide with peak Sr/Ca values, whereas in the male, they coincide with low Sr/Ca values. Both results indicate a 6-month difference in the apparent timing of density-band formation between genders. Examination of skeletal extension rates also show that the male has thicker tissue and extends faster, whereas the female has thinner tissue and a denser skeleton—but both calcify at the same rate. The correlation between extension and calcification, combined with the fact that density banding arises from thickening of the skeleton throughout the depth reached by the tissue layer, implies that S. siderea has the same growth strategy as massive Porites, investing its calcification resources into linear extension. In addition, differences in tissue thicknesses suggest that females offset the greater energy requirements of gamete production by generating less tissue, resulting in differences in the apparent timing of density-band formation. Such gender-related offsets may be common in other corals and require that environmental reconstructions be made from sexed colonies and that, in fossil corals where sex cannot be determined, reconstructions must be duplicated in different colonies.

Tidal extension and sea-level rise: recommendations for a research agenda

USGS Publications Warehouse

Ensign, Scott H.; Noe, Gregory

2018-01-01

Sea-level rise is pushing freshwater tides upstream into formerly non-tidal rivers. This tidal extension may increase the area of tidal freshwater ecosystems and offset loss of ecosystem functions due to salinization downstream. Without considering how gains in ecosystem functions could offset losses, landscape-scale assessments of ecosystem functions may be biased toward worst-case scenarios of loss. To stimulate research on this concept, we address three fundamental questions about tidal extension: Where will tidal extension be most evident, and can we measure it? What ecosystem functions are influenced by tidal extension, and how can we measure them? How do watershed processes, climate change, and tidal extension interact to affect ecosystem functions? Our preliminary answers lead to recommendations that will advance tidal extension research, enable better predictions of the impacts of sea-level rise, and help balance the landscape-scale benefits of ecosystem function with costs of response.

The 5-10 keV AGN luminosity function at 0.01 < z < 4.0

NASA Astrophysics Data System (ADS)

Fotopoulou, S.; Buchner, J.; Georgantopoulos, I.; Hasinger, G.; Salvato, M.; Georgakakis, A.; Cappelluti, N.; Ranalli, P.; Hsu, L. T.; Brusa, M.; Comastri, A.; Miyaji, T.; Nandra, K.; Aird, J.; Paltani, S.

2016-03-01

The active galactic nuclei (AGN) X-ray luminosity function traces actively accreting supermassive black holes and is essential for the study of the properties of the AGN population, black hole evolution, and galaxy-black hole coevolution. Up to now, the AGN luminosity function has been estimated several times in soft (0.5-2 keV) and hard X-rays (2-10 keV). AGN selection in these energy ranges often suffers from identification and redshift incompleteness and, at the same time, photoelectric absorption can obscure a significant amount of the X-ray radiation. We estimate the evolution of the luminosity function in the 5-10 keV band, where we effectively avoid the absorbed part of the spectrum, rendering absorption corrections unnecessary up to NH ~ 1023 cm-2. Our dataset is a compilation of six wide, and deep fields: MAXI, HBSS, XMM-COSMOS, Lockman Hole, XMM-CDFS, AEGIS-XD, Chandra-COSMOS, and Chandra-CDFS. This extensive sample of ~1110 AGN (0.01 < z < 4.0, 41 < log Lx < 46) is 98% redshift complete with 68% spectroscopic redshifts. For sources lacking a spectroscopic redshift estimation we use the probability distribution function of photometric redshift estimation specifically tuned for AGN, and a flat probability distribution function for sources with no redshift information. We use Bayesian analysis to select the best parametric model from simple pure luminosity and pure density evolution to more complicated luminosity and density evolution and luminosity-dependent density evolution (LDDE). We estimate the model parameters that describe best our dataset separately for each survey and for the combined sample. We show that, according to Bayesian model selection, the preferred model for our dataset is the LDDE. Our estimation of the AGN luminosity function does not require any assumption on the AGN absorption and is in good agreement with previous works in the 2-10 keV energy band based on X-ray hardness ratios to model the absorption in AGN up to redshift three. Our sample does not show evidence of a rapid decline of the AGN luminosity function up to redshift four.

Scattering of electromagnetic wave by the layer with one-dimensional random inhomogeneities

NASA Astrophysics Data System (ADS)

Kogan, Lev; Zaboronkova, Tatiana; Grigoriev, Gennadii., IV.

A great deal of attention has been paid to the study of probability characteristics of electro-magnetic waves scattered by one-dimensional fluctuations of medium dielectric permittivity. However, the problem of a determination of a density of a probability and average intensity of the field inside the stochastically inhomogeneous medium with arbitrary extension of fluc-tuations has not been considered yet. It is the purpose of the present report to find and to analyze the indicated functions for the plane electromagnetic wave scattered by the layer with one-dimensional fluctuations of permittivity. We assumed that the length and the amplitude of individual fluctuations as well the interval between them are random quantities. All of indi-cated fluctuation parameters are supposed as independent random values possessing Gaussian distribution. We considered the stationary time cases both small-scale and large-scale rarefied inhomogeneities. Mathematically such problem can be reduced to the solution of integral Fred-holm equation of second kind for Hertz potential (U). Using the decomposition of the field into the series of multiply scattered waves we obtained the expression for a probability density of the field of the plane wave and determined the moments of the scattered field. We have shown that all odd moments of the centered field (U-¡U¿) are equal to zero and the even moments depend on the intensity. It was obtained that the probability density of the field possesses the Gaussian distribution. The average field is small compared with the standard fluctuation of scattered field for all considered cases of inhomogeneities. The value of average intensity of the field is an order of a standard of fluctuations of field intensity and drops with increases the inhomogeneities length in the case of small-scale inhomogeneities. The behavior of average intensity is more complicated in the case of large-scale medium inhomogeneities. The value of average intensity is the oscillating function versus the average fluctuations length if the standard of fluctuations of inhomogeneities length is greater then the wave length. When the standard of fluctuations of medium inhomogeneities extension is smaller then the wave length, the av-erage intensity value weakly depends from the average fluctuations extension. The obtained results may be used for analysis of the electromagnetic wave propagation into the media with the fluctuating parameters caused by such factors as leafs of trees, cumulus, internal gravity waves with a chaotic phase and etc. Acknowledgment: This work was supported by the Russian Foundation for Basic Research (projects 08-02-97026 and 09-05-00450).

Reconstructing the galaxy density field with photometric redshifts - II. Environment-dependent galaxy evolution since z ≃ 3

NASA Astrophysics Data System (ADS)

Malavasi, Nicola; Pozzetti, Lucia; Cucciati, Olga; Bardelli, Sandro; Ilbert, Olivier; Cimatti, Andrea

2017-09-01

Although extensively investigated, the role of the environment in galaxy formation is still not well understood. In this context, the galaxy stellar mass function (GSMF) is a powerful tool to understand how environment relates to galaxy mass assembly and the quenching of star formation. In this work, we make use of the high-precision photometric redshifts of the UltraVISTA Survey to study the GSMF in different environments up to z ˜ 3, on physical scales from 0.3 to 2 Mpc, down to masses of M ˜ 1010 M⊙. We witness the appearance of environmental signatures for both quiescent and star-forming galaxies. We find that the shape of the GSMF of quiescent galaxies is different in high- and low-density environments up to z ˜ 2 with the high-mass end (M ≳ 1011 M⊙) being enhanced in high-density environments. On the contrary, for star-forming galaxies, a difference between the GSMF in high- and low-density environments is present for masses M ≲ 1011 M⊙. Star-forming galaxies in this mass range appear to be more frequent in low-density environments up to z < 1.5. Differences in the shape of the GSMF are not visible anymore at z > 2. Our results, in terms of general trends in the shape of the GSMF, are in agreement with a scenario in which galaxies are quenched when they enter hot gas-dominated massive haloes that are preferentially in high-density environments.

Grassmann phase space methods for fermions. II. Field theory

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

Dalton, B.J., E-mail: bdalton@swin.edu.au; Jeffers, J.; Barnett, S.M.

In both quantum optics and cold atom physics, the behaviour of bosonic photons and atoms is often treated using phase space methods, where mode annihilation and creation operators are represented by c-number phase space variables, with the density operator equivalent to a distribution function of these variables. The anti-commutation rules for fermion annihilation, creation operators suggests the possibility of using anti-commuting Grassmann variables to represent these operators. However, in spite of the seminal work by Cahill and Glauber and a few applications, the use of Grassmann phase space methods in quantum-atom optics to treat fermionic systems is rather rare, thoughmore » fermion coherent states using Grassmann variables are widely used in particle physics. This paper presents a phase space theory for fermion systems based on distribution functionals, which replace the density operator and involve Grassmann fields representing anti-commuting fermion field annihilation, creation operators. It is an extension of a previous phase space theory paper for fermions (Paper I) based on separate modes, in which the density operator is replaced by a distribution function depending on Grassmann phase space variables which represent the mode annihilation and creation operators. This further development of the theory is important for the situation when large numbers of fermions are involved, resulting in too many modes to treat separately. Here Grassmann fields, distribution functionals, functional Fokker–Planck equations and Ito stochastic field equations are involved. Typical applications to a trapped Fermi gas of interacting spin 1/2 fermionic atoms and to multi-component Fermi gases with non-zero range interactions are presented, showing that the Ito stochastic field equations are local in these cases. For the spin 1/2 case we also show how simple solutions can be obtained both for the untrapped case and for an optical lattice trapping potential.« less

Statistical analysis of Geopotential Height (GH) timeseries based on Tsallis non-extensive statistical mechanics

NASA Astrophysics Data System (ADS)

Karakatsanis, L. P.; Iliopoulos, A. C.; Pavlos, E. G.; Pavlos, G. P.

2018-02-01

In this paper, we perform statistical analysis of time series deriving from Earth's climate. The time series are concerned with Geopotential Height (GH) and correspond to temporal and spatial components of the global distribution of month average values, during the period (1948-2012). The analysis is based on Tsallis non-extensive statistical mechanics and in particular on the estimation of Tsallis' q-triplet, namely {qstat, qsens, qrel}, the reconstructed phase space and the estimation of correlation dimension and the Hurst exponent of rescaled range analysis (R/S). The deviation of Tsallis q-triplet from unity indicates non-Gaussian (Tsallis q-Gaussian) non-extensive character with heavy tails probability density functions (PDFs), multifractal behavior and long range dependences for all timeseries considered. Also noticeable differences of the q-triplet estimation found in the timeseries at distinct local or temporal regions. Moreover, in the reconstructive phase space revealed a lower-dimensional fractal set in the GH dynamical phase space (strong self-organization) and the estimation of Hurst exponent indicated multifractality, non-Gaussianity and persistence. The analysis is giving significant information identifying and characterizing the dynamical characteristics of the earth's climate.

Trajectory-based nonadiabatic dynamics with time-dependent density functional theory.

PubMed

Curchod, Basile F E; Rothlisberger, Ursula; Tavernelli, Ivano

2013-05-10

Understanding the fate of an electronically excited molecule constitutes an important task for theoretical chemistry, and practical implications range from the interpretation of atto- and femtosecond spectroscopy to the development of light-driven molecular machines, the control of photochemical reactions, and the possibility of capturing sunlight energy. However, many challenging conceptual and technical problems are involved in the description of these phenomena such as 1) the failure of the well-known Born-Oppenheimer approximation; 2) the need for accurate electronic properties such as potential energy surfaces, excited nuclear forces, or nonadiabatic coupling terms; and 3) the necessity of describing the dynamics of the photoexcited nuclear wavepacket. This review provides an overview of the current methods to address points 1) and 3) and shows how time-dependent density functional theory (TDDFT) and its linear-response extension can be used for point 2). First, the derivation of Ehrenfest dynamics and nonadiabatic Bohmian dynamics is discussed and linked to Tully's trajectory surface hopping. Second, the coupling of these trajectory-based nonadiabatic schemes with TDDFT is described in detail with special emphasis on the derivation of the required electronic structure properties. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Hydroxytyrosol in functional hydroxytyrosol-enriched biscuits is highly bioavailable and decreases oxidised low density lipoprotein levels in humans.

PubMed

Mateos, Raquel; Martínez-López, Sara; Baeza Arévalo, Gema; Amigo-Benavent, Miryam; Sarriá, Beatriz; Bravo-Clemente, Laura

2016-08-15

Hydroxytyrosol (HT) and its derivatives in olive oil protect low-density lipoproteins (LDL) against oxidation. Biscuits could be a convenient alternative to broaden consumers' choice of HT-rich foods, although the biscuit matrix could affect HT bioavailability. We performed a crossover, randomized, double-blind study to evaluate HT bioavailability in HT-enriched biscuits (HT-B) versus non-enriched biscuits (C-B), and the effects on oxidative postprandial status. On two separate days, 13 subjects consumed 30 g of C-B or HT-B (5.25mg HT) after overnight-fasting. Blood and urine were collected at different intervals and analysed by LC-MS-QToF. After HT-B consumption, plasma metabolites peaked between 0.5 and 1h and were extensively excreted in urine. HT-sulphate and 3,4-dihydroxyphenylacetic acid (DOPAC)-sulphate were the main metabolites, followed by DOPAC and homovanillic acid (HVA). HT-glucuronide, DOPAC-glucuronide, HVA-glucuronide and HVA-sulphate were also detected. Postprandial oxidised-LDL concentrations decreased with HT-B. HT is a promising functional ingredient and, in biscuits, it is highly bioavailable and lowers postprandial oxidised-LDL levels. Copyright © 2016 Elsevier Ltd. All rights reserved.

Rare reaction channels in real-time time-dependent density functional theory: the test case of electron attachment

NASA Astrophysics Data System (ADS)

Lacombe, Lionel; Dinh, P. Huong Mai; Reinhard, Paul-Gerhard; Suraud, Eric; Sanche, Leon

2015-08-01

We present an extension of standard time-dependent density functional theory (TDDFT) to include the evaluation of rare reaction channels, taking as an example of application the theoretical modelling of electron attachment to molecules. The latter process is of great importance in radiation-induced damage of biological tissue for which dissociative electron attachment plays a decisive role. As the attachment probability is very low, it cannot be extracted from the TDDFT propagation whose mean field provides an average over various reaction channels. To extract rare events, we augment TDDFT by a perturbative treatment to account for the occasional jumps, namely electron capture in our test case. We apply the modelling to electron attachment to H2O, H3O+, and (H2O)2. Dynamical calculations have been done at low energy (3-16 eV). We explore, in particular, how core-excited states of the targets show up as resonances in the attachment probability. Contribution to the Topical Issue "COST Action Nano-IBCT: Nano-scale Processes Behind Ion-Beam Cancer Therapy", edited by Andrey Solov'yov, Nigel Mason, Gustavo García, Eugene Surdutovich.

Droplets and the three-phase contact line at the nano-scale. Statics and dynamics

NASA Astrophysics Data System (ADS)

Yatsyshin, Petr; Sibley, David; Savva, Nikos; Kalliadasis, Serafim

2014-11-01

Understanding the behaviour of the solid-liquid-vapour contact line at the scale of several tens of molecular diameters is important in wetting hydrodynamics with applications in micro- and nano-fluidics, including the design of lab-on-a-chip devices and surfaces with specific wetting properties. Due to the fluid inhomogeneity at the nano-scale, the application of continuum-mechanical approaches is limited, and a natural way to remedy this is to seek descriptions accounting for the non-local molecular-level interactions. Density Functional Theory (DFT) for fluids offers a statistical-mechanical framework based on expressing the free energy of the fluid-solid pair as a functional of the spatially varying fluid density. DFT allows us to investigate small drops deposited on planar substrates whilst keeping track of the microscopic structural details of the fluid. Starting from a model of intermolecular forces, we systematically obtain interfaces, surface tensions, and the microscopic contact angle. Using a dynamic extension of equilibrium DFT, we investigate the diffusion-driven evolution of the three-phase contact line to gain insight into the dynamic behaviour of the microscopic contact angle, which is still under debate.

Advances in molecular quantum chemistry contained in the Q-Chem 4 program package

NASA Astrophysics Data System (ADS)

Shao, Yihan; Gan, Zhengting; Epifanovsky, Evgeny; Gilbert, Andrew T. B.; Wormit, Michael; Kussmann, Joerg; Lange, Adrian W.; Behn, Andrew; Deng, Jia; Feng, Xintian; Ghosh, Debashree; Goldey, Matthew; Horn, Paul R.; Jacobson, Leif D.; Kaliman, Ilya; Khaliullin, Rustam Z.; Kuś, Tomasz; Landau, Arie; Liu, Jie; Proynov, Emil I.; Rhee, Young Min; Richard, Ryan M.; Rohrdanz, Mary A.; Steele, Ryan P.; Sundstrom, Eric J.; Woodcock, H. Lee, III; Zimmerman, Paul M.; Zuev, Dmitry; Albrecht, Ben; Alguire, Ethan; Austin, Brian; Beran, Gregory J. O.; Bernard, Yves A.; Berquist, Eric; Brandhorst, Kai; Bravaya, Ksenia B.; Brown, Shawn T.; Casanova, David; Chang, Chun-Min; Chen, Yunqing; Chien, Siu Hung; Closser, Kristina D.; Crittenden, Deborah L.; Diedenhofen, Michael; DiStasio, Robert A., Jr.; Do, Hainam; Dutoi, Anthony D.; Edgar, Richard G.; Fatehi, Shervin; Fusti-Molnar, Laszlo; Ghysels, An; Golubeva-Zadorozhnaya, Anna; Gomes, Joseph; Hanson-Heine, Magnus W. D.; Harbach, Philipp H. P.; Hauser, Andreas W.; Hohenstein, Edward G.; Holden, Zachary C.; Jagau, Thomas-C.; Ji, Hyunjun; Kaduk, Benjamin; Khistyaev, Kirill; Kim, Jaehoon; Kim, Jihan; King, Rollin A.; Klunzinger, Phil; Kosenkov, Dmytro; Kowalczyk, Tim; Krauter, Caroline M.; Lao, Ka Un; Laurent, Adèle D.; Lawler, Keith V.; Levchenko, Sergey V.; Lin, Ching Yeh; Liu, Fenglai; Livshits, Ester; Lochan, Rohini C.; Luenser, Arne; Manohar, Prashant; Manzer, Samuel F.; Mao, Shan-Ping; Mardirossian, Narbe; Marenich, Aleksandr V.; Maurer, Simon A.; Mayhall, Nicholas J.; Neuscamman, Eric; Oana, C. Melania; Olivares-Amaya, Roberto; O'Neill, Darragh P.; Parkhill, John A.; Perrine, Trilisa M.; Peverati, Roberto; Prociuk, Alexander; Rehn, Dirk R.; Rosta, Edina; Russ, Nicholas J.; Sharada, Shaama M.; Sharma, Sandeep; Small, David W.; Sodt, Alexander; Stein, Tamar; Stück, David; Su, Yu-Chuan; Thom, Alex J. W.; Tsuchimochi, Takashi; Vanovschi, Vitalii; Vogt, Leslie; Vydrov, Oleg; Wang, Tao; Watson, Mark A.; Wenzel, Jan; White, Alec; Williams, Christopher F.; Yang, Jun; Yeganeh, Sina; Yost, Shane R.; You, Zhi-Qiang; Zhang, Igor Ying; Zhang, Xing; Zhao, Yan; Brooks, Bernard R.; Chan, Garnet K. L.; Chipman, Daniel M.; Cramer, Christopher J.; Goddard, William A., III; Gordon, Mark S.; Hehre, Warren J.; Klamt, Andreas; Schaefer, Henry F., III; Schmidt, Michael W.; Sherrill, C. David; Truhlar, Donald G.; Warshel, Arieh; Xu, Xin; Aspuru-Guzik, Alán; Baer, Roi; Bell, Alexis T.; Besley, Nicholas A.; Chai, Jeng-Da; Dreuw, Andreas; Dunietz, Barry D.; Furlani, Thomas R.; Gwaltney, Steven R.; Hsu, Chao-Ping; Jung, Yousung; Kong, Jing; Lambrecht, Daniel S.; Liang, WanZhen; Ochsenfeld, Christian; Rassolov, Vitaly A.; Slipchenko, Lyudmila V.; Subotnik, Joseph E.; Van Voorhis, Troy; Herbert, John M.; Krylov, Anna I.; Gill, Peter M. W.; Head-Gordon, Martin

2015-01-01

A summary of the technical advances that are incorporated in the fourth major release of the Q-Chem quantum chemistry program is provided, covering approximately the last seven years. These include developments in density functional theory methods and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and open-shell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces. In addition, a selection of example case studies that illustrate these capabilities is given. These include extensive benchmarks of the comparative accuracy of modern density functionals for bonded and non-bonded interactions, tests of attenuated second order Møller-Plesset (MP2) methods for intermolecular interactions, a variety of parallel performance benchmarks, and tests of the accuracy of implicit solvation models. Some specific chemical examples include calculations on the strongly correlated Cr2 dimer, exploring zeolite-catalysed ethane dehydrogenation, energy decomposition analysis of a charged ter-molecular complex arising from glycerol photoionisation, and natural transition orbitals for a Frenkel exciton state in a nine-unit model of a self-assembling nanotube.

Phase space explorations in time dependent density functional theory

NASA Astrophysics Data System (ADS)

Rajam, Aruna K.

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

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

PubMed

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

2016-05-01

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

Studies on spectral analysis of randomly sampled signals: Application to laser velocimetry data

NASA Technical Reports Server (NTRS)

Sree, David

1992-01-01

Spectral analysis is very useful in determining the frequency characteristics of many turbulent flows, for example, vortex flows, tail buffeting, and other pulsating flows. It is also used for obtaining turbulence spectra from which the time and length scales associated with the turbulence structure can be estimated. These estimates, in turn, can be helpful for validation of theoretical/numerical flow turbulence models. Laser velocimetry (LV) is being extensively used in the experimental investigation of different types of flows, because of its inherent advantages; nonintrusive probing, high frequency response, no calibration requirements, etc. Typically, the output of an individual realization laser velocimeter is a set of randomly sampled velocity data. Spectral analysis of such data requires special techniques to obtain reliable estimates of correlation and power spectral density functions that describe the flow characteristics. FORTRAN codes for obtaining the autocorrelation and power spectral density estimates using the correlation-based slotting technique were developed. Extensive studies have been conducted on simulated first-order spectrum and sine signals to improve the spectral estimates. A first-order spectrum was chosen because it represents the characteristics of a typical one-dimensional turbulence spectrum. Digital prefiltering techniques, to improve the spectral estimates from randomly sampled data were applied. Studies show that the spectral estimates can be increased up to about five times the mean sampling rate.

Unusual Structure and Magnetism in MnO Nanoclusters

NASA Astrophysics Data System (ADS)

Ganguly, Shreemoyee; Kabir, Mukul; Sanyal, Biplab; Mookerjee, Abhijit

2011-03-01

We report an unusual structural and magnetic evolution in stoichiometric MnO nanoclusters by an extensive and unbiased search through the potential energy surface within density functional theory. The (MnO)n nanoclusters adopt two-dimensional structures in size ranges in which Mnn nanoclusters are three-dimensional and regardless of the size of the nanocluster, the magnetic coupling is found to be antiferromagnetic, and is strikingly different from Mn-based molecular magnets. Both of these features are explained through the inherent electronic structures of the nanoclusters. We gratefully acknowledge financial support from Swedish Research Links program funded by VR/SIDA and Carl Tryggers Foundation, Sweden.

Experimental and theoretical debate on efficient second harmonic generation in Bis (Cinnamic acid): Hexamine cocrystal

NASA Astrophysics Data System (ADS)

Vijayalakshmi, S.; Kalyanaraman, S.; Ravindran, T. R.

2014-02-01

Second harmonic generation (SHG) in Bis (Cinnamic acid): Hexamine cocrystal was extensively analyzed through charge transfer (CT). The CT interactions through hydrogen bonding were well established with the aid of vibrational analysis and Natural Bond Orbital (NBO) analysis. The retentivity of coplanar nature of the cinnamic acid in the cocrystal was confirmed through UV-Visible spectroscopy and supported by Raman studies. Structural analysis indicated the quinoidal character of the given material presenting a high SHG efficiency. The first order hyperpolarizability value was calculated theoretically by density functional theory (DFT) and Hartree-Fock (HF) methods in support for the large value of SHG.

streamgap-pepper: Effects of peppering streams with many small impacts

NASA Astrophysics Data System (ADS)

Bovy, Jo; Erkal, Denis; Sanders, Jason

2017-02-01

streamgap-pepper computes the effect of subhalo fly-bys on cold tidal streams based on the action-angle representation of streams. A line-of-parallel-angle approach is used to calculate the perturbed distribution function of a given stream segment by undoing the effect of all impacts. This approach allows one to compute the perturbed stream density and track in any coordinate system in minutes for realizations of the subhalo distribution down to 10^5 Msun, accounting for the stream's internal dispersion and overlapping impacts. This code uses galpy (ascl:1411.008) and the streampepperdf.py galpy extension, which implements the fast calculation of the perturbed stream structure.

Further New Diterpenoids as PTP1B Inhibitors from the Xisha Soft Coral Sinularia polydactyla.

PubMed

Ye, Fei; Zhu, Zheng-Dan; Gu, Yu-Cheng; Li, Jia; Zhu, Wei-Liang; Guo, Yue-Wei

2018-03-25

A new prenyleudesmane type diterpene, sinupol ( 8 ), and a new capnosane type diterpenoid, sinulacetate ( 9 ), were isolated from the Xisha soft coral Sinularia polydactyla along with five known related diterpenes ( 4 - 7 and 10 ). Their structures, including absolute configurations, were determined by extensive spectroscopic analysis, the comparison of their NMR data with those of related compounds, and time-dependent density functional theory electronic circular dichroism (TDDFT ECD) calculations. Both new compounds ( 8 and 9 ) exhibited promising inhibitory activity against protein tyrosine phosphatase 1B (PTP1B), a potential drug target for the treatment of type II diabetes and obesity.

Defect pair formation in fluorine and nitrogen codoped TiO2

NASA Astrophysics Data System (ADS)

Kordatos, A.; Kelaidis, N.; Chroneos, A.

2018-04-01

Titanium oxide is extensively investigated because of its high chemical stability and its photocatalytic properties; nevertheless, the large band gap limits its activity to a small portion of the solar spectrum. Nitrogen and fluorine codoping is an efficient defect engineering strategy to increase the photocatalytic activity of titanium oxide. In the present study, we apply density functional theory to investigate the interaction of nitrogen with fluorine and the formation of defect pairs. We show that in fluorine and nitrogen codoped titanium oxide, the FiNi, FONi, and FiNTi defects can form. Their impact on the electronic structure of titanium oxide is discussed.

Energy dependence of directed flow over a wide range of pseudorapidity in Au + Au collisions at the BNL Relativistic Heavy Ion Collider.

PubMed

Back, B B; Baker, M D; Ballintijn, M; Barton, D S; Betts, R R; Bickley, A A; Bindel, R; Budzanowski, A; Busza, W; Carroll, A; Chai, Z; Decowski, M P; García, E; Gburek, T; George, N; Gulbrandsen, K; Gushue, S; Halliwell, C; Hamblen, J; Hauer, M; Heintzelman, G A; Henderson, C; Hofman, D J; Hollis, R S; Hołyński, R; Holzman, B; Iordanova, A; Johnson, E; Kane, J L; Katzy, J; Khan, N; Kucewicz, W; Kulinich, P; Kuo, C M; Lin, W T; Manly, S; McLeod, D; Mignerey, A C; Nouicer, R; Olszewski, A; Pak, R; Park, I C; Pernegger, H; Reed, C; Remsberg, L P; Reuter, M; Roland, C; Roland, G; Rosenberg, L; Sagerer, J; Sarin, P; Sawicki, P; Seals, H; Sedykh, I; Skulski, W; Smith, C E; Stankiewicz, M A; Steinberg, P; Stephans, G S F; Sukhanov, A; Tang, J-L; Tonjes, M B; Trzupek, A; Vale, C; van Nieuwenhuizen, G J; Vaurynovich, S S; Verdier, R; Veres, G I; Wenger, E; Wolfs, F L H; Wosiek, B; Woźniak, K; Wuosmaa, A H; Wysłouch, B

2006-07-07

We report on measurements of directed flow as a function of pseudorapidity in Au + Au collisions at energies of square root of SNN = 19.6, 62.4, 130 and 200 GeV as measured by the PHOBOS detector at the BNL Relativistic Heavy Ion Collider. These results are particularly valuable because of the extensive, continuous pseudorapidity coverage of the PHOBOS detector. There is no significant indication of structure near midrapidity and the data surprisingly exhibit extended longitudinal scaling similar to that seen for elliptic flow and charged particle pseudorapidity density.

Employing OpenCL to Accelerate Ab Initio Calculations on Graphics Processing Units.

PubMed

Kussmann, Jörg; Ochsenfeld, Christian

2017-06-13

We present an extension of our graphics processing units (GPU)-accelerated quantum chemistry package to employ OpenCL compute kernels, which can be executed on a wide range of computing devices like CPUs, Intel Xeon Phi, and AMD GPUs. Here, we focus on the use of AMD GPUs and discuss differences as compared to CUDA-based calculations on NVIDIA GPUs. First illustrative timings are presented for hybrid density functional theory calculations using serial as well as parallel compute environments. The results show that AMD GPUs are as fast or faster than comparable NVIDIA GPUs and provide a viable alternative for quantum chemical applications.

Scale matters

NASA Astrophysics Data System (ADS)

Margolin, L. G.

2018-04-01

The applicability of Navier-Stokes equations is limited to near-equilibrium flows in which the gradients of density, velocity and energy are small. Here I propose an extension of the Chapman-Enskog approximation in which the velocity probability distribution function (PDF) is averaged in the coordinate phase space as well as the velocity phase space. I derive a PDF that depends on the gradients and represents a first-order generalization of local thermodynamic equilibrium. I then integrate this PDF to derive a hydrodynamic model. I discuss the properties of that model and its relation to the discrete equations of computational fluid dynamics. This article is part of the theme issue `Hilbert's sixth problem'.

The large-scale distribution of galaxies

NASA Technical Reports Server (NTRS)

Geller, Margaret J.

1989-01-01

The spatial distribution of galaxies in the universe is characterized on the basis of the six completed strips of the Harvard-Smithsonian Center for Astrophysics redshift-survey extension. The design of the survey is briefly reviewed, and the results are presented graphically. Vast low-density voids similar to the void in Bootes are found, almost completely surrounded by thin sheets of galaxies. Also discussed are the implications of the results for the survey sampling problem, the two-point correlation function of the galaxy distribution, the possibility of detecting large-scale coherent flows, theoretical models of large-scale structure, and the identification of groups and clusters of galaxies.

ILP-based co-optimization of cut mask layout, dummy fill, and timing for sub-14nm BEOL technology

NASA Astrophysics Data System (ADS)

Han, Kwangsoo; Kahng, Andrew B.; Lee, Hyein; Wang, Lutong

2015-10-01

Self-aligned multiple patterning (SAMP), due to its low overlay error, has emerged as the leading option for 1D gridded back-end-of-line (BEOL) in sub-14nm nodes. To form actual routing patterns from a uniform "sea of wires", a cut mask is needed for line-end cutting or realization of space between routing segments. Constraints on cut shapes and minimum cut spacing result in end-of-line (EOL) extensions and non-functional (i.e. dummy fill) patterns; the resulting capacitance and timing changes must be consistent with signoff performance analyses and their impacts should be minimized. In this work, we address the co-optimization of cut mask layout, dummy fill, and design timing for sub-14nm BEOL design. Our central contribution is an optimizer based on integer linear programming (ILP) to minimize the timing impact due to EOL extensions, considering (i) minimum cut spacing arising in sub-14nm nodes; (ii) cut assignment to different cut masks (color assignment); and (iii) the eligibility to merge two unit-size cuts into a bigger cut. We also propose a heuristic approach to remove dummy fills after the ILP-based optimization by extending the usage of cut masks. Our heuristic can improve critical path performance under minimum metal density and mask density constraints. In our experiments, we study the impact of number of cut masks, minimum cut spacing and metal density under various constraints. Our studies of optimized cut mask solutions in these varying contexts give new insight into the tradeoff of performance and cost that is afforded by cut mask patterning technology options.

Fitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations.

PubMed

Porebski, Przemyslaw Jerzy; Cymborowski, Marcin; Pasenkiewicz-Gierula, Marta; Minor, Wladek

2016-02-01

Improvements in crystallographic hardware and software have allowed automated structure-solution pipelines to approach a near-`one-click' experience for the initial determination of macromolecular structures. However, in many cases the resulting initial model requires a laborious, iterative process of refinement and validation. A new method has been developed for the automatic modeling of side-chain conformations that takes advantage of rotamer-prediction methods in a crystallographic context. The algorithm, which is based on deterministic dead-end elimination (DEE) theory, uses new dense conformer libraries and a hybrid energy function derived from experimental data and prior information about rotamer frequencies to find the optimal conformation of each side chain. In contrast to existing methods, which incorporate the electron-density term into protein-modeling frameworks, the proposed algorithm is designed to take advantage of the highly discriminatory nature of electron-density maps. This method has been implemented in the program Fitmunk, which uses extensive conformational sampling. This improves the accuracy of the modeling and makes it a versatile tool for crystallographic model building, refinement and validation. Fitmunk was extensively tested on over 115 new structures, as well as a subset of 1100 structures from the PDB. It is demonstrated that the ability of Fitmunk to model more than 95% of side chains accurately is beneficial for improving the quality of crystallographic protein models, especially at medium and low resolutions. Fitmunk can be used for model validation of existing structures and as a tool to assess whether side chains are modeled optimally or could be better fitted into electron density. Fitmunk is available as a web service at http://kniahini.med.virginia.edu/fitmunk/server/ or at http://fitmunk.bitbucket.org/.

