Derivative discontinuity and exchange-correlation potential of meta-GGAs in density-functional theory

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

Eich, F. G., E-mail: eichf@missouri.edu; Hellgren, Maria

2014-12-14

We investigate fundamental properties of meta-generalized-gradient approximations (meta-GGAs) to the exchange-correlation energy functional, which have an implicit density dependence via the Kohn-Sham kinetic-energy density. To this purpose, we construct the most simple meta-GGA by expressing the local exchange-correlation energy per particle as a function of a fictitious density, which is obtained by inverting the Thomas-Fermi kinetic-energy functional. This simple functional considerably improves the total energy of atoms as compared to the standard local density approximation. The corresponding exchange-correlation potentials are then determined exactly through a solution of the optimized effective potential equation. These potentials support an additional bound state andmore » exhibit a derivative discontinuity at integer particle numbers. We further demonstrate that through the kinetic-energy density any meta-GGA incorporates a derivative discontinuity. However, we also find that for commonly used meta-GGAs the discontinuity is largely underestimated and in some cases even negative.« less

Density functional theory for d- and f-electron materials and compounds

DOE PAGES

Mattson, Ann E.; Wills, John M.

2016-02-12

Here, the fundamental requirements for a computationally tractable Density Functional Theory-based method for relativistic f- and (nonrelativistic) d-electron materials and compounds are presented. The need for basing the Kohn–Sham equations on the Dirac equation is discussed. The full Dirac scheme needs exchange-correlation functionals in terms of four-currents, but ordinary functionals, using charge density and spin-magnetization, can be used in an approximate Dirac treatment. The construction of a functional that includes the additional confinement physics needed for these materials is illustrated using the subsystem-functional scheme. If future studies show that a full Dirac, four-current based, exchange-correlation functional is needed, the subsystemmore » functional scheme is one of the few schemes that can still be used for constructing functional approximations.« less

New approach to canonical partition functions computation in Nf=2 lattice QCD at finite baryon density

NASA Astrophysics Data System (ADS)

Bornyakov, V. G.; Boyda, D. L.; Goy, V. A.; Molochkov, A. V.; Nakamura, Atsushi; Nikolaev, A. A.; Zakharov, V. I.

2017-05-01

We propose and test a new approach to computation of canonical partition functions in lattice QCD at finite density. We suggest a few steps procedure. We first compute numerically the quark number density for imaginary chemical potential i μq I . Then we restore the grand canonical partition function for imaginary chemical potential using the fitting procedure for the quark number density. Finally we compute the canonical partition functions using high precision numerical Fourier transformation. Additionally we compute the canonical partition functions using the known method of the hopping parameter expansion and compare results obtained by two methods in the deconfining as well as in the confining phases. The agreement between two methods indicates the validity of the new method. Our numerical results are obtained in two flavor lattice QCD with clover improved Wilson fermions.

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.

Derivation of the density functional theory from the cluster expansion.

PubMed

Hsu, J Y

2003-09-26

The density functional theory is derived from a cluster expansion by truncating the higher-order correlations in one and only one term in the kinetic energy. The formulation allows self-consistent calculation of the exchange correlation effect without imposing additional assumptions to generalize the local density approximation. The pair correlation is described as a two-body collision of bound-state electrons, and modifies the electron- electron interaction energy as well as the kinetic energy. The theory admits excited states, and has no self-interaction energy.

Density-functional expansion methods: Grand challenges.

PubMed

Giese, Timothy J; York, Darrin M

2012-03-01

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

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

NASA Astrophysics Data System (ADS)

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

2017-11-01

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

Ensemble density variational methods with self- and ghost-interaction-corrected functionals

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

Pastorczak, Ewa; Pernal, Katarzyna, E-mail: pernalk@gmail.com

2014-05-14

Ensemble density functional theory (DFT) offers a way of predicting excited-states energies of atomic and molecular systems without referring to a density response function. Despite a significant theoretical work, practical applications of the proposed approximations have been scarce and they do not allow for a fair judgement of the potential usefulness of ensemble DFT with available functionals. In the paper, we investigate two forms of ensemble density functionals formulated within ensemble DFT framework: the Gross, Oliveira, and Kohn (GOK) functional proposed by Gross et al. [Phys. Rev. A 37, 2809 (1988)] alongside the orbital-dependent eDFT form of the functional introducedmore » by Nagy [J. Phys. B 34, 2363 (2001)] (the acronym eDFT proposed in analogy to eHF – ensemble Hartree-Fock method). Local and semi-local ground-state density functionals are employed in both approaches. Approximate ensemble density functionals contain not only spurious self-interaction but also the so-called ghost-interaction which has no counterpart in the ground-state DFT. We propose how to correct the GOK functional for both kinds of interactions in approximations that go beyond the exact-exchange functional. Numerical applications lead to a conclusion that functionals free of the ghost-interaction by construction, i.e., eDFT, yield much more reliable results than approximate self- and ghost-interaction-corrected GOK functional. Additionally, local density functional corrected for self-interaction employed in the eDFT framework yields excitations energies of the accuracy comparable to that of the uncorrected semi-local eDFT functional.« less

Study on the Electronic Transport Properties of Zigzag GaN Nanotubes

NASA Astrophysics Data System (ADS)

Li, Enling; Wang, Xiqiang; Hou, Liping; Zhao, Danna; Dai, Yuanbin; Wang, Xuewen

2011-02-01

The electronic transport properties of zigzag GaN nanotubes (n, 0) (4 <= n <= 9) have been calculated using the density functional theory and non-equilibrium Green's functions method. Firstly, the density functional theory (DFT) is used to optimize and calculate the electronic structure of GaNNTs (n, 0) (4<=n<=9). Secondly, DFT and non-equilibrium Green function (NEGF) method are also used to predict the electronic transport properties of GaNNTs two-probe system. The results showed: there is a corresponding relation between the electronic transport properties and the valley of state density of each GaNNT. In addition, the volt-ampere curve of GaNNT is approximately linear.

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.

Site-occupation embedding theory using Bethe ansatz local density approximations

NASA Astrophysics Data System (ADS)

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

2018-06-01

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

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

PubMed

Beck, Thomas L

2015-12-21

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

On the subsystem formulation of linear-response time-dependent DFT.

PubMed

Pavanello, Michele

2013-05-28

A new and thorough derivation of linear-response subsystem time-dependent density functional theory (TD-DFT) is presented and analyzed in detail. Two equivalent derivations are presented and naturally yield self-consistent subsystem TD-DFT equations. One reduces to the subsystem TD-DFT formalism of Neugebauer [J. Chem. Phys. 126, 134116 (2007)]. The other yields Dyson type equations involving three types of subsystem response functions: coupled, uncoupled, and Kohn-Sham. The Dyson type equations for subsystem TD-DFT are derived here for the first time. The response function formalism reveals previously hidden qualities and complications of subsystem TD-DFT compared with the regular TD-DFT of the supersystem. For example, analysis of the pole structure of the subsystem response functions shows that each function contains information about the electronic spectrum of the entire supersystem. In addition, comparison of the subsystem and supersystem response functions shows that, while the correlated response is subsystem additive, the Kohn-Sham response is not. Comparison with the non-subjective partition DFT theory shows that this non-additivity is largely an artifact introduced by the subjective nature of the density partitioning in subsystem DFT.

Accuracy of ab initio electron correlation and electron densities in vanadium dioxide

DOE PAGES

Kylänpää, Ilkka; Balachandran, Janakiraman; Ganesh, Panchapakesan; ...

2017-11-27

Here, diffusion quantum Monte Carlo results are used as a reference to analyze properties related to phase stability and magnetism in vanadium dioxide computed with various formulations of density functional theory. We introduce metrics related to energetics, electron densities and spin densities that give us insight on both local and global variations in the antiferromagnetic M1 and R phases. Importantly, these metrics can address contributions arising from the challenging description of the 3d orbital physics in this material. We observe that the best description of energetics between the structural phases does not correspond to the best accuracy in the charge density, which is consistent with observations made recently by Medvedev et~al. in the context of isolated atoms. However, we do find evidence that an accurate spin density connects to correct energetic ordering of different magnetic states in VOmore » $$_2$$, although local, semilocal, and meta-GGA functionals tend to erroneously favor demagnetization of the vanadium sites. The recently developed SCAN functional stands out as remaining nearly balanced in terms of magnetization across the M1-R transition and correctly predicting the ground state crystal structure. In addition to ranking current density functionals, our reference energies and densities serve as important benchmarks for future functional development.« less

Accuracy of ab initio electron correlation and electron densities in vanadium dioxide

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

Kylänpää, Ilkka; Balachandran, Janakiraman; Ganesh, Panchapakesan

Here, diffusion quantum Monte Carlo results are used as a reference to analyze properties related to phase stability and magnetism in vanadium dioxide computed with various formulations of density functional theory. We introduce metrics related to energetics, electron densities and spin densities that give us insight on both local and global variations in the antiferromagnetic M1 and R phases. Importantly, these metrics can address contributions arising from the challenging description of the 3d orbital physics in this material. We observe that the best description of energetics between the structural phases does not correspond to the best accuracy in the charge density, which is consistent with observations made recently by Medvedev et~al. in the context of isolated atoms. However, we do find evidence that an accurate spin density connects to correct energetic ordering of different magnetic states in VOmore » $$_2$$, although local, semilocal, and meta-GGA functionals tend to erroneously favor demagnetization of the vanadium sites. The recently developed SCAN functional stands out as remaining nearly balanced in terms of magnetization across the M1-R transition and correctly predicting the ground state crystal structure. In addition to ranking current density functionals, our reference energies and densities serve as important benchmarks for future functional development.« less

On the way to a microscopic derivation of covariant density functionals in nuclei

NASA Astrophysics Data System (ADS)

Ring, Peter

2018-02-01

Several methods are discussed to derive covariant density functionals from the microscopic input of bare nuclear forces. In a first step there are semi-microscopic functionals, which are fitted to ab-initio calculations of nuclear matter and depend in addition on very few phenomenological parameters. They are able to describe nuclear properties with the same precision as fully phenomenological functionals. In a second step we present first relativistic Brueckner-Hartree-Fock calculations in finite nuclei in order to study properties of such functionals, which cannot be obtained from nuclear matter calculations.

Handling times and saturating transmission functions in a snail-worm symbiosis.

PubMed

Hopkins, Skylar R; McGregor, Cari M; Belden, Lisa K; Wojdak, Jeremy M

2018-06-16

All dynamic species interaction models contain an assumption that describes how contact rates scale with population density. Choosing an appropriate contact-density function is important, because different functions have different implications for population dynamics and stability. However, this choice can be challenging, because there are many possible functions, and most are phenomenological and thus difficult to relate to underlying ecological processes. Using one such phenomenological function, we described a nonlinear relationship between field transmission rates and host density in a common snail-oligochaete symbiosis. We then used a well-known contact function from predator-prey models, the Holling Type II functional response, to describe and predict host snail contact rates in the laboratory. The Holling Type II functional response accurately described both the nonlinear contact-density relationship and the average contact duration that we observed. Therefore, we suggest that contact rates saturate with host density in this system because each snail contact requires a non-instantaneous handling time, and additional possible contacts do not occur during that handling time. Handling times and nonlinear contact rates might also explain the nonlinear relationship between symbiont transmission and snail density that we observed in the field, which could be confirmed by future work that controls for other potential sources of seasonal variation in transmission rates. Because most animal contacts are not instantaneous, the Holling Type II functional response might be broadly relevant to diverse host-symbiont systems.

Use of total electron content data to analyze ionosphere electron density gradients

NASA Astrophysics Data System (ADS)

Nava, B.; Radicella, S. M.; Leitinger, R.; Coïsson, P.

In the presence of electron density gradients the thin shell approximation for the ionosphere, used together with a simple mapping function to convert slant total electron content (TEC) to vertical TEC, could lead to TEC conversion errors. These "mapping function errors" can therefore be used to detect the electron density gradients in the ionosphere. In the present work GPS derived slant TEC data have been used to investigate the effects of the electron density gradients in the middle and low latitude ionosphere under geomagnetic quiet and disturbed conditions. In particular the data corresponding to the geographic area of the American Sector for the days 5-7 April 2000 have been used to perform a complete analysis of mapping function errors based on the "coinciding pierce point technique". The results clearly illustrate the electron density gradient effects according to the locations considered and to the actual levels of disturbance of the ionosphere. In addition, the possibility to assess an ionospheric shell height able to minimize the mapping function errors has been verified.

Estimation of option-implied risk-neutral into real-world density by using calibration function

NASA Astrophysics Data System (ADS)

Bahaludin, Hafizah; Abdullah, Mimi Hafizah

2017-04-01

Option prices contain crucial information that can be used as a reflection of future development of an underlying assets' price. The main objective of this study is to extract the risk-neutral density (RND) and the risk-world density (RWD) of option prices. A volatility function technique is applied by using a fourth order polynomial interpolation to obtain the RNDs. Then, a calibration function is used to convert the RNDs into RWDs. There are two types of calibration function which are parametric and non-parametric calibrations. The density is extracted from the Dow Jones Industrial Average (DJIA) index options with a one month constant maturity from January 2009 until December 2015. The performance of RNDs and RWDs extracted are evaluated by using a density forecasting test. This study found out that the RWDs obtain can provide an accurate information regarding the price of the underlying asset in future compared to that of the RNDs. In addition, empirical evidence suggests that RWDs from a non-parametric calibration has a better accuracy than other densities.

Monte Carlo Simulations of Electron Energy-Loss Spectra with the Addition of Fine Structure from Density Functional Theory Calculations.

PubMed

Attarian Shandiz, Mohammad; Guinel, Maxime J-F; Ahmadi, Majid; Gauvin, Raynald

2016-02-01

A new approach is presented to introduce the fine structure of core-loss excitations into the electron energy-loss spectra of ionization edges by Monte Carlo simulations based on an optical oscillator model. The optical oscillator strength is refined using the calculated electron energy-loss near-edge structure by density functional theory calculations. This approach can predict the effects of multiple scattering and thickness on the fine structure of ionization edges. In addition, effects of the fitting range for background removal and the integration range under the ionization edge on signal-to-noise ratio are investigated.

Density, structure, and dynamics of water: The effect of van der Waals interactions

NASA Astrophysics Data System (ADS)

Wang, Jue; Román-Pérez, G.; Soler, Jose M.; Artacho, Emilio; Fernández-Serra, M.-V.

2011-01-01

It is known that ab initio molecular dynamics (AIMD) simulations of liquid water at ambient conditions, based on the generalized gradient approximation (GGA) to density functional theory (DFT), with commonly used functionals fail to produce structural and diffusive properties in reasonable agreement with experiment. This is true for canonical, constant temperature simulations where the density of the liquid is fixed to the experimental density. The equilibrium density, at ambient conditions, of DFT water has recently been shown by Schmidt et al. [J. Phys. Chem. B, 113, 11959 (2009)] to be underestimated by different GGA functionals for exchange and correlation, and corrected by the addition of interatomic pair potentials to describe van der Waals (vdW) interactions. In this contribution we present a DFT-AIMD study of liquid water using several GGA functionals as well as the van der Waals density functional (vdW-DF) of Dion et al. [Phys. Rev. Lett. 92, 246401 (2004)]. As expected, we find that the density of water is grossly underestimated by GGA functionals. When a vdW-DF is used, the density improves drastically and the experimental diffusivity is reproduced without the need of thermal corrections. We analyze the origin of the density differences between all the functionals. We show that the vdW-DF increases the population of non-H-bonded interstitial sites, at distances between the first and second coordination shells. However, it excessively weakens the H-bond network, collapsing the second coordination shell. This structural problem is partially associated to the choice of GGA exchange in the vdW-DF. We show that a different choice for the exchange functional is enough to achieve an overall improvement both in structure and diffusivity.

DFT benchmark study for the oxidative addition of CH 4 to Pd. Performance of various density functionals

NASA Astrophysics Data System (ADS)

de Jong, G. Theodoor; Geerke, Daan P.; Diefenbach, Axel; Matthias Bickelhaupt, F.