Three-dimensional autoradiographic localization of quench-corrected glycine receptor specific activity in the mouse brain using sup 3 H-strychnine as the ligand

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

White, W.F.; O'Gorman, S.; Roe, A.W.

1990-03-01

The autoradiographic analysis of neurotransmitter receptor distribution is a powerful technique that provides extensive information on the localization of neurotransmitter systems. Computer methodologies are described for the analysis of autoradiographic material which include quench correction, 3-dimensional display, and quantification based on anatomical boundaries determined from the tissue sections. These methodologies are applied to the problem of the distribution of glycine receptors measured by 3H-strychnine binding in the mouse CNS. The most distinctive feature of this distribution is its marked caudorostral gradient. The highest densities of binding sites within this gradient were seen in somatic motor and sensory areas; high densitiesmore » of binding were seen in branchial efferent and special sensory areas. Moderate levels were seen in nuclei related to visceral function. Densities within the reticular formation paralleled the overall gradient with high to moderate levels of binding. The colliculi had low and the diencephalon had very low levels of binding. No binding was seen in the cerebellum or the telencephalon with the exception of the amygdala, which had very low levels of specific binding. This distribution of glycine receptors correlates well with the known functional distribution of glycine synaptic function. These data are illustrated in 3 dimensions and discussed in terms of the significance of the analysis techniques on this type of data as well as the functional significance of the distribution of glycine receptors.« less

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

PubMed

Kvaal, Simen; Helgaker, Trygve

2015-11-14

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

Benchmarking Hydrogen and Carbon NMR Chemical Shifts at HF, DFT, and MP2 Levels.

PubMed

Flaig, Denis; Maurer, Marina; Hanni, Matti; Braunger, Katharina; Kick, Leonhard; Thubauville, Matthias; Ochsenfeld, Christian

2014-02-11

An extensive study of error distributions for calculating hydrogen and carbon NMR chemical shifts at Hartree-Fock (HF), density functional theory (DFT), and Møller-Plesset second-order perturbation theory (MP2) levels is presented. Our investigation employs accurate CCSD(T)/cc-pVQZ calculations for providing reference data for 48 hydrogen and 40 carbon nuclei within an extended set of chemical compounds covering a broad range of the NMR scale with high relevance to chemical applications, especially in organic chemistry. Besides the approximations of HF, a variety of DFT functionals, and conventional MP2, we also present results with respect to a spin component-scaled MP2 (GIAO-SCS-MP2) approach. For each method, the accuracy is analyzed in detail for various basis sets, allowing identification of efficient combinations of method and basis set approximations.

Lateral and Time Distributions of Extensive Air Showers for CHICOS

NASA Astrophysics Data System (ADS)

Jillings, C. J.; Wells, D.; Chan, K. C.; Hill, J.; Falkowski, B.; Sepikas, J.

2005-04-01

We report results of a series of detailed Monte-Carlo calculations to determine the density and arrival-time distribution of charged particles in extensive air showers. We have parameterized both distributions as a function of distance from the shower axis, energy of the primary cosmic-ray proton, and incident zenith angle. Muons and electrons are parameterized separately. These parameterizations can be easily used in maximum-likelihood reconstruction of air showers. Calculations were performed for primary energies between 10^18 and 10^21eV and zenith angles out to approximately 50^o. The calculations are appropriate for the California High School Cosmic Ray Observatory: a 400 km^2 array of scintillation detectors in Los Angeles county. The average elevation of the array is approximately 250 meters above sea level. Currently 64 of 90 sites are operational. The array will be completed this year. We thank the NSF, the CURE program at the Jet Propulsion Laboratory, the SURF program at Caltech, and the Chinese University of Hong Kong.

Specific arrangement of alpha-helical coiled coils in the core domain of the bacterial flagellar hook for the universal joint function.

PubMed

Fujii, Takashi; Kato, Takayuki; Namba, Keiichi

2009-11-11

The bacterial flagellar hook is a short, highly curved tubular structure connecting the rotary motor to the filament acting as a helical propeller. The bending flexibility of the hook allows it to work as a universal joint. A partial atomic model of the hook revealed a sliding intersubunit domain interaction along the protofilament to produce bending flexibility. However, it remained unclear how the tightly packed inner core domains can still permit axial extension and compression. We report advances in cryoEM image analysis for high-resolution, high-throughput structural analysis and a density map of the hook that reveals most of the secondary structures, including the terminal alpha helices forming a coiled coil. The orientations and axial packing interactions of these two alpha helices are distinctly different from those of the filament, allowing them to have a room for axial compression and extension for bending flexibility without impairing the mechanical stability of the hook.

Whole-genome fingerprint of the DNA methylome during human B cell differentiation.

PubMed

Kulis, Marta; Merkel, Angelika; Heath, Simon; Queirós, Ana C; Schuyler, Ronald P; Castellano, Giancarlo; Beekman, Renée; Raineri, Emanuele; Esteve, Anna; Clot, Guillem; Verdaguer-Dot, Néria; Duran-Ferrer, Martí; Russiñol, Nuria; Vilarrasa-Blasi, Roser; Ecker, Simone; Pancaldi, Vera; Rico, Daniel; Agueda, Lidia; Blanc, Julie; Richardson, David; Clarke, Laura; Datta, Avik; Pascual, Marien; Agirre, Xabier; Prosper, Felipe; Alignani, Diego; Paiva, Bruno; Caron, Gersende; Fest, Thierry; Muench, Marcus O; Fomin, Marina E; Lee, Seung-Tae; Wiemels, Joseph L; Valencia, Alfonso; Gut, Marta; Flicek, Paul; Stunnenberg, Hendrik G; Siebert, Reiner; Küppers, Ralf; Gut, Ivo G; Campo, Elías; Martín-Subero, José I

2015-07-01

We analyzed the DNA methylome of ten subpopulations spanning the entire B cell differentiation program by whole-genome bisulfite sequencing and high-density microarrays. We observed that non-CpG methylation disappeared upon B cell commitment, whereas CpG methylation changed extensively during B cell maturation, showing an accumulative pattern and affecting around 30% of all measured CpG sites. Early differentiation stages mainly displayed enhancer demethylation, which was associated with upregulation of key B cell transcription factors and affected multiple genes involved in B cell biology. Late differentiation stages, in contrast, showed extensive demethylation of heterochromatin and methylation gain at Polycomb-repressed areas, and genes with apparent functional impact in B cells were not affected. This signature, which has previously been linked to aging and cancer, was particularly widespread in mature cells with an extended lifespan. Comparing B cell neoplasms with their normal counterparts, we determined that they frequently acquire methylation changes in regions already undergoing dynamic methylation during normal B cell differentiation.

Heart-Derived Stem Cells in Miniature Swine with Coronary Microembolization: Novel Ischemic Cardiomyopathy Model to Assess the Efficacy of Cell-Based Therapy

PubMed Central

Young, Rebeccah F.; Leiker, Merced M.; Suzuki, Takayuki

2016-01-01

A major problem in translating stem cell therapeutics is the difficulty of producing stable, long-term severe left ventricular (LV) dysfunction in a large animal model. For that purpose, extensive infarction was created in sinclair miniswine by injecting microspheres (1.5 × 106 microspheres, 45 μm diameter) in LAD. At 2 months after embolization, animals (n = 11) were randomized to receive allogeneic cardiosphere-derived cells derived from atrium (CDCs: 20 × 106, n = 5) or saline (untreated, n = 6). Four weeks after therapy myocardial function, myocyte proliferation (Ki67), mitosis (phosphor-Histone H3; pHH3), apoptosis, infarct size (TTC), myocyte nuclear density, and cell size were evaluated. CDCs injected into infarcted and remodeled remote myocardium (global infusion) increased regional function and global function contrasting no change in untreated animals. CDCs reduced infarct volume and stimulated Ki67 and pHH3 positive myocytes in infarct and remote regions. As a result, myocyte number (nuclear density) increased and myocyte cell diameter decreased in both infarct and remote regions. Coronary microembolization produces stable long-term ischemic cardiomyopathy. Global infusion of CDCs stimulates myocyte regeneration and improves left ventricular ejection fraction. Thus, global infusion of CDCs could become a new therapy to reverse LV dysfunction in patients with asymptomatic heart failure. PMID:27738436

Performance of the strongly constrained and appropriately normed density functional for solid-state materials

DOE PAGES

Isaacs, Eric B.; Wolverton, Chris

2018-06-22

Constructed to satisfy 17 known exact constraints for a semilocal density functional, the strongly constrained and appropriately normed (SCAN) meta-generalized-gradient-approximation functional has shown early promise for accurately describing the electronic structure of molecules and solids. One open question is how well SCAN predicts the formation energy, a key quantity for describing the thermodynamic stability of solid-state compounds. To answer this question, we perform an extensive benchmark of SCAN by computing the formation energies for a diverse group of nearly 1000 crystalline compounds for which experimental values are known. Due to an enhanced exchange interaction in the covalent bonding regime, SCANmore » substantially decreases the formation energy errors for strongly bound compounds, by approximately 50% to 110 meV/atom, as compared to the generalized gradient approximation of Perdew, Burke, and Ernzerhof (PBE). However, for intermetallic compounds, SCAN performs moderately worse than PBE with an increase in formation energy error of approximately 20%, stemming from SCAN's distinct behavior in the weak bonding regime. The formation energy errors can be further reduced via elemental chemical potential fitting. We find that SCAN leads to significantly more accurate predicted crystal volumes, moderately enhanced magnetism, and mildly improved band gaps as compared to PBE. Altogether, SCAN represents a significant improvement in accurately describing the thermodynamics of strongly bound compounds.« less

Performance of the strongly constrained and appropriately normed density functional for solid-state materials

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

Isaacs, Eric B.; Wolverton, Chris

Constructed to satisfy 17 known exact constraints for a semilocal density functional, the strongly constrained and appropriately normed (SCAN) meta-generalized-gradient-approximation functional has shown early promise for accurately describing the electronic structure of molecules and solids. One open question is how well SCAN predicts the formation energy, a key quantity for describing the thermodynamic stability of solid-state compounds. To answer this question, we perform an extensive benchmark of SCAN by computing the formation energies for a diverse group of nearly 1000 crystalline compounds for which experimental values are known. Due to an enhanced exchange interaction in the covalent bonding regime, SCANmore » substantially decreases the formation energy errors for strongly bound compounds, by approximately 50% to 110 meV/atom, as compared to the generalized gradient approximation of Perdew, Burke, and Ernzerhof (PBE). However, for intermetallic compounds, SCAN performs moderately worse than PBE with an increase in formation energy error of approximately 20%, stemming from SCAN's distinct behavior in the weak bonding regime. The formation energy errors can be further reduced via elemental chemical potential fitting. We find that SCAN leads to significantly more accurate predicted crystal volumes, moderately enhanced magnetism, and mildly improved band gaps as compared to PBE. Altogether, SCAN represents a significant improvement in accurately describing the thermodynamics of strongly bound compounds.« less

Role of the Neuropathology of Alzheimer Disease in Dementia in the Oldest-Old

PubMed Central

Haroutunian, Vahram; Schnaider-Beeri, Michal; Schmeidler, James; Wysocki, Michael; Purohit, Dushyant P.; Perl, Daniel P.; Libow, Leslie S.; Lesser, Gerson T.; Maroukian, Maria; Grossman, Hillel T.

2011-01-01

Background Neuritic plaques (NPs) and neurofibrillary tangles (NFTs) in the brain, especially in the hippocampus, entorhinal cortex, and isocortex, are hallmark lesions of Alzheimer disease and dementia in the elderly. However, this association has not been extensively studied in the rapidly growing population of the very old. Objective To assess the relationship between estimates of cognitive function and NP and NFT pathologic conditions in 317 autopsied persons aged 60 to 107 years. Design We studied the relationship between severity of dementia and the density of these characteristic lesions of Alzheimer disease in young-old, middle-old, and oldest-old persons. The relationship of the severity of dementia as measured by the Clinical Dementia Rating scale to the density of NPs and NFTs was then assessed in each age group. Participants Three hundred seventeen brains of persons aged 60 years and older were selected to have either no remarkable neuropathological lesions or only NP and NFT lesions. Brains with any other neuropathological conditions, either alone or in addition to Alzheimer disease findings, were excluded. The study cohort was then stratified into the youngest quartile (aged 60–80 years), middle 2 quartiles (aged 81–89 years), and oldest quartile (aged 90–107 years). Results While the density of NPs and NFTs rose significantly by more than 10-fold as a function of the severity of dementia in the youngest-old group, significant increases in the densities of NPs and NFTs were absent in the brains of the oldest-old. This lack of difference in the densities of NPs and NFTs was due to reduced lesion densities in the brains of oldest-old persons with dementia rather than to increased density of these lesions in the brains of nondemented oldest-old persons. Conclusions These findings suggest that the neuropathological features of dementia in the oldest-old are not the same as those of cognitively impaired younger-old persons and compel a vigorous search for neuropathological indices of dementia in this most rapidly growing segment of the elderly population. PMID:18779425

Spin-Multiplet Components and Energy Splittings by Multistate Density Functional Theory.

PubMed

Grofe, Adam; Chen, Xin; Liu, Wenjian; Gao, Jiali

2017-10-05

Kohn-Sham density functional theory has been tremendously successful in chemistry and physics. Yet, it is unable to describe the energy degeneracy of spin-multiplet components with any approximate functional. This work features two contributions. (1) We present a multistate density functional theory (MSDFT) to represent spin-multiplet components and to determine multiplet energies. MSDFT is a hybrid approach, taking advantage of both wave function theory and density functional theory. Thus, the wave functions, electron densities and energy density-functionals for ground and excited states and for different components are treated on the same footing. The method is illustrated on valence excitations of atoms and molecules. (2) Importantly, a key result is that for cases in which the high-spin components can be determined separately by Kohn-Sham density functional theory, the transition density functional in MSDFT (which describes electronic coupling) can be defined rigorously. The numerical results may be explored to design and optimize transition density functionals for configuration coupling in multiconfigurational DFT.

Theory of dynamic barriers, activated hopping, and the glass transition in polymer melts

NASA Astrophysics Data System (ADS)

Schweizer, Kenneth S.; Saltzman, Erica J.

2004-07-01

A statistical mechanical theory of collective dynamic barriers, slow segmental relaxation, and the glass transition of polymer melts is developed by combining, and in some aspects extending, methods of mode coupling, density functional, and activated hopping transport theories. A coarse-grained description of polymer chains is adopted and the melt is treated as a liquid of segments. The theory is built on the idea that collective density fluctuations on length scales considerably longer than the local cage scale are of primary importance in the deeply supercooled regime. The barrier hopping or segmental relaxation time is predicted to be a function primarily of a single parameter that is chemical structure, temperature, and pressure dependent. This parameter depends on the material-specific dimensionless amplitude of thermal density fluctuations (compressibility) and a reduced segmental density determined by the packing length and backbone characteristic ratio. Analytic results are derived for a crossover temperature Tc, collective barrier, and glass transition temperature Tg. The relation of these quantities to structural and thermodynamic properties of the polymer melt is established. A universal power-law scaling behavior of the relaxation time below Tc is predicted based on identification of a reduced temperature variable that quantifies the breadth of the supercooled regime. Connections between the ratio Tc/Tg, two measures of dynamic fragility, and the magnitude of the local relaxation time at Tg logically follow. Excellent agreement with experiment is found for these generic aspects, and the crucial importance of the experimentally observed near universality of the dynamic crossover time is established. Extensions of the theory to treat the full chain dynamics, heterogeneity, barrier fluctuations, and nonpolymeric thermal glass forming liquids are briefly discussed.

An Analytical Planning Model to Estimate the Optimal Density of Charging Stations for Electric Vehicles.

PubMed

Ahn, Yongjun; Yeo, Hwasoo

2015-01-01

The charging infrastructure location problem is becoming more significant due to the extensive adoption of electric vehicles. Efficient charging station planning can solve deeply rooted problems, such as driving-range anxiety and the stagnation of new electric vehicle consumers. In the initial stage of introducing electric vehicles, the allocation of charging stations is difficult to determine due to the uncertainty of candidate sites and unidentified charging demands, which are determined by diverse variables. This paper introduces the Estimating the Required Density of EV Charging (ERDEC) stations model, which is an analytical approach to estimating the optimal density of charging stations for certain urban areas, which are subsequently aggregated to city level planning. The optimal charging station's density is derived to minimize the total cost. A numerical study is conducted to obtain the correlations among the various parameters in the proposed model, such as regional parameters, technological parameters and coefficient factors. To investigate the effect of technological advances, the corresponding changes in the optimal density and total cost are also examined by various combinations of technological parameters. Daejeon city in South Korea is selected for the case study to examine the applicability of the model to real-world problems. With real taxi trajectory data, the optimal density map of charging stations is generated. These results can provide the optimal number of chargers for driving without driving-range anxiety. In the initial planning phase of installing charging infrastructure, the proposed model can be applied to a relatively extensive area to encourage the usage of electric vehicles, especially areas that lack information, such as exact candidate sites for charging stations and other data related with electric vehicles. The methods and results of this paper can serve as a planning guideline to facilitate the extensive adoption of electric vehicles.

Charge localization and ordering in A 2 Mn 8 O 16 hollandite group oxides: Impact of density functional theory approaches

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

Kaltak, Merzuk; Fernandez-Serra, Marivi; Hybertsen, Mark S.

The phases of A 2Mn 8O 16 hollandite group oxides emerge from the competition between ionic interactions, Jahn-Teller effects, charge ordering, and magnetic interactions. Their balanced treatment with feasible computational approaches can be challenging for commonly used approximations in density functional theory. Three examples (A = Ag, Li, and K) are studied with a sequence of different approximate exchange-correlation functionals. Starting from a generalized gradient approximation (GGA), an extension to include van der Waals interactions and a recently proposed meta-GGA are considered. Then local Coulomb interactions for the Mn 3d electrons are more explicitly considered with the DFT + Umore » approach. Finally, selected results from a hybrid functional approach provide a reference. Results for the binding energy of the A species in the parent oxide highlight the role of van der Waals interactions. Relatively accurate results for insertion energies can be achieved with a low-U and a high-U approach. In the low-U case, the materials are described as band metals with a high-symmetry, tetragonal crystal structure. In the high-U case, the electrons donated by A result in formation of local Mn 3+ centers and corresponding Jahn-Teller distortions characterized by a local order parameter. The resulting degree of monoclinic distortion depends on charge ordering and magnetic interactions in the phase formed. The reference hybrid functional results show charge localization and ordering. Comparison to low-temperature experiments of related compounds suggests that charge localization is the physically correct result for the hollandite group oxides studied here. Lastly, while competing effects in the local magnetic coupling are subtle, the fully anisotropic implementation of DFT + U gives the best overall agreement with results from the hybrid functional.« less

Charge localization and ordering in A 2 Mn 8 O 16 hollandite group oxides: Impact of density functional theory approaches

DOE PAGES

Kaltak, Merzuk; Fernandez-Serra, Marivi; Hybertsen, Mark S.

2017-12-01

The phases of A 2Mn 8O 16 hollandite group oxides emerge from the competition between ionic interactions, Jahn-Teller effects, charge ordering, and magnetic interactions. Their balanced treatment with feasible computational approaches can be challenging for commonly used approximations in density functional theory. Three examples (A = Ag, Li, and K) are studied with a sequence of different approximate exchange-correlation functionals. Starting from a generalized gradient approximation (GGA), an extension to include van der Waals interactions and a recently proposed meta-GGA are considered. Then local Coulomb interactions for the Mn 3d electrons are more explicitly considered with the DFT + Umore » approach. Finally, selected results from a hybrid functional approach provide a reference. Results for the binding energy of the A species in the parent oxide highlight the role of van der Waals interactions. Relatively accurate results for insertion energies can be achieved with a low-U and a high-U approach. In the low-U case, the materials are described as band metals with a high-symmetry, tetragonal crystal structure. In the high-U case, the electrons donated by A result in formation of local Mn 3+ centers and corresponding Jahn-Teller distortions characterized by a local order parameter. The resulting degree of monoclinic distortion depends on charge ordering and magnetic interactions in the phase formed. The reference hybrid functional results show charge localization and ordering. Comparison to low-temperature experiments of related compounds suggests that charge localization is the physically correct result for the hollandite group oxides studied here. Lastly, while competing effects in the local magnetic coupling are subtle, the fully anisotropic implementation of DFT + U gives the best overall agreement with results from the hybrid functional.« less

Charge localization and ordering in A2Mn8O16 hollandite group oxides: Impact of density functional theory approaches

NASA Astrophysics Data System (ADS)

Kaltak, Merzuk; Fernández-Serra, Marivi; Hybertsen, Mark S.

2017-12-01

The phases of A2Mn8O16 hollandite group oxides emerge from the competition between ionic interactions, Jahn-Teller effects, charge ordering, and magnetic interactions. Their balanced treatment with feasible computational approaches can be challenging for commonly used approximations in density functional theory. Three examples (A = Ag, Li, and K) are studied with a sequence of different approximate exchange-correlation functionals. Starting from a generalized gradient approximation (GGA), an extension to include van der Waals interactions and a recently proposed meta-GGA are considered. Then local Coulomb interactions for the Mn 3 d electrons are more explicitly considered with the DFT + U approach. Finally, selected results from a hybrid functional approach provide a reference. Results for the binding energy of the A species in the parent oxide highlight the role of van der Waals interactions. Relatively accurate results for insertion energies can be achieved with a low-U and a high-U approach. In the low-U case, the materials are described as band metals with a high-symmetry, tetragonal crystal structure. In the high-U case, the electrons donated by A result in formation of local Mn3 + centers and corresponding Jahn-Teller distortions characterized by a local order parameter. The resulting degree of monoclinic distortion depends on charge ordering and magnetic interactions in the phase formed. The reference hybrid functional results show charge localization and ordering. Comparison to low-temperature experiments of related compounds suggests that charge localization is the physically correct result for the hollandite group oxides studied here. Finally, while competing effects in the local magnetic coupling are subtle, the fully anisotropic implementation of DFT + U gives the best overall agreement with results from the hybrid functional.

Forward and inverse functional variations in rotationally inelastic scattering

NASA Astrophysics Data System (ADS)

Guzman, Robert; Rabitz, Herschel

1986-09-01

This paper considers the response of various rotational energy transfer processes to functional variations about an assumed model intermolecular potential. Attention is focused on the scattering of an atom and a linear rigid rotor. The collision dynamics are approximated by employing both the infinite order sudden (IOS) and exponential distorted wave (EDW) methods to describe Ar-N2 and He-H2, respectively. The following cross sections are considered: state-to-state differential and integral, final state summed differential and integral, and effective diffusion and viscosity cross sections. Attention is first given to the forward sensitivity densities δ0/δV(R,r) where 0 denotes any of the aforementioned cross sections, R is the intermolecular distance, and r is the internal coordinates. These forward sensitivity densities (functional derivatives) offer a quantitative measure of the importance of different regions of the potential surface to a chosen cross section. Via knowledge of the forward sensitivities and a particular variation δV(R,r) the concomitant response δ0 is generated. It was found that locally a variation in the potential can give rise to a large response in the cross sections as measured by these forward densities. In contrast, a unit percent change in the overall potential produced a 1%-10% change in the cross sections studied indicating that the large + and - responses to local variations tend to cancel. In addition, inverse sensitivity densities δV(R,r)/δ0 are obtained. These inverse densities are of interest since they are the exact solution to the infinitesimal inverse scattering problem. Although the inverse sensitivity densities do not in themselves form an inversion algorithm, they do offer a quantitative measure of the importance of performing particular measurements for the ultimate purpose of inversion. Using a set of state-to-state integral cross sections we found that the resultant responses from the infinitesimal inversion were typically small such that ‖δV(R,r)‖≪‖V(R,r)‖. From the viewpoint of an actual inversion, these results indicate that only through an extensive effort will significant knowledge of the potential be gained from the cross sections. All of these calculations serve to illustrate the methodology, and other observables as well as dynamical schemes could be explored as desired.

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

PubMed

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

2015-02-10

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

Self-assembly of hard helices: a rich and unconventional polymorphism.

PubMed

Kolli, Hima Bindu; Frezza, Elisa; Cinacchi, Giorgio; Ferrarini, Alberta; Giacometti, Achille; Hudson, Toby S; De Michele, Cristiano; Sciortino, Francesco

2014-11-07

Hard helices can be regarded as a paradigmatic elementary model for a number of natural and synthetic soft matter systems, all featuring the helix as their basic structural unit, from natural polynucleotides and polypeptides to synthetic helical polymers, and from bacterial flagella to colloidal helices. Here we present an extensive investigation of the phase diagram of hard helices using a variety of methods. Isobaric Monte Carlo numerical simulations are used to trace the phase diagram; on going from the low-density isotropic to the high-density compact phases a rich polymorphism is observed, exhibiting a special chiral screw-like nematic phase and a number of chiral and/or polar smectic phases. We present full characterization of the latter, showing that they have unconventional features, ascribable to the helical shape of the constituent particles. Equal area construction is used to locate the isotropic-to-nematic phase transition, and the results are compared with those stemming from an Onsager-like theory. Density functional theory is also used to study the nematic-to-screw-nematic phase transition; within the simplifying assumption of perfectly parallel helices, we compare different levels of approximation, that is second- and third-virial expansions and a Parsons-Lee correction.

Tetrahedrality and hydrogen bonds in water

NASA Astrophysics Data System (ADS)

Székely, Eszter; Varga, Imre K.; Baranyai, András

2016-06-01

We carried out extensive calculations of liquid water at different temperatures and pressures using the BK3 model suggested recently [P. T. Kiss and A. Baranyai, J. Chem. Phys. 138, 204507 (2013)]. In particular, we were interested in undercooled regions to observe the propensity of water to form tetrahedral coordination of closest neighbors around a central molecule. We compared the found tetrahedral order with the number of hydrogen bonds and with the partial pair correlation functions unfolded as distributions of the closest, the second closest, etc. neighbors. We found that contrary to the number of hydrogen bonds, tetrahedrality changes substantially with state variables. Not only the number of tetrahedral arrangements increases with lowering the pressure, the density, and the temperature but the domain size of connecting tetrahedral structures as well. The difference in tetrahedrality is very pronounced between the two sides of the Widom line and even more so between the low density amorphous (LDA) and high density amorphous (HDA) phases. We observed that in liquid water and in HDA, the 5th water molecule, contrary to ice and LDA, is positioned between the first and the second coordination shell. We found no convincing evidence of structural heterogeneity or regions referring to structural transition.

Twist-averaged boundary conditions for nuclear pasta Hartree-Fock calculations

DOE PAGES

Schuetrumpf, B.; Nazarewicz, W.

2015-10-21

Nuclear pasta phases, present in the inner crust of neutron stars, are associated with nucleonic matter at subsaturation densities arranged in regular shapes. Those complex phases, residing in a layer which is approximately 100-m thick, impact many features of neutron stars. Theoretical quantum-mechanical simulations of nuclear pasta are usually carried out in finite three-dimensional boxes assuming periodic boundary conditions. The resulting solutions are affected by spurious finite-size effects. To remove spurious finite-size effects, it is convenient to employ twist-averaged boundary conditions (TABC) used in condensed matter, nuclear matter, and lattice quantum chromodynamics applications. In this work, we study the effectivenessmore » of TABC in the context of pasta phase simulations within nuclear density functional theory. We demonstrated that by applying TABC reliable results can be obtained from calculations performed in relatively small volumes. By studying various contributions to the total energy, we gain insights into pasta phases in mid-density range. Future applications will include the TABC extension of the adaptive multiresolution 3D Hartree-Fock solver and Hartree-Fock-Bogoliubov TABC applications to superfluid pasta phases and complex nucleonic topologies as in fission.« less

Thermodynamics, Kinetics and Structural Evolution of ε-LiVOPO 4 over Multiple Lithium Intercalation

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

Lin, Yuh-Chieh; Wen, Bohua; Wiaderek, Kamila M.

In this work, we demonstrate the stable cycling of more than one Li in solid-state-synthesized ε-LiVOPO4 over more than 20 cycles for the first time. Using a combination of density functional theory (DFT) calculations, X-ray pair distribution function (PDF) analysis and X-ray absorption near edge structure (XANES) measurements, we present a comprehensive analysis of the thermodynamics, kinetics, and structural evolution of ε-LixVOPO4 over the entire lithiation range. We identify two intermediate phases at x = 1.5 and 1.75 in the low-voltage regime using DFT calculations, and the computed and electrochemical voltage profiles are in excellent agreement. Operando PDF and EXAFSmore » techniques show a reversible hysteretic change in the short (<2 Å) V—O bond lengths coupled with an irreversible extension of the long V—O bond (>2.4 Å) during low-voltage cycling. Hydrogen intercalation from electrolyte decomposition is a possible explanation for the ~2.4 Å V—O bond and its irreversible extension. Finally, we show that ε-LixVOPO4 is likely a pseudo-1D ionic diffuser with low electronic conductivity using DFT calculations, which suggests that nanosizing and carbon coating is necessary to achieve good electrochemical performance in this material.« less

A proteomic analysis of the chromoplasts isolated from sweet orange fruits [Citrus sinensis (L.) Osbeck].

PubMed

Zeng, Yunliu; Pan, Zhiyong; Ding, Yuduan; Zhu, Andan; Cao, Hongbo; Xu, Qiang; Deng, Xiuxin

2011-11-01

Here, a comprehensive proteomic analysis of the chromoplasts purified from sweet orange using Nycodenz density gradient centrifugation is reported. A GeLC-MS/MS shotgun approach was used to identify the proteins of pooled chromoplast samples. A total of 493 proteins were identified from purified chromoplasts, of which 418 are putative plastid proteins based on in silico sequence homology and functional analyses. Based on the predicted functions of these identified plastid proteins, a large proportion (∼60%) of the chromoplast proteome of sweet orange is constituted by proteins involved in carbohydrate metabolism, amino acid/protein synthesis, and secondary metabolism. Of note, HDS (hydroxymethylbutenyl 4-diphosphate synthase), PAP (plastid-lipid-associated protein), and psHSPs (plastid small heat shock proteins) involved in the synthesis or storage of carotenoid and stress response are among the most abundant proteins identified. A comparison of chromoplast proteomes between sweet orange and tomato suggested a high level of conservation in a broad range of metabolic pathways. However, the citrus chromoplast was characterized by more extensive carotenoid synthesis, extensive amino acid synthesis without nitrogen assimilation, and evidence for lipid metabolism concerning jasmonic acid synthesis. In conclusion, this study provides an insight into the major metabolic pathways as well as some unique characteristics of the sweet orange chromoplasts at the whole proteome level.

Unconditionally energy stable time stepping scheme for Cahn–Morral equation: Application to multi-component spinodal decomposition and optimal space tiling

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

Tavakoli, Rouhollah, E-mail: rtavakoli@sharif.ir

An unconditionally energy stable time stepping scheme is introduced to solve Cahn–Morral-like equations in the present study. It is constructed based on the combination of David Eyre's time stepping scheme and Schur complement approach. Although the presented method is general and independent of the choice of homogeneous free energy density function term, logarithmic and polynomial energy functions are specifically considered in this paper. The method is applied to study the spinodal decomposition in multi-component systems and optimal space tiling problems. A penalization strategy is developed, in the case of later problem, to avoid trivial solutions. Extensive numerical experiments demonstrate themore » success and performance of the presented method. According to the numerical results, the method is convergent and energy stable, independent of the choice of time stepsize. Its MATLAB implementation is included in the appendix for the numerical evaluation of algorithm and reproduction of the presented results. -- Highlights: •Extension of Eyre's convex–concave splitting scheme to multiphase systems. •Efficient solution of spinodal decomposition in multi-component systems. •Efficient solution of least perimeter periodic space partitioning problem. •Developing a penalization strategy to avoid trivial solutions. •Presentation of MATLAB implementation of the introduced algorithm.« less

A novel function of WAVE in lamellipodia: WAVE1 is required for stabilization of lamellipodial protrusions during cell spreading.

PubMed

Yamazaki, Daisuke; Fujiwara, Takashi; Suetsugu, Shiro; Takenawa, Tadaomi

2005-05-01

When a cell spreads and moves, reorganization of the actin cytoskeleton pushes the cell membrane, and the resulting membrane protrusions create new points of contact with the substrate and generate the locomotive force. Membrane extension and adhesion to a substrate must be tightly coordinated for effective cell movement, but little is known about the mechanisms underlying these processes. WAVEs are critical regulators of Rac-induced actin reorganization. WAVE2 is essential for formation of lamellipodial structures at the cell periphery stimulated by growth factors, but it is thought that WAVE1 is dispensable for such processes in mouse embryonic fibroblasts (MEFs). Here we show a novel function of WAVE in lamellipodial protrusions during cell spreading. During spreading on fibronectin (FN), MEFs with knockouts (KOs) of WAVE1 and WAVE2 showed different membrane dynamics, suggesting that these molecules have distinct roles in lamellipodium formation. Formation of lamellipodial structures on FN was inhibited in WAVE2 KO MEFs. In contrast, WAVE1 is not essential for extension of lamellipodial protrusions but is required for stabilization of such structures. WAVE1-deficiency decreased the density of actin filaments and increased the speed of membrane extension, causing deformation of focal complex at the tip of spreading edges. Thus, at the tip of the lamellipodial protrusion, WAVE2 generates the membrane protrusive structures containing actin filaments, and modification by WAVE1 stabilizes these structures through cell-substrate adhesion. Coordination of WAVE1 and WAVE2 activities appears to be necessary for formation of proper actin structures in stable lamellipodia.