2005-06-01

We have evaluated the performance of 24 popular density functionals for describing the potential energy surface (PES) of the archetypal oxidative addition reaction of the methane C-H bond to the palladium atom by comparing the results with our recent ab initio [CCSD(T)] benchmark study of this reaction. The density functionals examined cover the local density approximation (LDA), the generalized gradient approximation (GGA), meta-GGAs as well as hybrid density functional theory. Relativistic effects are accounted for through the zeroth-order regular approximation (ZORA). The basis-set dependence of the density-functional-theory (DFT) results is assessed for the Becke-Lee-Yang-Parr (BLYP) functional using a hierarchical series of Slater-type orbital (STO) basis sets ranging from unpolarized double-ζ (DZ) to quadruply polarized quadruple-ζ quality (QZ4P). Stationary points on the reaction surface have been optimized using various GGA functionals, all of which yield geometries that differ only marginally. Counterpoise-corrected relative energies of stationary points are converged to within a few tenths of a kcal/mol if one uses the doubly polarized triple-ζ (TZ2P) basis set and the basis-set superposition error (BSSE) drops to 0.0 kcal/mol for our largest basis set (QZ4P). Best overall agreement with the ab initio benchmark PES is achieved by functionals of the GGA, meta-GGA, and hybrid-DFT type, with mean absolute errors of 1.3-1.4 kcal/mol and errors in activation energies ranging from +0.8 to -1.4 kcal/mol. Interestingly, the well-known BLYP functional compares very reasonably with an only slightly larger mean absolute error of 2.5 kcal/mol and an underestimation by -1.9 kcal/mol of the overall barrier (i.e., the difference in energy between the TS and the separate reactants). For comparison, with B3LYP we arrive at a mean absolute error of 3.8 kcal/mol and an overestimation of the overall barrier by 4.5 kcal/mol.

On the asymptotic improvement of supervised learning by utilizing additional unlabeled samples - Normal mixture density case

NASA Technical Reports Server (NTRS)

Shahshahani, Behzad M.; Landgrebe, David A.

1992-01-01

The effect of additional unlabeled samples in improving the supervised learning process is studied in this paper. Three learning processes. supervised, unsupervised, and combined supervised-unsupervised, are compared by studying the asymptotic behavior of the estimates obtained under each process. Upper and lower bounds on the asymptotic covariance matrices are derived. It is shown that under a normal mixture density assumption for the probability density function of the feature space, the combined supervised-unsupervised learning is always superior to the supervised learning in achieving better estimates. Experimental results are provided to verify the theoretical concepts.

Econometric studies of urban population density: a survey.

PubMed

Mcdonald, J F

1989-01-01

This paper presents the 1st reasonably comprehensive survey of empirical research of urban population densities since the publication of the book by Edmonston in 1975. The survey summarizes contributions to empirical knowledge that have been made since 1975 and points toward possible areas for additional research. The paper also provides a brief interpretative intellectual history of the topic. It begins with a personal overview of research in the field. The next section discusses econometric issues that arise in the estimation of population density functions in which density is a function only of a distance to the central business district of the urban area. Section 4 summarizes the studies of a single urban area that went beyond the estimation of simple distance-density functions, and Section 5 discusses studies that sought to explain the variations across urban areas in population density patterns. McDonald refers to the standard theory of urban population density throughout the paper. This basic model is presented in the textbook by Mills and Hamilton and it is assumed that the reader is familiar with the model.

Accuracy of ab initio electron correlation and electron densities in vanadium dioxide

NASA Astrophysics Data System (ADS)

Kylänpää, Ilkka; Balachandran, Janakiraman; Ganesh, Panchapakesan; Heinonen, Olle; Kent, Paul R. C.; Krogel, Jaron T.

2017-11-01

Diffusion quantum Monte Carlo results are used as a reference to analyze properties related to phase stability and magnetism in vanadium dioxide computed with various formulations of density functional theory. We introduce metrics related to energetics, electron densities and spin densities that give us insight on both local and global variations in the antiferromagnetic M1 and R phases. Importantly, these metrics can address contributions arising from the challenging description of the 3 d orbital physics in this material. We observe that the best description of energetics between the structural phases does not correspond to the best accuracy in the charge density, which is consistent with observations made recently by Medvedev et al. [Science 355, 371 (2017), 10.1126/science.aag0410] in the context of isolated atoms. However, we do find evidence that an accurate spin density connects to correct energetic ordering of different magnetic states in VO2, although local, semilocal, and meta-GGA functionals tend to erroneously favor demagnetization of the vanadium sites. The recently developed SCAN functional stands out as remaining nearly balanced in terms of magnetization across the M1-R transition and correctly predicting the ground state crystal structure. In addition to ranking current density functionals, our reference energies and densities serve as important benchmarks for future functional development. With our reference data, the accuracy of both the energy and the electron density can be monitored simultaneously, which is useful for functional development. So far, this kind of detailed high accuracy reference data for correlated materials has been absent from the literature.

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

PubMed

Patra, Abhilash; Jana, Subrata; Samal, Prasanjit

2018-04-07

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

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

NASA Astrophysics Data System (ADS)

Patra, Abhilash; Jana, Subrata; Samal, Prasanjit

2018-04-01

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

Quest for a universal density functional: the accuracy of density functionals across a broad spectrum of databases in chemistry and physics.

PubMed

Peverati, Roberto; Truhlar, Donald G

2014-03-13

Kohn-Sham density functional theory is in principle an exact formulation of quantum mechanical electronic structure theory, but in practice we have to rely on approximate exchange-correlation (xc) functionals. The objective of our work has been to design an xc functional with broad accuracy across as wide an expanse of chemistry and physics as possible, leading--as a long-range goal--to a functional with good accuracy for all problems, i.e. a universal functional. To guide our path towards that goal and to measure our progress, we have developed-building on earlier work of our group-a set of databases of reference data for a variety of energetic and structural properties in chemistry and physics. These databases include energies of molecular processes, such as atomization, complexation, proton addition and ionization; they also include molecular geometries and solid-state lattice constants, chemical reaction barrier heights, and cohesive energies and band gaps of solids. For this paper, we gather many of these databases into four comprehensive databases, two with 384 energetic data for chemistry and solid-state physics and another two with 68 structural data for chemistry and solid-state physics, and we test two wave function methods and 77 density functionals (12 Minnesota meta functionals and 65 others) in a consistent way across this same broad set of data. We especially highlight the Minnesota density functionals, but the results have broader implications in that one may see the successes and failures of many kinds of density functionals when they are all applied to the same data. Therefore, the results provide a status report on the quest for a universal functional.

Modeling of normal contact of elastic bodies with surface relief taken into account

NASA Astrophysics Data System (ADS)

Goryacheva, I. G.; Tsukanov, I. Yu

2018-04-01

An approach to account the surface relief in normal contact problems for rough bodies on the basis of an additional displacement function for asperities is considered. The method and analytic expressions for calculating the additional displacement function for one-scale and two-scale wavy relief are presented. The influence of the microrelief geometric parameters, including the number of scales and asperities density, on additional displacements of the rough layer is analyzed.

Generalized Pauli constraints in reduced density matrix functional theory.

PubMed

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

2015-04-21

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

Charge Transport Properties in Disordered Organic Semiconductor as a Function of Charge Density: Monte Carlo Simulation

NASA Astrophysics Data System (ADS)

Shukri, Seyfan Kelil

2017-01-01

We have done Kinetic Monte Carlo (KMC) simulations to investigate the effect of charge carrier density on the electrical conductivity and carrier mobility in disordered organic semiconductors using a lattice model. The density of state (DOS) of the system are considered to be Gaussian and exponential. Our simulations reveal that the mobility of the charge carrier increases with charge carrier density for both DOSs. In contrast, the mobility of charge carriers decreases as the disorder increases. In addition the shape of the DOS has a significance effect on the charge transport properties as a function of density which are clearly seen. On the other hand, for the same distribution width and at low carrier density, the change occurred on the conductivity and mobility for a Gaussian DOS is more pronounced than that for the exponential DOS.

Importance of the Kinetic Energy Density for Band Gap Calculations in Solids with Density Functional Theory.

PubMed

Tran, Fabien; Blaha, Peter

2017-05-04

Recently, exchange-correlation potentials in density functional theory were developed with the goal of providing improved band gaps in solids. Among them, the semilocal potentials are particularly interesting for large systems since they lead to calculations that are much faster than with hybrid functionals or methods like GW. We present an exhaustive comparison of semilocal exchange-correlation potentials for band gap calculations on a large test set of solids, and particular attention is paid to the potential HLE16 proposed by Verma and Truhlar. It is shown that the most accurate potential is the modified Becke-Johnson potential, which, most noticeably, is much more accurate than all other semilocal potentials for strongly correlated systems. This can be attributed to its additional dependence on the kinetic energy density. It is also shown that the modified Becke-Johnson potential is at least as accurate as the hybrid functionals and more reliable for solids with large band gaps.

Functional connectivity analysis of the neural bases of emotion regulation: A comparison of independent component method with density-based k-means clustering method.

PubMed

Zou, Ling; Guo, Qian; Xu, Yi; Yang, Biao; Jiao, Zhuqing; Xiang, Jianbo

2016-04-29

Functional magnetic resonance imaging (fMRI) is an important tool in neuroscience for assessing connectivity and interactions between distant areas of the brain. To find and characterize the coherent patterns of brain activity as a means of identifying brain systems for the cognitive reappraisal of the emotion task, both density-based k-means clustering and independent component analysis (ICA) methods can be applied to characterize the interactions between brain regions involved in cognitive reappraisal of emotion. Our results reveal that compared with the ICA method, the density-based k-means clustering method provides a higher sensitivity of polymerization. In addition, it is more sensitive to those relatively weak functional connection regions. Thus, the study concludes that in the process of receiving emotional stimuli, the relatively obvious activation areas are mainly distributed in the frontal lobe, cingulum and near the hypothalamus. Furthermore, density-based k-means clustering method creates a more reliable method for follow-up studies of brain functional connectivity.

Magnetic exchange couplings from constrained density functional theory: an efficient approach utilizing analytic derivatives.

PubMed

Phillips, Jordan J; Peralta, Juan E

2011-11-14

We introduce a method for evaluating magnetic exchange couplings based on the constrained density functional theory (C-DFT) approach of Rudra, Wu, and Van Voorhis [J. Chem. Phys. 124, 024103 (2006)]. Our method shares the same physical principles as C-DFT but makes use of the fact that the electronic energy changes quadratically and bilinearly with respect to the constraints in the range of interest. This allows us to use coupled perturbed Kohn-Sham spin density functional theory to determine approximately the corrections to the energy of the different spin configurations and construct a priori the relevant energy-landscapes obtained by constrained spin density functional theory. We assess this methodology in a set of binuclear transition-metal complexes and show that it reproduces very closely the results of C-DFT. This demonstrates a proof-of-concept for this method as a potential tool for studying a number of other molecular phenomena. Additionally, routes to improving upon the limitations of this method are discussed. © 2011 American Institute of Physics

Subsystem real-time time dependent density functional theory.

PubMed

Krishtal, Alisa; Ceresoli, Davide; Pavanello, Michele

2015-04-21

We present the extension of Frozen Density Embedding (FDE) formulation of subsystem Density Functional Theory (DFT) to real-time Time Dependent Density Functional Theory (rt-TDDFT). FDE is a DFT-in-DFT embedding method that allows to partition a larger Kohn-Sham system into a set of smaller, coupled Kohn-Sham systems. Additional to the computational advantage, FDE provides physical insight into the properties of embedded systems and the coupling interactions between them. The extension to rt-TDDFT is done straightforwardly by evolving the Kohn-Sham subsystems in time simultaneously, while updating the embedding potential between the systems at every time step. Two main applications are presented: the explicit excitation energy transfer in real time between subsystems is demonstrated for the case of the Na4 cluster and the effect of the embedding on optical spectra of coupled chromophores. In particular, the importance of including the full dynamic response in the embedding potential is demonstrated.

Screened exchange hybrid density functional for accurate and efficient structures and interaction energies.

PubMed

Brandenburg, Jan Gerit; Caldeweyher, Eike; Grimme, Stefan

2016-06-21

We extend the recently introduced PBEh-3c global hybrid density functional [S. Grimme et al., J. Chem. Phys., 2015, 143, 054107] by a screened Fock exchange variant based on the Henderson-Janesko-Scuseria exchange hole model. While the excellent performance of the global hybrid is maintained for small covalently bound molecules, its performance for computed condensed phase mass densities is further improved. Most importantly, a speed up of 30 to 50% can be achieved and especially for small orbital energy gap cases, the method is numerically much more robust. The latter point is important for many applications, e.g., for metal-organic frameworks, organic semiconductors, or protein structures. This enables an accurate density functional based electronic structure calculation of a full DNA helix structure on a single core desktop computer which is presented as an example in addition to comprehensive benchmark results.

π-π stacking tackled with density functional theory

PubMed Central

Swart, Marcel; van der Wijst, Tushar; Fonseca Guerra, Célia

2007-01-01

Through comparison with ab initio reference data, we have evaluated the performance of various density functionals for describing π-π interactions as a function of the geometry between two stacked benzenes or benzene analogs, between two stacked DNA bases, and between two stacked Watson–Crick pairs. Our main purpose is to find a robust and computationally efficient density functional to be used specifically and only for describing π-π stacking interactions in DNA and other biological molecules in the framework of our recently developed QM/QM approach "QUILD". In line with previous studies, most standard density functionals recover, at best, only part of the favorable stacking interactions. An exception is the new KT1 functional, which correctly yields bound π-stacked structures. Surprisingly, a similarly good performance is achieved with the computationally very robust and efficient local density approximation (LDA). Furthermore, we show that classical electrostatic interactions determine the shape and depth of the π-π stacking potential energy surface. Figure Additivity approximation for the π-π interaction between two stacked Watson–Crick base pairs in terms of pairwise interactions between individual bases Electronic supplementary material The online version of this article (doi:10.1007/s00894-007-0239-y) contains supplementary material, which is available to authorized users. PMID:17874150

Effect of altered reproductive function and lowered testosterone levels on bone density in male endurance athletes.

PubMed

Bennell, K L; Brukner, P D; Malcolm, S A

1996-09-01

It is apparent that bone density in male athletes can be reduced without a concomitant decrease in testosterone, suggesting that bone density and testosterone concentrations in the normal range are not closely related in male athletes. Further research is necessary to monitor concurrent changes in bone density and testosterone over a period of time in exercising males. In any case, the effect of exercise on the male reproductive system does not appear as extreme as that which can occur in female athletes, and any impact on bone density is not nearly as evident. These results imply that factors apart from testosterone concentrations must be responsible for the observed osteopenia in some male athletes. Many factors have the potential to adversely affect bone density, independently of alterations in reproductive function. These include low calcium intake, energy deficit, weight loss, psychological stress, and low body fat, all of which may be associated with intense endurance training. Future research investigating skeletal health in male athletes should include a thorough assessment of reproductive function in addition to these other factors.

van der Waals forces in density functional theory: a review of the vdW-DF method.

PubMed

Berland, Kristian; Cooper, Valentino R; Lee, Kyuho; Schröder, Elsebeth; Thonhauser, T; Hyldgaard, Per; Lundqvist, Bengt I

2015-06-01

A density functional theory (DFT) that accounts for van der Waals (vdW) interactions in condensed matter, materials physics, chemistry, and biology is reviewed. The insights that led to the construction of the Rutgers-Chalmers van der Waals density functional (vdW-DF) are presented with the aim of giving a historical perspective, while also emphasizing more recent efforts which have sought to improve its accuracy. In addition to technical details, we discuss a range of recent applications that illustrate the necessity of including dispersion interactions in DFT. This review highlights the value of the vdW-DF method as a general-purpose method, not only for dispersion bound systems, but also in densely packed systems where these types of interactions are traditionally thought to be negligible.

A very efficient approach to compute the first-passage probability density function in a time-changed Brownian model: Applications in finance

NASA Astrophysics Data System (ADS)

Ballestra, Luca Vincenzo; Pacelli, Graziella; Radi, Davide

2016-12-01

We propose a numerical method to compute the first-passage probability density function in a time-changed Brownian model. In particular, we derive an integral representation of such a density function in which the integrand functions must be obtained solving a system of Volterra equations of the first kind. In addition, we develop an ad-hoc numerical procedure to regularize and solve this system of integral equations. The proposed method is tested on three application problems of interest in mathematical finance, namely the calculation of the survival probability of an indebted firm, the pricing of a single-knock-out put option and the pricing of a double-knock-out put option. The results obtained reveal that the novel approach is extremely accurate and fast, and performs significantly better than the finite difference method.