Combined copper/zinc attachment to prion protein

NASA Astrophysics Data System (ADS)

Hodak, Miroslav; Bernholc, Jerry

2013-03-01

Misfolding of prion protein (PrP) is responsible for diseases such as ``mad-cow disease'' in cattle and Creutzfeldt-Jacob in humans. Extensive experimental investigation has established that this protein strongly interacts with copper ions, and this ability has been linked to its still unknown function. Attachment of other metal ions (zinc, iron, manganese) have been demonstrated as well, but none of them could outcompete copper. Recent finding, however, indicates that at intermediate concentrations both copper and zinc ions can attach to the PrP at the octarepeat region, which contains high affinity metal binding sites. Based on this evidence, we have performed density functional theory simulations to investigate the combined Cu/Zn attachment. We consider all previously reported binding modes of copper at the octarepeat region and examine a possibility simultaneous Cu/Zn attachment. We find that this can indeed occur for only one of the known binding sites, when copper changes its coordination mode to allow for attachment of zinc ion. The implications of the simultaneous attachment on neural function remain to be explored.

The Superstatistical Nature and Interoccurrence Time of Atmospheric Mercury Concentration Fluctuations

NASA Astrophysics Data System (ADS)

Carbone, F.; Bruno, A. G.; Naccarato, A.; De Simone, F.; Gencarelli, C. N.; Sprovieri, F.; Hedgecock, I. M.; Landis, M. S.; Skov, H.; Pfaffhuber, K. A.; Read, K. A.; Martin, L.; Angot, H.; Dommergue, A.; Magand, O.; Pirrone, N.

2018-01-01

The probability density function (PDF) of the time intervals between subsequent extreme events in atmospheric Hg0 concentration data series from different latitudes has been investigated. The Hg0 dynamic possesses a long-term memory autocorrelation function. Above a fixed threshold Q in the data, the PDFs of the interoccurrence time of the Hg0 data are well described by a Tsallis q-exponential function. This PDF behavior has been explained in the framework of superstatistics, where the competition between multiple mesoscopic processes affects the macroscopic dynamics. An extensive parameter μ, encompassing all possible fluctuations related to mesoscopic phenomena, has been identified. It follows a χ2 distribution, indicative of the superstatistical nature of the overall process. Shuffling the data series destroys the long-term memory, the distributions become independent of Q, and the PDFs collapse on to the same exponential distribution. The possible central role of atmospheric turbulence on extreme events in the Hg0 data is highlighted.

Vps35 loss promotes hyperresorptive osteoclastogenesis and osteoporosis via sustained RANKL signaling

PubMed Central

Xia, Wen-Fang; Tang, Fu-Lei; Xiong, Lei; Xiong, Shan; Jung, Ji-Ung; Lee, Dae-Hoon; Li, Xing-Sheng; Feng, Xu; Mei, Lin

2013-01-01

Receptor activator of NF-κB (RANK) plays a critical role in osteoclastogenesis, an essential process for the initiation of bone remodeling to maintain healthy bone mass and structure. Although the signaling and function of RANK have been investigated extensively, much less is known about the negative regulatory mechanisms of its signaling. We demonstrate in this paper that RANK trafficking, signaling, and function are regulated by VPS35, a major component of the retromer essential for selective endosome to Golgi retrieval of membrane proteins. VPS35 loss of function altered RANK ligand (RANKL)–induced RANK distribution, enhanced RANKL sensitivity, sustained RANKL signaling, and increased hyperresorptive osteoclast (OC) formation. Hemizygous deletion of the Vps35 gene in mice promoted hyperresorptive osteoclastogenesis, decreased bone formation, and caused a subsequent osteoporotic deficit, including decreased trabecular bone volumes and reduced trabecular thickness and density in long bones. These results indicate that VPS35 critically deregulates RANK signaling, thus restraining increased formation of hyperresorptive OCs and preventing osteoporotic deficits. PMID:23509071

Multiconfiguration Pair-Density Functional Theory.

PubMed

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

2014-09-09

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

A fast atlas-guided high density diffuse optical tomography system for brain imaging

NASA Astrophysics Data System (ADS)

Dai, Xianjin; Zhang, Tao; Yang, Hao; Jiang, Huabei

2017-02-01

Near infrared spectroscopy (NIRS) is an emerging functional brain imaging tool capable of assessing cerebral concentrations of oxygenated hemoglobin (HbO) and deoxygenated hemoglobin (HbR) during brain activation noninvasively. As an extension of NIRS, diffuse optical tomography (DOT) not only shares the merits of providing continuous readings of cerebral oxygenation, but also has the ability to provide spatial resolution in the millimeter scale. Based on the scattering and absorption properties of nonionizing near-infrared light in biological tissue, DOT has been successfully applied in the imaging of breast tumors, osteoarthritis and cortex activations. Here, we present a state-of-art fast high density DOT system suitable for brain imaging. It can achieve up to a 21 Hz sampling rate for a full set of two-wavelength data for 3-D DOT brain image reconstruction. The system was validated using tissue-mimicking brain-model phantom. Then, experiments on healthy subjects were conducted to demonstrate the capability of the system.

Fast visible imaging of turbulent plasma in TORPEX

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

Iraji, D.; Diallo, A.; Fasoli, A.

2008-10-15

Fast framing cameras constitute an important recent diagnostic development aimed at monitoring light emission from magnetically confined plasmas, and are now commonly used to study turbulence in plasmas. In the TORPEX toroidal device [A. Fasoli et al., Phys. Plasmas 13, 055902 (2006)], low frequency electrostatic fluctuations associated with drift-interchange waves are routinely measured by means of extensive sets of Langmuir probes. A Photron Ultima APX-RS fast framing camera has recently been acquired to complement Langmuir probe measurements, which allows comparing statistical and spectral properties of visible light and electrostatic fluctuations. A direct imaging system has been developed, which allows viewingmore » the light, emitted from microwave-produced plasmas tangentially and perpendicularly to the toroidal direction. The comparison of the probability density function, power spectral density, and autoconditional average of the camera data to those obtained using a multiple head electrostatic probe covering the plasma cross section shows reasonable agreement in the case of perpendicular view and in the plasma region where interchange modes dominate.« less

Quark-Meson-Coupling (QMC) model for finite nuclei, nuclear matter and beyond

NASA Astrophysics Data System (ADS)

Guichon, P. A. M.; Stone, J. R.; Thomas, A. W.

2018-05-01

The Quark-Meson-Coupling model, which self-consistently relates the dynamics of the internal quark structure of a hadron to the relativistic mean fields arising in nuclear matter, provides a natural explanation to many open questions in low energy nuclear physics, including the origin of many-body nuclear forces and their saturation, the spin-orbit interaction and properties of hadronic matter at a wide range of densities up to those occurring in the cores of neutron stars. Here we focus on four aspects of the model (i) a full comprehensive survey of the theory, including the latest developments, (ii) extensive application of the model to ground state properties of finite nuclei and hypernuclei, with a discussion of similarities and differences between the QMC and Skyrme energy density functionals, (iii) equilibrium conditions and composition of hadronic matter in cold and warm neutron stars and their comparison with the outcome of relativistic mean-field theories and, (iv) tests of the fundamental idea that hadron structure changes in-medium.

Branching habit and the allocation of reproductive resources in conifers.

PubMed

Leslie, Andrew B

2012-09-01

Correlated relationships between branch thickness, branch density, and twig and leaf size have been used extensively to study the evolution of plant canopy architecture, but fewer studies have explored the impact of these relationships on the allocation of reproductive resources. This study quantifies pollen cone production in conifers, which have similar basic reproductive biology but vary dramatically in branching habit, in order to test how differences in branch diameter influence pollen cone size and the density with which they are deployed in the canopy. Measurements of canopy branch density, the number of cones per branch and cone size were used to estimate the amount of pollen cone tissues produced by 16 species in three major conifer clades. The number of pollen grains produced was also estimated using direct counts from individual pollen cones. The total amount of pollen cone tissues in the conifer canopy varied little among species and clades, although vegetative traits such as branch thickness, branch density and pollen cone size varied over several orders of magnitude. However, branching habit controls the way these tissues are deployed: taxa with small branches produce small pollen cones at a high density, while taxa with large branches produce large cones relatively sparsely. Conifers appear to invest similar amounts of energy in pollen production independent of branching habit. However, similar associations between branch thickness, branch density and pollen cone size are seen across conifers, including members of living and extinct groups not directly studied here. This suggests that reproductive features relating to pollen cone size are in large part a function of the evolution of vegetative morphology and branching habit.

Second-principles method for materials simulations including electron and lattice degrees of freedom

NASA Astrophysics Data System (ADS)

García-Fernández, Pablo; Wojdeł, Jacek C.; Íñiguez, Jorge; Junquera, Javier

2016-05-01

We present a first-principles-based (second-principles) scheme that permits large-scale materials simulations including both atomic and electronic degrees of freedom on the same footing. The method is based on a predictive quantum-mechanical theory—e.g., density functional theory—and its accuracy can be systematically improved at a very modest computational cost. Our approach is based on dividing the electron density of the system into a reference part—typically corresponding to the system's neutral, geometry-dependent ground state—and a deformation part—defined as the difference between the actual and reference densities. We then take advantage of the fact that the bulk part of the system's energy depends on the reference density alone; this part can be efficiently and accurately described by a force field, thus avoiding explicit consideration of the electrons. Then, the effects associated to the difference density can be treated perturbatively with good precision by working in a suitably chosen Wannier function basis. Further, the electronic model can be restricted to the bands of interest. All these features combined yield a very flexible and computationally very efficient scheme. Here we present the basic formulation of this approach, as well as a practical strategy to compute model parameters for realistic materials. We illustrate the accuracy and scope of the proposed method with two case studies, namely, the relative stability of various spin arrangements in NiO (featuring complex magnetic interactions in a strongly-correlated oxide) and the formation of a two-dimensional electron gas at the interface between band insulators LaAlO3 and SrTiO3 (featuring subtle electron-lattice couplings and screening effects). We conclude by discussing ways to overcome the limitations of the present approach (most notably, the assumption of a fixed bonding topology), as well as its many envisioned possibilities and future extensions.

Classical density functional theory and Monte Carlo simulation study of electric double layer in the vicinity of a cylindrical electrode

NASA Astrophysics Data System (ADS)

Zhou, Shiqi; Lamperski, Stanisław; Sokołowska, Marta

2017-07-01

We have performed extensive Monte-Carlo simulations and classical density functional theory (DFT) calculations of the electrical double layer (EDL) near a cylindrical electrode in a primitive model (PM) modified by incorporating interionic dispersion interactions. It is concluded that (i) in general, an unsophisticated use of the mean field (MF) approximation for the interionic dispersion interactions does not distinctly worsen the classical DFT performance, even if the salt ions considered are highly asymmetrical in size (3:1) and charge (5:1), the bulk molar concentration considered is high up to a total bulk ion packing fraction of 0.314, and the surface charge density of up to 0.5 C m-2. (ii) More specifically, considering the possible noises in the simulation, the local volume charge density profiles are the most accurately predicted by the classical DFT in all situations, and the co- and counter-ion singlet distributions are also rather accurately predicted; whereas the mean electrostatic potential profile is relatively less accurately predicted due to an integral amplification of minor inaccuracy of the singlet distributions. (iii) It is found that the layered structure of the co-ion distribution is abnormally possible only if the surface charge density is high enough (for example 0.5 C m-2) moreover, the co-ion valence abnormally influences the peak height of the first counter-ion layer, which decreases with the former. (iv) Even if both the simulation and DFT indicate an insignificant contribution of the interionic dispersion interaction to the above three ‘local’ quantities, it is clearly shown by the classical DFT that the interionic dispersion interaction does significantly influence a ‘global’ quantity like the cylinder surface-aqueous electrolyte interfacial tension, and this may imply the role of the interionic dispersion interaction in explaining the specific Hofmeister effects. We elucidate all of the above observations based on the arguments from the liquid state theory and at the molecular scale.

Structural study of Al2O3-Na2O-CaO-P2O5 bioactive glasses as a function of aluminium content.

PubMed

Smith, J M; King, S P; Barney, E R; Hanna, J V; Newport, R J; Pickup, D M

2013-01-21

Calcium phosphate based biomaterials are extensively used in the context of tissue engineering: small changes in composition can lead to significant changes in properties allowing their use in a wide range of applications. Samples of composition (Al(2)O(3))(x)(Na(2)O)(0.11-x)(CaO)(0.445)(P(2)O(5))(0.445), where x = 0, 0.03, 0.05, and 0.08, were prepared by melt quenching. The atomic-scale structure has been studied using neutron diffraction and solid state (27)Al MAS NMR, and these data have been rationalised with the determined density of the final glass product. With increasing aluminium concentration the density increases initially, but beyond about 3 mol. % Al(2)O(3) the density starts to decrease. Neutron diffraction data show a concomitant change in the aluminium speciation, which is confirmed by (27)Al MAS NMR studies. The NMR data reveal that aluminium is present in 4, 5, and 6-fold coordination and that the relative concentrations of these environments change with increasing aluminium concentration. Materials containing aluminium in 6-fold coordination tend to have higher densities than analogous materials with the aluminium found in 4-fold coordination. Thus, the density changes may readily be explained in terms of an increase in the relative concentration of 4-coordinated aluminium at the expense of 6-fold aluminium as the Al(2)O(3) content is increased beyond 3 mol. %.

Normalized difference vegetation index (ndvi) analysis for land cover types using landsat 8 oli in besitang watershed, Indonesia

NASA Astrophysics Data System (ADS)

Zaitunah, A.; Samsuri; Ahmad, A. G.; Safitri, R. A.

2018-03-01

Watershed is an ecosystem area confined by topography and has function as a catcher, storage, and supplier of water, sediments, pollutants and nutrients in the river system and exit through a single outlet. Various activities around watershed areas of Besitang have changed the land cover and vegetation index (NDVI) that exist in the region. In order to detect changes in land cover and NDVI quickly and accurately, we used remote sensing technology and geographic information systems (GIS). The study aimed to assess changes in land cover and vegetation density (NDVI) between 2005 and 2015, as well as obtaining the density of vegetation (NDVI) on each of the land cover of 2005 and 2015. The research showed the extensive of forest area of 949.65 Ha and a decline of mangrove forest area covering an area of 2,884.06 Ha. The highest vegetation density reduced 39,714.58 Ha, and rather dense increased 24,410.72 Ha between 2005 and 2015. The land cover that have the highest NDVI value range with very dense vegetation density class is the primary dry forest (0.804 to 0.876), followed by secondary dry forest (0.737 to 0.804) for 2015. In 2015 the land cover has NDVI value range the primary dry forest (0.513 to 0.57), then secondary dry forest (0.456 to 0.513) with dense vegetation density class

Thermodynamics of RNA structures by Wang–Landau sampling

PubMed Central

Lou, Feng; Clote, Peter

2010-01-01

Motivation: Thermodynamics-based dynamic programming RNA secondary structure algorithms have been of immense importance in molecular biology, where applications range from the detection of novel selenoproteins using expressed sequence tag (EST) data, to the determination of microRNA genes and their targets. Dynamic programming algorithms have been developed to compute the minimum free energy secondary structure and partition function of a given RNA sequence, the minimum free-energy and partition function for the hybridization of two RNA molecules, etc. However, the applicability of dynamic programming methods depends on disallowing certain types of interactions (pseudoknots, zig-zags, etc.), as their inclusion renders structure prediction an nondeterministic polynomial time (NP)-complete problem. Nevertheless, such interactions have been observed in X-ray structures. Results: A non-Boltzmannian Monte Carlo algorithm was designed by Wang and Landau to estimate the density of states for complex systems, such as the Ising model, that exhibit a phase transition. In this article, we apply the Wang-Landau (WL) method to compute the density of states for secondary structures of a given RNA sequence, and for hybridizations of two RNA sequences. Our method is shown to be much faster than existent software, such as RNAsubopt. From density of states, we compute the partition function over all secondary structures and over all pseudoknot-free hybridizations. The advantage of the WL method is that by adding a function to evaluate the free energy of arbitary pseudoknotted structures and of arbitrary hybridizations, we can estimate thermodynamic parameters for situations known to be NP-complete. This extension to pseudoknots will be made in the sequel to this article; in contrast, the current article describes the WL algorithm applied to pseudoknot-free secondary structures and hybridizations. Availability: The WL RNA hybridization web server is under construction at http://bioinformatics.bc.edu/clotelab/. Contact: clote@bc.edu PMID:20529917

Reformulation of Density Functional Theory for N-Representable Densities and the Resolution of the v-Representability Problem

DOE PAGES

Gonis, A.; Zhang, X. G.; Stocks, G. M.; ...

2015-10-23

Density functional theory for the case of general, N-representable densities is reformulated in terms of density functional derivatives of expectation values of operators evaluated with wave functions leading to a density, making no reference to the concept of potential. The developments provide a complete solution of the v-representability problem by establishing a mathematical procedure that determines whether a density is v-representable and in the case of an affirmative answer determines the potential (within an additive constant) as a derivative with respect to the density of a constrained search functional. It also establishes the existence of an energy functional of themore » density that, for v-representable densities, assumes its minimum value at the density describing the ground state of an interacting many-particle system. The theorems of Hohenberg and Kohn emerge as special cases of the formalism.« less

Stochastic Geometric Network Models for Groups of Functional and Structural Connectomes

PubMed Central

Friedman, Eric J.; Landsberg, Adam S.; Owen, Julia P.; Li, Yi-Ou; Mukherjee, Pratik

2014-01-01

Structural and functional connectomes are emerging as important instruments in the study of normal brain function and in the development of new biomarkers for a variety of brain disorders. In contrast to single-network studies that presently dominate the (non-connectome) network literature, connectome analyses typically examine groups of empirical networks and then compare these against standard (stochastic) network models. Current practice in connectome studies is to employ stochastic network models derived from social science and engineering contexts as the basis for the comparison. However, these are not necessarily best suited for the analysis of connectomes, which often contain groups of very closely related networks, such as occurs with a set of controls or a set of patients with a specific disorder. This paper studies important extensions of standard stochastic models that make them better adapted for analysis of connectomes, and develops new statistical fitting methodologies that account for inter-subject variations. The extensions explicitly incorporate geometric information about a network based on distances and inter/intra hemispherical asymmetries (to supplement ordinary degree-distribution information), and utilize a stochastic choice of networks' density levels (for fixed threshold networks) to better capture the variance in average connectivity among subjects. The new statistical tools introduced here allow one to compare groups of networks by matching both their average characteristics and the variations among them. A notable finding is that connectomes have high “smallworldness” beyond that arising from geometric and degree considerations alone. PMID:25067815

Exchange-correlation energies of atoms from efficient density functionals: influence of the electron density

DOE PAGES

Tao, Jianmin; Ye, Lin -Hui; Duan, Yuhua

2017-11-20

The primary goal of Kohn–Sham density functional theory is to evaluate the exchange-correlation contribution to electronic properties. However, the accuracy of a density functional can be affected by the electron density. Here we apply the nonempirical Tao–Mo (TM) semilocal functional to study the influence of the electron density on the exchange and correlation energies of atoms and ions, and compare the results with the commonly used nonempirical semilocal functionals local spin-density approximation (LSDA), Perdew–Burke–Ernzerhof (PBE), Tao–Perdew–Staroverov–Scuseria (TPSS), and hybrid functional PBE0. We find that the spin-restricted Hartree–Fock density yields the exchange and correlation energies in good agreement with the Optimizedmore » Effective Potential method, particularly for spherical atoms and ions. However, the errors of these semilocal and hybrid functionals become larger for self-consistent densities. We further find that the quality of the electron density have greater effect on the exchange-correlation energies of kinetic energy density-dependent meta-GGA functionals TPSS and TM than on those of the LSDA and GGA, and therefore, should have greater influence on the performance of meta-GGA functionals. Lastly, we show that the influence of the density quality on PBE0 is slightly reduced, compared to that of PBE, due to the exact mixing.« less

Exchange-correlation energies of atoms from efficient density functionals: influence of the electron density

NASA Astrophysics Data System (ADS)

Tao, Jianmin; Ye, Lin-Hui; Duan, Yuhua

2017-12-01

The primary goal of Kohn-Sham density functional theory is to evaluate the exchange-correlation contribution to electronic properties. However, the accuracy of a density functional can be affected by the electron density. Here we apply the nonempirical Tao-Mo (TM) semilocal functional to study the influence of the electron density on the exchange and correlation energies of atoms and ions, and compare the results with the commonly used nonempirical semilocal functionals local spin-density approximation (LSDA), Perdew-Burke-Ernzerhof (PBE), Tao-Perdew-Staroverov-Scuseria (TPSS), and hybrid functional PBE0. We find that the spin-restricted Hartree-Fock density yields the exchange and correlation energies in good agreement with the Optimized Effective Potential method, particularly for spherical atoms and ions. However, the errors of these semilocal and hybrid functionals become larger for self-consistent densities. We further find that the quality of the electron density have greater effect on the exchange-correlation energies of kinetic energy density-dependent meta-GGA functionals TPSS and TM than on those of the LSDA and GGA, and therefore, should have greater influence on the performance of meta-GGA functionals. Finally, we show that the influence of the density quality on PBE0 is slightly reduced, compared to that of PBE, due to the exact mixing.

Exchange-correlation energies of atoms from efficient density functionals: influence of the electron density

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

Tao, Jianmin; Ye, Lin -Hui; Duan, Yuhua

The primary goal of Kohn–Sham density functional theory is to evaluate the exchange-correlation contribution to electronic properties. However, the accuracy of a density functional can be affected by the electron density. Here we apply the nonempirical Tao–Mo (TM) semilocal functional to study the influence of the electron density on the exchange and correlation energies of atoms and ions, and compare the results with the commonly used nonempirical semilocal functionals local spin-density approximation (LSDA), Perdew–Burke–Ernzerhof (PBE), Tao–Perdew–Staroverov–Scuseria (TPSS), and hybrid functional PBE0. We find that the spin-restricted Hartree–Fock density yields the exchange and correlation energies in good agreement with the Optimizedmore » Effective Potential method, particularly for spherical atoms and ions. However, the errors of these semilocal and hybrid functionals become larger for self-consistent densities. We further find that the quality of the electron density have greater effect on the exchange-correlation energies of kinetic energy density-dependent meta-GGA functionals TPSS and TM than on those of the LSDA and GGA, and therefore, should have greater influence on the performance of meta-GGA functionals. Lastly, we show that the influence of the density quality on PBE0 is slightly reduced, compared to that of PBE, due to the exact mixing.« less

Arc_Mat: a Matlab-based spatial data analysis toolbox

NASA Astrophysics Data System (ADS)

Liu, Xingjian; Lesage, James

2010-03-01

This article presents an overview of Arc_Mat, a Matlab-based spatial data analysis software package whose source code has been placed in the public domain. An earlier version of the Arc_Mat toolbox was developed to extract map polygon and database information from ESRI shapefiles and provide high quality mapping in the Matlab software environment. We discuss revisions to the toolbox that: utilize enhanced computing and graphing capabilities of more recent versions of Matlab, restructure the toolbox with object-oriented programming features, and provide more comprehensive functions for spatial data analysis. The Arc_Mat toolbox functionality includes basic choropleth mapping; exploratory spatial data analysis that provides exploratory views of spatial data through various graphs, for example, histogram, Moran scatterplot, three-dimensional scatterplot, density distribution plot, and parallel coordinate plots; and more formal spatial data modeling that draws on the extensive Spatial Econometrics Toolbox functions. A brief review of the design aspects of the revised Arc_Mat is described, and we provide some illustrative examples that highlight representative uses of the toolbox. Finally, we discuss programming with and customizing the Arc_Mat toolbox functionalities.

Liouville action as path-integral complexity: from continuous tensor networks to AdS/CFT

NASA Astrophysics Data System (ADS)

Caputa, Pawel; Kundu, Nilay; Miyaji, Masamichi; Takayanagi, Tadashi; Watanabe, Kento

2017-11-01

We propose an optimization procedure for Euclidean path-integrals that evaluate CFT wave functionals in arbitrary dimensions. The optimization is performed by minimizing certain functional, which can be interpreted as a measure of computational complexity, with respect to background metrics for the path-integrals. In two dimensional CFTs, this functional is given by the Liouville action. We also formulate the optimization for higher dimensional CFTs and, in various examples, find that the optimized hyperbolic metrics coincide with the time slices of expected gravity duals. Moreover, if we optimize a reduced density matrix, the geometry becomes two copies of the entanglement wedge and reproduces the holographic entanglement entropy. Our approach resembles a continuous tensor network renormalization and provides a concrete realization of the proposed interpretation of AdS/CFT as tensor networks. The present paper is an extended version of our earlier report arXiv:1703.00456 and includes many new results such as evaluations of complexity functionals, energy stress tensor, higher dimensional extensions and time evolutions of thermofield double states.

Synaptic genes are extensively downregulated across multiple brain regions in normal human aging and Alzheimer’s disease

PubMed Central

Berchtold, Nicole C.; Coleman, Paul D.; Cribbs, David H.; Rogers, Joseph; Gillen, Daniel L.; Cotman, Carl W.

2014-01-01

Synapses are essential for transmitting, processing, and storing information, all of which decline in aging and Alzheimer’s disease (AD). Because synapse loss only partially accounts for the cognitive declines seen in aging and AD, we hypothesized that existing synapses might undergo molecular changes that reduce their functional capacity. Microarrays were used to evaluate expression profiles of 340 synaptic genes in aging (20–99 years) and AD across 4 brain regions from 81 cases. The analysis revealed an unexpectedly large number of significant expression changes in synapse-related genes in aging, with many undergoing progressive downregulation across aging and AD. Functional classification of the genes showing altered expression revealed that multiple aspects of synaptic function are affected, notably synaptic vesicle trafficking and release, neurotransmitter receptors and receptor trafficking, postsynaptic density scaffolding, cell adhesion regulating synaptic stability, and neuromodulatory systems. The widespread declines in synaptic gene expression in normal aging suggests that function of existing synapses might be impaired, and that a common set of synaptic genes are vulnerable to change in aging and AD. PMID:23273601

Accurate donor electron wave functions from a multivalley effective mass theory.

NASA Astrophysics Data System (ADS)

Pendo, Luke; Hu, Xuedong

Multivalley effective mass (MEM) theories combine physical intuition with a marginal need for computational resources, but they tend to be insensitive to variations in the wavefunction. However, recent papers suggest full Bloch functions and suitable central cell donor potential corrections are essential to replicating qualitative and quantitative features of the wavefunction. In this talk, we consider a variational MEM method that can accurately predict both spectrum and wavefunction of isolated phosphorus donors. As per Gamble et. al, we employ a truncated series representation of the Bloch function with a tetrahedrally symmetric central cell correction. We use a dynamic dielectric constant, a feature commonly seen in tight-binding methods. Uniquely, we use a freely extensible basis of either all Slater- or all Gaussian-type functions. With a large basis able to capture the influence of higher energy eigenstates, this method is well positioned to consider the influence of external perturbations, such as electric field or applied strain, on the charge density. This work is supported by the US Army Research Office (W911NF1210609).

Self-Interaction Error in Density Functional Theory: An Appraisal.

PubMed

Bao, Junwei Lucas; Gagliardi, Laura; Truhlar, Donald G

2018-05-03

Self-interaction error (SIE) is considered to be one of the major sources of error in most approximate exchange-correlation functionals for Kohn-Sham density-functional theory (KS-DFT), and it is large with all local exchange-correlation functionals and with some hybrid functionals. In this work, we consider systems conventionally considered to be dominated by SIE. For these systems, we demonstrate that by using multiconfiguration pair-density functional theory (MC-PDFT), the error of a translated local density-functional approximation is significantly reduced (by a factor of 3) when using an MCSCF density and on-top density, as compared to using KS-DFT with the parent functional; the error in MC-PDFT with local on-top functionals is even lower than the error in some popular KS-DFT hybrid functionals. Density-functional theory, either in MC-PDFT form with local on-top functionals or in KS-DFT form with some functionals having 50% or more nonlocal exchange, has smaller errors for SIE-prone systems than does CASSCF, which has no SIE.

A DNS study of turbulent mixing of two passive scalars

NASA Astrophysics Data System (ADS)

Juneja, A.; Pope, S. B.

1996-08-01

We employ direct numerical simulations to study the mixing of two passive scalars in stationary, homogeneous, isotropic turbulence. The present work is a direct extension of that of Eswaran and Pope from one scalar to two scalars and the focus is on examining the evolution states of the scalar joint probability density function (jpdf) and the conditional expectation of the scalar diffusion to motivate better models for multi-scalar mixing. The initial scalar fields are chosen to conform closely to a ``triple-delta function'' jpdf corresponding to blobs of fluid in three distinct states. The effect of the initial length scales and diffusivity of the scalars on the evolution of the jpdf and the conditional diffusion is investigated in detail as the scalars decay from their prescribed initial state. Also examined is the issue of self-similarity of the scalar jpdf at large times and the rate of decay of the scalar variance and dissipation.

Roughness in the Kolmogorov Johnson Mehl Avrami framework: extension to (2+1)D of the Trofimov Park model

NASA Astrophysics Data System (ADS)

Pacchiarotti, Barbara; Fanfoni, Massimo; Tomellini, Massimo

2005-12-01

In this paper the reformulation of Trofimov-Park (TP) model, [V.I. Trofimov, Appl. Surf. Sci. 219 (2003) 93), of thin film roughness evolution during nucleation and growth of islands in case of simultaneous nucleation is presented. The calculation of TP restricted to one-dimensional triangular islands has been extended to both the one-dimensional elliptical case and to the pyramidal two-dimensional one. The kinetics of the interface width, w, and the height-height autocorrelation function G, through which the correlation length ξ has been defined, have been estimated. Moreover, w(Θ) and ξ(Θ), where Θ is the fraction of the covered substrate, if properly rescaled to the density of nuclei N and to the aspect ratio of islands, are universal functions that, for a conspicuous range of Θ, obey a power law with the exponent depending upon island shape.

Solution to urn models of pairwise interaction with application to social, physical, and biological sciences

NASA Astrophysics Data System (ADS)

Pickering, William; Lim, Chjan

2017-07-01

We investigate a family of urn models that correspond to one-dimensional random walks with quadratic transition probabilities that have highly diverse applications. Well-known instances of these two-urn models are the Ehrenfest model of molecular diffusion, the voter model of social influence, and the Moran model of population genetics. We also provide a generating function method for diagonalizing the corresponding transition matrix that is valid if and only if the underlying mean density satisfies a linear differential equation and express the eigenvector components as terms of ordinary hypergeometric functions. The nature of the models lead to a natural extension to interaction between agents in a general network topology. We analyze the dynamics on uncorrelated heterogeneous degree sequence networks and relate the convergence times to the moments of the degree sequences for various pairwise interaction mechanisms.

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

Yu, Liang; Abild-Pedersen, Frank

On the basis of an extensive set of density functional theory calculations, it is shown that a simple scheme provides a fundamental understanding of variations in the transition state energies and structures of reaction intermediates on transition metal surfaces across the periodic table. The scheme is built on the bond order conservation principle and requires a limited set of input data, still achieving transition state energies as a function of simple descriptors with an error smaller than those of approaches based on linear fits to a set of calculated transition state energies. Here, we have applied this approach together withmore » linear scaling of adsorption energies to obtain the energetics of the NH 3 decomposition reaction on a series of stepped fcc(211) transition metal surfaces. Moreover, this information is used to establish a microkinetic model for the formation of N 2 and H 2, thus providing insight into the components of the reaction that determines the activity.« less

Design of transparent conductors and periodic two-dimensional electron gases without doping

NASA Astrophysics Data System (ADS)

Zhang, Xiuwen; Zhang, Lijun; Zunger, Alex; Perkins, John; Materials by Design Team; John D. Perkins Collaboration

The functionality of transparency plus conductivity plays an important role in renewable energy and information technologies, including applications such as solar cells, touch-screen sensors, and flat panel display. However, materials with such seemingly contraindicated properties are difficult to come by. The traditional strategy for designing bulk transparent conductors (TCs) starts from a wide-gap insulator and finds ways to make it conductive by extensive doping. We propose a different strategy for TC design--starting with a metallic conductor and designing transparency by control of intrinsic interband transitions and intraband plasmonic frequency. We identified specific design principles for prototypical intrinsic TC classes and searched computationally for materials that satisfy them. The electron gases in the 3D intrinsic TCs demonstrate intriguing properties, such as periodic 2D electron gas regions with very high carrier density. We will discuss a more extended search of these functionalities, in parallel with stability and growability calculations

Statistical optics

NASA Astrophysics Data System (ADS)

Goodman, J. W.