Carbon-Hydrogen Bond Activation in Hydridotris(pyrazolyl)borate Platinum(IV) Complexes:  Comparison of Density Functionals, Basis Sets, and Bonding Patterns.

PubMed

Vastine, Benjamin Alan; Webster, Charles Edwin; Hall, Michael B

2007-11-01

The reaction mechanism for the cycle beginning with the reductive elimination (RE) of methane from κ(3)-TpPt(IV)(CH3)2H (1) (Tp = hydridotris(pyrazolyl)borate) and subsequent oxidative addition (OA) of benzene to form finally κ(3)-TpPt(IV)(Ph)2H (19) was investigated by density functional theory (DFT). Two mechanistic steps are of particular interest, namely the barrier to C-H coupling (barrier 1 - Ba1) and the barrier to methane release (barrier 2 - Ba2). For 31 density functionals, the calculated values for Ba1 and Ba2 were benchmarked against the experimentally reported values of 26 (Ba1) and 35 (Ba2) kcal·mol(-1), respectively. Specifically, the values for Ba1 and Ba2, calculated at the B3LYP/double-ζ plus polarization level of theory, are 24.6 and 34.3 kcal·mol(-1), respectively. Overall, the best performing functional was BPW91 where the mae associated with the calculated values of the two barriers is 0.68 kcal·mol(-1). The calculated B3LYP values of Ba1 ranged between 20 and 26 kcal·mol(-1) for 12 effective core potential basis sets for platinum and 29 all-electron basis sets for the first row elements. Polarization functions for the first row elements were important for accurate values, but the addition of diffuse functions to non-hydrogen (+) and hydrogen atoms (++) had little effect on the calculated values. Basis set saturation was achieved with APNO basis sets utilized for first-row atoms. Bader's "Atoms in Molecules" was used to analyze the electron density of several complexes, and the electron density at the Pt-Nax bond critical point (trans to the active site for C-H coupling) varied over a wider range than any of the other Pt-N bonds.

Large-scale structure of randomly jammed spheres

NASA Astrophysics Data System (ADS)

Ikeda, Atsushi; Berthier, Ludovic; Parisi, Giorgio

2017-05-01

We numerically analyze the density field of three-dimensional randomly jammed packings of monodisperse soft frictionless spherical particles, paying special attention to fluctuations occurring at large length scales. We study in detail the two-point static structure factor at low wave vectors in Fourier space. We also analyze the nature of the density field in real space by studying the large-distance behavior of the two-point pair correlation function, of density fluctuations in subsystems of increasing sizes, and of the direct correlation function. We show that such real space analysis can be greatly improved by introducing a coarse-grained density field to disentangle genuine large-scale correlations from purely local effects. Our results confirm that both Fourier and real space signatures of vanishing density fluctuations at large scale are absent, indicating that randomly jammed packings are not hyperuniform. In addition, we establish that the pair correlation function displays a surprisingly complex structure at large distances, which is however not compatible with the long-range negative correlation of hyperuniform systems but fully compatible with an analytic form for the structure factor. This implies that the direct correlation function is short ranged, as we also demonstrate directly. Our results reveal that density fluctuations in jammed packings do not follow the behavior expected for random hyperuniform materials, but display instead a more complex behavior.

Characterizing and Understanding the Remarkably Slow Basis Set Convergence of Several Minnesota Density Functionals for Intermolecular Interaction Energies

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

Mardirossian, Narbe; Head-Gordon, Martin

2013-08-22

For a set of eight equilibrium intermolecular complexes, it is discovered in this paper that the basis set limit (BSL) cannot be reached by aug-cc-pV5Z for three of the Minnesota density functionals: M06-L, M06-HF, and M11-L. In addition, the M06 and M11 functionals exhibit substantial, but less severe, difficulties in reaching the BSL. By using successively finer grids, it is demonstrated that this issue is not related to the numerical integration of the exchange-correlation functional. In addition, it is shown that the difficulty in reaching the BSL is not a direct consequence of the structure of the augmented functions inmore » Dunning’s basis sets, since modified augmentation yields similar results. By using a very large custom basis set, the BSL appears to be reached for the HF dimer for all of the functionals. As a result, it is concluded that the difficulties faced by several of the Minnesota density functionals are related to an interplay between the form of these functionals and the structure of standard basis sets. It is speculated that the difficulty in reaching the basis set limit is related to the magnitude of the inhomogeneity correction factor (ICF) of the exchange functional. A simple modification of the M06-L exchange functional that systematically reduces the basis set superposition error (BSSE) for the HF dimer in the aug-cc-pVQZ basis set is presented, further supporting the speculation that the difficulty in reaching the BSL is caused by the magnitude of the exchange functional ICF. In conclusion, the BSSE is plotted with respect to the internuclear distance of the neon dimer for two of the examined functionals.« less

Evidence for a π-junction in Nb/F/Nb' trilayers from superfluid density measurements

NASA Astrophysics Data System (ADS)

Lemberger, Thomas; Hinton, Michael; Steers, Stanley; Peters, Bryan; Yang, Fengyuan

Two-coil measurements of the sheet superfluid density of Nb/NiV/Nb' trilayers reveal the transition temperatures and volume superfluid densities of both Nb layers, as functions of the thickness, dF, of the intervening ferromagnetic (F) Ni0.96V0.04 layer. The upper transition occurs when the thicker Nb layer goes superconducting and superfluid first appears. Fitting the high-temperature superfluid density to an appropriate functional form reveals the presence of a lower ``transition'' where additional superfluid appears. This event is really a crossover, but the difference is irrelevant here. There is a surprising minimum in superfluid densities of both Nb layers at dF ~ 30 Å, followed by a slow rise. This behavior suggests that a π phase difference between the Nb layers develops at dF ~ 30 Å and continues to larger F thickness. Supported in part by NSF Grant DMR-0805227.

Spatial electron density and electric field strength measurements in microwave cavity experiments

NASA Technical Reports Server (NTRS)

Peters, M.; Rogers, J.; Whitehair, S.; Asmussen, J.; Kerber, R.

1984-01-01

Measurements of electron density and electric field strength have been made in an argon plasma contained in a resonant microwave cavity at 2.45 GHz. Spatial measurements of electron density, n sub e, are correlated with fluorescence observations of the discharge. Measurements of n sub e were made with Stark broadening and compared with n sub 3 calculated from measured plasma conductivity. Additional measurements of n sub 3 as a function of pressure and in mixtures of argon and oxygen are presented for pressures from 10 Torr to 1 atm. Measurements in flowing gases and in static systems are presented. In addition, limitations of these measurements are identified.

Bayesian spatiotemporal analysis of zero-inflated biological population density data by a delta-normal spatiotemporal additive model.

PubMed

Arcuti, Simona; Pollice, Alessio; Ribecco, Nunziata; D'Onghia, Gianfranco

2016-03-01

We evaluate the spatiotemporal changes in the density of a particular species of crustacean known as deep-water rose shrimp, Parapenaeus longirostris, based on biological sample data collected during trawl surveys carried out from 1995 to 2006 as part of the international project MEDITS (MEDiterranean International Trawl Surveys). As is the case for many biological variables, density data are continuous and characterized by unusually large amounts of zeros, accompanied by a skewed distribution of the remaining values. Here we analyze the normalized density data by a Bayesian delta-normal semiparametric additive model including the effects of covariates, using penalized regression with low-rank thin-plate splines for nonlinear spatial and temporal effects. Modeling the zero and nonzero values by two joint processes, as we propose in this work, allows to obtain great flexibility and easily handling of complex likelihood functions, avoiding inaccurate statistical inferences due to misclassification of the high proportion of exact zeros in the model. Bayesian model estimation is obtained by Markov chain Monte Carlo simulations, suitably specifying the complex likelihood function of the zero-inflated density data. The study highlights relevant nonlinear spatial and temporal effects and the influence of the annual Mediterranean oscillations index and of the sea surface temperature on the distribution of the deep-water rose shrimp density. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Analysis of Different Cost Functions in the Geosect Airspace Partitioning Tool

NASA Technical Reports Server (NTRS)

Wong, Gregory L.

2010-01-01

A new cost function representing air traffic controller workload is implemented in the Geosect airspace partitioning tool. Geosect currently uses a combination of aircraft count and dwell time to select optimal airspace partitions that balance controller workload. This is referred to as the aircraft count/dwell time hybrid cost function. The new cost function is based on Simplified Dynamic Density, a measure of different aspects of air traffic controller workload. Three sectorizations are compared. These are the current sectorization, Geosect's sectorization based on the aircraft count/dwell time hybrid cost function, and Geosect s sectorization based on the Simplified Dynamic Density cost function. Each sectorization is evaluated for maximum and average workload along with workload balance using the Simplified Dynamic Density as the workload measure. In addition, the Airspace Concept Evaluation System, a nationwide air traffic simulator, is used to determine the capacity and delay incurred by each sectorization. The sectorization resulting from the Simplified Dynamic Density cost function had a lower maximum workload measure than the other sectorizations, and the sectorization based on the combination of aircraft count and dwell time did a better job of balancing workload and balancing capacity. However, the current sectorization had the lowest average workload, highest sector capacity, and the least system delay.

Factors leading to different viability predictions for a grizzly bear data set

USGS Publications Warehouse

Mills, L.S.; Hayes, S.G.; Wisdom, M.J.; Citta, J.; Mattson, D.J.; Murphy, K.

1996-01-01

Population viability analysis programs are being used increasingly in research and management applications, but there has not been a systematic study of the congruence of different program predictions based on a single data set. We performed such an analysis using four population viability analysis computer programs: GAPPS, INMAT, RAMAS/AGE, and VORTEX. The standardized demographic rates used in all programs were generalized from hypothetical increasing and decreasing grizzly bear (Ursus arctos horribilis) populations. Idiosyncracies of input format for each program led to minor differences in intrinsic growth rates that translated into striking differences in estimates of extinction rates and expected population size. In contrast, the addition of demographic stochasticity, environmental stochasticity, and inbreeding costs caused only a small divergence in viability predictions. But, the addition of density dependence caused large deviations between the programs despite our best attempts to use the same density-dependent functions. Population viability programs differ in how density dependence is incorporated, and the necessary functions are difficult to parameterize accurately. Thus, we recommend that unless data clearly suggest a particular density-dependent model, predictions based on population viability analysis should include at least one scenario without density dependence. Further, we describe output metrics that may differ between programs; development of future software could benefit from standardized input and output formats across different programs.

Application of SEAWAT to select variable-density and viscosity problems

USGS Publications Warehouse

Dausman, Alyssa M.; Langevin, Christian D.; Thorne, Danny T.; Sukop, Michael C.

2010-01-01

SEAWAT is a combined version of MODFLOW and MT3DMS, designed to simulate three-dimensional, variable-density, saturated groundwater flow. The most recent version of the SEAWAT program, SEAWAT Version 4 (or SEAWAT_V4), supports equations of state for fluid density and viscosity. In SEAWAT_V4, fluid density can be calculated as a function of one or more MT3DMS species, and optionally, fluid pressure. Fluid viscosity is calculated as a function of one or more MT3DMS species, and the program also includes additional functions for representing the dependence of fluid viscosity on temperature. This report documents testing of and experimentation with SEAWAT_V4 with six previously published problems that include various combinations of density-dependent flow due to temperature variations and/or concentration variations of one or more species. Some of the problems also include variations in viscosity that result from temperature differences in water and oil. Comparisons between the results of SEAWAT_V4 and other published results are generally consistent with one another, with minor differences considered acceptable.

Freezing of soft spheres: A critical test for weighted-density-functional theories

NASA Astrophysics Data System (ADS)

Laird, Brian B.; Kroll, D. M.

1990-10-01

We study the freezing properties of systems with inverse-power and Yukawa interactions (soft spheres), using recently developed weighted-density-functional theories. We find that the modified weighted-density-functional approximation (MWDA) of Denton and Ashcroft yields results for the liquid to face-centered-cubic (fcc) structure transition that represent a significant improvement over those of earlier ``second-order'' density-functional freezing theories; however, this theory, like the earlier ones, fails to predict any liquid to body-centered-cubic (bcc) transition, even under conditions where the computer simulations indicate that this should be the equilibrium solid structure. In addition, we show that both the modified effective-liquid approximation (MELA) of Baus [J. Phys. Condens. Matter 2, 2111 (1990)] and the generalized effective-liquid approximation of Lutsko and Baus [Phys. Rev. Lett. 64, 761 (1990)], while giving excellent results for the freezing of hard spheres, fail completely to predict freezing into either fcc or bcc solid phases for soft inverse-power potentials. We also give an alternate derivation of the MWDA that makes clearer its connection to earlier theories.

Stability of the guanine endoperoxide intermediate: a computational challenge for density functional theory.

PubMed

Grüber, Raymond; Monari, Antonio; Dumont, Elise

2014-12-11

The addition of singlet molecular oxygen (1)O2 onto guanine is a most important and deleterious reaction in biological damage. We assess the efficiency of density functional theory for evaluating the respective stabilities of two intermediates that can form upon (1)O2 addition: a charge-separated adduct with a peroxide anion at the C8 position of guanine, and the corresponding cyclic endoperoxide across the 4,8-bond, of the imidazole ring. The reference post Hartree-Fock SCS-MP3/aug-cc-pVTZ//MP2/DZP++ level of theory provides an unambiguous assignment in favor of the endoperoxide intermediate, based on implicitly solvated structures, by -8.0 kcal·mol(-1). This value is taken as the reference for a systematic and extended benchmarck performed on 58 exchange--correlation functionals. While B3LYP remains commonly used for studying oxidative DNA lesions, we prove that the stability of the peroxide anion is overestimated by this functional, but also by other commonly used exchange-correlation functionals. The significant error (ca. +3 kcal·mol(-1) over a representative set of 58 functionals) arises from overdelocalization but also from the description of the dynamic correlation by the density functional. The significantly improved performance of several recently proposed functionals, including range-separated hybrids such as LC-BLYP, is outlined. We believe that our results will be of great help to further studies on the versatile chemistry of singlet oxygen-induced DNA damage, where complex reaction mechanisms are required to be depicted at a quantum level.

van der Waals forces in density functional theory: a review of the vdW-DF method

DOE PAGES

Berland, Kristian; Cooper, Valentino R.; Lee, Kyuho; ...

2015-05-15

We review a density functional theory (DFT) that accounts for van der Waals (vdW) interactions in condensed matter, materials physics, chemistry, and biology. The insights that led to the construction of the Rutgers–Chalmers van der Waals density functional (vdW-DF) are presented with the aim of giving a historical perspective, while also emphasizing more recent efforts which have sought to improve its accuracy. In addition to technical details, we discuss a range of recent applications that illustrate the necessity of including dispersion interactions in DFT. This review highlights the value of the vdW-DF method as a general-purpose method, not only formore » dispersion bound systems, but also in densely packed systems where these types of interactions are traditionally thought to be negligible.« less

Quantum computing without wavefunctions: time-dependent density functional theory for universal quantum computation.

PubMed

Tempel, David G; Aspuru-Guzik, Alán

2012-01-01

We prove that the theorems of TDDFT can be extended to a class of qubit Hamiltonians that are universal for quantum computation. The theorems of TDDFT applied to universal Hamiltonians imply that single-qubit expectation values can be used as the basic variables in quantum computation and information theory, rather than wavefunctions. From a practical standpoint this opens the possibility of approximating observables of interest in quantum computations directly in terms of single-qubit quantities (i.e. as density functionals). Additionally, we also demonstrate that TDDFT provides an exact prescription for simulating universal Hamiltonians with other universal Hamiltonians that have different, and possibly easier-to-realize two-qubit interactions. This establishes the foundations of TDDFT for quantum computation and opens the possibility of developing density functionals for use in quantum algorithms.

Time-Dependent Density Functional Theory Analysis of Triphenylamine-Functionalized Graphene Doped with Transition Metals for Photocatalytic Hydrogen Production.

PubMed

Mota, Elder A V; Neto, Abel F G; Marques, Francisco C; Mota, Gunar V S; Martins, Marcelo G; Costa, Fabio L P; Borges, Rosivaldo S; Neto, Antonio M J C

2018-07-01

The electronic structures and optical properties of triphenylamine-functionalized graphene (G-TPA) doped with transition metals, using water as a solvent, were theoretically investigated to verify the efficiency of photocatalytic hydrogen production with the use of transition metals. This study was performed by Density Functional Theory and Time-dependent Density Functional Theory through Gaussian 09W software, adopting the B3LYP functional for all structures. The 6-31g(d) basis set was used for H, C and N atoms, and the LANL2DZ basis set for transition metals using the Effective Core Potentials method. Two approaches were adopted: (1) using single metallic dopants (Ni, Pd, Fe, Os and Pt) and (2) using combinations of Ni with the other dopants (NiPd, NiPt, NiFe and NiOs). The DOS spectra reveal an increase of accessible states in the valence shell, in addition to a gap decrease for all dopants. This doping also increases the absorption in the visible region of solar radiation where sunlight is most intense (400 nm to 700 nm), with additional absorption peaks. The results lead us to propose the G-TPA structures doped with Ni, Pd, Pt, NiPt or NiPd to be novel catalysts for the conversion of solar energy for photocatalytic hydrogen production, since they improve the absorption of solar energy in the range of interest for solar radiation; and act as reaction centers, reducing the required overpotential for hydrogen production from water.

Generating the Infrared Spectra of Large Interstellar Molecules with Density Functional Theory

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Arnold, James (Technical Monitor)

1999-01-01

It is now possible to compute IR (infrared) spectra of large molecules with an accuracy of 30 per cm, or better, using density function theory. This is true for cations, anions, and neutrals. Thus it possible to generate synthetic IR spectra that can help interpret experimental spectra and fill in for missing experimental data. These synthetic spectra can be used as input into interstellar models. In addition to IR spectra, it is possible to compute energetic properties to help understand which molecules can be formed in the interstellar environment.

Experimental investigation of alternative transmission functions: Quantitative evidence for the importance of nonlinear transmission dynamics in host-parasite systems.

PubMed

Orlofske, Sarah A; Flaxman, Samuel M; Joseph, Maxwell B; Fenton, Andy; Melbourne, Brett A; Johnson, Pieter T J

2018-05-01

Understanding pathogen transmission is crucial for predicting and managing disease. Nonetheless, experimental comparisons of alternative functional forms of transmission remain rare, and those experiments that are conducted are often not designed to test the full range of possible forms. To differentiate among 10 candidate transmission functions, we used a novel experimental design in which we independently varied four factors-duration of exposure, numbers of parasites, numbers of hosts and parasite density-in laboratory infection experiments. We used interactions between amphibian hosts and trematode parasites as a model system and all candidate models incorporated parasite depletion. An additional manipulation involving anaesthesia addressed the effects of host behaviour on transmission form. Across all experiments, nonlinear transmission forms involving either a power law or a negative binomial function were the best-fitting models and consistently outperformed the linear density-dependent and density-independent functions. By testing previously published data for two other host-macroparasite systems, we also found support for the same nonlinear transmission forms. Although manipulations of parasite density are common in transmission studies, the comprehensive set of variables tested in our experiments revealed that variation in density alone was least likely to differentiate among competing transmission functions. Across host-pathogen systems, nonlinear functions may often more accurately represent transmission dynamics and thus provide more realistic predictions for infection. © 2017 The Authors. Journal of Animal Ecology published by John Wiley & Sons Ltd on behalf of British Ecological Society.

Subchondral bone density distribution of the talus in clinically normal Labrador Retrievers.

PubMed

Dingemanse, W; Müller-Gerbl, M; Jonkers, I; Vander Sloten, J; van Bree, H; Gielen, I

2016-03-15

Bones continually adapt their morphology to their load bearing function. At the level of the subchondral bone, the density distribution is highly correlated with the loading distribution of the joint. Therefore, subchondral bone density distribution can be used to study joint biomechanics non-invasively. In addition physiological and pathological joint loading is an important aspect of orthopaedic disease, and research focusing on joint biomechanics will benefit veterinary orthopaedics. This study was conducted to evaluate density distribution in the subchondral bone of the canine talus, as a parameter reflecting the long-term joint loading in the tarsocrural joint. Two main density maxima were found, one proximally on the medial trochlear ridge and one distally on the lateral trochlear ridge. All joints showed very similar density distribution patterns and no significant differences were found in the localisation of the density maxima between left and right limbs and between dogs. Based on the density distribution the lateral trochlear ridge is most likely subjected to highest loads within the tarsocrural joint. The joint loading distribution is very similar between dogs of the same breed. In addition, the joint loading distribution supports previous suggestions of the important role of biomechanics in the development of OC lesions in the tarsus. Important benefits of computed tomographic osteoabsorptiometry (CTOAM), i.e. the possibility of in vivo imaging and temporal evaluation, make this technique a valuable addition to the field of veterinary orthopaedic research.

Calculation of phonon dispersion relation using new correlation functional

NASA Astrophysics Data System (ADS)

Jitropas, Ukrit; Hsu, Chung-Hao

2017-06-01

To extend the use of Local Density Approximation (LDA), a new analytical correlation functional is introduced. Correlation energy is an essential ingredient within density functional theory and used to determine ground state energy and other properties including phonon dispersion relation. Except for high and low density limit, the general expression of correlation energy is unknown. The approximation approach is therefore required. The accuracy of the modelling system depends on the quality of correlation energy approximation. Typical correlation functionals used in LDA such as Vosko-Wilk-Nusair (VWN) and Perdew-Wang (PW) were obtained from parameterizing the near-exact quantum Monte Carlo data of Ceperley and Alder. These functionals are presented in complex form and inconvenient to implement. Alternatively, the latest published formula of Chachiyo correlation functional provides a comparable result for those much more complicated functionals. In addition, it provides more predictive power based on the first principle approach, not fitting functionals. Nevertheless, the performance of Chachiyo formula for calculating phonon dispersion relation (a key to the thermal properties of materials) has not been tested yet. Here, the implementation of new correlation functional to calculate phonon dispersion relation is initiated. The accuracy and its validity will be explored.

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

San Fabián, J.; Omar, S.; García de la Vega, J. M., E-mail: garcia.delavega@uam.es

The effect of a fraction of Hartree-Fock exchange on the calculated spin-spin coupling constants involving fluorine through a hydrogen bond is analyzed in detail. Coupling constants calculated using wavefunction methods are revisited in order to get high-level calculations using the same basis set. Accurate MCSCF results are obtained using an additive approach. These constants and their contributions are used as a reference for density functional calculations. Within the density functional theory, the Hartree-Fock exchange functional is split in short- and long-range using a modified version of the Coulomb-attenuating method with the SLYP functional as well as with the original B3LYP.more » Results support the difficulties for calculating hydrogen bond coupling constants using density functional methods when fluorine nuclei are involved. Coupling constants are very sensitive to the Hartree-Fock exchange and it seems that, contrary to other properties, it is important to include this exchange for short-range interactions. Best functionals are tested in two different groups of complexes: those related with anionic clusters of type [F(HF){sub n}]{sup −} and those formed by difluoroacetylene and either one or two hydrogen fluoride molecules.« less

Measuring the economic effects of Japan's Mikawa Port: Pre- and-post disaster assessments

NASA Astrophysics Data System (ADS)

Shibusawa, Hiroyuki; Miyata, Yuzuru

2017-10-01

This study examines the economic effects of Japan's Mikawa Port on Aichi Prefecture before and after a natural disaster interrupts its operations for one year. Using a regional input-output model, backward and forward linkage impacts are calculated along the waterfront where the auto industry is concentrated. In addition, economic damage from natural disasters is estimated. We assess the economic implications on the hinterland of Mikawa Port. Density functions of the backward and forward linkage impacts are derived. A production stoppage along the waterfront of Mikawa Port generates large indirect negative effects on the regional economy. Results found that density functions of the total impacts are decreasing function of distance but that several sectors are characterized by non-decreasing functions.

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

Jiménez, Jose Beltrán; Heisenberg, Lavinia; Olmo, Gonzalo J., E-mail: jose.beltran@uclouvain.be, E-mail: Lavinia.Heisenberg@unige.ch, E-mail: gonzalo.olmo@csic.es

We generalize the ultraviolet sector of gravitation via a Born-Infeld action using lessons from massive gravity. The theory contains all of the elementary symmetric polynomials and is treated in the Palatini formalism. We show how the connection can be solved algebraically to be the Levi-Civita connection of an effective metric. The non-linearity of the algebraic equations yields several branches, one of which always reduces to General Relativity at low curvatures. We explore in detail a minimal version of the theory, for which we study solutions in the presence of a perfect fluid with special attention to the cosmological evolution. Inmore » vacuum we recover Ricci-flat solutions, but also an additional physical solution corresponding to an Einstein space. The existence of two physical branches remains for non-vacuum solutions and, in addition, the branch that connects to the Einstein space in vacuum is not very sensitive to the specific value of the energy density. For the branch that connects to the General Relativity limit we generically find three behaviours for the Hubble function depending on the equation of state of the fluid, namely: either there is a maximum value for the energy density that connects continuously with vacuum, or the energy density can be arbitrarily large but the Hubble function saturates and remains constant at high energy densities, or the energy density is unbounded and the Hubble function grows faster than in General Relativity. The second case is particularly interesting because it could offer an interesting inflationary epoch even in the presence of a dust component. Finally, we discuss the possibility of avoiding certain types of singularities within the minimal model.« less

Magnetic Exchange Couplings from Semilocal Functionals Evaluated Nonself-Consistently on Hybrid Densities: Insights on Relative Importance of Exchange, Correlation, and Delocalization.

PubMed

Phillips, Jordan J; Peralta, Juan E

2012-09-11

Semilocal functionals generally yield poor magnetic exchange couplings for transition-metal complexes, typically overpredicting in magnitude the experimental values. Here we show that semilocal functionals evaluated nonself-consistently on densities from hybrid functionals can yield magnetic exchange couplings that are greatly improved with respect to their self-consistent semilocal values. Furthermore, when semilocal functionals are evaluated nonself-consistently on densities from a "half-and-half" hybrid, their errors with respect to experimental values can actually be lower than those from self-consistent calculations with standard hybrid functionals such as PBEh or TPSSh. This illustrates that despite their notoriously poor performance for exchange couplings, for many systems semilocal functionals are capable of delivering accurate relative energies for magnetic states provided that their electron delocalization error is corrected. However, while self-consistent calculations with hybrids uniformly improve results for all complexes, evaluating nonself-consistently with semilocal functionals does not give a balanced improvement for both ferro- and antiferromagnetically coupled complexes, indicating that there is more at play with the overestimation problem than simply the delocalization error. Additionally, we show that for some systems the conventional wisdom of choice of exchange functional mattering more than correlation does not hold. This combined with results from the nonself-consistent calculations provide insight on clarifying the relative roles of exchange, correlation, and delocalization in calculating magnetic exchange coupling parameters in Kohn-Sham Density Functional Theory.

Communication: Evaluating non-empirical double hybrid functionals for spin-state energetics in transition-metal complexes

NASA Astrophysics Data System (ADS)

Wilbraham, Liam; Adamo, Carlo; Ciofini, Ilaria

2018-01-01

The computationally assisted, accelerated design of inorganic functional materials often relies on the ability of a given electronic structure method to return the correct electronic ground state of the material in question. Outlining difficulties with current density functionals and wave function-based approaches, we highlight why double hybrid density functionals represent promising candidates for this purpose. In turn, we show that PBE0-DH (and PBE-QIDH) offers a significant improvement over its hybrid parent functional PBE0 [as well as B3LYP* and coupled cluster singles and doubles with perturbative triples (CCSD(T))] when computing spin-state splitting energies, using high-level diffusion Monte Carlo calculations as a reference. We refer to the opposing influence of Hartree-Fock (HF) exchange and MP2, which permits higher levels of HF exchange and a concomitant reduction in electronic density error, as the reason for the improved performance of double-hybrid functionals relative to hybrid functionals. Additionally, using 16 transition metal (Fe and Co) complexes, we show that low-spin states are stabilised by increasing contributions from MP2 within the double hybrid formulation. Furthermore, this stabilisation effect is more prominent for high field strength ligands than low field strength ligands.

Non-additive non-interacting kinetic energy of rare gas dimers

NASA Astrophysics Data System (ADS)

Jiang, Kaili; Nafziger, Jonathan; Wasserman, Adam

2018-03-01

Approximations of the non-additive non-interacting kinetic energy (NAKE) as an explicit functional of the density are the basis of several electronic structure methods that provide improved computational efficiency over standard Kohn-Sham calculations. However, within most fragment-based formalisms, there is no unique exact NAKE, making it difficult to develop general, robust approximations for it. When adjustments are made to the embedding formalisms to guarantee uniqueness, approximate functionals may be more meaningfully compared to the exact unique NAKE. We use numerically accurate inversions to study the exact NAKE of several rare-gas dimers within partition density functional theory, a method that provides the uniqueness for the exact NAKE. We find that the NAKE decreases nearly exponentially with atomic separation for the rare-gas dimers. We compute the logarithmic derivative of the NAKE with respect to the bond length for our numerically accurate inversions as well as for several approximate NAKE functionals. We show that standard approximate NAKE functionals do not reproduce the correct behavior for this logarithmic derivative and propose two new NAKE functionals that do. The first of these is based on a re-parametrization of a conjoint Perdew-Burke-Ernzerhof (PBE) functional. The second is a simple, physically motivated non-decomposable NAKE functional that matches the asymptotic decay constant without fitting.

Pair correlation functions and the wavevector-dependent surface tension in a simple density functional treatment of the liquid-vapour interface.

PubMed

Parry, A O; Rascón, C; Willis, G; Evans, R

2014-09-03

We study the density-density correlation function G(r, r') in the interfacial region of a fluid (or Ising-like magnet) with short-ranged interactions using square gradient density functional theory. Adopting a simple double parabola approximation for the bulk free-energy density, we first show that the parallel Fourier transform G(z, z'; q) and local structure factor S(z; q) separate into bulk and excess contributions. We attempt to account for both contributions by deriving an interfacial Hamiltonian, characterised by a wavevector dependent surface tension σ(q), and then reconstructing density correlations from correlations in the interface position. We show that the standard crossing criterion identification of the interface, as a surface of fixed density (or magnetization), does not explain the separation of G(z, z'; q) and the form of the excess contribution. We propose an alternative definition of the interface position based on the properties of correlations between points that 'float' with the surface and show that this describes the full q and z dependence of the excess contributions to both G and S. However, neither the 'crossing-criterion' nor the new 'floating interface' definition of σ(q) are quantities directly measurable from the total structure factor S(tot)(q) which contains additional q dependence arising from the non-local relation between fluctuations in the interfacial position and local density. Since it is the total structure factor that is measured experimentally or in simulations, our results have repercussions for earlier attempts to extract and interpret σ(q).

An open-source framework for analyzing N-electron dynamics. II. Hybrid density functional theory/configuration interaction methodology.