This book is based on the thesis that some training in the area of statistical optics should be included as a standard part of any advanced optics curriculum. Random variables are discussed, taking into account definitions of probability and random variables, distribution functions and density functions, an extension to two or more random variables, statistical averages, transformations of random variables, sums of real random variables, Gaussian random variables, complex-valued random variables, and random phasor sums. Other subjects examined are related to random processes, some first-order properties of light waves, the coherence of optical waves, some problems involving high-order coherence, effects of partial coherence on imaging systems, imaging in the presence of randomly inhomogeneous media, and fundamental limits in photoelectric detection of light. Attention is given to deterministic versus statistical phenomena and models, the Fourier transform, and the fourth-order moment of the spectrum of a detected speckle image.

Collapsing radiating stars with various equations of state

NASA Astrophysics Data System (ADS)

Brassel, Byron P.; Goswami, Rituparno; Maharaj, Sunil D.

2017-06-01

We study the gravitational collapse of radiating stars in the context of the cosmic censorship conjecture. We consider a generalized Vaidya spacetime with three concentric regions. The local internal atmosphere is a two-component system consisting of standard pressure-free, null radiation and an additional string fluid with energy density and nonzero pressure obeying all physically realistic energy conditions. The middle region is purely radiative which matches to a third region which is the Schwarzschild exterior. We outline the general mathematical framework to study the conditions on the mass function so that future-directed nonspacelike geodesics can terminate at the singularity in the past. Mass functions for several equations of state are analyzed using this framework and it is shown that the collapse in each case terminates at a locally naked central singularity. We calculate the strength of these singularities to show that they are strong curvature singularities which implies that no extension of spacetime through them is possible.

Reprint of "Theoretical description of metal/oxide interfacial properties: The case of MgO/Ag(001)"

NASA Astrophysics Data System (ADS)

Prada, Stefano; Giordano, Livia; Pacchioni, Gianfranco; Goniakowski, Jacek

2017-02-01

We compare the performances of different DFT functionals applied to ultra-thin MgO(100) films supported on the Ag(100) surface, a prototypical system of a weakly interacting oxide/metal interface, extensively studied in the past. Beyond semi-local DFT-GGA approximation, we also use the hybrid DFT-HSE approach to improve the description of the oxide electronic structure. Moreover, to better account for the interfacial adhesion, we include the van de Waals interactions by means of either the semi-empirical force fields by Grimme (DFT-D2 and DFT-D2*) or the self-consistent density functional optB88-vdW. We compare and discuss the results on the structural, electronic, and adhesion characteristics of the interface as obtained for pristine and oxygen-deficient Ag-supported MgO films in the 1-4 ML thickness range.

Theoretical description of metal/oxide interfacial properties: The case of MgO/Ag(001)

NASA Astrophysics Data System (ADS)

Prada, Stefano; Giordano, Livia; Pacchioni, Gianfranco; Goniakowski, Jacek

2016-12-01

We compare the performances of different DFT functionals applied to ultra-thin MgO(100) films supported on the Ag(100) surface, a prototypical system of a weakly interacting oxide/metal interface, extensively studied in the past. Beyond semi-local DFT-GGA approximation, we also use the hybrid DFT-HSE approach to improve the description of the oxide electronic structure. Moreover, to better account for the interfacial adhesion, we include the van de Waals interactions by means of either the semi-empirical force fields by Grimme (DFT-D2 and DFT-D2*) or the self-consistent density functional optB88-vdW. We compare and discuss the results on the structural, electronic, and adhesion characteristics of the interface as obtained for pristine and oxygen-deficient Ag-supported MgO films in the 1-4 ML thickness range.

Hardware Evaluation of the Horizontal Exercise Fixture with Weight Stack

NASA Technical Reports Server (NTRS)

Newby, Nate; Leach, Mark; Fincke, Renita; Sharp, Carwyn

2009-01-01

HEF with weight stack seems to be a very sturdy and reliable exercise device that should function well in a bed rest training setting. A few improvements should be made to both the hardware and software to improve usage efficiency, but largely, this evaluation has demonstrated HEF's robustness. The hardware offers loading to muscles, bones, and joints, potentially sufficient to mitigate the loss of muscle mass and bone mineral density during long-duration bed rest campaigns. With some minor modifications, the HEF with weight stack equipment provides the best currently available means of performing squat, heel raise, prone row, bench press, and hip flexion/extension exercise in a supine orientation.

Statistics of multi-look AIRSAR imagery: A comparison of theory with measurements

NASA Technical Reports Server (NTRS)

Lee, J. S.; Hoppel, K. W.; Mango, S. A.

1993-01-01

The intensity and amplitude statistics of SAR images, such as L-Band HH for SEASAT and SIR-B, and C-Band VV for ERS-1 have been extensively investigated for various terrain, ground cover and ocean surfaces. Less well-known are the statistics between multiple channels of polarimetric of interferometric SAR's, especially for the multi-look processed data. In this paper, we investigate the probability density functions (PDF's) of phase differences, the magnitude of complex products and the amplitude ratios, between polarization channels (i.e. HH, HV, and VV) using 1-look and 4-look AIRSAR polarimetric data. Measured histograms are compared with theoretical PDF's which were recently derived based on a complex Gaussian model.

Improving Olefin Purification Using Metal Organic Frameworks with Open Metal Sites.

PubMed

Luna-Triguero, A; Vicent-Luna, J M; Poursaeidesfahani, A; Vlugt, T J H; Sánchez-de-Armas, R; Gómez-Álvarez, P; Calero, S

2018-05-16

The separation and purification of light hydrocarbons is challenging in the industry. Recently, a ZJNU-30 metal-organic framework (MOF) has been found to have the potential for adsorption-based separation of olefins and diolefins with four carbon atoms [H. M. Liu et al. Chem.-Eur. J. 2016, 22, 14988-14997]. Our study corroborates this finding but reveals Fe-MOF-74 as a more efficient candidate for the separation because of the open metal sites. We performed adsorption-based separation, transient breakthrough curves, and density functional theory calculations. This combination of techniques provides an extensive understanding of the studied system. Using this MOF, we propose a separation scheme to obtain a high-purity product.

Microscopic description of fission properties for r-process nuclei

NASA Astrophysics Data System (ADS)

Giuliani, S. A.; Martínez-Pinedo, G.; Robledo, L. M.

2018-01-01

Fission properties of 886 even-even nuclei in the region 84 ≤ Z ≤ 120 and 118 ≤ Z ≤ 250 were computed using the Barcelona-Catania-Paris-Madrid energy density functional. An extensive study of both the potential energy surfaces and collectives inertias was performed. Spontaneous fission half-lives are computed using the semiclassical Wentzel-Kramers-Brillouin formalism. By comparing these three quantities we found that the stability of the nucleus against the fission process is driven by the interplay between both the potential energy and the collective inertias. In our calculations, nuclei with relative long half-lives were found in two regions around Z = 120, N = 182 and Z = 104, N = 222.

Dynamics of quantum turbulence of different spectra

PubMed Central

Walmsley, Paul; Zmeev, Dmitry; Pakpour, Fatemeh; Golov, Andrei

2014-01-01

Turbulence in a superfluid in the zero-temperature limit consists of a dynamic tangle of quantized vortex filaments. Different types of turbulence are possible depending on the level of correlations in the orientation of vortex lines. We provide an overview of turbulence in superfluid 4He with a particular focus on recent experiments probing the decay of turbulence in the zero-temperature regime below 0.5 K. We describe extensive measurements of the vortex line density during the free decay of different types of turbulence: ultraquantum and quasiclassical turbulence in both stationary and rotating containers. The observed decays and the effective dissipation as a function of temperature are compared with theoretical models and numerical simulations. PMID:24704876

In situ, operando measurements of rechargeable batteries

DOE PAGES

Wang, Howard; Wang, Feng

2016-08-01

This article reviews recent in operando measurements (IOMs) for addressing challenges in advancing rechargeable battery (RB) technologies. As the demands on energy and power density of RBs for broader applications continue to grow, current RB technologies are pushed to their theoretical and engineering limits while new approaches are being extensively investigated. Also, IOMs have become more powerful and effective research tools in recent years; they will play an essential role in developing next generation RBs. This review is organized around outstanding issues in battery science and engineering. Finally, we emphasize the critical need for quantifying the distribution and transport ofmore » active ions in functioning batteries over wide temporal and spatial scales in real time.« less

Solid-state NMR studies of form I of atorvastatin calcium.

PubMed

Wang, Wei David; Gao, Xudong; Strohmeier, Mark; Wang, Wei; Bai, Shi; Dybowski, Cecil

2012-03-22

Solid-state (13)C, (19)F, and (15)N magic angle spinning NMR studies of Form I of atorvastatin calcium are reported, including chemical shift tensors of all resolvable carbon sites and fluorine sites. The complete (13)C and (19)F chemical shift assignments are given based on an extensive analysis of (13)C-(1)H HETCOR and (13)C-(19)F HETCOR results. The solid-state NMR data indicate that the asymmetric unit of this material contains two atorvastatin molecules. A possible structure of Form I of atorvastatin calcium (ATC-I), derived from solid-state NMR data and density functional theory calculations of various structures, is proposed for this important active pharmaceutical ingredient (API).

Knee extension range of motion and self-report physical function in total knee arthroplasty: mediating effects of knee extensor strength

PubMed Central

2013-01-01

Background Knee extensor strength and knee extension range of motion (ROM) are important predictors of physical function in patients with a total knee arthroplasty (TKA). However, the relationship between the two knee measures remains unclear. The purpose of this study was to examine whether changes in knee extensor strength mediate the association between changes in knee extension ROM and self-report physical function. Methods Data from 441 patients with a TKA were collected preoperatively and 6 months postoperatively. Self-report measure of physical function was assessed by the Short Form 36 (SF-36) questionnaire. Knee extensor strength was measured by handheld dynamometry and knee extension ROM by goniometry. A bootstrapped cross product of coefficients approach was used to evaluate mediation effects. Results Mediation analyses, adjusted for clinicodemographic measures, revealed that the association between changes in knee extension ROM and SF-36 physical function was mediated by changes in knee extensor strength. Conclusions In patients with TKA, knee extensor strength mediated the influence of knee extension ROM on physical function. These results suggest that interventions to improve the range of knee extension may be useful in improving knee extensor performance. PMID:23332039

Lattice cluster theory for dense, thin polymer films.

PubMed

Freed, Karl F

2015-04-07

While the application of the lattice cluster theory (LCT) to study the miscibility of polymer blends has greatly expanded our understanding of the monomer scale molecular details influencing miscibility, the corresponding theory for inhomogeneous systems has not yet emerged because of considerable technical difficulties and much greater complexity. Here, we present a general formulation enabling the extension of the LCT to describe the thermodynamic properties of dense, thin polymer films using a high dimension, high temperature expansion. Whereas the leading order of the LCT for bulk polymer systems is essentially simple Flory-Huggins theory, the highly non-trivial leading order inhomogeneous LCT (ILCT) for a film with L layers already involves the numerical solution of 3(L - 1) coupled, highly nonlinear equations for the various density profiles in the film. The new theory incorporates the essential "transport" constraints of Helfand and focuses on the strict imposition of excluded volume constraints, appropriate to dense polymer systems, rather than the maintenance of chain connectivity as appropriate for lower densities and as implemented in self-consistent theories of polymer adsorption at interfaces. The ILCT is illustrated by presenting examples of the computed profiles of the density, the parallel and perpendicular bonds, and the chain ends for free standing and supported films as a function of average film density, chain length, temperature, interaction with support, and chain stiffness. The results generally agree with expected general trends.

High cell density cultivation of probiotics and lactic acid production.

PubMed

Schiraldi, Chiara; Adduci, Vincenzo; Valli, Vivien; Maresca, Carmelina; Giuliano, Mariateresa; Lamberti, Monica; Cartenì, Maria; De Rosa, Mario

2003-04-20

The commercial interest in functional foods that contain live microorganisms, also named probiotics, is paralleled by the increasing scientific attention to their functionality in the digestive tract. This is especially true of yogurts that contain strains of lactic-acid bacteria of intestinal origin, among these, Lactobacillus delbrueckii ssp. bulgaricus is extensively used in the dairy industry and it has been demonstrated to be a probiotic strain. In this work we describe high cell density cultivations of this microorganism also focusing on the stereospecific production of lactic acid. Key parameters such as medium composition (bactocasitone concentration) and diverse aeration conditions were explored. The results showed that the final concentration of biomass in anaerobic fermentation was lower than the one obtained in microaerophilic conditions, while it gave a very high productivity of lactic acid which was present as a racemic mixture in the permeate. Fermentation experiments carried out with air sparging, even at very low flow-rate, led to the production of the sole L(+) lactic acid giving sevenfold increase in biomass yield in respect to the batch cultivation. Finally, a mathematical model was developed to describe the microfiltration bioprocess applied in this research considering an inhibition kinetic and enucleating a suitable mathematical description for the decrease of the transmembrane flux. Copyright 2003 Wiley Periodicals, Inc.

Density functional theory calculations in stereochemical determination of terpecurcumins J-W, cytotoxic terpene-conjugated curcuminoids from Curcuma longa L.

PubMed

Lin, Xionghao; Ji, Shuai; Qiao, Xue; Hu, Hongbo; Chen, Ni; Dong, Yinhui; Huang, Yun; Guo, Dean; Tu, Pengfei; Ye, Min

2013-12-06

Fourteen novel terpene-conjugated curcuminoids, terpecurcumins J-W (1-14), have been isolated from the rhizomes of Curcuma longa L. Among them, terpecurcumins J-Q and V represent four unprecedented skeletons featuring an unusual core of hydrobenzannulated[6,6]-spiroketal (1 and 2), bicyclo[2.2.2]octene (3-7), bicyclo[3.1.3]octene (8), and spiroepoxide (13), respectively. The structures of compounds 1-14 were elucidated by extensive spectroscopic analysis, and their absolute configurations were established by electronic circular dichroism, vibrational circular dichroism, and (13)C NMR spectroscopic data analysis, together with density functional theory calculations. The structure and configuration of 1 was further confirmed by single-crystal X-ray diffraction (Cu Kα). The biogenetic pathways of 1-14 were proposed, involving Michael addition, condensation, Diels-Alder cycloaddition, and electrophilic substitution reactions. Terpecurcumins showed more potent cytotoxic activities than curcumin and ar-/β-turmerone. Among them, terpecurcumin Q (8) exhibited IC50 of 3.9 μM against MCF-7 human breast cancer cells, and mitochondria-mediated apoptosis played an important role in the overall growth inhibition. Finally, LC/MS/MS quantitative analysis of five representative terpecurcumins indicated these novel compounds were present in C. longa at parts per million level.

Theory of L -edge spectroscopy of strongly correlated systems

NASA Astrophysics Data System (ADS)

Lüder, Johann; Schött, Johan; Brena, Barbara; Haverkort, Maurits W.; Thunström, Patrik; Eriksson, Olle; Sanyal, Biplab; Di Marco, Igor; Kvashnin, Yaroslav O.

2017-12-01

X-ray absorption spectroscopy measured at the L edge of transition metals (TMs) is a powerful element-selective tool providing direct information about the correlation effects in the 3 d states. The theoretical modeling of the 2 p →3 d excitation processes remains to be challenging for contemporary ab initio electronic structure techniques, due to strong core-hole and multiplet effects influencing the spectra. In this work, we present a realization of the method combining the density-functional theory with multiplet ligand field theory, proposed in Haverkort et al. [Phys. Rev. B 85, 165113 (2012), 10.1103/PhysRevB.85.165113]. In this approach, a single-impurity Anderson model (SIAM) is constructed, with almost all parameters obtained from first principles, and then solved to obtain the spectra. In our implementation, we adopt the language of the dynamical mean-field theory and utilize the local density of states and the hybridization function, projected onto TM 3 d states, in order to construct the SIAM. The developed computational scheme is applied to calculate the L -edge spectra for several TM monoxides. A very good agreement between the theory and experiment is found for all studied systems. The effect of core-hole relaxation, hybridization discretization, possible extensions of the method as well as its limitations are discussed.

A structural insight into mechanical strength of graphene-like carbon and carbon nitride networks

NASA Astrophysics Data System (ADS)

Rahaman, Obaidur; Mortazavi, Bohayra; Dianat, Arezoo; Cuniberti, Gianaurelio; Rabczuk, Timon

2017-02-01

Graphene, one of the strongest materials ever discovered, triggered the exploration of many 2D materials in the last decade. However, the successful synthesis of a stable nanomaterial requires a rudimentary understanding of the relationship between its structure and strength. In the present study, we investigate the mechanical properties of eight different carbon-based 2D nanomaterials by performing extensive density functional theory calculations. The considered structures were just recently either experimentally synthesized or theoretically predicted. The corresponding stress-strain curves and elastic moduli are reported. They can be useful in training force field parameters for large scale simulations. A comparative analysis of these results revealed a direct relationship between atomic density per area and elastic modulus. Furthermore, for the networks that have an armchair and a zigzag orientation, we observed that they were more stretchable in the zigzag direction than the armchair direction. A critical analysis of the angular distributions and radial distribution functions suggested that it could be due to the higher ability of the networks to suppress the elongations of the bonds in the zigzag direction by deforming the bond angles. The structural interpretations provided in this work not only improve the general understanding of a 2D material’s strength but also enables us to rationally design them for higher qualities.

Calibrating the Spatiotemporal Root Density Distribution for Macroscopic Water Uptake Models Using Tikhonov Regularization

NASA Astrophysics Data System (ADS)

Li, N.; Yue, X. Y.

2018-03-01

Macroscopic root water uptake models proportional to a root density distribution function (RDDF) are most commonly used to model water uptake by plants. As the water uptake is difficult and labor intensive to measure, these models are often calibrated by inverse modeling. Most previous inversion studies assume RDDF to be constant with depth and time or dependent on only depth for simplification. However, under field conditions, this function varies with type of soil and root growth and thus changes with both depth and time. This study proposes an inverse method to calibrate both spatially and temporally varying RDDF in unsaturated water flow modeling. To overcome the difficulty imposed by the ill-posedness, the calibration is formulated as an optimization problem in the framework of the Tikhonov regularization theory, adding additional constraint to the objective function. Then the formulated nonlinear optimization problem is numerically solved with an efficient algorithm on the basis of the finite element method. The advantage of our method is that the inverse problem is translated into a Tikhonov regularization functional minimization problem and then solved based on the variational construction, which circumvents the computational complexity in calculating the sensitivity matrix involved in many derivative-based parameter estimation approaches (e.g., Levenberg-Marquardt optimization). Moreover, the proposed method features optimization of RDDF without any prior form, which is applicable to a more general root water uptake model. Numerical examples are performed to illustrate the applicability and effectiveness of the proposed method. Finally, discussions on the stability and extension of this method are presented.

Ocean acidification affects coral growth by reducing skeletal density.

PubMed

Mollica, Nathaniel R; Guo, Weifu; Cohen, Anne L; Huang, Kuo-Fang; Foster, Gavin L; Donald, Hannah K; Solow, Andrew R

2018-02-20

Ocean acidification (OA) is considered an important threat to coral reef ecosystems, because it reduces the availability of carbonate ions that reef-building corals need to produce their skeletons. However, while theory predicts that coral calcification rates decline as carbonate ion concentrations decrease, this prediction is not consistently borne out in laboratory manipulation experiments or in studies of corals inhabiting naturally low-pH reefs today. The skeletal growth of corals consists of two distinct processes: extension (upward growth) and densification (lateral thickening). Here, we show that skeletal density is directly sensitive to changes in seawater carbonate ion concentration and thus, to OA, whereas extension is not. We present a numerical model of Porites skeletal growth that links skeletal density with the external seawater environment via its influence on the chemistry of coral calcifying fluid. We validate the model using existing coral skeletal datasets from six Porites species collected across five reef sites and use this framework to project the impact of 21st century OA on Porites skeletal density across the global tropics. Our model predicts that OA alone will drive up to 20.3 ± 5.4% decline in the skeletal density of reef-building Porites corals.

Visualization of electronic density

DOE PAGES

Grosso, Bastien; Cooper, Valentino R.; Pine, Polina; ...

2015-04-22

An atom’s volume depends on its electronic density. Although this density can only be evaluated exactly for hydrogen-like atoms, there are many excellent numerical algorithms and packages to calculate it for other materials. 3D visualization of charge density is challenging, especially when several molecular/atomic levels are intertwined in space. We explore several approaches to 3D charge density visualization, including the extension of an anaglyphic stereo visualization application based on the AViz package to larger structures such as nanotubes. We will describe motivations and potential applications of these tools for answering interesting questions about nanotube properties.

Extensive TD-DFT Benchmark: Singlet-Excited States of Organic Molecules.

PubMed

Jacquemin, Denis; Wathelet, Valérie; Perpète, Eric A; Adamo, Carlo

2009-09-08

Extensive Time-Dependent Density Functional Theory (TD-DFT) calculations have been carried out in order to obtain a statistically meaningful analysis of the merits of a large number of functionals. To reach this goal, a very extended set of molecules (∼500 compounds, >700 excited states) covering a broad range of (bio)organic molecules and dyes have been investigated. Likewise, 29 functionals including LDA, GGA, meta-GGA, global hybrids, and long-range-corrected hybrids have been considered. Comparisons with both theoretical references and experimental measurements have been carried out. On average, the functionals providing the best match with reference data are, one the one hand, global hybrids containing between 22% and 25% of exact exchange (X3LYP, B98, PBE0, and mPW1PW91) and, on the other hand, a long-range-corrected hybrid with a less-rapidly increasing HF ratio, namely LC-ωPBE(20). Pure functionals tend to be less consistent, whereas functionals incorporating a larger fraction of exact exchange tend to underestimate significantly the transition energies. For most treated cases, the M05 and CAM-B3LYP schemes deliver fairly small deviations but do not outperform standard hybrids such as X3LYP or PBE0, at least within the vertical approximation. With the optimal functionals, one obtains mean absolute deviations smaller than 0.25 eV, though the errors significantly depend on the subset of molecules or states considered. As an illustration, PBE0 and LC-ωPBE(20) provide a mean absolute error of only 0.14 eV for the 228 states related to neutral organic dyes but are completely off target for cyanine-like derivatives. On the basis of comparisons with theoretical estimates, it also turned out that CC2 and TD-DFT errors are of the same order of magnitude, once the above-mentioned hybrids are selected.

Dynamic multipopulation and density dependent evolutionary games related to replicator dynamics. A metasimplex concept.

PubMed

Argasinski, Krzysztof

2006-07-01

This paper contains the basic extensions of classical evolutionary games (multipopulation and density dependent models). It is shown that classical bimatrix approach is inconsistent with other approaches because it does not depend on proportion between populations. The main conclusion is that interspecific proportion parameter is important and must be considered in multipopulation models. The paper provides a synthesis of both extensions (a metasimplex concept) which solves the problem intrinsic in the bimatrix model. It allows us to model interactions among any number of subpopulations including density dependence effects. We prove that all modern approaches to evolutionary games are closely related. All evolutionary models (except classical bimatrix approaches) can be reduced to a single population general model by a simple change of variables. Differences between classic bimatrix evolutionary games and a new model which is dependent on interspecific proportion are shown by examples.

On the synthesis of resonance lines in dynamical models of structured hot-star winds

NASA Technical Reports Server (NTRS)

Puls, J.; Owocki, S. P.; Fullerton, A. W.

1993-01-01

We examine basic issues involved in synthesizing resonance-line profiles from 1-D, dynamical models of highly structured hot-star winds. Although these models exhibit extensive variations in density as well as velocity, the density scale length is still typically much greater than the Sobolev length. The line transfer is thus treated using a Sobolev approach, as generalized by Rybicki & Hummer (1978) to take proper account of the multiple Sobolev resonances arising from the nonmonotonic velocity field. The resulting reduced-lambda-matrix equation describing nonlocal coupling of the source function is solved by iteration, and line profiles are then derived from formal solution integration using this source function. Two more approximate methods that instead use either a stationary or a structured, local source function yield qualitatively similar line-profiles, but are found to violate photon conservation by 10% or more. The full results suggest that such models may indeed be able to reproduce naturally some of the qualitative properties long noted in observed UV line profiles, such as discrete absorption components in unsaturated lines, or the blue-edge variability in saturated lines. However, these particular models do not yet produce the black absorption troughs commonly observed in saturated lines, and it seems that this and other important discrepancies (e.g., in acceleration time scale of absorption components) may require development of more complete models that include rotation and other 2-D and/or 3-D effects.

Fluctuations at the blue edge of saturated wind lines in IUE spectra of O-type stars

NASA Technical Reports Server (NTRS)

Owocki, Stanley P.; Fullerton, Alex

1993-01-01

We examine basic issues involved in synthesizing resonance-line profiles from 1-D, dynamical models of highly structured hot-star winds. Although these models exhibit extensive variations in density as well as velocity, the density scale length is still typically much greater than the Sobolev length. The line transfer is thus treated using a Sobolev approach, as generalized by Rybicki & Hummer (1978) to take proper account of the multiple Sobolev resonances arising from the nonmonotonic velocity field. The resulting reduced-Lambda-matrix equation describing nonlocal coupling of the source function is solved by iteration, and line profiles and then derived from formal solution integration using this source function. The more appropriate methods that instead use either a stationary or a structured, local source function yield qualitatively similar line-profiles, but are found to violate photon conservation by 10 percent or more. The full results suggest that such models may indeed be able to reproduce naturally some of the qualitative properties long noted in observed UV line profiles, such as discrete absorption components in unsaturated lines, or the blue-edge variability in saturated lines. However, these particular models do not yet produce the black absorption troughs commonly observed in saturated lines, and it seems that this and other important discrepancies (e.g., in acceleration time scale of absorption components) may require development of more complete models that include rotation and other 2-D and/or 3-D effects.

Wave generation by contaminant ions near a large spacecraft

NASA Technical Reports Server (NTRS)

Singh, N.

1993-01-01

Measurements from the space shuttle flights have revealed that a large spacecraft in a low earth orbit is accompanied by an extensive gas cloud which is primarily made up of water. The charge exchange between the water molecule and the ionospheric O(+) ions produces a water ion beam traversing downstream of the spacecraft. In this report we present results from a study on the generation of plasma waves by the interaction of the water ion beams with the ionospheric plasma. Since velocity distribution function is key to the understanding of the wave generation process, we have performed a test particle simulation to determine the nature of H2O(+) ions velocity distribution function. The simulations show that at the time scales shorter than the ion cyclotron period tau(sub c), the distribution function can be described by a beam. On the other hand, when the time scales are larger than tau(sub c), a ring distribution forms. A brief description of the linear instabilities driven by an ion beam streaming across a magnetic field in a plasma is presented. We have identified two types of instabilities occurring in low and high frequency bands; the low-frequency instability occurs over the frequency band from zero to about the lower hybrid frequency for a sufficiently low beam density. As the beam density increases, the linear instability occurs at decreasing frequencies below the lower-hybrid frequency. The high frequency instability occurs near the electron cyclotron frequency and its harmonics.

AUC-based biomarker ensemble with an application on gene scores predicting low bone mineral density.

PubMed

Zhao, X G; Dai, W; Li, Y; Tian, L

2011-11-01

The area under the receiver operating characteristic (ROC) curve (AUC), long regarded as a 'golden' measure for the predictiveness of a continuous score, has propelled the need to develop AUC-based predictors. However, the AUC-based ensemble methods are rather scant, largely due to the fact that the associated objective function is neither continuous nor concave. Indeed, there is no reliable numerical algorithm identifying optimal combination of a set of biomarkers to maximize the AUC, especially when the number of biomarkers is large. We have proposed a novel AUC-based statistical ensemble methods for combining multiple biomarkers to differentiate a binary response of interest. Specifically, we propose to replace the non-continuous and non-convex AUC objective function by a convex surrogate loss function, whose minimizer can be efficiently identified. With the established framework, the lasso and other regularization techniques enable feature selections. Extensive simulations have demonstrated the superiority of the new methods to the existing methods. The proposal has been applied to a gene expression dataset to construct gene expression scores to differentiate elderly women with low bone mineral density (BMD) and those with normal BMD. The AUCs of the resulting scores in the independent test dataset has been satisfactory. Aiming for directly maximizing AUC, the proposed AUC-based ensemble method provides an efficient means of generating a stable combination of multiple biomarkers, which is especially useful under the high-dimensional settings. lutian@stanford.edu. Supplementary data are available at Bioinformatics online.

A molecular scale perspective: Monte Carlo simulation for rupturing of ultra thin polymer film melts

NASA Astrophysics Data System (ADS)

Singh, Satya Pal

2017-04-01

Monte Carlo simulation has been performed to study the rupturing process of thin polymer film under strong confinement. The change in mean square displacement; pair correlation function; density distribution; average bond length and microscopic viscosity are sampled by varying the molecular interaction parameters such as the strength and the equilibrium positions of the bonding, non-bonding potentials and the sizes of the beads. The variation in mean square angular displacement χθ = [ < Δθ2 > - < Δθ>2 ] fits very well to a function of type y (t) = A + B *e-t/τ. This may help to study the viscous properties of the films and its dependence on different parameters. The ultra thin film annealed at high temperature gets ruptured and holes are created in the film mimicking spinodal dewetting. The pair correlation function and density profile reveal rich information about the equilibrium structure of the film. The strength and equilibrium bond length of finite extensible non-linear elastic potential (FENE) and non-bonding Morse potential have clear impact on microscopic rupturing of the film. The beads show Rouse or repetition motion forming rim like structures near the holes created inside the film. The higher order interaction as dipole-quadrupole may get prominence under strong confinement. The enhanced excluded volume interaction under strong confinement may overlap with the molecular dispersion forces. It can work to reorganize the molecules at the bottom of the scale and can imprint its signature in complex patterns evolved.

Density-functional theory for internal magnetic fields

NASA Astrophysics Data System (ADS)

Tellgren, Erik I.

2018-01-01

A density-functional theory is developed based on the Maxwell-Schrödinger equation with an internal magnetic field in addition to the external electromagnetic potentials. The basic variables of this theory are the electron density and the total magnetic field, which can equivalently be represented as a physical current density. Hence, the theory can be regarded as a physical current density-functional theory and an alternative to the paramagnetic current density-functional theory due to Vignale and Rasolt. The energy functional has strong enough convexity properties to allow a formulation that generalizes Lieb's convex analysis formulation of standard density-functional theory. Several variational principles as well as a Hohenberg-Kohn-like mapping between potentials and ground-state densities follow from the underlying convex structure. Moreover, the energy functional can be regarded as the result of a standard approximation technique (Moreau-Yosida regularization) applied to the conventional Schrödinger ground-state energy, which imposes limits on the maximum curvature of the energy (with respect to the magnetic field) and enables construction of a (Fréchet) differentiable universal density functional.

The 2-10 keV unabsorbed luminosity function of AGN from the LSS, CDFS, and COSMOS surveys

NASA Astrophysics Data System (ADS)

Ranalli, P.; Koulouridis, E.; Georgantopoulos, I.; Fotopoulou, S.; Hsu, L.-T.; Salvato, M.; Comastri, A.; Pierre, M.; Cappelluti, N.; Carrera, F. J.; Chiappetti, L.; Clerc, N.; Gilli, R.; Iwasawa, K.; Pacaud, F.; Paltani, S.; Plionis, E.; Vignali, C.

2016-05-01

The XMM-Large scale structure (XMM-LSS), XMM-Cosmological evolution survey (XMM-COSMOS), and XMM-Chandra deep field south (XMM-CDFS) surveys are complementary in terms of sky coverage and depth. Together, they form a clean sample with the least possible variance in instrument effective areas and point spread function. Therefore this is one of the best samples available to determine the 2-10 keV luminosity function of active galactic nuclei (AGN) and their evolution. The samples and the relevant corrections for incompleteness are described. A total of 2887 AGN is used to build the LF in the luminosity interval 1042-1046 erg s-1 and in the redshift interval 0.001-4. A new method to correct for absorption by considering the probability distribution for the column density conditioned on the hardness ratio is presented. The binned luminosity function and its evolution is determined with a variant of the Page-Carrera method, which is improved to include corrections for absorption and to account for the full probability distribution of photometric redshifts. Parametric models, namely a double power law with luminosity and density evolution (LADE) or luminosity-dependent density evolution (LDDE), are explored using Bayesian inference. We introduce the Watanabe-Akaike information criterion (WAIC) to compare the models and estimate their predictive power. Our data are best described by the LADE model, as hinted by the WAIC indicator. We also explore the recently proposed 15-parameter extended LDDE model and find that this extension is not supported by our data. The strength of our method is that it provides unabsorbed, non-parametric estimates, credible intervals for luminosity function parameters, and a model choice based on predictive power for future data. Based on observations obtained with XMM-Newton, an ESA science mission with instruments and contributions directly funded by ESA member states and NASA.Tables with the samples of the posterior probability distributions are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/590/A80

CR extension from hypersurfaces of higher type

NASA Astrophysics Data System (ADS)

Baracco, Luca

2007-07-01

We prove extension of CR functions from a hypersurface M of in presence of the so-called sector property. If M has finite type in the Bloom-Graham sense, then our result is already contained in [C. Rea, Prolongement holomorphe des fonctions CR, conditions suffisantes, C. R. Acad. Sci. Paris 297 (1983) 163-166] by Rea. We think however, that the argument of our proof carries an expressive geometric meaning and deserves interest on its own right. Also, our method applies in some case to hypersurfaces of infinite type; note that for these, the classical methods fail. CR extension is treated by many authors mainly in two frames: extension in directions of iterated of commutators of CR vector fields (cf., for instance, [A. Boggess, J. Pitts, CR extension near a point of higher type, Duke Math. J. 52 (1) (1985) 67-102; A. Boggess, J.C. Polking, Holomorphic extension of CR functions, Duke Math. J. 49 (1982) 757-784. ; M.S. Baouendi, L. Rothschild, Normal forms for generic manifolds and holomorphic extension of CR functions, J. Differential Geom. 25 (1987) 431-467. ]); extension through minimality towards unprecised directions [A.E. Tumanov, Extension of CR-functions into a wedge, Mat. Sb. 181 (7) (1990) 951-964. ; A.E. Tumanov, Analytic discs and the extendibility of CR functions, in: Integral Geometry, Radon Transforms and Complex Analysis, Venice, 1996, in: Lecture Notes in Math., vol. 1684, Springer, Berlin, 1998, pp. 123-141].