PubMed

Hermann, Gunter; Pohl, Vincent; Tremblay, Jean Christophe

2017-10-30

In this contribution, we extend our framework for analyzing and visualizing correlated many-electron dynamics to non-variational, highly scalable electronic structure method. Specifically, an explicitly time-dependent electronic wave packet is written as a linear combination of N-electron wave functions at the configuration interaction singles (CIS) level, which are obtained from a reference time-dependent density functional theory (TDDFT) calculation. The procedure is implemented in the open-source Python program detCI@ORBKIT, which extends the capabilities of our recently published post-processing toolbox (Hermann et al., J. Comput. Chem. 2016, 37, 1511). From the output of standard quantum chemistry packages using atom-centered Gaussian-type basis functions, the framework exploits the multideterminental structure of the hybrid TDDFT/CIS wave packet to compute fundamental one-electron quantities such as difference electronic densities, transient electronic flux densities, and transition dipole moments. The hybrid scheme is benchmarked against wave function data for the laser-driven state selective excitation in LiH. It is shown that all features of the electron dynamics are in good quantitative agreement with the higher-level method provided a judicious choice of functional is made. Broadband excitation of a medium-sized organic chromophore further demonstrates the scalability of the method. In addition, the time-dependent flux densities unravel the mechanistic details of the simulated charge migration process at a glance. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Density function theoretical study on the complex involved in Th atom-activated C-C bond in C2H6

NASA Astrophysics Data System (ADS)

Qing-Qing, Wang; Peng, Li; Tao, Gao; Hong-Yan, Wang; Bing-Yun, Ao

2016-06-01

Density functional theory (DFT) calculations are performed to investigate the reactivity of Th atom toward ethane C-C bond activation. A comprehensive description of the reaction mechanisms leading to two different reaction products is presented. We report a complete exploration of the potential energy surfaces by taking into consideration different spin states. In addition, the intermediate and transition states along the reaction paths are characterized. Total, partial, and overlap population density of state diagrams and analyses are also presented. Furthermore, the natures of the chemical bonding of intermediate and transition states are studied by using topological method combined with electron localization function (ELF) and Mayer bond order. Infrared spectrum (IR) is obtained and further discussed based on the optimized geometries. Project supported by the National Natural Science Foundation of China (Grant Nos. 21371160, 21401173, and 11364023).

The risks and returns of stock investment in a financial market

NASA Astrophysics Data System (ADS)

Li, Jiang-Cheng; Mei, Dong-Cheng

2013-03-01

The risks and returns of stock investment are discussed via numerically simulating the mean escape time and the probability density function of stock price returns in the modified Heston model with time delay. Through analyzing the effects of delay time and initial position on the risks and returns of stock investment, the results indicate that: (i) There is an optimal delay time matching minimal risks of stock investment, maximal average stock price returns and strongest stability of stock price returns for strong elasticity of demand of stocks (EDS), but the opposite results for weak EDS; (ii) The increment of initial position recedes the risks of stock investment, strengthens the average stock price returns and enhances stability of stock price returns. Finally, the probability density function of stock price returns and the probability density function of volatility and the correlation function of stock price returns are compared with other literatures. In addition, good agreements are found between them.

Oxygen reduction on a Pt(111) catalyst in HT-PEM fuel cells by density functional theory

NASA Astrophysics Data System (ADS)

Sun, Hong; Li, Jie; Almheiri, Saif; Xiao, Jianyu

2017-08-01

The oxygen reduction reaction plays an important role in the performance of high-temperature proton exchange membrane (HT-PEM) fuel cells. In this study, a molecular dynamics model, which is based on the density functional theory and couples the system's energy, the exchange-correlation energy functional, the charge density distribution function, and the simplified Kohn-Sham equation, was developed to simulate the oxygen reduction reaction on a Pt(111) surface. Additionally, an electrochemical reaction system on the basis of a four-electron reaction mechanism was also developed for this simulation. The reaction path of the oxygen reduction reaction, the product structure of each reaction step and the system's energy were simulated. It is found that the first step reaction of the first hydrogen ion with the oxygen molecule is the controlling step of the overall reaction. Increasing the operating temperature speeds up the first step reaction rate and slightly decreases its reaction energy barrier. Our results provide insight into the working principles of HT-PEM fuel cells.

Changes in Structure and Functioning of Protist (Testate Amoebae) Communities Due to Conversion of Lowland Rainforest into Rubber and Oil Palm Plantations.

PubMed

Krashevska, Valentyna; Klarner, Bernhard; Widyastuti, Rahayu; Maraun, Mark; Scheu, Stefan

2016-01-01

Large areas of tropical rainforest are being converted to agricultural and plantation land uses, but little is known of biodiversity and ecological functioning under these replacement land uses. We investigated the effects of conversion of rainforest into jungle rubber, intensive rubber and oil palm plantations on testate amoebae, diverse and functionally important protists in litter and soil. Living testate amoebae species richness, density and biomass were all lower in replacement land uses than in rainforest, with the impact being more pronounced in litter than in soil. Similar abundances of species of high and low trophic level in rainforest suggest that trophic interactions are more balanced, with a high number of functionally redundant species, than in rubber and oil palm. In contrast, plantations had a low density of high trophic level species indicating losses of functions. This was particularly so in oil palm plantations. In addition, the relative density of species with siliceous shells was >50% lower in the litter layer of oil palm and rubber compared to rainforest and jungle rubber. This difference suggests that rainforest conversion changes biogenic silicon pools and increases silicon losses. Overall, the lower species richness, density and biomass in plantations than in rainforest, and the changes in the functional composition of the testate amoebae community, indicate detrimental effects of rainforest conversion on the structure and functioning of microbial food webs.

Effect of the powder characteristics of Sisub3Nsub4 on the microstructure of sintered bodies

NASA Technical Reports Server (NTRS)

Woetting, G.; Hausner, H.

1981-01-01

Silicon nitride powders sintered with the addition of 2 wt% Mg0 to 95% theoretical density after attrition milling and subsequent purification were evaluated. Preparation of the powders is described. The powder characteristics (specific surfaces, iron concentration, and oxygen content), and density, weight loss, and phase state of the sinter bodies as a function of powder preparation are presented.

Thermodynamic DFT analysis of natural gas.

PubMed

Neto, Abel F G; Huda, Muhammad N; Marques, Francisco C; Borges, Rosivaldo S; Neto, Antonio M J C

2017-08-01

Density functional theory was performed for thermodynamic predictions on natural gas, whose B3LYP/6-311++G(d,p), B3LYP/6-31+G(d), CBS-QB3, G3, and G4 methods were applied. Additionally, we carried out thermodynamic predictions using G3/G4 averaged. The calculations were performed for each major component of seven kinds of natural gas and to their respective air + natural gas mixtures at a thermal equilibrium between room temperature and the initial temperature of a combustion chamber during the injection stage. The following thermodynamic properties were obtained: internal energy, enthalpy, Gibbs free energy and entropy, which enabled us to investigate the thermal resistance of fuels. Also, we estimated an important parameter, namely, the specific heat ratio of each natural gas; this allowed us to compare the results with the empirical functions of these parameters, where the B3LYP/6-311++G(d,p) and G3/G4 methods showed better agreements. In addition, relevant information on the thermal and mechanic resistance of natural gases were investigated, as well as the standard thermodynamic properties for the combustion of natural gas. Thus, we show that density functional theory can be useful for predicting the thermodynamic properties of natural gas, enabling the production of more efficient compositions for the investigated fuels. Graphical abstract Investigation of the thermodynamic properties of natural gas through the canonical ensemble model and the density functional theory.

Hydrogen atom addition to the surface of graphene nanoflakes: A density functional theory study

NASA Astrophysics Data System (ADS)

Tachikawa, Hiroto

2017-02-01

Polycyclic aromatic hydrocarbons (PAHs) provide a 2-dimensional (2D) reaction surface in 3-dimensional (3D) interstellar space and have been utilized as a model of graphene surfaces. In the present study, the reaction of PAHs with atomic hydrogen was investigated by means of density functional theory (DFT) to systematically elucidate the binding nature of atomic hydrogen to graphene nanoflakes. PAHs with n = 4-37 were chosen, where n indicates the number of benzene rings. Activation energies of hydrogen addition to the graphene surface were calculated to be 5.2-7.0 kcal/mol at the CAM-B3LYP/6-311G(d,p) level, which is almost constant for all PAHs. The binding energies of hydrogen atom were slightly dependent on the size (n): 14.8-28.5 kcal/mol. The absorption spectra showed that a long tail is generated at the low-energy region after hydrogen addition to the graphene surface. The electronic states of hydrogenated graphenes were discussed on the basis of theoretical results.

Density functional theory study on the influence of pyrrolidine substituent of C60 bisadduct on its supramolecular interaction with porphine

NASA Astrophysics Data System (ADS)

Zhao, Li-Hong; Weng, Jun-Ying; Zhao, Wei; Ruan, Wen-Juan; Xin, Fei; Zhang, Ying-Hui

2013-09-01

Calculation using three kinds of density functional theory (DFT) methods revealed that the nonbonded interaction of pyrrolidine-functionalized C60 bisadducts with porphine derivatives (MP: M = Zn, 2H) was significantly affected by pyrrolidine substituents. Several types of the stable interaction configurations of trans-3 C60 bisadduct/ZnP complex (abbreviated as tran-3/ZnP) were compared. The association energy predicted by the wB97XD method was larger than that predicted by CAM-B3LYP and BHandH functionals. The results showed that the closer approach of porphine ring to the two pyrrolidine substituents, the larger the association energy of the complex. This trend was ascribed to the additional C-H⋯π interaction between the pyrrolidine and porphine rings. The natural bond orbital analysis proved the existence of an additional charge transfer process between the porphine and pyrrolidine rings for the t-I type of trans-3/porphine complexes. The red shift of absorption peaks of porphine were predicted in consistent with general experimental results.

Watching excitons move: the time-dependent transition density matrix

NASA Astrophysics Data System (ADS)

Ullrich, Carsten

2012-02-01

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

Robust control algorithms for Mars aerobraking

NASA Technical Reports Server (NTRS)

Shipley, Buford W., Jr.; Ward, Donald T.

1992-01-01

Four atmospheric guidance concepts have been adapted to control an interplanetary vehicle aerobraking in the Martian atmosphere. The first two offer improvements to the Analytic Predictor Corrector (APC) to increase its robustness to density variations. The second two are variations of a new Liapunov tracking exit phase algorithm, developed to guide the vehicle along a reference trajectory. These four new controllers are tested using a six degree of freedom computer simulation to evaluate their robustness. MARSGRAM is used to develop realistic atmospheres for the study. When square wave density pulses perturb the atmosphere all four controllers are successful. The algorithms are tested against atmospheres where the inbound and outbound density functions are different. Square wave density pulses are again used, but only for the outbound leg of the trajectory. Additionally, sine waves are used to perturb the density function. The new algorithms are found to be more robust than any previously tested and a Liapunov controller is selected as the most robust control algorithm overall examined.

Evolution of the Blue and Far-Infrared Galaxy Luminosity Functions

NASA Technical Reports Server (NTRS)

Lonsdale, Carol J.; Chokshi, Arati

1993-01-01

The space density of blue-selected galaxies at moderate redshifts is determined here directly by deriving the luminosity function. Evidence is found for density evolution for moderate luminosity galaxies at a rate of (1+z) exp delta, with a best fit of delta + 4 +/- 2, between the current epoch and Z greater than about 0.1. At M(b) less than -22 evidence is found for about 0.5-1.5 mag of luminosity evolution in addition to the density evolution, corresponding to an evolutionary rate of about (1+z) exp gamma, with gamma = 0.5-2.5, but a redshift of about 0.4. Assuming a steeper faint end slope of alpha = -1.3 similar to that observed in the Virgo cluster, could explain the data with a luminosity evolution rate of gamma = 1-2, without need for any density evolution. Acceptable fits are found by comparing composite density and luminosity evolution models to faint IRAS 60 micron source counts, implying that the blue and far-IR evolutionary rates may be similar.

First-principle study of structural, electronic and magnetic properties of (FeC)n (n = 1-8) and (FeC)8TM (TM = V, Cr, Mn and Co) clusters.

PubMed

Li, Cheng-Gang; Zhang, Jie; Zhang, Wu-Qin; Tang, Ya-Nan; Ren, Bao-Zeng; Hu, Yan-Fei

2017-12-13

The structural, electronic and magnetic properties of the (FeC) n (n = 1-8) clusters are studied using the unbiased CALYPSO structure search method and density functional theory. A combination of the PBE functional and 6-311 + G* basis set is used for determining global minima on potential energy surfaces of (FeC) n clusters. Relatively stabilities are analyzed via computing their binding energies, second order difference and HOMO-LUMO gaps. In addition, the origin of magnetic properties, spin density and density of states are discussed in detail, respectively. At last, based on the same computational method, the structures, magnetic properties and density of states are systemically investigated for the 3d (V, Cr, Mn and Co) atom doped (FeC) 8 cluster.

How the climate limits the wood density of angiosperms

NASA Astrophysics Data System (ADS)

Choi, Jin Woo; Kim, Ho-Young

2017-11-01

Flowering trees have various types of wood structure to perform multiple functions under their environmental conditions. In addition to transporting water from the roots to the canopy and providing mechanical support, the structure should provide resistance to embolism to maintain soil-plant-atmosphere continuum. By investigating existing data of the resistivity to embolism and wood density of 165 angiosperm species, here we show that the climate can limit the intrinsic properties of trees. Trees living in the dry environments require a high wood density to slow down the pressure decrease as it loses water relatively fast by evaporation. However, building too much tissues will result in the decrease of hydraulic conductivity and moisture concentration around mesophyll cells. To rationalize the biologically observed lower bound of the wood density, we construct a mechanical model to predict the wood density as a function of the vulnerability to embolism and the time for the recovery. Also, we build an artificial system using hydrogel microchannels that can test the probability of embolism as a function of conduit distributions. Our theoretical prediction is shown to be consistent with the results obtained from the artificial system and the biological data.

Origin of the 20-electron structure of Mg3 MnH7 : Density functional calculations

NASA Astrophysics Data System (ADS)

Gupta, M.; Singh, D. J.; Gupta, R.

2005-03-01

The electronic structure and stability of the 20-electron complex hydride, Mg3MnH7 is studied using density functional calculations. The heat of formation is larger in magnitude than that of MgH2 . The deviation from the 18-electron rule is explained by the predominantly ionic character of the band structure and a large crystal-field splitting of the Mn d bands. In particular, each H provides one deep band accomodating two electrons, while the Mn t2g bands hold an additional six electrons per formula unit.

Grand canonical electronic density-functional theory: Algorithms and applications to electrochemistry

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

Sundararaman, Ravishankar; Goddard, III, William A.; Arias, Tomas A.

First-principles calculations combining density-functional theory and continuum solvation models enable realistic theoretical modeling and design of electrochemical systems. When a reaction proceeds in such systems, the number of electrons in the portion of the system treated quantum mechanically changes continuously, with a balancing charge appearing in the continuum electrolyte. A grand-canonical ensemble of electrons at a chemical potential set by the electrode potential is therefore the ideal description of such systems that directly mimics the experimental condition. We present two distinct algorithms: a self-consistent field method and a direct variational free energy minimization method using auxiliary Hamiltonians (GC-AuxH), to solvemore » the Kohn-Sham equations of electronic density-functional theory directly in the grand canonical ensemble at fixed potential. Both methods substantially improve performance compared to a sequence of conventional fixed-number calculations targeting the desired potential, with the GC-AuxH method additionally exhibiting reliable and smooth exponential convergence of the grand free energy. Lastly, we apply grand-canonical density-functional theory to the under-potential deposition of copper on platinum from chloride-containing electrolytes and show that chloride desorption, not partial copper monolayer formation, is responsible for the second voltammetric peak.« less

Grand canonical electronic density-functional theory: Algorithms and applications to electrochemistry.

PubMed

Sundararaman, Ravishankar; Goddard, William A; Arias, Tomas A

2017-03-21

First-principles calculations combining density-functional theory and continuum solvation models enable realistic theoretical modeling and design of electrochemical systems. When a reaction proceeds in such systems, the number of electrons in the portion of the system treated quantum mechanically changes continuously, with a balancing charge appearing in the continuum electrolyte. A grand-canonical ensemble of electrons at a chemical potential set by the electrode potential is therefore the ideal description of such systems that directly mimics the experimental condition. We present two distinct algorithms: a self-consistent field method and a direct variational free energy minimization method using auxiliary Hamiltonians (GC-AuxH), to solve the Kohn-Sham equations of electronic density-functional theory directly in the grand canonical ensemble at fixed potential. Both methods substantially improve performance compared to a sequence of conventional fixed-number calculations targeting the desired potential, with the GC-AuxH method additionally exhibiting reliable and smooth exponential convergence of the grand free energy. Finally, we apply grand-canonical density-functional theory to the under-potential deposition of copper on platinum from chloride-containing electrolytes and show that chloride desorption, not partial copper monolayer formation, is responsible for the second voltammetric peak.