Multiconfiguration Pair-Density Functional Theory Outperforms Kohn-Sham Density Functional Theory and Multireference Perturbation Theory for Ground-State and Excited-State Charge Transfer.

PubMed

Ghosh, Soumen; Sonnenberger, Andrew L; Hoyer, Chad E; Truhlar, Donald G; Gagliardi, Laura

2015-08-11

The correct description of charge transfer in ground and excited states is very important for molecular interactions, photochemistry, electrochemistry, and charge transport, but it is very challenging for Kohn-Sham (KS) density functional theory (DFT). KS-DFT exchange-correlation functionals without nonlocal exchange fail to describe both ground- and excited-state charge transfer properly. We have recently proposed a theory called multiconfiguration pair-density functional theory (MC-PDFT), which is based on a combination of multiconfiguration wave function theory with a new type of density functional called an on-top density functional. Here we have used MC-PDFT to study challenging ground- and excited-state charge-transfer processes by using on-top density functionals obtained by translating KS exchange-correlation functionals. For ground-state charge transfer, MC-PDFT performs better than either the PBE exchange-correlation functional or CASPT2 wave function theory. For excited-state charge transfer, MC-PDFT (unlike KS-DFT) shows qualitatively correct behavior at long-range with great improvement in predicted excitation energies.

Extension of Coronal Structure Into Interplanetary Space

NASA Technical Reports Server (NTRS)

Woo, Richard; Habbal, Shadia Rifai

1996-01-01

The evolution of the solar corona and its imprint on the solar wind is investigated by comparing Ulysses radio occultation measurements of path-integrated electron density and density fluctuations in the heliocentric distance range of 21-32R(sub o) with simultaneous measurements of the solasr corona by the HAO Mauna Loa K-coronameter.

Construction of a high-density high-resolution genetic map and its integration with BAC-based physical map in channel catfish

USDA-ARS?s Scientific Manuscript database

Construction of genetic linkage map is essential for genetic and genomic studies. Recent advances in sequencing and genotyping technologies made it possible to generate high-density and high-resolution genetic linkage maps, especially for the organisms lacking extensive genomic resources. In the pre...

Long-distance Movements by Female White-footed Mice, Peromyscus leucopus, in Extensive Mixed-wood Forest

Treesearch

Thomas J. Maier

2002-01-01

Two adult female White-footed Mice (Peromyscus leucopus) were recovered 14,730 m and 6840 m from where they were originally captured and tagged in central Massachusetts. Similar combinations of factors throughout an extensive forested landscape, including poor acorn (Quercus spp.) crops, high population densities of mice, and the...

A Fast Algorithm for the Convolution of Functions with Compact Support Using Fourier Extensions

DOE PAGES

Xu, Kuan; Austin, Anthony P.; Wei, Ke

2017-12-21

In this paper, we present a new algorithm for computing the convolution of two compactly supported functions. The algorithm approximates the functions to be convolved using Fourier extensions and then uses the fast Fourier transform to efficiently compute Fourier extension approximations to the pieces of the result. Finally, the complexity of the algorithm is O(N(log N) 2), where N is the number of degrees of freedom used in each of the Fourier extensions.

A Fast Algorithm for the Convolution of Functions with Compact Support Using Fourier Extensions

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

Xu, Kuan; Austin, Anthony P.; Wei, Ke

In this paper, we present a new algorithm for computing the convolution of two compactly supported functions. The algorithm approximates the functions to be convolved using Fourier extensions and then uses the fast Fourier transform to efficiently compute Fourier extension approximations to the pieces of the result. Finally, the complexity of the algorithm is O(N(log N) 2), where N is the number of degrees of freedom used in each of the Fourier extensions.

Interactions among forest age, valley and channel morphology, and log jams regulate animal production in mountain streams

NASA Astrophysics Data System (ADS)

Walters, D. M.; Venarsky, M. P.; Hall, R. O., Jr.; Herdrich, A.; Livers, B.; Winkelman, D.; Wohl, E.

2014-12-01

Forest age and local valley morphometry strongly influence the form and function of mountain streams in Colorado. Streams in valleys with old growth forest (>350 years) have extensive log jam complexes that create multi-thread channel reaches with extensive pool habitat and large depositional areas. Streams in younger unmanaged forests (e.g., 120 years old) and intensively managed forests have much fewer log jams and lower wood loads. These are single-thread streams dominated by riffles and with little depositional habitat. We hypothesized that log jam streams would retain more organic matter and have higher metabolism, leading to greater production of stream macroinvertebrates and trout. Log jam reaches should also have greater emergence of adult aquatic insects, and consequently have higher densities of riparian spiders taking advantage of these prey. Surficial organic matter was 3-fold higher in old-growth streams, and these streams had much higher ecosystem respiration. Insect production (g m2 y-1) was similar among forest types, but fish density was four times higher in old-growth streams with copious log jams. However, at the valley scale, insect production (g m-1 valley-1) and trout density (number m-1 valley-1) was 2-fold and 10-fold higher, respectively, in old growth streams. This finding is because multi-thread reaches created by log jams have much greater stream area and stream length per meter of valley than single-thread channels. The more limited response of macroinvertebrates may be related to fish predation. Trout in old growth streams had similar growth rates and higher fat content than fish in other streams in spite of occurring at higher densities and higher elevation/colder temperatures. This suggests that the positive fish effect observed in old growth streams is related to greater availability of invertebrate prey, which is consistent with our original hypothesis. Preliminary analyses suggest that spider densities do not respond strongly to differences in stream morphology, but rather to changes in elevation and associated air temperatures. These results demonstrate strong indirect effects of forest age and valley morphometry on organic matter storage and animal secondary production in streams that is mediated by direct effects associated with the presence or absence of logjams.

A functional ABCA1 gene variant is associated with low HDL-cholesterol levels and shows evidence of positive selection in Native Americans

PubMed Central

Acuña-Alonzo, Víctor; Flores-Dorantes, Teresa; Kruit, Janine K.; Villarreal-Molina, Teresa; Arellano-Campos, Olimpia; Hünemeier, Tábita; Moreno-Estrada, Andrés; Ortiz-López, Ma Guadalupe; Villamil-Ramírez, Hugo; León-Mimila, Paola; Villalobos-Comparan, Marisela; Jacobo-Albavera, Leonor; Ramírez-Jiménez, Salvador; Sikora, Martin; Zhang, Lin-Hua; Pape, Terry D.; de Ángeles Granados-Silvestre, Ma; Montufar-Robles, Isela; Tito-Alvarez, Ana M.; Zurita-Salinas, Camilo; Bustos-Arriaga, José; Cedillo-Barrón, Leticia; Gómez-Trejo, Celta; Barquera-Lozano, Rodrigo; Vieira-Filho, Joao P.; Granados, Julio; Romero-Hidalgo, Sandra; Huertas-Vázquez, Adriana; González-Martín, Antonio; Gorostiza, Amaya; Bonatto, Sandro L.; Rodríguez-Cruz, Maricela; Wang, Li; Tusié-Luna, Teresa; Aguilar-Salinas, Carlos A.; Lisker, Ruben; Moises, Regina S.; Menjivar, Marta; Salzano, Francisco M.; Knowler, William C.; Bortolini, M. Cátira; Hayden, Michael R.; Baier, Leslie J.; Canizales-Quinteros, Samuel

2010-01-01

It has been suggested that the higher susceptibility of Hispanics to metabolic disease is related to their Native American heritage. A frequent cholesterol transporter ABCA1 (ATP-binding cassette transporter A1) gene variant (R230C, rs9282541) apparently exclusive to Native American individuals was associated with low high-density lipoprotein cholesterol (HDL-C) levels, obesity and type 2 diabetes in Mexican Mestizos. We performed a more extensive analysis of this variant in 4405 Native Americans and 863 individuals from other ethnic groups to investigate genetic evidence of positive selection, to assess its functional effect in vitro and to explore associations with HDL-C levels and other metabolic traits. The C230 allele was found in 29 of 36 Native American groups, but not in European, Asian or African individuals. C230 was observed on a single haplotype, and C230-bearing chromosomes showed longer relative haplotype extension compared with other haplotypes in the Americas. Additionally, single-nucleotide polymorphism data from the Human Genome Diversity Panel Native American populations were enriched in significant integrated haplotype score values in the region upstream of the ABCA1 gene. Cells expressing the C230 allele showed a 27% cholesterol efflux reduction (P< 0.001), confirming this variant has a functional effect in vitro. Moreover, the C230 allele was associated with lower HDL-C levels (P = 1.77 × 10−11) and with higher body mass index (P = 0.0001) in the combined analysis of Native American populations. This is the first report of a common functional variant exclusive to Native American and descent populations, which is a major determinant of HDL-C levels and may have contributed to the adaptive evolution of Native American populations. PMID:20418488

Branching habit and the allocation of reproductive resources in conifers

PubMed Central

Leslie, Andrew B.

2012-01-01

Background and Aims Correlated relationships between branch thickness, branch density, and twig and leaf size have been used extensively to study the evolution of plant canopy architecture, but fewer studies have explored the impact of these relationships on the allocation of reproductive resources. This study quantifies pollen cone production in conifers, which have similar basic reproductive biology but vary dramatically in branching habit, in order to test how differences in branch diameter influence pollen cone size and the density with which they are deployed in the canopy. Methods Measurements of canopy branch density, the number of cones per branch and cone size were used to estimate the amount of pollen cone tissues produced by 16 species in three major conifer clades. The number of pollen grains produced was also estimated using direct counts from individual pollen cones. Key Results The total amount of pollen cone tissues in the conifer canopy varied little among species and clades, although vegetative traits such as branch thickness, branch density and pollen cone size varied over several orders of magnitude. However, branching habit controls the way these tissues are deployed: taxa with small branches produce small pollen cones at a high density, while taxa with large branches produce large cones relatively sparsely. Conclusions Conifers appear to invest similar amounts of energy in pollen production independent of branching habit. However, similar associations between branch thickness, branch density and pollen cone size are seen across conifers, including members of living and extinct groups not directly studied here. This suggests that reproductive features relating to pollen cone size are in large part a function of the evolution of vegetative morphology and branching habit. PMID:22782240

Micro-computed tomography: Applications for high-resolution skeletal density determinations: An example using annually banded crustose coralline algae

NASA Astrophysics Data System (ADS)

Chan, P.; Halfar, J.; Norley, C. J. D.; Pollmann, S. I.; Adey, W.; Holdsworth, D. W.

2017-09-01

Warming and acidification of the world's oceans are expected to have widespread consequences for marine biodiversity and ecosystem functioning. However, due to the relatively short record of instrumental observations, one has to rely upon geochemical and physical proxy information stored in biomineralized shells and skeletons of calcareous marine organisms as in situ recorders of past environments. Of particular interest is the response of marine calcifiers to ocean acidification through the examination of structural growth characteristics. Here we demonstrate the application of micro-computed tomography (micro-CT) for three-dimensional visualization and analysis of growth, skeletal density, and calcification in a slow-growing, annually banded crustose coralline alga Clathromorphum nereostratum (increment width ˜380 µm). X-ray images and time series of skeletal density were generated at 20 µm resolution and rebinned to 40, 60, 80, and 100 µm for comparison in a sensitivity analysis. Calcification rates were subsequently calculated as the product of density and growth (linear extension). While both skeletal density and calcification rates do not significantly differ at varying spatial resolutions (the latter being strongly influenced by growth rates), clear visualization of micron-scale growth features and the quantification of structural changes on subannual time scales requires higher scanning resolutions. In the present study, imaging at 20 µm resolution reveals seasonal cycles in density that correspond to summer/winter variations in skeletal structure observed using scanning electron microscopy (SEM). Micro-CT is a fast, nondestructive, and high-resolution technique for structural and morphometric analyses of temporally banded paleoclimate archives, particularly those that exhibit slow or compressed growth or micron-scale structures.

An Analytical Planning Model to Estimate the Optimal Density of Charging Stations for Electric Vehicles

PubMed Central

Ahn, Yongjun; Yeo, Hwasoo

2015-01-01

The charging infrastructure location problem is becoming more significant due to the extensive adoption of electric vehicles. Efficient charging station planning can solve deeply rooted problems, such as driving-range anxiety and the stagnation of new electric vehicle consumers. In the initial stage of introducing electric vehicles, the allocation of charging stations is difficult to determine due to the uncertainty of candidate sites and unidentified charging demands, which are determined by diverse variables. This paper introduces the Estimating the Required Density of EV Charging (ERDEC) stations model, which is an analytical approach to estimating the optimal density of charging stations for certain urban areas, which are subsequently aggregated to city level planning. The optimal charging station’s density is derived to minimize the total cost. A numerical study is conducted to obtain the correlations among the various parameters in the proposed model, such as regional parameters, technological parameters and coefficient factors. To investigate the effect of technological advances, the corresponding changes in the optimal density and total cost are also examined by various combinations of technological parameters. Daejeon city in South Korea is selected for the case study to examine the applicability of the model to real-world problems. With real taxi trajectory data, the optimal density map of charging stations is generated. These results can provide the optimal number of chargers for driving without driving-range anxiety. In the initial planning phase of installing charging infrastructure, the proposed model can be applied to a relatively extensive area to encourage the usage of electric vehicles, especially areas that lack information, such as exact candidate sites for charging stations and other data related with electric vehicles. The methods and results of this paper can serve as a planning guideline to facilitate the extensive adoption of electric vehicles. PMID:26575845

A note on the accuracy of KS-DFT densities

NASA Astrophysics Data System (ADS)

Ranasinghe, Duminda S.; Perera, Ajith; Bartlett, Rodney J.

2017-11-01

The accuracy of the density of wave function methods and Kohn-Sham (KS) density functionals is studied using moments of the density, ⟨rn ⟩ =∫ ρ (r )rnd τ =∫0∞4 π r2ρ (r ) rnd r ,where n =-1 ,-2,0,1,2 ,and 3 provides information about the short- and long-range behavior of the density. Coupled cluster (CC) singles, doubles, and perturbative triples (CCSD(T)) is considered as the reference density. Three test sets are considered: boron through neon neutral atoms, two and four electron cations, and 3d transition metals. The total density and valence only density are distinguished by dropping appropriate core orbitals. Among density functionals tested, CAMQTP00 and ωB97x show the least deviation for boron through neon neutral atoms. They also show accurate eigenvalues for the HOMO indicating that they should have a more correct long-range behavior for the density. For transition metals, some density functional approximations outperform some wave function methods, suggesting that the KS determinant could be a better starting point for some kinds of correlated calculations. By using generalized many-body perturbation theory (MBPT), the convergence of second-, third-, and fourth-order KS-MBPT for the density is addressed as it converges to the infinite-order coupled cluster result. For the transition metal test set, the deviations in the KS density functional theory methods depend on the amount of exact exchange the functional uses. Functionals with exact exchange close to 25% show smaller deviations from the CCSD(T) density.

LSPRAY-IV: A Lagrangian Spray Module

NASA Technical Reports Server (NTRS)

Raju, M. S.

2012-01-01

LSPRAY-IV is a Lagrangian spray solver developed for application with parallel computing and unstructured grids. It is designed to be massively parallel and could easily be coupled with any existing gas-phase flow and/or Monte Carlo Probability Density Function (PDF) solvers. The solver accommodates the use of an unstructured mesh with mixed elements of either triangular, quadrilateral, and/or tetrahedral type for the gas flow grid representation. It is mainly designed to predict the flow, thermal and transport properties of a rapidly vaporizing spray. Some important research areas covered as a part of the code development are: (1) the extension of combined CFD/scalar-Monte- Carlo-PDF method to spray modeling, (2) the multi-component liquid spray modeling, and (3) the assessment of various atomization models used in spray calculations. The current version contains the extension to the modeling of superheated sprays. The manual provides the user with an understanding of various models involved in the spray formulation, its code structure and solution algorithm, and various other issues related to parallelization and its coupling with other solvers.

Limnological study of Shasta Lake, Shasta County, California, with emphasis on the effects of the 1977 drought

USGS Publications Warehouse

Rettig, S.A.; Bortleson, Gilbert C.

1983-01-01

An intensive limnological study of Shasta Lake was made in conjunction with the California Department of Water Resources during the 1977 drought. Water-quality data were collected from March 1977 through September 1978 at six lake stations and four lake tributary stations. Data collected during and after the drought were compared. Lake water quality is described as a function of lake morphometry, climate, hydrology, and reservoir hydraulics. Results indicate Shasta Lake is a warm monomictic lake. Tributary inflow to the lake and outflow through the dam generate density currents which promote mixing at depth and the development of an extensive metalimnion. During the drought, record low lake levels resulted in the exposure of an extensive nearshore sediment zone. Resuspended sediments caused a deterioration of water quality. The most notable effects, in comparison with post-drought conditions, were decreased light penetration, increased dissolved-solids concentration and specific conductance, decreased dissolved-oxygen concentrations, and elevated nutrient levels. A hypolimnetic anoxic condition was observed at the upstream stations of the lake. (USGS)

Nitric oxide inhibitory daphnane diterpenoids as potential anti-neuroinflammatory agents for AD from the twigs of Trigonostemon thyrsoideus.

PubMed

Liu, Feng; Yang, Xueyuan; Ma, Jun; Yang, Yuling; Xie, Chunfeng; Tuerhong, Muhetaer; Jin, Da-Qing; Xu, Jing; Lee, Dongho; Ohizumi, Yasushi; Guo, Yuanqiang

2017-12-01

The extensive pathology studies revealed that Alzheimer's disease (AD) is closely related to neuroinflammation and anti-neuroinflammatory agents may be potentially useful for the treatment of AD. A continuous search for new nitric oxide (NO) inhibitory compounds as anti-neuroinflammatory agents for AD resulted in the isolation of four new (1-4) and eight known (5-12) daphnane diterpenoids from the twigs of Trigonostemon thyrsoideus. Their structures were elucidated on the basis of extensive nuclear magnetic resonance (NMR) spectroscopic data analysis and the time-dependent density functional theory (TDDFT) electronic circular dichroism (ECD) calculations. Compounds 1-4 represent new examples of daphnane diterpenoid orthoesters and 4 features a rare and complex macroring diterpenoid structure. The anti-neuroinflammatory effects were examined by inhibiting NO release in lipopolysaccharide (LPS)-induced murine microglial BV-2 cells. The possible mechanism of NO inhibition of some bioactive compounds was also investigated using molecular docking, which revealed the interactions of bioactive compounds with the inducible nitric oxide synthase (iNOS) protein. Copyright © 2017 Elsevier Inc. All rights reserved.

The electronics system for the LBNL positron emission mammography (PEM) camera

NASA Astrophysics Data System (ADS)

Moses, W. W.; Young, J. W.; Baker, K.; Jones, W.; Lenox, M.; Ho, M. H.; Weng, M.

2001-06-01

Describes the electronics for a high-performance positron emission mammography (PEM) camera. It is based on the electronics for a human brain positron emission tomography (PET) camera (the Siemens/CTI HRRT), modified to use a detector module that incorporates a photodiode (PD) array. An application-specified integrated circuit (ASIC) services the photodetector (PD) array, amplifying its signal and identifying the crystal of interaction. Another ASIC services the photomultiplier tube (PMT), measuring its output and providing a timing signal. Field-programmable gate arrays (FPGAs) and lookup RAMs are used to apply crystal-by-crystal correction factors and measure the energy deposit and the interaction depth (based on the PD/PMT ratio). Additional FPGAs provide event multiplexing, derandomization, coincidence detection, and real-time rebinning. Embedded PC/104 microprocessors provide communication, real-time control, and configure the system. Extensive use of FPGAs make the overall design extremely flexible, allowing many different functions (or design modifications) to be realized without hardware changes. Incorporation of extensive onboard diagnostics, implemented in the FPGAs, is required by the very high level of integration and density achieved by this system.

Segmentation Algorithms for Detection of Targets in IR Imagery (Algorithmes de Segmentation pour la Detection de Cibles sur Images IR),

DTIC Science & Technology

1981-01-01

This fact being established, leptokurtic and platykurtic density functions are defined in terms of deviations from the normal density function. Thus...the usual definitions (Ref. 6) are: Leptokurtic - A density function that is peaked, K > 0, [18] and Platykurtic - A density function that is flat, K...has long Deen accepted that a symmetrical platykurtic density function, with K<O, is characterized by a flatter top and more abrupt terminals than the

A divide-conquer-recombine algorithmic paradigm for large spatiotemporal quantum molecular dynamics simulations

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

Shimojo, Fuyuki; Hattori, Shinnosuke; Department of Physics, Kumamoto University, Kumamoto 860-8555

We introduce an extension of the divide-and-conquer (DC) algorithmic paradigm called divide-conquer-recombine (DCR) to perform large quantum molecular dynamics (QMD) simulations on massively parallel supercomputers, in which interatomic forces are computed quantum mechanically in the framework of density functional theory (DFT). In DCR, the DC phase constructs globally informed, overlapping local-domain solutions, which in the recombine phase are synthesized into a global solution encompassing large spatiotemporal scales. For the DC phase, we design a lean divide-and-conquer (LDC) DFT algorithm, which significantly reduces the prefactor of the O(N) computational cost for N electrons by applying a density-adaptive boundary condition at themore » peripheries of the DC domains. Our globally scalable and locally efficient solver is based on a hybrid real-reciprocal space approach that combines: (1) a highly scalable real-space multigrid to represent the global charge density; and (2) a numerically efficient plane-wave basis for local electronic wave functions and charge density within each domain. Hybrid space-band decomposition is used to implement the LDC-DFT algorithm on parallel computers. A benchmark test on an IBM Blue Gene/Q computer exhibits an isogranular parallel efficiency of 0.984 on 786 432 cores for a 50.3 × 10{sup 6}-atom SiC system. As a test of production runs, LDC-DFT-based QMD simulation involving 16 661 atoms is performed on the Blue Gene/Q to study on-demand production of hydrogen gas from water using LiAl alloy particles. As an example of the recombine phase, LDC-DFT electronic structures are used as a basis set to describe global photoexcitation dynamics with nonadiabatic QMD (NAQMD) and kinetic Monte Carlo (KMC) methods. The NAQMD simulations are based on the linear response time-dependent density functional theory to describe electronic excited states and a surface-hopping approach to describe transitions between the excited states. A series of techniques are employed for efficiently calculating the long-range exact exchange correction and excited-state forces. The NAQMD trajectories are analyzed to extract the rates of various excitonic processes, which are then used in KMC simulation to study the dynamics of the global exciton flow network. This has allowed the study of large-scale photoexcitation dynamics in 6400-atom amorphous molecular solid, reaching the experimental time scales.« less

Quantum confinement effects on electronic photomobilities at nanostructured semiconductor surfaces: Si(111) without and with adsorbed Ag clusters

NASA Astrophysics Data System (ADS)

Hembree, Robert H.; Vazhappilly, Tijo; Micha, David A.

2017-12-01

The conductivity of holes and electrons photoexcited in Si slabs is affected by the slab thickness and by adsorbates. The mobilities of those charged carriers depend on how many layers compose the slab, and this has important scientific and technical consequences for the understanding of photovoltaic materials. A previously developed general computational procedure combining density matrix and electronic band structure treatments has been applied to extensive calculations of mobilities of photoexcited electrons and holes at Si(111) nanostructured surfaces with varying slab thickness and for varying photon energies, to investigate the expected change in mobility magnitudes as the slab thickness is increased. Results have been obtained with and without adsorbed silver clusters for comparison of their optical and photovoltaic properties. Band states were generated using a modified ab initio density functional treatment with the PBE exchange and correlation density functionals and with periodic boundary conditions for large atomic supercells. An energy gap correction was applied to the unoccupied orbital energies of each band structure by running more accurate HSE hybrid functional calculations for a Si(111) slab. Photoexcited state populations for slabs with 6, 8, 10, and 12 layers were generated using a steady state reduced density matrix including dissipative effects due to energy exchange with excitons and phonons in the medium. Mobilities have been calculated from the derivatives of voltage-driven electronic energies with respect to electronic momentum, for each energy band and for the average over bands. Results show two clear trends: (a) adding Ag increases the hole photomobilities and (b) decreasing the slab thickness increases hole photomobilities. The increased hole populations in 6- and 8-layer systems and the large increase in hole mobility for these thinner slabs can be interpreted as a quantum confinement effect of hole orbitals. As the slab thickness increases to ten and twelve layers, the effect of silver adsorbates decreases leading to smaller relative enhancements to the conduction electron and hole mobilities, but the addition of the silver nanoclusters still increases the absorbance of light and the mobility of holes compared to their mobilities in the pure Si slabs.

Differential geometry-based solvation and electrolyte transport models for biomolecular modeling: a review

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

Wei, Guowei; Baker, Nathan A.

2016-11-11

This chapter reviews the differential geometry-based solvation and electrolyte transport for biomolecular solvation that have been developed over the past decade. A key component of these methods is the differential geometry of surfaces theory, as applied to the solvent-solute boundary. In these approaches, the solvent-solute boundary is determined by a variational principle that determines the major physical observables of interest, for example, biomolecular surface area, enclosed volume, electrostatic potential, ion density, electron density, etc. Recently, differential geometry theory has been used to define the surfaces that separate the microscopic (solute) domains for biomolecules from the macroscopic (solvent) domains. In thesemore » approaches, the microscopic domains are modeled with atomistic or quantum mechanical descriptions, while continuum mechanics models (including fluid mechanics, elastic mechanics, and continuum electrostatics) are applied to the macroscopic domains. This multiphysics description is integrated through an energy functional formalism and the resulting Euler-Lagrange equation is employed to derive a variety of governing partial differential equations for different solvation and transport processes; e.g., the Laplace-Beltrami equation for the solvent-solute interface, Poisson or Poisson-Boltzmann equations for electrostatic potentials, the Nernst-Planck equation for ion densities, and the Kohn-Sham equation for solute electron density. Extensive validation of these models has been carried out over hundreds of molecules, including proteins and ion channels, and the experimental data have been compared in terms of solvation energies, voltage-current curves, and density distributions. We also propose a new quantum model for electrolyte transport.« less

Maximum current density and beam brightness achievable by laser-driven electron sources

NASA Astrophysics Data System (ADS)

Filippetto, D.; Musumeci, P.; Zolotorev, M.; Stupakov, G.

2014-02-01

This paper discusses the extension to different electron beam aspect ratio of the Child-Langmuir law for the maximum achievable current density in electron guns. Using a simple model, we derive quantitative formulas in good agreement with simulation codes. The new scaling laws for the peak current density of temporally long and transversely narrow initial beam distributions can be used to estimate the maximum beam brightness and suggest new paths for injector optimization.

Increased InAs quantum dot size and density using bismuth as a surfactant

NASA Astrophysics Data System (ADS)

Dasika, Vaishno D.; Krivoy, E. M.; Nair, H. P.; Maddox, S. J.; Park, K. W.; Jung, D.; Lee, M. L.; Yu, E. T.; Bank, S. R.

2014-12-01

We have investigated the growth of self-assembled InAs quantum dots using bismuth as a surfactant to control the dot size and density. We find that the bismuth surfactant increases the quantum dot density, size, and uniformity, enabling the extension of the emission wavelength with increasing InAs deposition without a concomitant reduction in dot density. We show that these effects are due to bismuth acting as a reactive surfactant to kinetically suppress the surface adatom mobility. This mechanism for controlling quantum dot density and size has the potential to extend the operating wavelength and enhance the performance of various optoelectronic devices.

Long-term decline in krill stock and increase in salps within the Southern Ocean.

PubMed

Atkinson, Angus; Siegel, Volker; Pakhomov, Evgeny; Rothery, Peter

2004-11-04

Antarctic krill (Euphausia superba) and salps (mainly Salpa thompsoni) are major grazers in the Southern Ocean, and krill support commercial fisheries. Their density distributions have been described in the period 1926-51, while recent localized studies suggest short-term changes. To examine spatial and temporal changes over larger scales, we have combined all available scientific net sampling data from 1926 to 2003. This database shows that the productive southwest Atlantic sector contains >50% of Southern Ocean krill stocks, but here their density has declined since the 1970s. Spatially, within their habitat, summer krill density correlates positively with chlorophyll concentrations. Temporally, within the southwest Atlantic, summer krill densities correlate positively with sea-ice extent the previous winter. Summer food and the extent of winter sea ice are thus key factors in the high krill densities observed in the southwest Atlantic Ocean. Krill need the summer phytoplankton blooms of this sector, where winters of extensive sea ice mean plentiful winter food from ice algae, promoting larval recruitment and replenishing the stock. Salps, by contrast, occupy the extensive lower-productivity regions of the Southern Ocean and tolerate warmer water than krill. As krill densities decreased last century, salps appear to have increased in the southern part of their range. These changes have had profound effects within the Southern Ocean food web.

Electronic Excited States of Tungsten(0) Arylisocyanides.

PubMed

Kvapilová, Hana; Sattler, Wesley; Sattler, Aaron; Sazanovich, Igor V; Clark, Ian P; Towrie, Michael; Gray, Harry B; Záliš, Stanislav; Vlček, Antonín

2015-09-08

W(CNAryl)6 complexes containing 2,6-diisopropylphenyl isocyanide (CNdipp) are powerful photoreductants with strongly emissive long-lived excited states. These properties are enhanced upon appending another aryl ring, e.g., W(CNdippPh(OMe2))6; CNdippPh(OMe2) = 4-(3,5-dimethoxyphenyl)-2,6-diisopropylphenylisocyanide (Sattler et al. J. Am. Chem. Soc. 2015, 137, 1198-1205). Electronic transitions and low-lying excited states of these complexes were investigated by time-dependent density functional theory (TDDFT); the lowest triplet state was characterized by time-resolved infrared spectroscopy (TRIR) supported by density functional theory (DFT). The intense absorption band of W(CNdipp)6 at 460 nm and that of W(CNdippPh(OMe2))6 at 500 nm originate from transitions of mixed ππ*(C≡N-C)/MLCT(W → Aryl) character, whereby W is depopulated by ca. 0.4 e(-) and the electron-density changes are predominantly localized along two equatorial molecular axes. The red shift and intensity rise on going from W(CNdipp)6 to W(CNdippPh(OMe2))6 are attributable to more extensive delocalization of the MLCT component. The complexes also exhibit absorptions in the 300-320 nm region, owing to W → C≡N MLCT transitions. Electronic absorptions in the spectrum of W(CNXy)6 (Xy = 2,6-dimethylphenyl), a complex with orthogonal aryl orientation, have similar characteristics, although shifted to higher energies. The relaxed lowest W(CNAryl)6 triplet state combines ππ* excitation of a trans pair of C≡N-C moieties with MLCT (0.21 e(-)) and ligand-to-ligand charge transfer (LLCT, 0.24-0.27 e(-)) from the other four CNAryl ligands to the axial aryl and, less, to C≡N groups; the spin density is localized along a single Aryl-N≡C-W-C≡N-Aryl axis. Delocalization of excited electron density on outer aryl rings in W(CNdippPh(OMe2))6 likely promotes photoinduced electron-transfer reactions to acceptor molecules. TRIR spectra show an intense broad bleach due to ν(C≡N), a prominent transient upshifted by 60-65 cm(-1), and a weak down-shifted feature due to antisymmetric C≡N stretch along the axis of high spin density. The TRIR spectral pattern remains unchanged on the femtosecond-nanosecond time scale, indicating that intersystem crossing and electron-density localization are ultrafast (<100 fs).