Density-functional energy gaps of solids demystified

NASA Astrophysics Data System (ADS)

Perdew, John P.; Ruzsinszky, Adrienn

2018-06-01

The fundamental energy gap of a solid is a ground-state second energy difference. Can one find the fundamental gap from the gap in the band structure of Kohn-Sham density functional theory? An argument of Williams and von Barth (WB), 1983, suggests that one can. In fact, self-consistent band-structure calculations within the local density approximation or the generalized gradient approximation (GGA) yield the fundamental gap within the same approximation for the energy. Such a calculation with the exact density functional would yield a band gap that also underestimates the fundamental gap, because the exact Kohn-Sham potential in a solid jumps up by an additive constant when one electron is added, and the WB argument does not take this effect into account. The WB argument has been extended recently to generalized Kohn-Sham theory, the simplest way to implement meta-GGAs and hybrid functionals self-consistently, with an exchange-correlation potential that is a non-multiplication operator. Since this operator is continuous, the band gap is again the fundamental gap within the same approximation, but, because the approximations are more realistic, so is the band gap. What approximations might be even more realistic?

A density functional approach to ferrogels

NASA Astrophysics Data System (ADS)

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

2017-07-01

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

Neural network approach to quantum-chemistry data: accurate prediction of density functional theory energies.

PubMed

Balabin, Roman M; Lomakina, Ekaterina I

2009-08-21

Artificial neural network (ANN) approach has been applied to estimate the density functional theory (DFT) energy with large basis set using lower-level energy values and molecular descriptors. A total of 208 different molecules were used for the ANN training, cross validation, and testing by applying BLYP, B3LYP, and BMK density functionals. Hartree-Fock results were reported for comparison. Furthermore, constitutional molecular descriptor (CD) and quantum-chemical molecular descriptor (QD) were used for building the calibration model. The neural network structure optimization, leading to four to five hidden neurons, was also carried out. The usage of several low-level energy values was found to greatly reduce the prediction error. An expected error, mean absolute deviation, for ANN approximation to DFT energies was 0.6+/-0.2 kcal mol(-1). In addition, the comparison of the different density functionals with the basis sets and the comparison of multiple linear regression results were also provided. The CDs were found to overcome limitation of the QD. Furthermore, the effective ANN model for DFT/6-311G(3df,3pd) and DFT/6-311G(2df,2pd) energy estimation was developed, and the benchmark results were provided.

Grand canonical electronic density-functional theory: Algorithms and applications to electrochemistry

DOE PAGES

Sundararaman, Ravishankar; Goddard, III, William A.; Arias, Tomas A.

2017-03-16

First-principles calculations combining density-functional theory and continuum solvation models enable realistic theoretical modeling and design of electrochemical systems. When a reaction proceeds in such systems, the number of electrons in the portion of the system treated quantum mechanically changes continuously, with a balancing charge appearing in the continuum electrolyte. A grand-canonical ensemble of electrons at a chemical potential set by the electrode potential is therefore the ideal description of such systems that directly mimics the experimental condition. We present two distinct algorithms: a self-consistent field method and a direct variational free energy minimization method using auxiliary Hamiltonians (GC-AuxH), to solvemore » the Kohn-Sham equations of electronic density-functional theory directly in the grand canonical ensemble at fixed potential. Both methods substantially improve performance compared to a sequence of conventional fixed-number calculations targeting the desired potential, with the GC-AuxH method additionally exhibiting reliable and smooth exponential convergence of the grand free energy. Lastly, we apply grand-canonical density-functional theory to the under-potential deposition of copper on platinum from chloride-containing electrolytes and show that chloride desorption, not partial copper monolayer formation, is responsible for the second voltammetric peak.« less

Non-Fickian dispersion of groundwater age

PubMed Central

Engdahl, Nicholas B.; Ginn, Timothy R.; Fogg, Graham E.

2014-01-01

We expand the governing equation of groundwater age to account for non-Fickian dispersive fluxes using continuous random walks. Groundwater age is included as an additional (fifth) dimension on which the volumetric mass density of water is distributed and we follow the classical random walk derivation now in five dimensions. The general solution of the random walk recovers the previous conventional model of age when the low order moments of the transition density functions remain finite at their limits and describes non-Fickian age distributions when the transition densities diverge. Previously published transition densities are then used to show how the added dimension in age affects the governing differential equations. Depending on which transition densities diverge, the resulting models may be nonlocal in time, space, or age and can describe asymptotic or pre-asymptotic dispersion. A joint distribution function of time and age transitions is developed as a conditional probability and a natural result of this is that time and age must always have identical transition rate functions. This implies that a transition density defined for age can substitute for a density in time and this has implications for transport model parameter estimation. We present examples of simulated age distributions from a geologically based, heterogeneous domain that exhibit non-Fickian behavior and show that the non-Fickian model provides better descriptions of the distributions than the Fickian model. PMID:24976651

Non-pairwise additivity of the leading-order dispersion energy

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

Hollett, Joshua W., E-mail: j.hollett@uwinnipeg.ca

2015-02-28

The leading-order (i.e., dipole-dipole) dispersion energy is calculated for one-dimensional (1D) and two-dimensional (2D) infinite lattices, and an infinite 1D array of infinitely long lines, of doubly occupied locally harmonic wells. The dispersion energy is decomposed into pairwise and non-pairwise additive components. By varying the force constant and separation of the wells, the non-pairwise additive contribution to the dispersion energy is shown to depend on the overlap of density between neighboring wells. As well separation is increased, the non-pairwise additivity of the dispersion energy decays. The different rates of decay for 1D and 2D lattices of wells is explained inmore » terms of a Jacobian effect that influences the number of nearest neighbors. For an array of infinitely long lines of wells spaced 5 bohrs apart, and an inter-well spacing of 3 bohrs within a line, the non-pairwise additive component of the leading-order dispersion energy is −0.11 kJ mol{sup −1} well{sup −1}, which is 7% of the total. The polarizability of the wells and the density overlap between them are small in comparison to that of the atomic densities that arise from the molecular density partitioning used in post-density-functional theory (DFT) damped dispersion corrections, or DFT-D methods. Therefore, the nonadditivity of the leading-order dispersion observed here is a conservative estimate of that in molecular clusters.« less

A proposed simulation method for directed self-assembly of nanographene

NASA Astrophysics Data System (ADS)

Geraets, J. A.; Baldwin, J. P. C.; Twarock, R.; Hancock, Y.

2017-09-01

A methodology for predictive kinetic self-assembly modeling of bottom-up chemical synthesis of nanographene is proposed. The method maintains physical transparency in using a novel array format to efficiently store molecule information and by using array operations to determine reaction possibilities. Within a minimal model approach, the parameter space for the bond activation energies (i.e. molecule functionalization) at fixed reaction temperature and initial molecule concentrations is explored. Directed self-assembly of nanographene from functionalized tetrabenzanthracene and benzene is studied with regions in the activation energy phase-space showing length-to-width ratio tunability. The degree of defects and reaction reproducibility in the simulations is also determined, with the rate of functionalized benzene addition providing additional control of the dimension and quality of the nanographene. Comparison of the reaction energetics to available density functional theory data suggests the synthesis may be experimentally tenable using aryl-halide cross-coupling and noble metal surface-assisted catalysis. With full access to the intermediate reaction network and with dynamic coupling to density functional theory-informed tight-binding simulation, the method is proposed as a computationally efficient means towards detailed simulation-driven design of new nanographene systems.

12-h abstinence-induced functional connectivity density changes and craving in young smokers: a resting-state study.

PubMed

Zhao, Shuzhi; Li, Yangding; Li, Min; Wang, Ruonan; Bi, Yanzhi; Zhang, Yajuan; Lu, Xiaoqi; Yu, Dahua; Yang, Likun; Yuan, Kai

2018-06-20

Studying the neural correlates of craving to smoke is of great importance to improve treatment outcomes in smoking addiction. According to previous studies, the critical roles of striatum and frontal brain regions had been revealed in addiction. However, few studies focused on the hub of brain regions in the 12 h abstinence induced craving in young smokers. Thirty-one young male smokers were enrolled in the present study. A within-subject experiment design was carried out to compare functional connectivity density between 12-h smoking abstinence and smoking satiety conditions during resting state in young adult smokers by using functional connectivity density mapping (FCDM). Then, the functional connectivity density changes during smoking abstinence versus satiety were further used to examine correlations with abstinence-induced changes in subjective craving. We found young adult smokers in abstinence state (vs satiety) had higher local functional connectivity density (lFCD) and global functional connectivity density (gFCD) in brain regions including striatal subregions (i.e., bilateral caudate and putamen), frontal regions (i.e., anterior cingulate cortex (ACC) and orbital frontal cortex (OFC)) and bilateral insula. We also found higher lFCD during smoking abstinence (vs satiety) in bilateral thalamus. Additionally, the lFCD changes of the left ACC, bilateral caudate and right OFC were positively correlated with the changes in craving induced by abstinence (i.e., abstinence minus satiety) in young adult smokers. The present findings improve the understanding of the effects of acute smoking abstinence on the hubs of brain gray matter in the abstinence-induces craving and may contribute new insights into the neural mechanism of abstinence-induced craving in young smokers in smoking addiction.

A family of triaxial modified Hubble mass models: Effects of the additional radial functions

NASA Astrophysics Data System (ADS)

Das, Mousumi; Thakur, Parijat; Ann, H. B.

2005-03-01

The projected properties of triaxial generalization of the modified Hubble mass models are studied. These models are constructed by adding the additional radial functions, each multiplied by a low-order spherical harmonic, to the models of [Chakraborty, D.K., Thakur, P., 2000. MNRAS 318, 1273]. The projected surface density of mass models can be calculated analytically which allows us to derive the analytic expressions of axial ratio and position angle of major axis of constant density elliptical contours at asymptotic radii. The models are more general than those studied earlier in the sense that the inclusions of additional terms in density distribution, allow one to produce varieties of the radial profile of axial ratio and position angle, in particular, their small scale variations at inner radii. Strong correlations are found to exist between the observed axial ratio evaluated at 0.25Re and at 4Re which occupy well-separated regions in the parameter space for different choices of the intrinsic axial ratios. These correlations can be exploited to predict the intrinsic shape of the mass model, independent of the viewing angles. Using Bayesian statistics, the result of a test case launched for an estimation of the shape of a model galaxy is found to be satisfactory.

Density functional theory calculations for armchair stanene nanoribbons with fluorine and sulfur functionalization

NASA Astrophysics Data System (ADS)

Zhang, J.; Lang, X. Y.; Jiang, Q.

2018-07-01

A systematic density functional theory calculation has been carried out to study the effect of edge terminating of F and S elements with different edge natures on the structure and electronic properties of armchair stanene nanoribbons (ASnNRs). Moreover, the corresponding size (ribbon width Na) dependence on these properties is also considered. The energy gap was found to be oscillated as a function of Na and could be classified into three distinct groups of 3m, 3m + 1 and 3m + 2. In addition, the energy gaps of ASnNRs saturated by S atoms differ from that did by F and H atoms in vibration trends as well VBM and CBM changes, where the energy gap is a direct energy gap with a moderate size.

Spiral Galaxy Lensing: A Model with Twist

NASA Astrophysics Data System (ADS)

Bell, Steven R.; Ernst, Brett; Fancher, Sean; Keeton, Charles R.; Komanduru, Abi; Lundberg, Erik

2014-12-01

We propose a single galaxy gravitational lensing model with a mass density that has a spiral structure. Namely, we extend the arcsine gravitational lens (a truncated singular isothermal elliptical model), adding an additional parameter that controls the amount of spiraling in the structure of the mass density. An important feature of our model is that, even though the mass density is sophisticated, we succeed in integrating the deflection term in closed form using a Gauss hypergeometric function. When the spiraling parameter is set to zero, this reduces to the arcsine lens.

Statistical properties of swarms of self-propelled particles with repulsions across the order-disorder transition

NASA Astrophysics Data System (ADS)

Romenskyy, Maksym; Lobaskin, Vladimir

2013-03-01

We study dynamic self-organisation and order-disorder transitions in a two-dimensional system of self-propelled particles. Our model is a variation of the Vicsek model, where particles align the motion to their neighbours but repel each other at short distances. We use computer simulations to measure the orientational order parameter for particle velocities as a function of intensity of internal noise or particle density. We show that in addition to the transition to an ordered state on increasing the particle density, as reported previously, there exists a transition into a disordered phase at the higher densities, which can be attributed to the destructive action of the repulsions. We demonstrate that the transition into the ordered phase is accompanied by the onset of algebraic behaviour of the two-point velocity correlation function and by a non-monotonous variation of the velocity relaxation time. The critical exponent for the decay of the velocity correlation function in the ordered phase depends on particle concentration at low densities but assumes a universal value in more dense systems.

Stochastic Optimally Tuned Range-Separated Hybrid Density Functional Theory.

PubMed

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

2016-05-19

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

Tigers and their prey: Predicting carnivore densities from prey abundance

USGS Publications Warehouse

Karanth, K.U.; Nichols, J.D.; Kumar, N.S.; Link, W.A.; Hines, J.E.

2004-01-01

The goal of ecology is to understand interactions that determine the distribution and abundance of organisms. In principle, ecologists should be able to identify a small number of limiting resources for a species of interest, estimate densities of these resources at different locations across the landscape, and then use these estimates to predict the density of the focal species at these locations. In practice, however, development of functional relationships between abundances of species and their resources has proven extremely difficult, and examples of such predictive ability are very rare. Ecological studies of prey requirements of tigers Panthera tigris led us to develop a simple mechanistic model for predicting tiger density as a function of prey density. We tested our model using data from a landscape-scale long-term (1995-2003) field study that estimated tiger and prey densities in 11 ecologically diverse sites across India. We used field techniques and analytical methods that specifically addressed sampling and detectability, two issues that frequently present problems in macroecological studies of animal populations. Estimated densities of ungulate prey ranged between 5.3 and 63.8 animals per km2. Estimated tiger densities (3.2-16.8 tigers per 100 km2) were reasonably consistent with model predictions. The results provide evidence of a functional relationship between abundances of large carnivores and their prey under a wide range of ecological conditions. In addition to generating important insights into carnivore ecology and conservation, the study provides a potentially useful model for the rigorous conduct of macroecological science.

Fundamental gaps with approximate density functionals: The derivative discontinuity revealed from ensemble considerations

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

Kraisler, Eli; Kronik, Leeor

2014-05-14

The fundamental gap is a central quantity in the electronic structure of matter. Unfortunately, the fundamental gap is not generally equal to the Kohn-Sham gap of density functional theory (DFT), even in principle. The two gaps differ precisely by the derivative discontinuity, namely, an abrupt change in slope of the exchange-correlation energy as a function of electron number, expected across an integer-electron point. Popular approximate functionals are thought to be devoid of a derivative discontinuity, strongly compromising their performance for prediction of spectroscopic properties. Here we show that, in fact, all exchange-correlation functionals possess a derivative discontinuity, which arises naturallymore » from the application of ensemble considerations within DFT, without any empiricism. This derivative discontinuity can be expressed in closed form using only quantities obtained in the course of a standard DFT calculation of the neutral system. For small, finite systems, addition of this derivative discontinuity indeed results in a greatly improved prediction for the fundamental gap, even when based on the most simple approximate exchange-correlation density functional – the local density approximation (LDA). For solids, the same scheme is exact in principle, but when applied to LDA it results in a vanishing derivative discontinuity correction. This failure is shown to be directly related to the failure of LDA in predicting fundamental gaps from total energy differences in extended systems.« less

Artificial cognitive memory—changing from density driven to functionality driven

NASA Astrophysics Data System (ADS)

Shi, L. P.; Yi, K. J.; Ramanathan, K.; Zhao, R.; Ning, N.; Ding, D.; Chong, T. C.