A proteomic analysis of the chromoplasts isolated from sweet orange fruits [Citrus sinensis (L.) Osbeck

PubMed Central

Zeng, Yunliu; Pan, Zhiyong; Ding, Yuduan; Zhu, Andan; Cao, Hongbo; Xu, Qiang; Deng, Xiuxin

2011-01-01

Here, a comprehensive proteomic analysis of the chromoplasts purified from sweet orange using Nycodenz density gradient centrifugation is reported. A GeLC-MS/MS shotgun approach was used to identify the proteins of pooled chromoplast samples. A total of 493 proteins were identified from purified chromoplasts, of which 418 are putative plastid proteins based on in silico sequence homology and functional analyses. Based on the predicted functions of these identified plastid proteins, a large proportion (∼60%) of the chromoplast proteome of sweet orange is constituted by proteins involved in carbohydrate metabolism, amino acid/protein synthesis, and secondary metabolism. Of note, HDS (hydroxymethylbutenyl 4-diphosphate synthase), PAP (plastid-lipid-associated protein), and psHSPs (plastid small heat shock proteins) involved in the synthesis or storage of carotenoid and stress response are among the most abundant proteins identified. A comparison of chromoplast proteomes between sweet orange and tomato suggested a high level of conservation in a broad range of metabolic pathways. However, the citrus chromoplast was characterized by more extensive carotenoid synthesis, extensive amino acid synthesis without nitrogen assimilation, and evidence for lipid metabolism concerning jasmonic acid synthesis. In conclusion, this study provides an insight into the major metabolic pathways as well as some unique characteristics of the sweet orange chromoplasts at the whole proteome level. PMID:21841170

Solute-solvent cavity and bridge functions. I. Varying size of the solute

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

Vyalov, I., E-mail: ivan.vyalov@iit.it; Chuev, G., E-mail: genchuev@rambler.ru; Georgi, N., E-mail: georgi@mis.mpg.de

2014-08-21

In this work we present the results of the extensive molecular simulations of solute-solvent cavity and bridge functions. The mixtures of Lennard-Jones solvent with Lennard-Jones solute at infinite dilution are considered for different solute-solvent size ratios—up to 4:1. The Percus-Yevick and hypernetted chain closures deviate substantially from simulation results in the investigated temperature and density ranges. We also find that the behavior of the indirect and cavity correlation functions is non-monotonous within the hard-core region, but the latter can be successfully approximated by mean-field theory if the solute-solvent interaction energy is divided into repulsive and attractive contribution, according to Weeks-Chandler-Andersenmore » theory. Furthermore, in spite of the non-monotonous behavior of logarithm of the cavity function and the indirect correlation function, their difference, i.e., the bridge function remains constant within the hard-core region. Such behavior of the bridge and indirect correlation functions at small distances and for small values of indirect correlation function is well known from the Duh-Haymet plots, where the non-unique relationship results in loops of the bridge function vs. indirect correlation function graphs. We show that the same pathological behavior appears also when distance is small and indirect correlation function is large. We further show that the unique functional behavior of the bridge function can be established when bridge is represented as a function of the renormalized, repulsive indirect correlation function.« less

Dynamic Structure Factor: An Introduction

NASA Astrophysics Data System (ADS)

Sturm, K.

1993-02-01

The doubly differential cross-section for weak inelastic scattering of waves or particles by manybody systems is derived in Born approximation and expressed in terms of the dynamic structure factor according to van Hove. The application of this very general scheme to scattering of neutrons, x-rays and high-energy electrons is discussed briefly. The dynamic structure factor, which is the space and time Fourier transform of the density-density correlation function, is a property of the many-body system independent of the external probe and carries information on the excitation spectrum of the system. The relation of the electronic structure factor to the density-density response function defined in linear-response theory is shown using the fluctuation-dissipation theorem. This is important for calculations, since the response function can be calculated approximately from the independent-particle response function in self-consistent field approximations, such as the random-phase approximation or the local-density approximation of the density functional theory. Since the density-density response function also determines the dielectric function, the dynamic structure can be expressed by the dielectric function.

Vacuum ultraviolet photoionization of carbohydrates and nucleotides

NASA Astrophysics Data System (ADS)

Shin, Joong-Won; Bernstein, Elliot R.

2014-01-01

Carbohydrates (2-deoxyribose, ribose, and xylose) and nucleotides (adenosine-, cytidine-, guanosine-, and uridine-5'-monophosphate) are generated in the gas phase, and ionized with vacuum ultraviolet photons (VUV, 118.2 nm). The observed time of flight mass spectra of the carbohydrate fragmentation are similar to those observed [J.-W. Shin, F. Dong, M. Grisham, J. J. Rocca, and E. R. Bernstein, Chem. Phys. Lett. 506, 161 (2011)] for 46.9 nm photon ionization, but with more intensity in higher mass fragment ions. The tendency of carbohydrate ions to fragment extensively following ionization seemingly suggests that nucleic acids might undergo radiation damage as a result of carbohydrate, rather than nucleobase fragmentation. VUV photoionization of nucleotides (monophosphate-carbohydrate-nucleobase), however, shows that the carbohydrate-nucleobase bond is the primary fragmentation site for these species. Density functional theory (DFT) calculations indicate that the removed carbohydrate electrons by the 118.2 nm photons are associated with endocyclic C-C and C-O ring centered orbitals: loss of electron density in the ring bonds of the nascent ion can thus account for the observed fragmentation patterns following carbohydrate ionization. DFT calculations also indicate that electrons removed from nucleotides under these same conditions are associated with orbitals involved with the nucleobase-saccharide linkage electron density. The calculations give a general mechanism and explanation of the experimental results.

Simulations of material mixing in laser-driven reshock experiments

NASA Astrophysics Data System (ADS)

Haines, Brian M.; Grinstein, Fernando F.; Welser-Sherrill, Leslie; Fincke, James R.

2013-02-01

We perform simulations of a laser-driven reshock experiment [Welser-Sherrill et al., High Energy Density Phys. (unpublished)] in the strong-shock high energy-density regime to better understand material mixing driven by the Richtmyer-Meshkov instability. Validation of the simulations is based on direct comparison of simulation and radiographic data. Simulations are also compared with published direct numerical simulation and the theory of homogeneous isotropic turbulence. Despite the fact that the flow is neither homogeneous, isotropic nor fully turbulent, there are local regions in which the flow demonstrates characteristics of homogeneous isotropic turbulence. We identify and isolate these regions by the presence of high levels of turbulent kinetic energy (TKE) and vorticity. After reshock, our analysis shows characteristics consistent with those of incompressible isotropic turbulence. Self-similarity and effective Reynolds number assessments suggest that the results are reasonably converged at the finest resolution. Our results show that in shock-driven transitional flows, turbulent features such as self-similarity and isotropy only fully develop once de-correlation, characteristic vorticity distributions, and integrated TKE, have decayed significantly. Finally, we use three-dimensional simulation results to test the performance of two-dimensional Reynolds-averaged Navier-Stokes simulations. In this context, we also test a presumed probability density function turbulent mixing model extensively used in combustion applications.

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

Huang, Chen, E-mail: chuang3@fsu.edu

A key element in the density functional embedding theory (DFET) is the embedding potential. We discuss two major issues related to the embedding potential: (1) its non-uniqueness and (2) the numerical difficulty for solving for it, especially for the spin-polarized systems. To resolve the first issue, we extend DFET to finite temperature: all quantities, such as the subsystem densities and the total system’s density, are calculated at a finite temperature. This is a physical extension since materials work at finite temperatures. We show that the embedding potential is strictly unique at T > 0. To resolve the second issue, wemore » introduce an efficient iterative embedding potential solver. We discuss how to relax the magnetic moments in subsystems and how to equilibrate the chemical potentials across subsystems. The solver is robust and efficient for several non-trivial examples, in all of which good quality spin-polarized embedding potentials were obtained. We also demonstrate the solver on an extended periodic system: iron body-centered cubic (110) surface, which is related to the modeling of the heterogeneous catalysis involving iron, such as the Fischer-Tropsch and the Haber processes. This work would make it efficient and accurate to perform embedding simulations of some challenging material problems, such as the heterogeneous catalysis and the defects of complicated spin configurations in electronic materials.« less

Distinguishability notion based on Wootters statistical distance: Application to discrete maps

NASA Astrophysics Data System (ADS)

Gomez, Ignacio S.; Portesi, M.; Lamberti, P. W.

2017-08-01

We study the distinguishability notion given by Wootters for states represented by probability density functions. This presents the particularity that it can also be used for defining a statistical distance in chaotic unidimensional maps. Based on that definition, we provide a metric d ¯ for an arbitrary discrete map. Moreover, from d ¯ , we associate a metric space with each invariant density of a given map, which results to be the set of all distinguished points when the number of iterations of the map tends to infinity. Also, we give a characterization of the wandering set of a map in terms of the metric d ¯ , which allows us to identify the dissipative regions in the phase space. We illustrate the results in the case of the logistic and the circle maps numerically and analytically, and we obtain d ¯ and the wandering set for some characteristic values of their parameters. Finally, an extension of the metric space associated for arbitrary probability distributions (not necessarily invariant densities) is given along with some consequences. The statistical properties of distributions given by histograms are characterized in terms of the cardinal of the associated metric space. For two conjugate variables, the uncertainty principle is expressed in terms of the diameters of the associated metric space with those variables.

Vacuum ultraviolet photoionization of carbohydrates and nucleotides.

PubMed

Shin, Joong-Won; Bernstein, Elliot R

2014-01-28

Carbohydrates (2-deoxyribose, ribose, and xylose) and nucleotides (adenosine-, cytidine-, guanosine-, and uridine-5(')-monophosphate) are generated in the gas phase, and ionized with vacuum ultraviolet photons (VUV, 118.2 nm). The observed time of flight mass spectra of the carbohydrate fragmentation are similar to those observed [J.-W. Shin, F. Dong, M. Grisham, J. J. Rocca, and E. R. Bernstein, Chem. Phys. Lett. 506, 161 (2011)] for 46.9 nm photon ionization, but with more intensity in higher mass fragment ions. The tendency of carbohydrate ions to fragment extensively following ionization seemingly suggests that nucleic acids might undergo radiation damage as a result of carbohydrate, rather than nucleobase fragmentation. VUV photoionization of nucleotides (monophosphate-carbohydrate-nucleobase), however, shows that the carbohydrate-nucleobase bond is the primary fragmentation site for these species. Density functional theory (DFT) calculations indicate that the removed carbohydrate electrons by the 118.2 nm photons are associated with endocyclic C-C and C-O ring centered orbitals: loss of electron density in the ring bonds of the nascent ion can thus account for the observed fragmentation patterns following carbohydrate ionization. DFT calculations also indicate that electrons removed from nucleotides under these same conditions are associated with orbitals involved with the nucleobase-saccharide linkage electron density. The calculations give a general mechanism and explanation of the experimental results.

Quantification of cell response to polymeric composites using a two-dimensional gradient platform.

PubMed

Lin, Nancy J; Hu, Haiqing; Sung, Lipin; Lin-Gibson, Sheng

2009-07-01

A simple and straightforward screening process to assess the toxicity and corresponding cell response of dental composites would be useful prior to extensive in vitro or in vivo characterization. To this end, gradient composite samples were prepared with variations in filler content/type and in degree of conversion (DC). The DC was determined using near infrared spectroscopy (NIR), and the surface morphology was evaluated by laser scanning confocal microscopy (LSCM). RAW 264.7 macrophage-like cells were cultured directly on the composite gradient samples, and cell viability, density, and area were measured at 24 h. All three measures of cell response varied as a function of material properties. For instance, compositions with higher filler content had no reduction in cell viability or cell density, even at low conversions of 52%, whereas significant decreases in viability and density were present when the filler content was 35% or below (by mass). The overall results demonstrate the complexity of the cell-material interactions, with properties including DC, filler type, filler mass ratio, and surface morphology influencing the cell response. The combinatorial approach described herein enables simultaneous screening of multiple compositions and material properties, providing a more thorough characterization of cell response for the improved selection of biocompatible composite formulations and processing conditions.

Comparing ab initio density-functional and wave function theories: the impact of correlation on the electronic density and the role of the correlation potential.

PubMed

Grabowski, Ireneusz; Teale, Andrew M; Śmiga, Szymon; Bartlett, Rodney J

2011-09-21

The framework of ab initio density-functional theory (DFT) has been introduced as a way to provide a seamless connection between the Kohn-Sham (KS) formulation of DFT and wave-function based ab initio approaches [R. J. Bartlett, I. Grabowski, S. Hirata, and S. Ivanov, J. Chem. Phys. 122, 034104 (2005)]. Recently, an analysis of the impact of dynamical correlation effects on the density of the neon atom was presented [K. Jankowski, K. Nowakowski, I. Grabowski, and J. Wasilewski, J. Chem. Phys. 130, 164102 (2009)], contrasting the behaviour for a variety of standard density functionals with that of ab initio approaches based on second-order Møller-Plesset (MP2) and coupled cluster theories at the singles-doubles (CCSD) and singles-doubles perturbative triples [CCSD(T)] levels. In the present work, we consider ab initio density functionals based on second-order many-body perturbation theory and coupled cluster perturbation theory in a similar manner, for a range of small atomic and molecular systems. For comparison, we also consider results obtained from MP2, CCSD, and CCSD(T) calculations. In addition to this density based analysis, we determine the KS correlation potentials corresponding to these densities and compare them with those obtained for a range of ab initio density functionals via the optimized effective potential method. The correlation energies, densities, and potentials calculated using ab initio DFT display a similar systematic behaviour to those derived from electronic densities calculated using ab initio wave function theories. In contrast, typical explicit density functionals for the correlation energy, such as VWN5 and LYP, do not show behaviour consistent with this picture of dynamical correlation, although they may provide some degree of correction for already erroneous explicitly density-dependent exchange-only functionals. The results presented here using orbital dependent ab initio density functionals show that they provide a treatment of exchange and correlation contributions within the KS framework that is more consistent with traditional ab initio wave function based methods.

Local and linear chemical reactivity response functions at finite temperature in density functional theory

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

Franco-Pérez, Marco, E-mail: francopj@mcmaster.ca, E-mail: ayers@mcmaster.ca, E-mail: jlgm@xanum.uam.mx, E-mail: avela@cinvestav.mx; Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco 186, México, D.F. 09340; Ayers, Paul W., E-mail: francopj@mcmaster.ca, E-mail: ayers@mcmaster.ca, E-mail: jlgm@xanum.uam.mx, E-mail: avela@cinvestav.mx

2015-12-28

We explore the local and nonlocal response functions of the grand canonical potential density functional at nonzero temperature. In analogy to the zero-temperature treatment, local (e.g., the average electron density and the local softness) and nonlocal (e.g., the softness kernel) intrinsic response functions are defined as partial derivatives of the grand canonical potential with respect to its thermodynamic variables (i.e., the chemical potential of the electron reservoir and the external potential generated by the atomic nuclei). To define the local and nonlocal response functions of the electron density (e.g., the Fukui function, the linear density response function, and the dualmore » descriptor), we differentiate with respect to the average electron number and the external potential. The well-known mathematical relationships between the intrinsic response functions and the electron-density responses are generalized to nonzero temperature, and we prove that in the zero-temperature limit, our results recover well-known identities from the density functional theory of chemical reactivity. Specific working equations and numerical results are provided for the 3-state ensemble model.« less

Local and linear chemical reactivity response functions at finite temperature in density functional theory.

PubMed

Franco-Pérez, Marco; Ayers, Paul W; Gázquez, José L; Vela, Alberto

2015-12-28

We explore the local and nonlocal response functions of the grand canonical potential density functional at nonzero temperature. In analogy to the zero-temperature treatment, local (e.g., the average electron density and the local softness) and nonlocal (e.g., the softness kernel) intrinsic response functions are defined as partial derivatives of the grand canonical potential with respect to its thermodynamic variables (i.e., the chemical potential of the electron reservoir and the external potential generated by the atomic nuclei). To define the local and nonlocal response functions of the electron density (e.g., the Fukui function, the linear density response function, and the dual descriptor), we differentiate with respect to the average electron number and the external potential. The well-known mathematical relationships between the intrinsic response functions and the electron-density responses are generalized to nonzero temperature, and we prove that in the zero-temperature limit, our results recover well-known identities from the density functional theory of chemical reactivity. Specific working equations and numerical results are provided for the 3-state ensemble model.

High-density collagen patch prevents stricture after endoscopic circumferential submucosal dissection of the esophagus: a porcine model.

PubMed

Aoki, Shigehisa; Sakata, Yasuhisa; Shimoda, Ryo; Takezawa, Toshiaki; Oshikata-Miyazaki, Ayumi; Kimura, Hiromi; Yamamoto, Mihoko; Iwakiri, Ryuichi; Fujimoto, Kazuma; Toda, Shuji

2017-05-01

Extensive excision of the esophageal mucosa by endoscopic submucosal dissection (ESD) frequently evokes a luminal stricture. This study aimed to determine the efficacy of a high-density collagen patch for the prevention of esophageal stricture in extensive ESD. Six pigs underwent circumferential esophageal ESD under general anesthesia. In 3 pigs, artificial ulcers were covered by 2 collagen patches. The other 3 pigs underwent circumferential ESD only. The 2 collagen patches were settled onto the ulcer surface using a general endoscope and instruments. The collagen patch-treated group showed significantly better patency rates on both the oral and anal sides of the wound area compared with the control group at day 14. The mucosal re-epithelization ratio was significantly promoted, and the extent of mucosal inflammation and fibrosis was significantly decreased with the collagen patch treatment in the wound area. The frequency of cells positive α-smooth muscle actin was significantly reduced in the collagen patch-treated group compared with the control group. We have established a high-density collagen device that can reduce the esophageal stricture associated with extensive ESD. This easy-to-handle device would be useful during superficial esophageal cancer treatment by ESD. Copyright © 2017 American Society for Gastrointestinal Endoscopy. Published by Elsevier Inc. All rights reserved.

Multiconfiguration pair-density functional theory: barrier heights and main group and transition metal energetics.

PubMed

Carlson, Rebecca K; Li Manni, Giovanni; Sonnenberger, Andrew L; Truhlar, Donald G; Gagliardi, Laura

2015-01-13

Kohn-Sham density functional theory, resting on the representation of the electronic density and kinetic energy by a single Slater determinant, has revolutionized chemistry, but for open-shell systems, the Kohn-Sham Slater determinant has the wrong symmetry properties as compared to an accurate wave function. We have recently proposed a theory, called multiconfiguration pair-density functional theory (MC-PDFT), in which the electronic kinetic energy and classical Coulomb energy are calculated from a multiconfiguration wave function with the correct symmetry properties, and the rest of the energy is calculated from a density functional, called the on-top density functional, that depends on the density and the on-top pair density calculated from this wave function. We also proposed a simple way to approximate the on-top density functional by translation of Kohn-Sham exchange-correlation functionals. The method is much less expensive than other post-SCF methods for calculating the dynamical correlation energy starting with a multiconfiguration self-consistent-field wave function as the reference wave function, and initial tests of the theory were quite encouraging. Here, we provide a broader test of the theory by applying it to bond energies of main-group molecules and transition metal complexes, barrier heights and reaction energies for diverse chemical reactions, proton affinities, and the water dimerization energy. Averaged over 56 data points, the mean unsigned error is 3.2 kcal/mol for MC-PDFT, as compared to 6.9 kcal/mol for Kohn-Sham theory with a comparable density functional. MC-PDFT is more accurate on average than complete active space second-order perturbation theory (CASPT2) for main-group small-molecule bond energies, alkyl bond dissociation energies, transition-metal-ligand bond energies, proton affinities, and the water dimerization energy.

Dissepiments, density bands and signatures of thermal stress in Porites skeletons

NASA Astrophysics Data System (ADS)

DeCarlo, Thomas M.; Cohen, Anne L.

2017-09-01

The skeletons of many reef-building corals are accreted with rhythmic structural patterns that serve as valuable sclerochronometers. Annual high- and low-density band couplets, visible in X-radiographs or computed tomography scans, are used to construct age models for paleoclimate reconstructions and to track variability in coral growth over time. In some corals, discrete, anomalously high-density bands, called "stress bands," preserve information about coral bleaching. However, the mechanisms underlying the formation of coral skeletal density banding remain unclear. Dissepiments—thin, horizontal sheets of calcium carbonate accreted by the coral to support the living polyp—play a key role in the upward growth of the colony. Here, we first conducted a vital staining experiment to test whether dissepiments were accreted with lunar periodicity in Porites coral skeleton, as previously hypothesized. Over 6, 15, and 21 months, dissepiments consistently formed in a 1:1 ratio to the number of full moons elapsed over each study period. We measured dissepiment spacing to reconstruct multiple years of monthly skeletal extension rates in two Porites colonies from Palmyra Atoll and in another from Palau that bleached in 1998 under anomalously high sea temperatures. Spacing between successive dissepiments exhibited strong seasonality in corals containing annual density bands, with narrow (wide) spacing associated with high (low) density, respectively. A high-density "stress band" accreted during the 1998 bleaching event was associated with anomalously low dissepiment spacing and missed dissepiments, implying that thermal stress disrupts skeletal extension. Further, uranium/calcium ratios increased within stress bands, indicating a reduction in the carbonate ion concentration of the coral's calcifying fluid under stress. Our study verifies the lunar periodicity of dissepiments, provides a mechanistic basis for the formation of annual density bands in Porites, and reveals the underlying cause of high-density stress bands.

Graphical and Numerical Descriptive Analysis: Exploratory Tools Applied to Vietnamese Data

ERIC Educational Resources Information Center

Haughton, Dominique; Phong, Nguyen

2004-01-01

This case study covers several exploratory data analysis ideas, the histogram and boxplot, kernel density estimates, the recently introduced bagplot--a two-dimensional extension of the boxplot--as well as the violin plot, which combines a boxplot with a density shape plot. We apply these ideas and demonstrate how to interpret the output from these…

Utility of Megavoltage Fan-Beam CT for Treatment Planning in a Head-And-Neck Cancer Patient with Extensive Dental Fillings Undergoing Helical Tomotherapy

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

Yang, Claus; Liu Tianxiao; Jennelle, Richard L.

The purpose of this study was to demonstrate the potential utility of megavoltage fan-beam computed tomography (MV-FBCT) for treatment planning in a patient undergoing helical tomotherapy for nasopharyngeal carcinoma in the presence of extensive dental artifact. A 28-year-old female with locally advanced nasopharyngeal carcinoma presented for radiation therapy. Due to the extensiveness of the dental artifact present in the oral cavity kV-CT scan acquired at simulation, which made treatment planning impossible on tomotherapy planning system, MV-FBCT imaging was obtained using the HI-ART tomotherapy treatment machine, with the patient in the treatment position, and this information was registered with her originalmore » kV-CT scan for the purposes of structure delineation, dose calculation, and treatment planning. To validate the feasibility of the MV-FBCT-generated treatment plan, an electron density CT phantom (model 465, Gammex Inc., Middleton, WI) was scanned using MV-FBCT to obtain CT number to density table. Additionally, both a 'cheese' phantom (which came with the tomotherapy treatment machine) with 2 inserted ion chambers and a generic phantom called Quasar phantom (Modus Medical Devices Inc., London, ON, Canada) with one inserted chamber were used to confirm dosimetric accuracy. The MV-FBCT could be used to clearly visualize anatomy in the region of the dental artifact and provide sufficient soft-tissue contrast to assist in the delineation of normal tissue structures and fat planes. With the elimination of the dental artifact, the MV-FBCT images allowed more accurate dose calculation by the tomotherapy system. It was confirmed that the phantom material density was determined correctly by the tomotherapy MV-FBCT number to density table. The ion chamber measurements agreed with the calculations from the MV-FBCT generated phantom plan within 2%. MV-FBCT may be useful in radiation treatment planning for nasopharyngeal cancer patients in the setting of extensive dental artifacts.« less

On the origin of heavy-tail statistics in equations of the Nonlinear Schrödinger type

NASA Astrophysics Data System (ADS)

Onorato, Miguel; Proment, Davide; El, Gennady; Randoux, Stephane; Suret, Pierre

2016-09-01

We study the formation of extreme events in incoherent systems described by the Nonlinear Schrödinger type of equations. We consider an exact identity that relates the evolution of the normalized fourth-order moment of the probability density function of the wave envelope to the rate of change of the width of the Fourier spectrum of the wave field. We show that, given an initial condition characterized by some distribution of the wave envelope, an increase of the spectral bandwidth in the focusing/defocusing regime leads to an increase/decrease of the probability of formation of rogue waves. Extensive numerical simulations in 1D+1 and 2D+1 are also performed to confirm the results.

Proximity effects in ferromagnet-superconductor structures

NASA Astrophysics Data System (ADS)

Halterman, Klaus Byron

I present an extensive theoretical investigation of the proximity effects that occur in ferromagnet/superconductor systems. I use a numerical method to solve self consistently the Bogoliubov-de Gennes equations in the continuum. I obtain the pair amplitude and the local density of states (DOS), and use these results to extract the relevant lengths characterizing both the leakage of superconductivity into the magnet and to study spin splitting induced in the superconductor. These phenomena are investigated as a function of parameters such as temperature, magnet polarization, interfacial scattering, sample size and Fermi wave vector mismatch, all of which turn out to have an important influence on the results. These comprehensive results should help characterize and analyze future data, and are shown to be in agreement with existing experiments.

Consensus structures of the Mo(v) sites of sulfite-oxidizing enzymes derived from variable frequency pulsed EPR spectroscopy, isotopic labelling and DFT calculations.

PubMed

Enemark, John H

2017-10-10

Sulfite-oxidizing enzymes from eukaryotes and prokaryotes have five-coordinate distorted square-pyramidal coordination about the molybdenum atom. The paramagnetic Mo(v) state is easily generated, and over the years four distinct CW EPR spectra have been identified, depending upon enzyme source and the reaction conditions, namely high and low pH (hpH and lpH), phosphate inhibited (P i ) and sulfite (or blocked). Extensive studies of these paramagnetic forms of sulfite-oxidizing enzymes using variable frequency pulsed electron spin echo (ESE) spectroscopy, isotopic labeling and density functional theory (DFT) calculations have led to the consensus structures that are described here. Errors in some of the previously proposed structures are corrected.

A composition joint PDF method for the modeling of spray flames

NASA Technical Reports Server (NTRS)

Raju, M. S.

1995-01-01

This viewgraph presentation discusses an extension of the probability density function (PDF) method to the modeling of spray flames to evaluate the limitations and capabilities of this method in the modeling of gas-turbine combustor flows. The comparisons show that the general features of the flowfield are correctly predicted by the present solution procedure. The present solution appears to provide a better representation of the temperature field, particularly, in the reverse-velocity zone. The overpredictions in the centerline velocity could be attributed to the following reasons: (1) the use of k-epsilon turbulence model is known to be less precise in highly swirling flows and (2) the swirl number used here is reported to be estimated rather than measured.

The electronic and optical properties of CH3NH3MoI3 perovskite

NASA Astrophysics Data System (ADS)

Kansara, Shivam; Sonvane, Yogesh; Gupta, Sanjeev K.

2018-05-01

In this work, a first-principles theoretical study of hybrid perovskite CH3NH3MoI3 is performed using PBE exchange-correlation approximations in density functional theory. The results of electronic band structure are 0.90 eV (M-point: Direct) and 0.60 eV (R-X point: Indirect), respectively. We have also calculated the dielectric properties such as real, imaginary, extension coefficient (K) and reflectivity (R) properties of hybrid perovskite CH3NH3MoI3. The low-bandgap molecules are used to absorb near-IR range and typically having a bandgap smaller than 1.6 eV. This is particularly attractive in organic photovoltaics (OPV), photodetectors (PDs), and ambipolar field-effect transistors (FETs).

Dynamic sensor management of dispersed and disparate sensors for tracking resident space objects

NASA Astrophysics Data System (ADS)

El-Fallah, A.; Zatezalo, A.; Mahler, R.; Mehra, R. K.; Donatelli, D.

2008-04-01

Dynamic sensor management of dispersed and disparate sensors for space situational awareness presents daunting scientific and practical challenges as it requires optimal and accurate maintenance of all Resident Space Objects (RSOs) of interest. We demonstrate an approach to the space-based sensor management problem by extending a previously developed and tested sensor management objective function, the Posterior Expected Number of Targets (PENT), to disparate and dispersed sensors. This PENT extension together with observation models for various sensor platforms, and a Probability Hypothesis Density Particle Filter (PHD-PF) tracker provide a powerful tool for tackling this challenging problem. We demonstrate the approach using simulations for tracking RSOs by a Space Based Visible (SBV) sensor and ground based radars.

Application of an extended random-phase approximation to giant resonances in light-, medium-, and heavy-mass nuclei

NASA Astrophysics Data System (ADS)

Tselyaev, V.; Lyutorovich, N.; Speth, J.; Krewald, S.; Reinhard, P.-G.

2016-09-01

We present results of the time blocking approximation (TBA) for giant resonances in light-, medium-, and heavy-mass nuclei. The TBA is an extension of the widely used random-phase approximation (RPA) adding complex configurations by coupling to phonon excitations. A new method for handling the single-particle continuum is developed and applied in the present calculations. We investigate in detail the dependence of the numerical results on the size of the single-particle space and the number of phonons as well as on nuclear matter properties. Our approach is self-consistent, based on an energy-density functional of Skyrme type where we used seven different parameter sets. The numerical results are compared with experimental data.

On the symmetry of the boundary conditions of the volume potential

NASA Astrophysics Data System (ADS)

Kal'menov, Tynysbek Sh.; Arepova, Gaukhar; Suragan, Durvudkhan

2017-09-01

It is well known that the volume potential determines the mass or the charge distributed over the domain with density f. The volume potential is extensively used in function theory and embedding theorems. It is also well known that the volume potential gives a solution to an inhomogeneous equation. And it generates a linear self-adjoint operator. It is known that self-adjoint differential operators are generated by boundary conditions. In our previous papers for an arbitrary domain a boundary condition on the volume potential is given. In the past, it was not possible to prove the self-adjointness of these obtained boundary conditions. In the present paper, we prove the symmetry of boundary condition for the volume potential.

Challenges in Optical Emission Spectroscopy

NASA Astrophysics Data System (ADS)

Siepa, Sarah; Berger, Birk; Schulze, Julian; Schuengel, Edmund; von Keudell, Achim

2016-09-01

Collisional-radiative models (CRMs) are widely used to investigate plasma properties such as electron density, electron temperature and the form of the electron energy distribution function. In this work an extensive CRM for argon is presented, which models 30 excited states and various kinds of processes including electron impact excitation/de-excitation, radiation and radiation trapping. The CRM is evaluated in several test cases, i.e. inductively and capacitively coupled plasmas at various pressures, powers/voltages and gas admixtures. Deviations are found between modelled and measured spectra. The escape factor as a means of describing radiation trapping is discussed as well as the cross section data for electron impact processes. This work was supported by the Ruhr University Research School PLUS, funded by Germany's Excellence Initiative [DFG GSC 98/3].

Inflation in random Gaussian landscapes

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

Masoumi, Ali; Vilenkin, Alexander; Yamada, Masaki, E-mail: ali@cosmos.phy.tufts.edu, E-mail: vilenkin@cosmos.phy.tufts.edu, E-mail: Masaki.Yamada@tufts.edu

2017-05-01

We develop analytic and numerical techniques for studying the statistics of slow-roll inflation in random Gaussian landscapes. As an illustration of these techniques, we analyze small-field inflation in a one-dimensional landscape. We calculate the probability distributions for the maximal number of e-folds and for the spectral index of density fluctuations n {sub s} and its running α {sub s} . These distributions have a universal form, insensitive to the correlation function of the Gaussian ensemble. We outline possible extensions of our methods to a large number of fields and to models of large-field inflation. These methods do not suffer frommore » potential inconsistencies inherent in the Brownian motion technique, which has been used in most of the earlier treatments.« less

The evolution history of the extended solar neighbourhood

NASA Astrophysics Data System (ADS)

Just, Andreas; Sysoliatina, Kseniia; Koutsouridou, Ioanna

2018-04-01

Our detailed analytic local disc model (JJ-model) quantifies the interrelation between kinematic properties (e.g. velocity dispersions and asymmetric drift), spatial parameters (scale-lengths and vertical density profiles), and properties of stellar sub-populations (age and abundance distributions). We discuss a radial extension of the disc evolution model representing an inside-out growth of the thin disc with constant thickness. Based on metallicity distributions of APOGEE red clump stars we derive the AMR as function of galactrocentric distance and show that mono-abundance as well as mono-age populations are flaring. The predictions of the JJ-model are consistent with the TGAS-RAVE data, which provide a significant improvement of the kinematic data and unbiased distances for more than 250,000 stars.

The structure-property relationships of powder processed Fe-Al-Si alloys

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

Prichard, Paul D.

1998-02-23

Iron-aluminum alloys have been extensively evaluated as semi-continuous product such as sheet and bar, but have not been evaluated by net shape P/M processing techniques such as metal injection molding. The alloy compositions of iron-aluminum alloys have been optimized for room temperature ductility, but have limited high temperature strength. Hot extruded powder alloys in the Fe-Al-Si system have developed impressive mechanical properties, but the effects of sintering on mechanical properties have not been explored. This investigation evaluated three powder processed Fe-Al-Si alloys: Fe-15Al, Fe-15Al-2.8Si, Fe-15Al-5Si (atomic %). The powder alloys were produced with a high pressure gas atomization (HPGA) processmore » to obtain a high fraction of metal injection molding (MIM) quality powder (D 84 < 32 μm). The powders were consolidated either by P/M hot extrusion or by vacuum sintering. The extruded materials were near full density with grain sizes ranging from 30 to 50 μm. The vacuum sintering conditions produced samples with density ranging from 87% to 99% of theoretical density, with an average grain size ranging from 26 μm to 104 μm. Mechanical property testing was conducted on both extruded and sintered material using a small punch test. Tensile tests were conducted on extruded bar for comparison with the punch test data. Punch tests were conducted from 25 to 550 C to determine the yield strength, and fracture energy for each alloy as a function of processing condition. The ductile to brittle transition temperature (DBTT) was observed to increase with an increasing silicon content. The Fe-15Al-2.8Si alloy was selected for more extensive testing due to the combination of high temperature strength and low temperature toughness due to the two phase α + DO 3 structure. This investigation provided a framework for understanding the effects of silicon in powder processing and mechanical property behavior of Fe-Al-Si alloys.« less

Track structure in biological models.

PubMed

Curtis, S B

1986-01-01

High-energy heavy ions in the galactic cosmic radiation (HZE particles) may pose a special risk during long term manned space flights outside the sheltering confines of the earth's geomagnetic field. These particles are highly ionizing, and they and their nuclear secondaries can penetrate many centimeters of body tissue. The three dimensional patterns of ionizations they create as they lose energy are referred to as their track structure. Several models of biological action on mammalian cells attempt to treat track structure or related quantities in their formulation. The methods by which they do this are reviewed. The proximity function is introduced in connection with the theory of Dual Radiation Action (DRA). The ion-gamma kill (IGK) model introduces the radial energy-density distribution, which is a smooth function characterizing both the magnitude and extension of a charged particle track. The lethal, potentially lethal (LPL) model introduces lambda, the mean distance between relevant ion clusters or biochemical species along the track. Since very localized energy depositions (within approximately 10 nm) are emphasized, the proximity function as defined in the DRA model is not of utility in characterizing track structure in the LPL formulation.

A Discrete Probability Function Method for the Equation of Radiative Transfer

NASA Technical Reports Server (NTRS)

Sivathanu, Y. R.; Gore, J. P.

1993-01-01

A discrete probability function (DPF) method for the equation of radiative transfer is derived. The DPF is defined as the integral of the probability density function (PDF) over a discrete interval. The derivation allows the evaluation of the PDF of intensities leaving desired radiation paths including turbulence-radiation interactions without the use of computer intensive stochastic methods. The DPF method has a distinct advantage over conventional PDF methods since the creation of a partial differential equation from the equation of transfer is avoided. Further, convergence of all moments of intensity is guaranteed at the basic level of simulation unlike the stochastic method where the number of realizations for convergence of higher order moments increases rapidly. The DPF method is described for a representative path with approximately integral-length scale-sized spatial discretization. The results show good agreement with measurements in a propylene/air flame except for the effects of intermittency resulting from highly correlated realizations. The method can be extended to the treatment of spatial correlations as described in the Appendix. However, information regarding spatial correlations in turbulent flames is needed prior to the execution of this extension.

Athermal brittle-to-ductile transition in amorphous solids.

PubMed

Dauchot, Olivier; Karmakar, Smarajit; Procaccia, Itamar; Zylberg, Jacques

2011-10-01

Brittle materials exhibit sharp dynamical fractures when meeting Griffith's criterion, whereas ductile materials blunt a sharp crack by plastic responses. Upon continuous pulling, ductile materials exhibit a necking instability that is dominated by a plastic flow. Usually one discusses the brittle to ductile transition as a function of increasing temperature. We introduce an athermal brittle to ductile transition as a function of the cutoff length of the interparticle potential. On the basis of extensive numerical simulations of the response to pulling the material boundaries at a constant speed we offer an explanation of the onset of ductility via the increase in the density of plastic modes as a function of the potential cutoff length. Finally we can resolve an old riddle: In experiments brittle materials can be strained under grip boundary conditions and exhibit a dynamic crack when cut with a sufficiently long initial slot. Mysteriously, in molecular dynamics simulations it appeared that cracks refused to propagate dynamically under grip boundary conditions, and continuous pulling was necessary to achieve fracture. We argue that this mystery is removed when one understands the distinction between brittle and ductile athermal amorphous materials.

Space-time-modulated stochastic processes

NASA Astrophysics Data System (ADS)

Giona, Massimiliano

2017-10-01

Starting from the physical problem associated with the Lorentzian transformation of a Poisson-Kac process in inertial frames, the concept of space-time-modulated stochastic processes is introduced for processes possessing finite propagation velocity. This class of stochastic processes provides a two-way coupling between the stochastic perturbation acting on a physical observable and the evolution of the physical observable itself, which in turn influences the statistical properties of the stochastic perturbation during its evolution. The definition of space-time-modulated processes requires the introduction of two functions: a nonlinear amplitude modulation, controlling the intensity of the stochastic perturbation, and a time-horizon function, which modulates its statistical properties, providing irreducible feedback between the stochastic perturbation and the physical observable influenced by it. The latter property is the peculiar fingerprint of this class of models that makes them suitable for extension to generic curved-space times. Considering Poisson-Kac processes as prototypical examples of stochastic processes possessing finite propagation velocity, the balance equations for the probability density functions associated with their space-time modulations are derived. Several examples highlighting the peculiarities of space-time-modulated processes are thoroughly analyzed.

Magnetic-Field Density-Functional Theory (BDFT): Lessons from the Adiabatic Connection.

PubMed

Reimann, Sarah; Borgoo, Alex; Tellgren, Erik I; Teale, Andrew M; Helgaker, Trygve

2017-09-12

We study the effects of magnetic fields in the context of magnetic field density-functional theory (BDFT), where the energy is a functional of the electron density ρ and the magnetic field B. We show that this approach is a worthwhile alternative to current-density functional theory (CDFT) and may provide a viable route to the study of many magnetic phenomena using density-functional theory (DFT). The relationship between BDFT and CDFT is developed and clarified within the framework of the four-way correspondence of saddle functions and their convex and concave parents in convex analysis. By decomposing the energy into its Kohn-Sham components, we demonstrate that the magnetizability is mainly determined by those energy components that are related to the density. For existing density functional approximations, this implies that, for the magnetizability, improvements of the density will be more beneficial than introducing a magnetic-field dependence in the correlation functional. However, once a good charge density is achieved, we show that high accuracy is likely only obtainable by including magnetic-field dependence. We demonstrate that adiabatic-connection (AC) curves at different field strengths resemble one another closely provided each curve is calculated at the equilibrium geometry of that field strength. In contrast, if all AC curves are calculated at the equilibrium geometry of the field-free system, then the curves change strongly with increasing field strength due to the increasing importance of static correlation. This holds also for density functional approximations, for which we demonstrate that the main error encountered in the presence of a field is already present at zero field strength, indicating that density-functional approximations may be applied to systems in strong fields, without the need to treat additional static correlation.

The Hpp Rule with Memory and the Density Classification Task

NASA Astrophysics Data System (ADS)

Alonso-Sanz, Ramón

This article considers an extension to the standard framework of cellular automata by implementing memory capability in cells. It is shown that the important block HPP rule behaves as an excellent classifier of the density in the initial configuration when applied to cells endowed with pondered memory of their previous states. If the weighing is made so that the most recent state values are assigning the highest weights, the HPP rule surpasses the performance of the best two-dimensional density classifiers reported in the literature.

Superfluid density and condensate fraction in the BCS-BEC crossover regime at finite temperatures

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

Fukushima, N.; Ohashi, Y.; Faculty of Science and Technology, Keio University, Hiyoshi, Yokohama 223

2007-03-15

The superfluid density is a fundamental quantity describing the response to a rotation as well as in two-fluid collisional hydrodynamics. We present extensive calculations of the superfluid density {rho}{sub s} in the BCS-BEC crossover regime of a uniform superfluid Fermi gas at finite temperatures. We include strong-coupling or fluctuation effects on these quantities within a Gaussian approximation. We also incorporate the same fluctuation effects into the BCS single-particle excitations described by the superfluid order parameter {delta} and Fermi chemical potential {mu}, using the Nozieres-Schmitt-Rink approximation. This treatment is shown to be necessary for consistent treatment of {rho}{sub s} over themore » entire BCS-BEC crossover. We also calculate the condensate fraction N{sub c} as a function of the temperature, a quantity which is quite different from the superfluid density {rho}{sub s}. We show that the mean-field expression for the condensate fraction N{sub c} is a good approximation even in the strong-coupling BEC regime. Our numerical results show how {rho}{sub s} and N{sub c} depend on temperature, from the weak-coupling BCS region to the BEC region of tightly bound Cooper pair molecules. In a companion paper [Phys. Rev. A 74, 063626 (2006)], we derive an equivalent expression for {rho}{sub s} from the thermodynamic potential, which exhibits the role of the pairing fluctuations in a more explicit manner.« less

On the modelling of scalar and mass transport in combustor flows

NASA Technical Reports Server (NTRS)

Nikjooy, M.; So, R. M. C.

1989-01-01

Results are presented of a numerical study of swirling and nonswirling combustor flows with and without density variations. Constant-density arguments are used to justify closure assumptions invoked for the transport equations for turbulent momentum and scalar fluxes, which are written in terms of density-weighted variables. Comparisons are carried out with measurements obtained from three different axisymmetric model combustor experiments covering recirculating flow, swirling flow, and variable-density swirling flow inside the model combustors. Results show that the Reynolds stress/flux models do a credible job of predicting constant-density swirling and nonswirling combustor flows with passive scalar transport. However, their improvements over algebraic stress/flux models are marginal. The extension of the constant-density models to variable-density flow calculations shows that the models are equally valid for such flows.

Influence of halide composition on the structural, electronic, and optical properties of mixed CH3NH3Pb (I1-xBrx) 3 perovskites calculated using the virtual crystal approximation method

NASA Astrophysics Data System (ADS)

Jong, Un-Gi; Yu, Chol-Jun; Ri, Jin-Song; Kim, Nam-Hyok; Ri, Guk-Chol

2016-09-01

Extensive studies have demonstrated the promising capability of the organic-inorganic hybrid halide perovskite CH3NH3PbI3 in solar cells with a high power conversion efficiency exceeding 20%. However, the intrinsic as well as extrinsic instabilities of this material remain the major challenge to the commercialization of perovskite-based solar cells. Mixing halides is expected to resolve this problem. Here, we investigate the effect of chemical substitution in the position of the halogen atom on the structural, electronic, and optical properties of mixed halide perovskites CH3NH3Pb (I1-xBrx) 3 with a pseudocubic phase using the virtual crystal approximation method within density functional theory. With an increase of Br content x from 0.0 to 1.0, the lattice constant decreases in proportion to x with the function of a (x )=6.420 -0.333 x (Å), while the band gap and the exciton binding energy increase with the quadratic function of Eg(x ) =1.542 +0.374 x +0.185 x2 (eV) and the linear function of Eb(x ) =0.045 +0.057 x (eV), respectively. The photoabsorption coefficients are also calculated, showing a blueshift of the absorption onsets for higher Br contents. We calculate the phase decomposition energy of these materials and analyze the electronic charge density difference to estimate the material stability. Based on the calculated results, we suggest that the best match between efficiency and stability can be achieved at x ≈0.2 in CH3NH3Pb (I1-xBrx) 3 perovskites.

Efficient time-dependent density functional theory approximations for hybrid density functionals: analytical gradients and parallelization.

PubMed

Petrenko, Taras; Kossmann, Simone; Neese, Frank

2011-02-07

In this paper, we present the implementation of efficient approximations to time-dependent density functional theory (TDDFT) within the Tamm-Dancoff approximation (TDA) for hybrid density functionals. For the calculation of the TDDFT/TDA excitation energies and analytical gradients, we combine the resolution of identity (RI-J) algorithm for the computation of the Coulomb terms and the recently introduced "chain of spheres exchange" (COSX) algorithm for the calculation of the exchange terms. It is shown that for extended basis sets, the RIJCOSX approximation leads to speedups of up to 2 orders of magnitude compared to traditional methods, as demonstrated for hydrocarbon chains. The accuracy of the adiabatic transition energies, excited state structures, and vibrational frequencies is assessed on a set of 27 excited states for 25 molecules with the configuration interaction singles and hybrid TDDFT/TDA methods using various basis sets. Compared to the canonical values, the typical error in transition energies is of the order of 0.01 eV. Similar to the ground-state results, excited state equilibrium geometries differ by less than 0.3 pm in the bond distances and 0.5° in the bond angles from the canonical values. The typical error in the calculated excited state normal coordinate displacements is of the order of 0.01, and relative error in the calculated excited state vibrational frequencies is less than 1%. The errors introduced by the RIJCOSX approximation are, thus, insignificant compared to the errors related to the approximate nature of the TDDFT methods and basis set truncation. For TDDFT/TDA energy and gradient calculations on Ag-TB2-helicate (156 atoms, 2732 basis functions), it is demonstrated that the COSX algorithm parallelizes almost perfectly (speedup ~26-29 for 30 processors). The exchange-correlation terms also parallelize well (speedup ~27-29 for 30 processors). The solution of the Z-vector equations shows a speedup of ~24 on 30 processors. The parallelization efficiency for the Coulomb terms can be somewhat smaller (speedup ~15-25 for 30 processors), but their contribution to the total calculation time is small. Thus, the parallel program completes a Becke3-Lee-Yang-Parr energy and gradient calculation on the Ag-TB2-helicate in less than 4 h on 30 processors. We also present the necessary extension of the Lagrangian formalism, which enables the calculation of the TDDFT excited state properties in the frozen-core approximation. The algorithms described in this work are implemented into the ORCA electronic structure system.

Atomic-scale defects and electronic properties of a transferred synthesized MoS2 monolayer

NASA Astrophysics Data System (ADS)

Delač Marion, Ida; Čapeta, Davor; Pielić, Borna; Faraguna, Fabio; Gallardo, Aurelio; Pou, Pablo; Biel, Blanca; Vujičić, Nataša; Kralj, Marko

2018-07-01

MoS2 monolayer samples were synthesized on a SiO2/Si wafer and transferred to Ir(111) for nano-scale characterization. The samples were extensively characterized during every step of the transfer process, and MoS2 on the final substrate was examined down to the atomic level by scanning tunneling microscopy (STM). The procedures conducted yielded high-quality monolayer MoS2 of milimeter-scale size with an average defect density of 2 × 1013 cm–2. The lift-off from the growth substrate was followed by a release of the tensile strain, visible in a widening of the optical band gap measured by photoluminescence. Subsequent transfer to the Ir(111) surface led to a strong drop of this optical signal but without further shifts of characteristic peaks. The electronic band gap was measured by scanning tunneling spectroscopy (STS), revealing n-doping and lateral nano-scale variations. The combined use of STM imaging and density functional theory (DFT) calculations allows us to identify the most recurring point-like defects as S vacancies.

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

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

The reduction in fatigue crack growth resistance of dentin with depth.

PubMed

Ivancik, J; Neerchal, N K; Romberg, E; Arola, D

2011-08-01

The fatigue crack growth resistance of dentin was characterized as a function of depth from the dentino-enamel junction. Compact tension (CT) specimens were prepared from the crowns of third molars in the deep, middle, and peripheral dentin. The microstructure was quantified in terms of the average tubule dimensions and density. Fatigue cracks were grown in-plane with the tubules and characterized in terms of the initiation and growth responses. Deep dentin exhibited the lowest resistance to the initiation of fatigue crack growth, as indicated by the stress intensity threshold (ΔK(th) ≈ 0.8 MPa•m(0.5)) and the highest incremental fatigue crack growth rate (over 1000 times that in peripheral dentin). Cracks in deep dentin underwent incremental extension under cyclic stresses that were 40% lower than those required in peripheral dentin. The average fatigue crack growth rates increased significantly with tubule density, indicating the importance of microstructure on the potential for tooth fracture. Molars with deep restorations are more likely to suffer from the cracked-tooth syndrome, because of the lower fatigue crack growth resistance of deep dentin.

Temperature-driven band inversion in Pb 0.77 Sn 0.23 Se : Optical and Hall effect studies

DOE PAGES

Anand, Naween; Buvaev, Sanal; Hebard, A. F.; ...

2014-12-23

Optical and Hall-effect measurements have been performed on single crystals of Pb₀.₇₇Sn₀.₂₃Se, a IV-VI mixed chalcogenide. The temperature dependent (10–300 K) reflectance was measured over 40–7000 cm⁻¹ (5–870 meV) with an extension to 15,500 cm⁻¹ (1.92 eV) at room temperature. The reflectance was fit to the Drude-Lorentz model using a single Drude component and several Lorentz oscillators. The optical properties at the measured temperatures were estimated via Kramers-Kronig analysis as well as by the Drude-Lorentz fit. The carriers were p-type with the carrier density determined by Hall measurements. A signature of valence intraband transition is found in the low-energy opticalmore » spectra. It is found that the valence-conduction band transition energy as well as the free carrier effective mass reach minimum values at 100 K, suggesting temperature-driven band inversion in the material. Thus, density function theory calculation for the electronic band structure also make similar predictions.« less

Radiation Transport in Random Media With Large Fluctuations

NASA Astrophysics Data System (ADS)

Olson, Aaron; Prinja, Anil; Franke, Brian

2017-09-01

Neutral particle transport in media exhibiting large and complex material property spatial variation is modeled by representing cross sections as lognormal random functions of space and generated through a nonlinear memory-less transformation of a Gaussian process with covariance uniquely determined by the covariance of the cross section. A Karhunen-Loève decomposition of the Gaussian process is implemented to effciently generate realizations of the random cross sections and Woodcock Monte Carlo used to transport particles on each realization and generate benchmark solutions for the mean and variance of the particle flux as well as probability densities of the particle reflectance and transmittance. A computationally effcient stochastic collocation method is implemented to directly compute the statistical moments such as the mean and variance, while a polynomial chaos expansion in conjunction with stochastic collocation provides a convenient surrogate model that also produces probability densities of output quantities of interest. Extensive numerical testing demonstrates that use of stochastic reduced-order modeling provides an accurate and cost-effective alternative to random sampling for particle transport in random media.

A kinetic theory for age-structured stochastic birth-death processes

NASA Astrophysics Data System (ADS)

Chou, Tom; Greenman, Chris

Classical age-structured mass-action models such as the McKendrick-von Foerster equation have been extensively studied but they are structurally unable to describe stochastic fluctuations or population-size-dependent birth and death rates. Conversely, current theories that include size-dependent population dynamics (e.g., carrying capacity) cannot be easily extended to take into account age-dependent birth and death rates. In this paper, we present a systematic derivation of a new fully stochastic kinetic theory for interacting age-structured populations. By defining multiparticle probability density functions, we derive a hierarchy of kinetic equations for the stochastic evolution of an aging population undergoing birth and death. We show that the fully stochastic age-dependent birth-death process precludes factorization of the corresponding probability densities, which then must be solved by using a BBGKY-like hierarchy. Our results generalize both deterministic models and existing master equation approaches by providing an intuitive and efficient way to simultaneously model age- and population-dependent stochastic dynamics applicable to the study of demography, stem cell dynamics, and disease evolution. NSF.

Interacting hadron resonance gas model in the K -matrix formalism

NASA Astrophysics Data System (ADS)

Dash, Ashutosh; Samanta, Subhasis; Mohanty, Bedangadas

2018-05-01

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

Investigations of static properties of model bulk polymer fluids

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

Bishop, M.; Ceperley, D.; Frisch, H.L.

1980-03-01

The static properties of continuum, multichain systems are investigated by a ''reptation'' Monte Carlo algorithm. All beads interact via a repulsive (shifted) Lennard-Jones potential. In addition, nearest neighbors along chains are linked by a quasiharmonic potential which permits limited pair extensions. Chain lengths of 5, 10, 20, 32, 50, and 70 beads have been studied. Studies at densities of 0.1, 0.3, and 0.5 demonstrate that chain dimensions are compressed as the concentration is increased. Both the mean square end-to-end distance, , and the mean square radius of gyration, , have a power law dependence upon l-1, the number of bonds,more » with exponent approximately 1.16 for rho=0.1 and 1.07 for rho=0.3 and 0.5. and scale with density as rho/sup -gamma/ where ..gamma..approx.-0.22 +- 0.02 for long chains, in reasonable agreement with the scaling prediction of -0.25. The asphericity ratios, the pair correlation functions of the center of masses, and the extent of chain overlaps indicate the nonideal behavior of these systems.« less

Halogen Bonding versus Hydrogen Bonding: A Molecular Orbital Perspective

PubMed Central

Wolters, Lando P; Bickelhaupt, F Matthias

2012-01-01

We have carried out extensive computational analyses of the structure and bonding mechanism in trihalides DX⋅⋅⋅A− and the analogous hydrogen-bonded complexes DH⋅⋅⋅A− (D, X, A=F, Cl, Br, I) using relativistic density functional theory (DFT) at zeroth-order regular approximation ZORA-BP86/TZ2P. One purpose was to obtain a set of consistent data from which reliable trends in structure and stability can be inferred over a large range of systems. The main objective was to achieve a detailed understanding of the nature of halogen bonds, how they resemble, and also how they differ from, the better understood hydrogen bonds. Thus, we present an accurate physical model of the halogen bond based on quantitative Kohn–Sham molecular orbital (MO) theory, energy decomposition analyses (EDA) and Voronoi deformation density (VDD) analyses of the charge distribution. It appears that the halogen bond in DX⋅⋅⋅A− arises not only from classical electrostatic attraction but also receives substantial stabilization from HOMO–LUMO interactions between the lone pair of A− and the σ* orbital of D–X. PMID:24551497

“Smooth” Semiparametric Regression Analysis for Arbitrarily Censored Time-to-Event Data

PubMed Central

Zhang, Min; Davidian, Marie

2008-01-01

Summary A general framework for regression analysis of time-to-event data subject to arbitrary patterns of censoring is proposed. The approach is relevant when the analyst is willing to assume that distributions governing model components that are ordinarily left unspecified in popular semiparametric regression models, such as the baseline hazard function in the proportional hazards model, have densities satisfying mild “smoothness” conditions. Densities are approximated by a truncated series expansion that, for fixed degree of truncation, results in a “parametric” representation, which makes likelihood-based inference coupled with adaptive choice of the degree of truncation, and hence flexibility of the model, computationally and conceptually straightforward with data subject to any pattern of censoring. The formulation allows popular models, such as the proportional hazards, proportional odds, and accelerated failure time models, to be placed in a common framework; provides a principled basis for choosing among them; and renders useful extensions of the models straightforward. The utility and performance of the methods are demonstrated via simulations and by application to data from time-to-event studies. PMID:17970813

Lateral distributions of EAS muons (Eμ > 800 MeV) measured with the KASCADE-Grande Muon Tracking Detector in the primary energy range 1016 -1017 eV

NASA Astrophysics Data System (ADS)

Apel, W. D.; Arteaga-Velázquez, J. C.; Bekk, K.; Bertaina, M.; Blümer, J.; Bozdog, H.; Brancus, I. M.; Cantoni, E.; Chiavassa, A.; Cossavella, F.; Daumiller, K.; de Souza, V.; Di Pierro, F.; Doll, P.; Engel, R.; Engler, J.; Fuchs, B.; Fuhrmann, D.; Gherghel-Lascu, A.; Gils, H. J.; Glasstetter, R.; Grupen, C.; Haungs, A.; Heck, D.; Hörandel, J. R.; Huber, D.; Huege, T.; Kampert, K.-H.; Kang, D.; Klages, H. O.; Link, K.; Łuczak, P.; Mathes, H. J.; Mayer, H. J.; Milke, J.; Mitrica, B.; Morello, C.; Oehlschläger, J.; Ostapchenko, S.; Palmieri, N.; Petcu, M.; Pierog, T.; Rebel, H.; Roth, M.; Schieler, H.; Schoo, S.; Schröder, F. G.; Sima, O.; Toma, G.; Trinchero, G. C.; Ulrich, H.; Weindl, A.; Wochele, J.; Zabierowski, J.

2015-05-01

The KASCADE-Grande large area (128 m2) Muon Tracking Detector has been built with the aim to identify muons ( Eμthr = 800 MeV) in Extensive Air Showers by track measurements under 18 r.l. shielding. This detector provides high-accuracy angular information (approx. 0.3 °) for muons up to 700 m distance from the shower core. In this work we present the lateral density distributions of muons in EAS measured with the Muon Tracking Detector of the KASCADE-Grande experiment. The density is calculated by counting muon tracks in a muon-to-shower-axis distance range from 100 m to 610 m from showers with reconstructed energy of 1016 -1017 eV and zenith angle θ < 18 ° . In the distance range covered by the experiment, these distributions are well described by functions phenomenologically determined already in the fifties (of the last century) by Greisen. They are compared also with the distributions obtained with the KASCADE scintillator array (Eμthr = 230 MeV) and with distributions obtained using simulated showers.

Atomic-scale defects and electronic properties of a transferred synthesized MoS2 monolayer.

PubMed

Delač Marion, Ida; Čapeta, Davor; Pielić, Borna; Faraguna, Fabio; Gallardo, Aurelio; Pou, Pablo; Biel, Blanca; Vujičić, Nataša; Kralj, Marko

2018-07-27

MoS 2 monolayer samples were synthesized on a SiO 2 /Si wafer and transferred to Ir(111) for nano-scale characterization. The samples were extensively characterized during every step of the transfer process, and MoS 2 on the final substrate was examined down to the atomic level by scanning tunneling microscopy (STM). The procedures conducted yielded high-quality monolayer MoS 2 of milimeter-scale size with an average defect density of 2 × 10 13 cm -2 . The lift-off from the growth substrate was followed by a release of the tensile strain, visible in a widening of the optical band gap measured by photoluminescence. Subsequent transfer to the Ir(111) surface led to a strong drop of this optical signal but without further shifts of characteristic peaks. The electronic band gap was measured by scanning tunneling spectroscopy (STS), revealing n-doping and lateral nano-scale variations. The combined use of STM imaging and density functional theory (DFT) calculations allows us to identify the most recurring point-like defects as S vacancies.

Virus-based surface patterning of biological molecules, probes, and inorganic materials.

PubMed

Ahn, Suji; Jeon, Seongho; Kwak, Eun-A; Kim, Jong-Man; Jaworski, Justyn

2014-10-01

An essential requirement for continued technological advancement in many areas of biology, physics, chemistry, and materials science is the growing need to generate custom patterned materials. Building from recent achievements in the site-specific modification of virus for covalent surface tethering, we show in this work that stable 2D virus patterns can be generated in custom geometries over large area glass surfaces to yield templates of biological, biochemical, and inorganic materials in high density. As a nanomaterial building block, filamentous viruses have been extensively used in recent years to produce materials with interesting properties, owing to their ease of genetic and chemical modification. By utilizing un-natural amino acids generated at specific locations on the filamentous fd bacteriophage protein coat, surface immobilization is carried out on APTES patterned glass resulting in precise geometries of covalently linked virus material. This technique facilitated the surface display of a high density of virus that were labeled with biomolecules, fluorescent probes, and gold nanoparticles, thereby opening the possibility of integrating virus as functional components for surface engineering. Copyright © 2014 Elsevier B.V. All rights reserved.

High resolution electrolyte for thinning InP by anodic dissolution and its applications to EC-V profiling, defect revealing and surface passivation

NASA Technical Reports Server (NTRS)

Faur, Maria; Faur, Mircea; Weinberg, Irving; Goradia, Manju; Vargas, Carlos

1991-01-01

An extensive experimental study was conducted using various electrolytes in an effort to find an appropriate electrolyte for anodic dissolution of InP. From the analysis of electrochemical characteristics in the dark and under different illumination levels, x ray photoelectron spectroscopy and SEM/Nomarski inspection of the surfaces, it was determined that the anodic dissolution of InP front surface layers by FAP electrolyte is a very good choice for rendering smooth surfaces, free of oxides and contaminants and with good electrical characteristics. The FAP electrolyte, based on HF, CH3COOH, and H2O2 appears to be inherently superior to previously reported electrolytes for performing accurate EC-V profiling of InP at current densities of up to 0.3 mA/sq cm. It can also be used for accurate electrochemical revealing of either precipitates or dislocation density with application to EPD mapping as a function of depth, and for defect revealing of multilayer InP structures at any depth and/or at the interfaces.

Multiconfiguration Pair-Density Functional Theory Is as Accurate as CASPT2 for Electronic Excitation.

PubMed

Hoyer, Chad E; Ghosh, Soumen; Truhlar, Donald G; Gagliardi, Laura

2016-02-04

A correct description of electronically excited states is critical to the interpretation of visible-ultraviolet spectra, photochemical reactions, and excited-state charge-transfer processes in chemical systems. We have recently proposed a theory called multiconfiguration pair-density functional theory (MC-PDFT), which is based on a combination of multiconfiguration wave function theory and a new kind of density functional called an on-top density functional. Here, we show that MC-PDFT with a first-generation on-top density functional performs as well as CASPT2 for an organic chemistry database including valence, Rydberg, and charge-transfer excitations. The results are very encouraging for practical applications.

Nanostructured hematite for photoelectrochemical water splitting

NASA Astrophysics Data System (ADS)

Ling, Yichuan

Solar water splitting is an environmentally friendly reaction of producing hydrogen gas. Since Honda and Fujishima first demonstrated solar water splitting in 1972 by using semiconductor titanium dioxide (TiO2) as photoanode in a photoelectrochemical (PEC) cell, extensive efforts have been invested into improving the solar-to-hydrogen (STH) conversion efficiency and lower the production cost of photoelectrochemical devices. In the last few years, hematite (alpha-Fe2O3) nanostructures have been extensively studied as photoanodes for PEC water splitting. Although nanostructured hematite can improve its photoelectrochemical water splitting performance to some extent, by increasing active sites for water oxidation and shortening photogenerated hole path length to semiconductor/electrolyte interface, the photoactivity of pristine hematite nanostructures is still limited by a number of factors, such as poor electrical conductivities and slow oxygen evolution reaction kinetics. Previous studies have shown that tin (Sn) as an n-type dopant can substantially enhance the photoactivity of hematite photoanodes by modifying their optical and electrical properties. In this thesis, I will first demonstrate an unintentional Sn-doping method via high temperature annealing of hematite nanowires grown on fluorine-doped tin oxide (FTO) substrate to enhance the donor density. In addition to introducing extrinsic dopants into semiconductors, the carrier densities of hematite can also be enhanced by creating intrinsic defects. Oxygen vacancies function as shallow donors for a number of hematite. In this regard, I have investigated the influence of oxygen content on thermal decomposition of FeOOH to induce oxygen vacancies in hematite. In the end, I have studied low temperature activation of hematite nanostructures.

Analysis of medium-BTU gasification condensates, June 1985-June 1986

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

Elliott, D.C.

1987-05-01

This report provides the final results of chemical and physical analysis of condensates from biomass gasification systems which are part of the US Department of Energy Biomass Thermochemical Conversion Program. The work described in detail in this report involves extensive analysis of condensates from four medium-BTU gasifiers. The analyses include elemental analysis, ash, moisture, heating value, density, specific chemical analysis, ash, moisture, heating value, density, specific chemical analysis (gas chromatography/mass spectrometry, infrared spectrophotometry, Carbon-13 nuclear magnetic resonance spectrometry) and Ames Assay. This work was an extension of a broader study earlier completed of the condensates of all the gasifers andmore » pyrolyzers in the Biomass Thermochemical Conversion Program. The analytical data demonstrates the wide range of chemical composition of the organics recoverd in the condensates and suggests a direct relationship between operating temperature and chemical composition of the condensates. A continuous pathway of thermal degradation of the tar components as a function of temperature is proposed. Variations in the chemical composition of the organic in the tars are reflected in the physical properties of tars and phase stability in relation to water in the condensate. The biological activity appears to be limited to the tars produced at high temperatures as a result of formation of polycyclic aromatic hydrocarbons in high concentrations. Future studies of the time/temperature relationship to tar composition and the effect of processing atmosphere should be undertaken. Further processing of the condensates either as wastewater treatment or upgrading of the organics to useful products is also recommended. 15 refs., 4 figs., 4 tabs.« less

Skyrme forces and decay of the Rf266*104 nucleus synthesized via different incoming channels

NASA Astrophysics Data System (ADS)

Niyti, Deep, Aman; Kharab, Rajesh; Chopra, Sahila; Gupta, Raj K.

2017-03-01

The excitation functions for the production of 262Rf, 261Rf, and 260Rf isotopes via 4 n -, 5 n -, and 6 n -decay channels from the *266Rf compound nucleus are studied within the dynamical cluster-decay model (DCM), including deformations β2 i and so-called hot-optimum orientations θi which support symmetric fission, in agreement with experiments. The data are available for 18O+248Cm and 22Ne+244Pu reactions, respectively, at the energy ranges of Elab=88.2 to 101.3 and 109.0 to 124.8 MeV. For the nuclear interaction potentials, we use the Skyrme energy density functional (SEDF) based on semiclassical extended Thomas Fermi (ETF) approach, which means an extension of the earlier study of excitation functions of *266Rf formed in 18O+248Cm reaction, based on the DCM using the pocket formula for nuclear proximity potential, showing interaction dependence. The Skyrme forces used here are the old SIII and SIV and new GSkI and KDE0(v1) given for both normal and isospin-rich nuclei, with densities added in frozen density approximation. Interestingly, the DCM gives an excellent fit to the measured data on fusion evaporation residue (ER) for both the incoming channels (18O+248Cm and 22Ne+244Pu ) at the energy range Elab=88.2 to 124.8 MeV, independent of the entrance channel and Skyrme force used. The possible fusion-fission (ff) and quasifission (qf) mass regions of fragments on DCM are also predicted. The DCM with Skyrme forces is further used to look for all the possible target-projectile (t-p) combinations forming the cold compound nucleus (CN) *266Rf at the CN excitation energy of Elab for hot compact configurations. The fusion evaporation residue cross sections, for the proposed new reactions in synthesizing the CN *266Rf, are also estimated for the future experiments, and role of mass asymmetry of nuclei is indicated.

On the use of the noncentral chi-square density function for the distribution of helicopter spectral estimates

NASA Technical Reports Server (NTRS)

Garber, Donald P.