2011-03-01

Increasing density based on bit size reduction is currently a main driving force for the development of data storage technologies. However, it is expected that all of the current available storage technologies might approach their physical limits in around 15 to 20 years due to miniaturization. To further advance the storage technologies, it is required to explore a new development trend that is different from density driven. One possible direction is to derive insights from biological counterparts. Unlike physical memories that have a single function of data storage, human memory is versatile. It contributes to functions of data storage, information processing, and most importantly, cognitive functions such as adaptation, learning, perception, knowledge generation, etc. In this paper, a brief review of current data storage technologies are presented, followed by discussions of future storage technology development trend. We expect that the driving force will evolve from density to functionality, and new memory modules associated with additional functions other than only data storage will appear. As an initial step toward building a future generation memory technology, we propose Artificial Cognitive Memory (ACM), a memory based intelligent system. We also present the characteristics of ACM, new technologies that can be used to develop ACM components such as bioinspired element cells (silicon, memristor, phase change, etc.), and possible methodologies to construct a biologically inspired hierarchical system.

Ensemble Averaged Probability Density Function (APDF) for Compressible Turbulent Reacting Flows

NASA Technical Reports Server (NTRS)

Shih, Tsan-Hsing; Liu, Nan-Suey

2012-01-01

In this paper, we present a concept of the averaged probability density function (APDF) for studying compressible turbulent reacting flows. The APDF is defined as an ensemble average of the fine grained probability density function (FG-PDF) with a mass density weighting. It can be used to exactly deduce the mass density weighted, ensemble averaged turbulent mean variables. The transport equation for APDF can be derived in two ways. One is the traditional way that starts from the transport equation of FG-PDF, in which the compressible Navier- Stokes equations are embedded. The resulting transport equation of APDF is then in a traditional form that contains conditional means of all terms from the right hand side of the Navier-Stokes equations except for the chemical reaction term. These conditional means are new unknown quantities that need to be modeled. Another way of deriving the transport equation of APDF is to start directly from the ensemble averaged Navier-Stokes equations. The resulting transport equation of APDF derived from this approach appears in a closed form without any need for additional modeling. The methodology of ensemble averaging presented in this paper can be extended to other averaging procedures: for example, the Reynolds time averaging for statistically steady flow and the Reynolds spatial averaging for statistically homogeneous flow. It can also be extended to a time or spatial filtering procedure to construct the filtered density function (FDF) for the large eddy simulation (LES) of compressible turbulent reacting flows.

On the Mechanistic Origins of Toughness in Bone

DTIC Science & Technology

2010-01-01

the cement lines provide the prime sites for microcrack formation, the increased osteon density gives rise to (a) a higher microcrack density, which...organs. The diversity of structures within this family reflects the fine-tuning or adaptation of the structure to its function. In addition , a remarkable...material (16, 20, 21). Unfortunately, excessive remodeling and other aging-related changes to the mus- culoskeletal system increase susceptibility to bone

Dielectric properties of organic solvents from non-polarizable molecular dynamics simulation with electronic continuum model and density functional theory.

PubMed

Lee, Sanghun; Park, Sung Soo

2011-11-03

Dielectric constants of electrolytic organic solvents are calculated employing nonpolarizable Molecular Dynamics simulation with Electronic Continuum (MDEC) model and Density Functional Theory. The molecular polarizabilities are obtained by the B3LYP/6-311++G(d,p) level of theory to estimate high-frequency refractive indices while the densities and dipole moment fluctuations are computed using nonpolarizable MD simulations. The dielectric constants reproduced from these procedures are evaluated to provide a reliable approach for estimating the experimental data. An additional feature, two representative solvents which have similar molecular weights but are different dielectric properties, i.e., ethyl methyl carbonate and propylene carbonate, are compared using MD simulations and the distinctly different dielectric behaviors are observed at short times as well as at long times.

Magnetism, structures and stabilities of cluster assembled TM@Si nanotubes (TM = Cr, Mn and Fe): a density functional study.

PubMed

Dhaka, Kapil; Bandyopadhyay, Debashis

2016-08-02

The present study reports transition metal (TM = Cr, Mn and Fe) doped silicon nanotubes with tunable band structures and magnetic properties by careful selection of cluster assemblies as building blocks using the first-principles density functional theory. We found that the transition metal doping and in addition, the hydrogen termination process can stabilize the pure silicon nanoclusters or cluster assemblies and then it could be extended as magnetic nanotubes with finite magnetic moments. Study of the band structures and density of states (DOS) of different empty and TM doped nanotubes (Type 1 to Type 4) show that these nanotubes are useful as metals, semiconductors, semi-metals and half-metals. These designer magnetic materials could be useful in spintronics and magnetic devices of nanoscale order.

Infrared lessons for ultraviolet gravity: the case of massive gravity and Born-Infeld

NASA Astrophysics Data System (ADS)

Beltrán Jiménez, Jose; Heisenberg, Lavinia; Olmo, Gonzalo J.

2014-11-01

We generalize the ultraviolet sector of gravitation via a Born-Infeld action using lessons from massive gravity. The theory contains all of the elementary symmetric polynomials and is treated in the Palatini formalism. We show how the connection can be solved algebraically to be the Levi-Civita connection of an effective metric. The non-linearity of the algebraic equations yields several branches, one of which always reduces to General Relativity at low curvatures. We explore in detail a minimal version of the theory, for which we study solutions in the presence of a perfect fluid with special attention to the cosmological evolution. In vacuum we recover Ricci-flat solutions, but also an additional physical solution corresponding to an Einstein space. The existence of two physical branches remains for non-vacuum solutions and, in addition, the branch that connects to the Einstein space in vacuum is not very sensitive to the specific value of the energy density. For the branch that connects to the General Relativity limit we generically find three behaviours for the Hubble function depending on the equation of state of the fluid, namely: either there is a maximum value for the energy density that connects continuously with vacuum, or the energy density can be arbitrarily large but the Hubble function saturates and remains constant at high energy densities, or the energy density is unbounded and the Hubble function grows faster than in General Relativity. The second case is particularly interesting because it could offer an interesting inflationary epoch even in the presence of a dust component. Finally, we discuss the possibility of avoiding certain types of singularities within the minimal model.

Performance of exchange-correlation functionals in density functional theory calculations for liquid metal: A benchmark test for sodium.

PubMed

Han, Jeong-Hwan; Oda, Takuji

2018-04-14

The performance of exchange-correlation functionals in density-functional theory (DFT) calculations for liquid metal has not been sufficiently examined. In the present study, benchmark tests of Perdew-Burke-Ernzerhof (PBE), Armiento-Mattsson 2005 (AM05), PBE re-parameterized for solids, and local density approximation (LDA) functionals are conducted for liquid sodium. The pair correlation function, equilibrium atomic volume, bulk modulus, and relative enthalpy are evaluated at 600 K and 1000 K. Compared with the available experimental data, the errors range from -11.2% to 0.0% for the atomic volume, from -5.2% to 22.0% for the bulk modulus, and from -3.5% to 2.5% for the relative enthalpy depending on the DFT functional. The generalized gradient approximation functionals are superior to the LDA functional, and the PBE and AM05 functionals exhibit the best performance. In addition, we assess whether the error tendency in liquid simulations is comparable to that in solid simulations, which would suggest that the atomic volume and relative enthalpy performances are comparable between solid and liquid states but that the bulk modulus performance is not. These benchmark test results indicate that the results of liquid simulations are significantly dependent on the exchange-correlation functional and that the DFT functional performance in solid simulations can be used to roughly estimate the performance in liquid simulations.

Performance of exchange-correlation functionals in density functional theory calculations for liquid metal: A benchmark test for sodium

NASA Astrophysics Data System (ADS)

Han, Jeong-Hwan; Oda, Takuji

2018-04-01

The performance of exchange-correlation functionals in density-functional theory (DFT) calculations for liquid metal has not been sufficiently examined. In the present study, benchmark tests of Perdew-Burke-Ernzerhof (PBE), Armiento-Mattsson 2005 (AM05), PBE re-parameterized for solids, and local density approximation (LDA) functionals are conducted for liquid sodium. The pair correlation function, equilibrium atomic volume, bulk modulus, and relative enthalpy are evaluated at 600 K and 1000 K. Compared with the available experimental data, the errors range from -11.2% to 0.0% for the atomic volume, from -5.2% to 22.0% for the bulk modulus, and from -3.5% to 2.5% for the relative enthalpy depending on the DFT functional. The generalized gradient approximation functionals are superior to the LDA functional, and the PBE and AM05 functionals exhibit the best performance. In addition, we assess whether the error tendency in liquid simulations is comparable to that in solid simulations, which would suggest that the atomic volume and relative enthalpy performances are comparable between solid and liquid states but that the bulk modulus performance is not. These benchmark test results indicate that the results of liquid simulations are significantly dependent on the exchange-correlation functional and that the DFT functional performance in solid simulations can be used to roughly estimate the performance in liquid simulations.

Benchmark study of ionization potentials and electron affinities of armchair single-walled carbon nanotubes using density functional theory

NASA Astrophysics Data System (ADS)

Zhou, Bin; Hu, Zhubin; Jiang, Yanrong; He, Xiao; Sun, Zhenrong; Sun, Haitao

2018-05-01

The intrinsic parameters of carbon nanotubes (CNTs) such as ionization potential (IP) and electron affinity (EA) are closely related to their unique properties and associated applications. In this work, we demonstrated the success of optimal tuning method based on range-separated (RS) density functionals for both accurate and efficient prediction of vertical IPs and electron affinities (EAs) of a series of armchair single-walled carbon nanotubes C20n H20 (n  =  2–6) compared to the high-level IP/EA equation-of-motion coupled-cluster method with single and double substitutions (IP/EA-EOM-CCSD). Notably, the resulting frontier orbital energies (–ε HOMO and –ε LUMO) from the tuning method exhibit an excellent approximation to the corresponding IPs and EAs, that significantly outperform other conventional density functionals. In addition, it is suggested that the RS density functionals that possess both a fixed amount of exact exchange in the short-range and a correct long-range asymptotic behavior are suitable for calculating electronic structures of finite-sized CNTs. Next the performance of density functionals for description of various molecular properties such as chemical potential, hardness and electrophilicity are assessed as a function of tube length. Thanks to the efficiency and accuracy of this tuning method, the related behaviors of much longer armchair single-walled CNTs until C200H20 were studied. Lastly, the present work is proved to provide an efficient theoretical tool for future materials design and reliable characterization of other interesting properties of CNT-based systems.

The Density Functional Theory of Flies: Predicting distributions of interacting active organisms

NASA Astrophysics Data System (ADS)

Kinkhabwala, Yunus; Valderrama, Juan; Cohen, Itai; Arias, Tomas

On October 2nd, 2016, 52 people were crushed in a stampede when a crowd panicked at a religious gathering in Ethiopia. The ability to predict the state of a crowd and whether it is susceptible to such transitions could help prevent such catastrophes. While current techniques such as agent based models can predict transitions in emergent behaviors of crowds, the assumptions used to describe the agents are often ad hoc and the simulations are computationally expensive making their application to real-time crowd prediction challenging. Here, we pursue an orthogonal approach and ask whether a reduced set of variables, such as the local densities, are sufficient to describe the state of a crowd. Inspired by the theoretical framework of Density Functional Theory, we have developed a system that uses only measurements of local densities to extract two independent crowd behavior functions: (1) preferences for locations and (2) interactions between individuals. With these two functions, we have accurately predicted how a model system of walking Drosophila melanogaster distributes itself in an arbitrary 2D environment. In addition, this density-based approach measures properties of the crowd from only observations of the crowd itself without any knowledge of the detailed interactions and thus it can make predictions about the resulting distributions of these flies in arbitrary environments, in real-time. This research was supported in part by ARO W911NF-16-1-0433.

Using Density Functional Theory (DFT) for the Calculation of Atomization Energies

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Partridge, Harry; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

The calculation of atomization energies using density functional theory (DFT), using the B3LYP hybrid functional, is reported. The sensitivity of the atomization energy to basis set is studied and compared with the coupled cluster singles and doubles approach with a perturbational estimate of the triples (CCSD(T)). Merging the B3LYP results with the G2(MP2) approach is also considered. It is found that replacing the geometry optimization and calculation of the zero-point energy by the analogous quantities computed using the B3LYP approach reduces the maximum error in the G2(MP2) approach. In addition to the 55 G2 atomization energies, some results for transition metal containing systems will also be presented.

Statistics of Point Vortex Turbulence in Non-neutral Flows and in Flows with Translational and Rotational Symmetries

NASA Astrophysics Data System (ADS)

Esler, J. G.

2017-12-01

A theory (Esler and Ashbee in J Fluid Mech 779:275-308, 2015) describing the statistics of N freely-evolving point vortices in a bounded two-dimensional domain is extended. First, the case of a non-neutral vortex gas is addressed, and it is shown that the density of states function can be identified with the probability density function of an infinite sum of independent non-central chi-squared random variables, the details of which depend only on the shape of the domain. Equations for the equilibrium energy spectrum and other statistical quantities follow, the validity of which are verified against direct numerical simulations of the equations of motion. Second, domains with additional conserved quantities associated with a symmetry (e.g., circle, periodic channel) are investigated, and it is shown that the treatment of the non-neutral case can be modified to account for the additional constraint.

Hartree-Fock theory of the inhomogeneous electron gas at a jellium metal surface: Rigorous upper bounds to the surface energy and accurate work functions

NASA Astrophysics Data System (ADS)

Sahni, V.; Ma, C. Q.

1980-12-01

The inhomogeneous electron gas at a jellium metal surface is studied in the Hartree-Fock approximation by Kohn-Sham density functional theory. Rigorous upper bounds to the surface energy are derived by application of the Rayleigh-Ritz variational principle for the energy, the surface kinetic, electrostatic, and nonlocal exchange energy functionals being determined exactly for the accurate linear-potential model electronic wave functions. The densities obtained by the energy minimization constraint are then employed to determine work-function results via the variationally accurate "displaced-profile change-in-self-consistent-field" expression. The theoretical basis of this non-self-consistent procedure and its demonstrated accuracy for the fully correlated system (as treated within the local-density approximation for exchange and correlation) leads us to conclude these results for the surface energies and work functions to be essentially exact. Work-function values are also determined by the Koopmans'-theorem expression, both for these densities as well as for those obtained by satisfaction of the constraint set on the electrostatic potential by the Budd-Vannimenus theorem. The use of the Hartree-Fock results in the accurate estimation of correlation-effect contributions to these surface properties of the nonuniform electron gas is also indicated. In addition, the original work and approximations made by Bardeen in this attempt at a solution of the Hartree-Fock problem are briefly reviewed in order to contrast with the present work.

Changes in Structure and Functioning of Protist (Testate Amoebae) Communities Due to Conversion of Lowland Rainforest into Rubber and Oil Palm Plantations

PubMed Central

Krashevska, Valentyna; Klarner, Bernhard; Widyastuti, Rahayu; Maraun, Mark; Scheu, Stefan

2016-01-01

Large areas of tropical rainforest are being converted to agricultural and plantation land uses, but little is known of biodiversity and ecological functioning under these replacement land uses. We investigated the effects of conversion of rainforest into jungle rubber, intensive rubber and oil palm plantations on testate amoebae, diverse and functionally important protists in litter and soil. Living testate amoebae species richness, density and biomass were all lower in replacement land uses than in rainforest, with the impact being more pronounced in litter than in soil. Similar abundances of species of high and low trophic level in rainforest suggest that trophic interactions are more balanced, with a high number of functionally redundant species, than in rubber and oil palm. In contrast, plantations had a low density of high trophic level species indicating losses of functions. This was particularly so in oil palm plantations. In addition, the relative density of species with siliceous shells was >50% lower in the litter layer of oil palm and rubber compared to rainforest and jungle rubber. This difference suggests that rainforest conversion changes biogenic silicon pools and increases silicon losses. Overall, the lower species richness, density and biomass in plantations than in rainforest, and the changes in the functional composition of the testate amoebae community, indicate detrimental effects of rainforest conversion on the structure and functioning of microbial food webs. PMID:27463805

A Keystone Ant Species Provides Robust Biological Control of the Coffee Berry Borer Under Varying Pest Densities.