1993-01-01

A probability density function for the variability of ensemble averaged spectral estimates from helicopter acoustic signals in Gaussian background noise was evaluated. Numerical methods for calculating the density function and for determining confidence limits were explored. Density functions were predicted for both synthesized and experimental data and compared with observed spectral estimate variability.

Stretched hydrogen molecule from a constrained-search density-functional perspective

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

Valone, Steven M; Levy, Mel

2009-01-01

Constrained-search density functional theory gives valuable insights into the fundamentals of density functional theory. It provides exact results and bounds on the ground- and excited-state density functionals. An important advantage of the theory is that it gives guidance in the construction of functionals. Here they engage constrained search theory to explore issues associated with the functional behavior of 'stretched bonds' in molecular hydrogen. A constrained search is performed with familiar valence bond wavefunctions ordinarily used to describe molecular hydrogen. The effective, one-electron hamiltonian is computed and compared to the corresponding uncorrelated, Hartree-Fock effective hamiltonian. Analysis of the functional suggests themore » need to construct different functionals for the same density and to allow a competition among these functions. As a result the correlation energy functional is composed explicitly of energy gaps from the different functionals.« less

Spatial-size scaling of pedestrian groups under growing density conditions

NASA Astrophysics Data System (ADS)

Zanlungo, Francesco; Brščić, Dražen; Kanda, Takayuki

2015-06-01

We study the dependence on crowd density of the spatial size, configuration, and velocity of pedestrian social groups. We find that, in the investigated density range, the extension of pedestrian groups in the direction orthogonal to that of motion decreases linearly with the pedestrian density around them, both for two- and three-person groups. Furthermore, we observe that at all densities, three-person groups walk slower than two-person groups, and the latter are slower than individual pedestrians, the differences in velocities being weakly affected by density. Finally, we observe that three-person groups walk in a V-shaped formation regardless of density, with a distance between the pedestrians in the front and back again almost independent of density, although the configuration appears to be less stable at higher densities. These findings may facilitate the development of more realistic crowd dynamics models and simulators.

Modeling quorum sensing trade-offs between bacterial cell density and system extension from open boundaries

NASA Astrophysics Data System (ADS)

Marenda, Mattia; Zanardo, Marina; Trovato, Antonio; Seno, Flavio; Squartini, Andrea

2016-12-01

Bacterial communities undergo collective behavioural switches upon producing and sensing diffusible signal molecules; a mechanism referred to as Quorum Sensing (QS). Exemplarily, biofilm organic matrices are built concertedly by bacteria in several environments. QS scope in bacterial ecology has been debated for over 20 years. Different perspectives counterpose the role of density reporter for populations to that of local environment diffusivity probe for individual cells. Here we devise a model system where tubes of different heights contain matrix-embedded producers and sensors. These tubes allow non-limiting signal diffusion from one open end, thereby showing that population spatial extension away from an open boundary can be a main critical factor in QS. Experimental data, successfully recapitulated by a comprehensive mathematical model, demonstrate how tube height can overtake the role of producer density in triggering sensor activation. The biotic degradation of the signal is found to play a major role and to be species-specific and entirely feedback-independent.

Modeling quorum sensing trade-offs between bacterial cell density and system extension from open boundaries.

PubMed

Marenda, Mattia; Zanardo, Marina; Trovato, Antonio; Seno, Flavio; Squartini, Andrea

2016-12-14

Bacterial communities undergo collective behavioural switches upon producing and sensing diffusible signal molecules; a mechanism referred to as Quorum Sensing (QS). Exemplarily, biofilm organic matrices are built concertedly by bacteria in several environments. QS scope in bacterial ecology has been debated for over 20 years. Different perspectives counterpose the role of density reporter for populations to that of local environment diffusivity probe for individual cells. Here we devise a model system where tubes of different heights contain matrix-embedded producers and sensors. These tubes allow non-limiting signal diffusion from one open end, thereby showing that population spatial extension away from an open boundary can be a main critical factor in QS. Experimental data, successfully recapitulated by a comprehensive mathematical model, demonstrate how tube height can overtake the role of producer density in triggering sensor activation. The biotic degradation of the signal is found to play a major role and to be species-specific and entirely feedback-independent.

Active Space Dependence in Multiconfiguration Pair-Density Functional Theory.

PubMed

Sharma, Prachi; Truhlar, Donald G; Gagliardi, Laura

2018-02-13

In multiconfiguration pair-density functional theory (MC-PDFT), multiconfiguration self-consistent-field calculations and on-top density functionals are combined to describe both static and dynamic correlation. Here, we investigate how the MC-PDFT total energy and its components depend on the active space choice in the case of the H 2 and N 2 molecules. The active space dependence of the on-top pair density, the total density, the ratio of on-top pair density to half the square of the electron density, and the satisfaction of the virial theorem are also explored. We find that the density and on-top pair density do not change significantly with changes in the active space. However, the on-top ratio does change significantly with respect to active space change, and this affects the on-top energy. This study provides a foundation for designing on-top density functionals and automatizing the active space choice in MC-PDFT.

Optimization of Systems with Uncertainty: Initial Developments for Performance, Robustness and Reliability Based Designs

NASA Technical Reports Server (NTRS)

Crespo, Luis G.; Bushnell, Dennis M. (Technical Monitor)

2002-01-01

This paper presents a study on the optimization of systems with structured uncertainties, whose inputs and outputs can be exhaustively described in the probabilistic sense. By propagating the uncertainty from the input to the output in the space of the probability density functions and the moments, optimization problems that pursue performance, robustness and reliability based designs are studied. Be specifying the desired outputs in terms of desired probability density functions and then in terms of meaningful probabilistic indices, we settle a computationally viable framework for solving practical optimization problems. Applications to static optimization and stability control are used to illustrate the relevance of incorporating uncertainty in the early stages of the design. Several examples that admit a full probabilistic description of the output in terms of the design variables and the uncertain inputs are used to elucidate the main features of the generic problem and its solution. Extensions to problems that do not admit closed form solutions are also evaluated. Concrete evidence of the importance of using a consistent probabilistic formulation of the optimization problem and a meaningful probabilistic description of its solution is provided in the examples. In the stability control problem the analysis shows that standard deterministic approaches lead to designs with high probability of running into instability. The implementation of such designs can indeed have catastrophic consequences.

Pressure-induced structural change in liquid GeI4.

PubMed

Fuchizaki, Kazuhiro; Nishimura, Hironori; Hase, Takaki; Saitoh, Hiroyuki

2017-12-27

The similarity in the shape of the melting curve of GeI 4 to that of SnI 4 suggests that a liquid-liquid transition as observed in liquid SnI 4 is also expected to occur in liquid GeI 4 . Because the slope of the melting curve of GeI 4 abruptly changes at around 3 GPa, in situ synchrotron diffraction measurements were conducted to examine closely the structural changes upon compression at around 3 GPa. The reduced radial distribution functions of the high- and low-pressure liquid states of GeI 4 share the same feature inherent in the high-pressure (high-density) and low-pressure (low-density) radial distribution functions of liquid SnI 4 . This feature allows us to introduce local order parameters that we may use to observe the transition. Unlike the transition in liquid SnI 4 , the transition from the low-pressure to the high-pressure structure seems sluggish. We speculate that the liquid-liquid critical point of GeI 4 is no longer a thermodynamically stable state and is slightly located below the melting curve. As a result, the structural change is said to be a crossover rather than a transition. The behavior of the local-order parameters implies a metastable extension of the liquid-liquid phase boundary with a negative slope.

Ab initio study of friction of graphene flake on graphene/graphite or SiC surface

NASA Astrophysics Data System (ADS)

Gulseren, Oguz; Tayran, Ceren; Sayin, Ceren Sibel

Recently, the rich dynamics of graphene flake on graphite or SiC surfaces are revealed from atomic force microcopy experiments. The studies toward to the understanding of microscopic origin of friction are getting a lot of attention. Despite the several studies of these systems using molecular dynamics methods, density functional theory based investigations are limited because of the huge system sizes. In this study, we investigated the frictional force on graphene flake on graphite or SiC surfaces from pseudopotential planewave calculations based on density functional theory. In both cases, graphene flake (24 C) on graphite or SiC surface, bilayer flake is introduced by freezing the top layer as well as the bottom layer of the surface slab. After fixing the load with these frozen layers, we checked the relative motion of the flake over the surface. A minimum energy is reached when the flake is moved on graphene to attain AB stacking. We also conclude that edge reconstruction because of the finite size of the flake is very critical for frictional properties of the flake; therefore the saturation of dangling bonds with hydrogen is also addressed. Not only the symmetric configurations remaining parameter space is extensively studied. Supported by TUBITAK Project No: 114F162. This work is supported by TUBITAK Project No: 114F162.

Kinetics of Cell Fusion Induced by a Syncytia-Producing Mutant of Herpes Simplex Virus Type I

PubMed Central

Person, Stanley; Knowles, Robert W.; Read, G. Sullivan; Warner, Susan C.; Bond, Vincent C.

1976-01-01

We have isolated a number of plaque-morphology mutants from a strain of herpes simplex virus type I which, unlike the wild type, cause extensive cell fusion during a productive viral infection. After the onset of fusion, there is an exponential decrease in the number of single cells as a function of time after infection. At a multiplicity of infection (MOI) of 3.8 plaque-forming units per cell, fusion begins 5.3 h after infection with the number of single cells decreasing to 10% of the original number 10.2 h after infection. As the MOI is gradually increased from 0.4 to 8, the onset of fusion occurs earlier during infection. However, when the MOI is increased from 8 to 86, the onset of fusion does not occur any earlier. The rate of fusion is independent of the MOI for an MOI greater than 1. The rate of fusion varies linearly with initial cell density up to 3.5 × 104 cells/cm2 and is independent of initial cell density at higher cell concentrations. To assay cell fusion we have developed a simple quantitative assay using a Coulter counter to measure the number of single cells as a function of time after infection. Data obtained using a Coulter counter are similar to those obtained with a microscope assay. PMID:173881

Molecular Gas in Starburts: Understanding Mergers using High Density Gas Tracers

NASA Astrophysics Data System (ADS)

Manohar, Swarnima; Scoville, N.; Walter, F.; Sheth, K.

2014-01-01

NGC 6240 and Arp 220 can be considered the founding members of a very active class of objects called Ultraluminous Infrared Galaxies or ULIRGs. They are in different stages of mergers and hence are excellent case studies to enhance our knowledge about the merging process. We have imaged the dense star-forming regions of these galaxies at sub-arcsec resolution with ALMA and CARMA. Multi-band imaging allows multilevel excitation analysis of HCN, HCO+ and CS transitions which will constrain the properties of the gas as a function of position and velocity (across line profiles). We are doing an extensive multilevel excitation analysis of the merger as a function of radius which enables in depth understanding of the gas dynamics and gas properties such as temperature and density. This in turn probes the homogeneity of the gas in the merging system and hence the regions that facilitate high star formation rates. This tandem use of CARMA with ALMA to map these systems at different merger stages will assemble a more integrated picture of the merger process. We are probing the distribution and dynamics of star forming gas and star formation activity in the dense disk structures to enable new theoretical understanding of the physics, dynamics, star formation activity and associated feedback in the most active and rapidly evolving galactic nuclei. Here we present preliminary observations of Arp 220 and NGC 6240 from ALMA and CARMA.

Maximum size-density relationships for mixed softwoods in the northeastern USA

Treesearch

Dale S. Solomon; Lianjun Zhang

2002-01-01

The maximum size-density relationships or self-thinning lines were developed for three mix .ed-softwood climax forest habitats (hemlock-red spruce, spruce-fir, and cedar-black spruce) in the northeastern USA. The plot data were collected from an extensive data base used in growth studies from 1950 to 1970, and represented a wide range of species compositions, sites,...

Multicomponent density functional theory embedding formulation.

PubMed

Culpitt, Tanner; Brorsen, Kurt R; Pak, Michael V; Hammes-Schiffer, Sharon

2016-07-28

Multicomponent density functional theory (DFT) methods have been developed to treat two types of particles, such as electrons and nuclei, quantum mechanically at the same level. In the nuclear-electronic orbital (NEO) approach, all electrons and select nuclei, typically key protons, are treated quantum mechanically. For multicomponent DFT methods developed within the NEO framework, electron-proton correlation functionals based on explicitly correlated wavefunctions have been designed and used in conjunction with well-established electronic exchange-correlation functionals. Herein a general theory for multicomponent embedded DFT is developed to enable the accurate treatment of larger systems. In the general theory, the total electronic density is separated into two subsystem densities, denoted as regular and special, and different electron-proton correlation functionals are used for these two electronic densities. In the specific implementation, the special electron density is defined in terms of spatially localized Kohn-Sham electronic orbitals, and electron-proton correlation is included only for the special electron density. The electron-proton correlation functional depends on only the special electron density and the proton density, whereas the electronic exchange-correlation functional depends on the total electronic density. This scheme includes the essential electron-proton correlation, which is a relatively local effect, as well as the electronic exchange-correlation for the entire system. This multicomponent DFT-in-DFT embedding theory is applied to the HCN and FHF(-) molecules in conjunction with two different electron-proton correlation functionals and three different electronic exchange-correlation functionals. The results illustrate that this approach provides qualitatively accurate nuclear densities in a computationally tractable manner. The general theory is also easily extended to other types of partitioning schemes for multicomponent systems.

Multicomponent density functional theory embedding formulation

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

Culpitt, Tanner; Brorsen, Kurt R.; Pak, Michael V.

Multicomponent density functional theory (DFT) methods have been developed to treat two types of particles, such as electrons and nuclei, quantum mechanically at the same level. In the nuclear-electronic orbital (NEO) approach, all electrons and select nuclei, typically key protons, are treated quantum mechanically. For multicomponent DFT methods developed within the NEO framework, electron-proton correlation functionals based on explicitly correlated wavefunctions have been designed and used in conjunction with well-established electronic exchange-correlation functionals. Herein a general theory for multicomponent embedded DFT is developed to enable the accurate treatment of larger systems. In the general theory, the total electronic density ismore » separated into two subsystem densities, denoted as regular and special, and different electron-proton correlation functionals are used for these two electronic densities. In the specific implementation, the special electron density is defined in terms of spatially localized Kohn-Sham electronic orbitals, and electron-proton correlation is included only for the special electron density. The electron-proton correlation functional depends on only the special electron density and the proton density, whereas the electronic exchange-correlation functional depends on the total electronic density. This scheme includes the essential electron-proton correlation, which is a relatively local effect, as well as the electronic exchange-correlation for the entire system. This multicomponent DFT-in-DFT embedding theory is applied to the HCN and FHF{sup −} molecules in conjunction with two different electron-proton correlation functionals and three different electronic exchange-correlation functionals. The results illustrate that this approach provides qualitatively accurate nuclear densities in a computationally tractable manner. The general theory is also easily extended to other types of partitioning schemes for multicomponent systems.« less

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

PubMed

Kananenka, Alexei A; Zgid, Dominika

2017-11-14

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

Pollution-tolerant invertebrates enhance greenhouse gas flux in urban wetlands.

PubMed

Mehring, Andrew S; Cook, Perran L M; Evrard, Victor; Grant, Stanley B; Levin, Lisa A

2017-09-01

One of the goals of urban ecology is to link community structure to ecosystem function in urban habitats. Pollution-tolerant wetland invertebrates have been shown to enhance greenhouse gas (GHG) flux in controlled laboratory experiments, suggesting that they may influence urban wetland roles as sources or sinks of GHG. However, it is unclear if their effects can be detected in highly variable conditions in a field setting. Here we use an extensive data set on carbon dioxide (CO 2 ), methane (CH 4 ), and nitrous oxide (N 2 O) flux in sediment cores (n = 103) collected from 10 urban wetlands in Melbourne, Australia during summer and winter in order to test for invertebrate enhancement of GHG flux. We detected significant multiplicative enhancement effects of temperature, sediment carbon content, and invertebrate density on CH 4 and CO 2 flux. Each doubling in density of oligochaete worms or large benthic invertebrates (oligochaete worms and midge larvae) corresponded to ~42% and ~15% increases in average CH 4 and CO 2 flux, respectively. However, despite exceptionally high densities, invertebrates did not appear to enhance N 2 O flux. This was likely due to fairly high organic carbon content in sediments (range 2.1-12.6%), and relatively low nitrate availability (median 1.96 μmol/L NO 3 - -N), which highlights the context-dependent nature of community structural effects on ecosystem function. The invertebrates enhancing GHG flux in this study are ubiquitous, and frequently dominate faunal communities in impaired aquatic ecosystems. Therefore, invertebrate effects on CO 2 and CH 4 flux may be common in wetlands impacted by urbanization, and urban wetlands may make greater contributions to the total GHG budgets of cities if the negative impacts of urbanization on wetlands are left unchecked. © 2017 by the Ecological Society of America.

Bit patterned media with composite structure for microwave assisted magnetic recording

NASA Astrophysics Data System (ADS)

Eibagi, Nasim

Patterned magnetic nano-structures are under extensive research due to their interesting emergent physics and promising applications in high-density magnetic data storage, through magnetic logic to bio-magnetic functionality. Bit-patterned media is an example of such structures which is a leading candidate to reach magnetic densities which cannot be achieved by conventional magnetic media. Patterned arrays of complex heterostructures such as exchange-coupled composites are studied in this thesis as a potential for next generation of magnetic recording media. Exchange-coupled composites have shown new functionality and performance advantages in magnetic recording and bit patterned media provide unique capability to implement such architectures. Due to unique resonant properties of such structures, their possible application in spin transfer torque memory and microwave assisted switching is also studied. This dissertation is divided into seven chapters. The first chapter covers the history of magnetic recording, the need to increase magnetic storage density, and the challenges in the field. The second chapter introduces basic concepts of magnetism. The third chapter explains the fabrication methods for thin films and various lithographic techniques that were used to pattern the devices under study for this thesis. The fourth chapter introduces the exchanged coupled system with the structure of [Co/Pd] / Fe / [Co/Pd], where the thickness of Fe is varied, and presents the magnetic properties of such structures using conventional magnetometers. The fifth chapter goes beyond what is learned in the fourth chapter and utilizes polarized neutron reflectometry to study the vertical exchange coupling and reversal mechanism in patterned structures with such structure. The sixth chapter explores the dynamic properties of the patterned samples, and their reversal mechanism under microwave field. The final chapter summarizes the results and describes the prospects for future applications of these structures.

Modeling and Density Estimation of an Urban Freeway Network Based on Dynamic Graph Hybrid Automata

PubMed Central

Chen, Yangzhou; Guo, Yuqi; Wang, Ying

2017-01-01

In this paper, in order to describe complex network systems, we firstly propose a general modeling framework by combining a dynamic graph with hybrid automata and thus name it Dynamic Graph Hybrid Automata (DGHA). Then we apply this framework to model traffic flow over an urban freeway network by embedding the Cell Transmission Model (CTM) into the DGHA. With a modeling procedure, we adopt a dual digraph of road network structure to describe the road topology, use linear hybrid automata to describe multi-modes of dynamic densities in road segments and transform the nonlinear expressions of the transmitted traffic flow between two road segments into piecewise linear functions in terms of multi-mode switchings. This modeling procedure is modularized and rule-based, and thus is easily-extensible with the help of a combination algorithm for the dynamics of traffic flow. It can describe the dynamics of traffic flow over an urban freeway network with arbitrary topology structures and sizes. Next we analyze mode types and number in the model of the whole freeway network, and deduce a Piecewise Affine Linear System (PWALS) model. Furthermore, based on the PWALS model, a multi-mode switched state observer is designed to estimate the traffic densities of the freeway network, where a set of observer gain matrices are computed by using the Lyapunov function approach. As an example, we utilize the PWALS model and the corresponding switched state observer to traffic flow over Beijing third ring road. In order to clearly interpret the principle of the proposed method and avoid computational complexity, we adopt a simplified version of Beijing third ring road. Practical application for a large-scale road network will be implemented by decentralized modeling approach and distributed observer designing in the future research. PMID:28353664

Modeling and Density Estimation of an Urban Freeway Network Based on Dynamic Graph Hybrid Automata.

PubMed

Chen, Yangzhou; Guo, Yuqi; Wang, Ying

2017-03-29

In this paper, in order to describe complex network systems, we firstly propose a general modeling framework by combining a dynamic graph with hybrid automata and thus name it Dynamic Graph Hybrid Automata (DGHA). Then we apply this framework to model traffic flow over an urban freeway network by embedding the Cell Transmission Model (CTM) into the DGHA. With a modeling procedure, we adopt a dual digraph of road network structure to describe the road topology, use linear hybrid automata to describe multi-modes of dynamic densities in road segments and transform the nonlinear expressions of the transmitted traffic flow between two road segments into piecewise linear functions in terms of multi-mode switchings. This modeling procedure is modularized and rule-based, and thus is easily-extensible with the help of a combination algorithm for the dynamics of traffic flow. It can describe the dynamics of traffic flow over an urban freeway network with arbitrary topology structures and sizes. Next we analyze mode types and number in the model of the whole freeway network, and deduce a Piecewise Affine Linear System (PWALS) model. Furthermore, based on the PWALS model, a multi-mode switched state observer is designed to estimate the traffic densities of the freeway network, where a set of observer gain matrices are computed by using the Lyapunov function approach. As an example, we utilize the PWALS model and the corresponding switched state observer to traffic flow over Beijing third ring road. In order to clearly interpret the principle of the proposed method and avoid computational complexity, we adopt a simplified version of Beijing third ring road. Practical application for a large-scale road network will be implemented by decentralized modeling approach and distributed observer designing in the future research.

Patterns in hydraulic architecture from roots to branches in six tropical tree species from cacao agroforestry and their relation to wood density and stem growth.

PubMed

Kotowska, Martyna M; Hertel, Dietrich; Rajab, Yasmin Abou; Barus, Henry; Schuldt, Bernhard

2015-01-01

For decades it has been assumed that the largest vessels are generally found in roots and that vessel size and corresponding sapwood area-specific hydraulic conductivity are acropetally decreasing toward the distal twigs. However, recent studies from the perhumid tropics revealed a hump-shaped vessel size distribution. Worldwide tropical perhumid forests are extensively replaced by agroforestry systems often using introduced species of various biogeographical and climatic origins. Nonetheless, it is unknown so far what kind of hydraulic architectural patterns are developed in those agroforestry tree species and which impact this exerts regarding important tree functional traits, such as stem growth, hydraulic efficiency and wood density (WD). We investigated wood anatomical and hydraulic properties of the root, stem and branch wood in Theobroma cacao and five common shade tree species in agroforestry systems on Sulawesi (Indonesia); three of these were strictly perhumid tree species, and the other three tree species are tolerating seasonal drought. The overall goal of our study was to relate these properties to stem growth and other tree functional traits such as foliar nitrogen content and sapwood to leaf area ratio. Our results confirmed a hump-shaped vessel size distribution in nearly all species. Drought-adapted species showed divergent patterns of hydraulic conductivity, vessel density, and relative vessel lumen area between root, stem and branch wood compared to wet forest species. Confirming findings from natural old-growth forests in the same region, WD showed no relationship to specific conductivity. Overall, aboveground growth performance was better predicted by specific hydraulic conductivity than by foliar traits and WD. Our study results suggest that future research on conceptual trade-offs of tree hydraulic architecture should consider biogeographical patterns underlining the importance of anatomical adaptation mechanisms to environment.

Revealing the z ~ 2.5 Cosmic Web with 3D Lyα Forest Tomography: a Deformation Tensor Approach

NASA Astrophysics Data System (ADS)

Lee, Khee-Gan; White, Martin

2016-11-01

Studies of cosmological objects should take into account their positions within the cosmic web of large-scale structure. Unfortunately, the cosmic web has only been extensively mapped at low redshifts (z\\lt 1), using galaxy redshifts as tracers of the underlying density field. At z\\gt 1, the required galaxy densities are inaccessible for the foreseeable future, but 3D reconstructions of Lyα forest absorption in closely separated background QSOs and star-forming galaxies already offer a detailed window into z˜ 2-3 large-scale structure. We quantify the utility of such maps for studying the cosmic web by using realistic z = 2.5 Lyα forest simulations matched to observational properties of upcoming surveys. A deformation tensor-based analysis is used to classify voids, sheets, filaments, and nodes in the flux, which are compared to those determined from the underlying dark matter (DM) field. We find an extremely good correspondence, with 70% of the volume in the flux maps correctly classified relative to the DM web, and 99% classified to within one eigenvalue. This compares favorably to the performance of galaxy-based classifiers with even the highest galaxy densities from low-redshift surveys. We find that narrow survey geometries can degrade the recovery of the cosmic web unless the survey is ≳ 60 {h}-1 {Mpc} or ≳ 1 deg on the sky. We also examine halo abundances as a function of the cosmic web, and find a clear dependence as a function of flux overdensity, but little explicit dependence on the cosmic web. These methods will provide a new window on cosmological environments of galaxies at this very special time in galaxy formation, “high noon,” and on overall properties of cosmological structures at this epoch.

The Synthesis of Cellulose Graft Copolymers Using Cu(0)-Mediated Polymerization

NASA Astrophysics Data System (ADS)

Donaldson, Jason L.

Cellulose is the most abundant renewable polymer on the planet and there is great interest in expanding its use beyond its traditional applications. However, its hydrophilicity and insolubility in most common solvent systems are obstacles to its widespread use in advanced materials. One way to counteract this is to attach hydrophobic polymer chains to cellulose: this allows the properties of the copolymer to be tailored by the molecular weight, density, and physical properties of the grafts. Two methods were used here to synthesize the graft copolymers: a 'grafting-from' approach, where synthetic chains were grown outward from bromoester moieties on cellulose (Cell-BiB) via Cu(0)-mediated polymerization; and a 'grafting-to' approach, where fully formed synthetic chains with terminal sulfide functionality were added to cellulose acetate with methacrylate functionality (CA-MAA) via thiol-ene Michael addition. The Cell-BiB was synthesized in the ionic liquid 1-butyl-3-methylimidazolium chloride and had a degree of substitution of 1.13. Polymerization from Cell-BiB proceeded at similar but slightly slower rate than an analogous non-polymeric initiator (EBiB). The average graft density of poly(methyl acrylate) chains was 0.71 chains/ring, with a maximum of 1.0 obtained. The graft density when grafting poly(methyl methacrylate) was only 0.15, and this appeared to be due to the slow initiation of BiB groups. Using EBiB to model the reaction and improve the design should allow this to be overcome. Chain extension experiments demonstrated the living behaviour of the polymer. The CA-MAA was synthesized by esterification with methacrylic acid. Reactions of CA-MAA with thiophenol and dodecanethiol resulted in quantitative addition of the thiol to the alkene. The grafts were synthesized by Cu(0)-mediated polymerization from a bifunctional initiator containing a disulfide bond, followed by reduction to sulfides. The synthetic polymers were successfully grafted to CA-MAA but the grafting yield was limited by the low sulfide functionality. Better retention of sulfide functionality is necessary for more efficient grafting.

Correlation of structural stability with functional remodeling of high-density lipoproteins: the importance of being disordered.

PubMed

Guha, Madhumita; Gao, Xuan; Jayaraman, Shobini; Gursky, Olga

2008-11-04

High-density lipoproteins (HDLs) are protein-lipid assemblies that remove excess cell cholesterol and prevent atherosclerosis. HDLs are stabilized by kinetic barriers that decelerate protein dissociation and lipoprotein fusion. We propose that similar barriers modulate metabolic remodeling of plasma HDLs; hence, changes in particle composition that destabilize HDLs and accelerate their denaturation may accelerate their metabolic remodeling. To test this notion, we correlate existing reports on HDL-mediated cell cholesterol efflux and esterification, which are obligatory early steps in cholesterol removal, with our kinetic studies of HDL stability. The results support our hypothesis and show that factors accelerating cholesterol efflux and esterification in model discoidal lipoproteins (including reduced protein size, reduced fatty acyl chain length, and/or increased level of cis unsaturation) destabilize lipoproteins and accelerate their fusion and apolipoprotein dissociation. Oxidation studies of plasma spherical HDLs show a similar trend: mild oxidation by Cu(2+) or OCl(-) accelerates cell cholesterol efflux, protein dissociation, and HDL fusion, while extensive oxidation inhibits these reactions. Consequently, moderate destabilization may be beneficial for HDL functions by facilitating insertion of cholesterol and lipophilic enzymes, promoting dissociation of lipid-poor apolipoproteins, which are primary acceptors of cell cholesterol, and thereby accelerating HDL metabolism. Therefore, HDL stability must be delicately balanced to maintain the structural integrity of the lipoprotein assembly and ensure structural specificity necessary for interactions of HDL with its metabolic partners, while facilitating rapid HDL remodeling and turnover at key junctures of cholesterol transport. The inverse correlation between HDL stability and remodeling illustrates the functional importance of structural disorder in macromolecular assemblies stabilized by kinetic barriers.

Integrating resource selection into spatial capture-recapture models for large carnivores

USGS Publications Warehouse

Proffitt, Kelly M.; Goldberg, Joshua; Hebblewite, Mark; Russell, Robin E.; Jimenez, Ben; Robinson, Hugh S.; Pilgrim, Kristine; Schwartz, Michael K.

2015-01-01

Wildlife managers need reliable methods to estimate large carnivore densities and population trends; yet large carnivores are elusive, difficult to detect, and occur at low densities making traditional approaches intractable. Recent advances in spatial capture-recapture (SCR) models have provided new approaches for monitoring trends in wildlife abundance and these methods are particularly applicable to large carnivores. We applied SCR models in a Bayesian framework to estimate mountain lion densities in the Bitterroot Mountains of west central Montana. We incorporate an existing resource selection function (RSF) as a density covariate to account for heterogeneity in habitat use across the study area and include data collected from harvested lions. We identify individuals through DNA samples collected by (1) biopsy darting mountain lions detected in systematic surveys of the study area, (2) opportunistically collecting hair and scat samples, and (3) sampling all harvested mountain lions. We included 80 DNA samples collected from 62 individuals in the analysis. Including information on predicted habitat use as a covariate on the distribution of activity centers reduced the median estimated density by 44%, the standard deviation by 7%, and the width of 95% credible intervals by 10% as compared to standard SCR models. Within the two management units of interest, we estimated a median mountain lion density of 4.5 mountain lions/100 km2 (95% CI = 2.9, 7.7) and 5.2 mountain lions/100 km2 (95% CI = 3.4, 9.1). Including harvested individuals (dead recovery) did not create a significant bias in the detection process by introducing individuals that could not be detected after removal. However, the dead recovery component of the model did have a substantial effect on results by increasing sample size. The ability to account for heterogeneity in habitat use provides a useful extension to SCR models, and will enhance the ability of wildlife managers to reliably and economically estimate density of wildlife populations, particularly large carnivores.

Exact conditions on the temperature dependence of density functionals

DOE PAGES

Burke, K.; Smith, J. C.; Grabowski, P. E.; ...

2016-05-15

Universal exact conditions guided the construction of most ground-state density functional approximations in use today. Here, we derive the relation between the entropy and Mermin free energy density functionals for thermal density functional theory. Both the entropy and sum of kinetic and electron-electron repulsion functionals are shown to be monotonically increasing with temperature, while the Mermin functional is concave downwards. Analogous relations are found for both exchange and correlation. The importance of these conditions is illustrated in two extremes: the Hubbard dimer and the uniform gas.

Galilei group with multiple central extension, vorticity, and entropy generation: Exotic fluid in 3 +1 dimensions

NASA Astrophysics Data System (ADS)

Das, Praloy; Ghosh, Subir

2017-12-01

A noncommutative extension of an ideal (Hamiltonian) fluid model in 3 +1 dimensions is proposed. The model enjoys several interesting features: it allows a multiparameter central extension in Galilean boost algebra (which is significant being contrary to the existing belief that a similar feature can appear only in 2 +1 -dimensions); noncommutativity generates vorticity in a canonically irrotational fluid; it induces a nonbarotropic pressure leading to a nonisentropic system. (Barotropic fluids are entropy preserving as the pressure depends only on the matter density.) Our fluid model is termed "exotic" since it has a close resemblance with the extensively studied planar (2 +1 dimensions) exotic models and exotic (noncommutative) field theories.

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

PubMed

Patra, Bikash; Jana, Subrata; Samal, Prasanjit

2018-03-28

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

Beyond Kohn-Sham Approximation: Hybrid Multistate Wave Function and Density Functional Theory.

PubMed

Gao, Jiali; Grofe, Adam; Ren, Haisheng; Bao, Peng

2016-12-15

A multistate density functional theory (MSDFT) is presented in which the energies and densities for the ground and excited states are treated on the same footing using multiconfigurational approaches. The method can be applied to systems with strong correlation and to correctly describe the dimensionality of the conical intersections between strongly coupled dissociative potential energy surfaces. A dynamic-then-static framework for treating electron correlation is developed to first incorporate dynamic correlation into contracted state functions through block-localized Kohn-Sham density functional theory (KSDFT), followed by diagonalization of the effective Hamiltonian to include static correlation. MSDFT can be regarded as a hybrid of wave function and density functional theory. The method is built on and makes use of the current approximate density functional developed in KSDFT, yet it retains its computational efficiency to treat strongly correlated systems that are problematic for KSDFT but too large for accurate WFT. The results presented in this work show that MSDFT can be applied to photochemical processes involving conical intersections.