PubMed

Morris, Jonathan R; Vandermeer, John; Perfecto, Ivette

2015-01-01

Species' functional traits are an important part of the ecological complexity that determines the provisioning of ecosystem services. In biological pest control, predator response to pest density variation is a dynamic trait that impacts the provision of this service in agroecosystems. When pest populations fluctuate, farmers relying on biocontrol services need to know how natural enemies respond to these changes. Here we test the effect of variation in coffee berry borer (CBB) density on the biocontrol efficiency of a keystone ant species (Azteca sericeasur) in a coffee agroecosystem. We performed exclosure experiments to measure the infestation rate of CBB released on coffee branches in the presence and absence of ants at four different CBB density levels. We measured infestation rate as the number of CBB bored into fruits after 24 hours, quantified biocontrol efficiency (BCE) as the proportion of infesting CBB removed by ants, and estimated functional response from ant attack rates, measured as the difference in CBB infestation between branches. Infestation rates of CBB on branches with ants were significantly lower (71%-82%) than on those without ants across all density levels. Additionally, biocontrol efficiency was generally high and did not significantly vary across pest density treatments. Furthermore, ant attack rates increased linearly with increasing CBB density, suggesting a Type I functional response. These results demonstrate that ants can provide robust biological control of CBB, despite variation in pest density, and that the response of predators to pest density variation is an important factor in the provision of biocontrol services. Considering how natural enemies respond to changes in pest densities will allow for more accurate biocontrol predictions and better-informed management of this ecosystem service in agroecosystems.

A Keystone Ant Species Provides Robust Biological Control of the Coffee Berry Borer Under Varying Pest Densities

PubMed Central

Morris, Jonathan R.; Vandermeer, John; Perfecto, Ivette

2015-01-01

Species’ functional traits are an important part of the ecological complexity that determines the provisioning of ecosystem services. In biological pest control, predator response to pest density variation is a dynamic trait that impacts the provision of this service in agroecosystems. When pest populations fluctuate, farmers relying on biocontrol services need to know how natural enemies respond to these changes. Here we test the effect of variation in coffee berry borer (CBB) density on the biocontrol efficiency of a keystone ant species (Azteca sericeasur) in a coffee agroecosystem. We performed exclosure experiments to measure the infestation rate of CBB released on coffee branches in the presence and absence of ants at four different CBB density levels. We measured infestation rate as the number of CBB bored into fruits after 24 hours, quantified biocontrol efficiency (BCE) as the proportion of infesting CBB removed by ants, and estimated functional response from ant attack rates, measured as the difference in CBB infestation between branches. Infestation rates of CBB on branches with ants were significantly lower (71%-82%) than on those without ants across all density levels. Additionally, biocontrol efficiency was generally high and did not significantly vary across pest density treatments. Furthermore, ant attack rates increased linearly with increasing CBB density, suggesting a Type I functional response. These results demonstrate that ants can provide robust biological control of CBB, despite variation in pest density, and that the response of predators to pest density variation is an important factor in the provision of biocontrol services. Considering how natural enemies respond to changes in pest densities will allow for more accurate biocontrol predictions and better-informed management of this ecosystem service in agroecosystems. PMID:26562676

Chemical insight from density functional modeling of molecular adsorption: Tracking the bonding and diffusion of anthracene derivatives on Cu(111) with molecular orbitals

NASA Astrophysics Data System (ADS)

Wyrick, Jonathan; Einstein, T. L.; Bartels, Ludwig

2015-03-01

We present a method of analyzing the results of density functional modeling of molecular adsorption in terms of an analogue of molecular orbitals. This approach permits intuitive chemical insight into the adsorption process. Applied to a set of anthracene derivates (anthracene, 9,10-anthraquinone, 9,10-dithioanthracene, and 9,10-diselenonanthracene), we follow the electronic states of the molecules that are involved in the bonding process and correlate them to both the molecular adsorption geometry and the species' diffusive behavior. We additionally provide computational code to easily repeat this analysis on any system.

Fullerene Cyanation Does Not Always Increase Electron Affinity: Experimental and Theoretical Study

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

Clikeman, Tyler T.; Deng, Shihu; Popov, Alexey A.

2015-01-01

The electron affinities of C70 derivatives with trifluoromethyl, methyl and cyano groups were studied experimentally and theoretically using low-temperature photoelectron spectroscopy (LT PES) and density functional theory (DFT). The electronic effects of these functional groups were determined and found to be highly dependent on the addition patterns. Substitution of CF3 for CN for the same addition pattern increases the experimental electron affinity by 70 meV per substitution. The synthesis of a new fullerene derivative, C70(CF3)10(CN)2, is reported for the first time

Human islet viability and function is maintained during high density shipment in silicone rubber membrane vessels

PubMed Central

Kitzmann, Jennifer P; Pepper, Andrew R; Lopez, Boris G; Pawlick, Rena; Kin, Tatsuya; O’Gorman, Doug; Mueller, Kathryn R; Gruessner, Angelika C; Avgoustiniatos, Efstathios S; Karatzas, Theodore; Szot, Greg L; Posselt, Andrew M; Stock, Peter G; Wilson, John R; Shapiro, AM; Papas, Klearchos K

2014-01-01

The shipment of human islets from processing centers to distant laboratories is beneficial for both research and clinical applications. The maintenance of islet viability and function in transit is critically important. Gas-permeable silicone rubber membrane (SRM) vessels reduce the risk of hypoxia-induced death or dysfunction during high-density islet culture or shipment. SRM vessels may offer additional advantages: they are cost-effective (fewer flasks, less labor needed), safer (lower contamination risk), and simpler (culture vessel can also be used for shipment). Human islets(IE) were isolated from two manufacturing centers and shipped in 10cm2 surface area SRM vessels in temperature and pressure controlled containers to a distant center following at least two days of culture (n = 6). Three conditions were examined: low density (LD), high density (HD), and a micro centrifuge tube negative control (NC). LD was designed to mimic the standard culture density for human islet preparations (200 IE/cm2), while HD was designed to have a 20-fold higher tissue density, which would enable the culture of an entire human isolation in 1–3 vessels. Upon receipt, islets were assessed for viability, measured by oxygen consumption rate normalized to DNA content (OCR/DNA), and quantity, measured by DNA, and, when possible, potency and function with dynamic glucose-stimulated insulin secretion (GSIS) measurements and transplants in immunodeficient B6 rag mice. Post-shipment OCR/DNA was not reduced in HD versus LD, and was substantially reduced in the NC condition. HD islets exhibited normal function post-shipment. Based on the data we conclude that entire islet isolations (up to 400,000 IE) may be shipped using a single, larger SRM vessel with no negative effect on viability and ex vivo and in vivo function. PMID:25131090

Human islet viability and function is maintained during high-density shipment in silicone rubber membrane vessels.

PubMed

Kitzmann, J P; Pepper, A R; Gala-Lopez, B; Pawlick, R; Kin, T; O'Gorman, D; Mueller, K R; Gruessner, A C; Avgoustiniatos, E S; Karatzas, T; Szot, G L; Posselt, A M; Stock, P G; Wilson, J R; Shapiro, A M; Papas, K K

2014-01-01

The shipment of human islets (IE) from processing centers to distant laboratories is beneficial for both research and clinical applications. The maintenance of islet viability and function in transit is critically important. Gas-permeable silicone rubber membrane (SRM) vessels reduce the risk of hypoxia-induced death or dysfunction during high-density islet culture or shipment. SRM vessels may offer additional advantages: they are cost-effective (fewer flasks, less labor needed), safer (lower contamination risk), and simpler (culture vessel can also be used for shipment). IE were isolated from two manufacturing centers and shipped in 10-cm(2) surface area SRM vessels in temperature- and pressure-controlled containers to a distant center after at least 2 days of culture (n = 6). Three conditions were examined: low density (LD), high density (HD), and a microcentrifuge tube negative control (NC). LD was designed to mimic the standard culture density for IE preparations (200 IE/cm(2)), while HD was designed to have a 20-fold higher tissue density, which would enable the culture of an entire human isolation in 1-3 vessels. Upon receipt, islets were assessed for viability (measured by oxygen consumption rate normalized to DNA content [OCR/DNA)]), quantity (measured by DNA), and, when possible, potency and function (measured by dynamic glucose-stimulated insulin secretion measurements and transplants in immunodeficient B6 Rag(+/-) mice). Postshipment OCR/DNA was not reduced in HD vs LD and was substantially reduced in the NC condition. HD islets exhibited normal function postshipment. Based on the data, we conclude that entire islet isolations (up to 400,000 IE) may be shipped using a single, larger SRM vessel with no negative effect on viability and ex vivo and in vivo function. Copyright © 2014 Elsevier Inc. All rights reserved.

Global hybrids from the semiclassical atom theory satisfying the local density linear response.

PubMed

Fabiano, Eduardo; Constantin, Lucian A; Cortona, Pietro; Della Sala, Fabio

2015-01-13

We propose global hybrid approximations of the exchange-correlation (XC) energy functional which reproduce well the modified fourth-order gradient expansion of the exchange energy in the semiclassical limit of many-electron neutral atoms and recover the full local density approximation (LDA) linear response. These XC functionals represent the hybrid versions of the APBE functional [Phys. Rev. Lett. 2011, 106, 186406] yet employing an additional correlation functional which uses the localization concept of the correlation energy density to improve the compatibility with the Hartree-Fock exchange as well as the coupling-constant-resolved XC potential energy. Broad energetic and structural testing, including thermochemistry and geometry, transition metal complexes, noncovalent interactions, gold clusters and small gold-molecule interfaces, as well as an analysis of the hybrid parameters, show that our construction is quite robust. In particular, our testing shows that the resulting hybrid, including 20% of Hartree-Fock exchange and named hAPBE, performs remarkably well for a broad palette of systems and properties, being generally better than popular hybrids (PBE0 and B3LYP). Semiempirical dispersion corrections are also provided.

Evolution of the orbitals Dy-4f in the DyB2 compound using the LDA, PBE approximations, and the PBE0 hybrid functional

NASA Astrophysics Data System (ADS)

Rasero Causil, Diego; Ortega López, César; Espitia Rico, Miguel

2018-04-01

Computational calculations of total energy based on density functional theory were used to investigate the structural, electronic, and magnetic properties of the DyB2 compounds in the hexagonal structure. The calculations were carried out by means of the full-potential linearized augmented plane wave (FP-LAPW) method, employing the computational Wien2k package. The local density approximation (LDA) and the generalized gradient approximation (GGA) were used for the electron-electron interactions. Additionally, we used the functional hybrid PBE0 for a better description the electronic and magnetic properties, because the DyB2 compound is a strongly-correlated system. We found that the calculated lattice constant agrees well with the values reported theoretically and experimentally. The density of states (DOS) calculation shows that the compound exhibits a metallic behavior and has magnetic properties, with a total magnetic moment of 5.47 μ0/cell determined mainly by the 4f states of the rare earth elements. The functional PBE0 shows a strong localization of the Dy-4f orbitals.

Influence of additive laser manufacturing parameters on surface using density of partially melted particles

NASA Astrophysics Data System (ADS)

Rosa, Benoit; Brient, Antoine; Samper, Serge; Hascoët, Jean-Yves

2016-12-01

Mastering the additive laser manufacturing surface is a real challenge and would allow functional surfaces to be obtained without finishing. Direct Metal Deposition (DMD) surfaces are composed by directional and chaotic textures that are directly linked to the process principles. The aim of this work is to obtain surface topographies by mastering the operating process parameters. Based on experimental investigation, the influence of operating parameters on the surface finish has been modeled. Topography parameters and multi-scale analysis have been used in order to characterize the DMD obtained surfaces. This study also proposes a methodology to characterize DMD chaotic texture through topography filtering and 3D image treatment. In parallel, a new parameter is proposed: density of particles (D p). Finally, this study proposes a regression modeling between process parameters and density of particles parameter.

Spectroscopic imaging of metal halide high-intensity discharge lamps

NASA Astrophysics Data System (ADS)

Bonvallet, Geoffrey A.

The body of this work consists of three main research projects. An optical- and near-ultraviolet-wavelength absorption study sought to determine absolute densities of ground and excited level Sc atoms, ground level Sc + ions, and ground level Na atoms in a commercial 250 W metal halide high intensity discharge lamp during operation. These measurements also allowed the determination of the arc temperature and absolute electron density as functions of radius. Through infrared emission spectroscopy, relative densities of sodium and scandium were determined as functions of radius. Using the absolute densities gained from the optical experiment, these relative densities were calibrated. In addition, direct observation of the infrared emission allowed us to characterize the infrared power losses of the lamp. When considered as a fraction of the overall power consumption, the near-infrared spectral power losses were not substantial enough to warrant thorough investigation of their reduction in these lamps. The third project was an attempt to develop a portable x-ray diagnostic experiment. Two-dimensional spatial maps of the lamps were analyzed to determine absolute elemental mercury densities and the arc temperature as a function of radius. Two methods were used to improve the calibration of the density measurements and to correct for the spread in x-ray energy: known solutions of mercury in nitric acid, and an arc lamp which was uniformly heated to evaporate the mercury content. Although many complexities arose in this experiment, its goal was successfully completed.

ωB97X-V: A 10-parameter, range-separated hybrid, generalized gradient approximation density functional with nonlocal correlation, designed by a survival-of-the-fittest strategy

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

Mardirossian, Narbe; Head-Gordon, Martin

2013-12-18

A 10-parameter, range-separated hybrid (RSH), generalized gradient approximation (GGA) density functional with nonlocal correlation (VV10) is presented in this paper. Instead of truncating the B97-type power series inhomogeneity correction factors (ICF) for the exchange, same-spin correlation, and opposite-spin correlation functionals uniformly, all 16 383 combinations of the linear parameters up to fourth order (m = 4) are considered. These functionals are individually fit to a training set and the resulting parameters are validated on a primary test set in order to identify the 3 optimal ICF expansions. Through this procedure, it is discovered that the functional that performs best onmore » the training and primary test sets has 7 linear parameters, with 3 additional nonlinear parameters from range-separation and nonlocal correlation. The resulting density functional, ωB97X-V, is further assessed on a secondary test set, the parallel-displaced coronene dimer, as well as several geometry datasets. Finally and furthermore, the basis set dependence and integration grid sensitivity of ωB97X-V are analyzed and documented in order to facilitate the use of the functional.« less

On-line prognosis of fatigue crack propagation based on Gaussian weight-mixture proposal particle filter.

PubMed

Chen, Jian; Yuan, Shenfang; Qiu, Lei; Wang, Hui; Yang, Weibo

2018-01-01

Accurate on-line prognosis of fatigue crack propagation is of great meaning for prognostics and health management (PHM) technologies to ensure structural integrity, which is a challenging task because of uncertainties which arise from sources such as intrinsic material properties, loading, and environmental factors. The particle filter algorithm has been proved to be a powerful tool to deal with prognostic problems those are affected by uncertainties. However, most studies adopted the basic particle filter algorithm, which uses the transition probability density function as the importance density and may suffer from serious particle degeneracy problem. This paper proposes an on-line fatigue crack propagation prognosis method based on a novel Gaussian weight-mixture proposal particle filter and the active guided wave based on-line crack monitoring. Based on the on-line crack measurement, the mixture of the measurement probability density function and the transition probability density function is proposed to be the importance density. In addition, an on-line dynamic update procedure is proposed to adjust the parameter of the state equation. The proposed method is verified on the fatigue test of attachment lugs which are a kind of important joint components in aircraft structures. Copyright © 2017 Elsevier B.V. All rights reserved.

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.

The effects of the one-step replica symmetry breaking on the Sherrington-Kirkpatrick spin glass model in the presence of random field with a joint Gaussian probability density function for the exchange interactions and random fields

NASA Astrophysics Data System (ADS)

Hadjiagapiou, Ioannis A.; Velonakis, Ioannis N.

2018-07-01

The Sherrington-Kirkpatrick Ising spin glass model, in the presence of a random magnetic field, is investigated within the framework of the one-step replica symmetry breaking. The two random variables (exchange integral interaction Jij and random magnetic field hi) are drawn from a joint Gaussian probability density function characterized by a correlation coefficient ρ, assuming positive and negative values. The thermodynamic properties, the three different phase diagrams and system's parameters are computed with respect to the natural parameters of the joint Gaussian probability density function at non-zero and zero temperatures. The low temperature negative entropy controversy, a result of the replica symmetry approach, has been partly remedied in the current study, leading to a less negative result. In addition, the present system possesses two successive spin glass phase transitions with characteristic temperatures.

JDFTx: Software for joint density-functional theory

DOE PAGES

Sundararaman, Ravishankar; Letchworth-Weaver, Kendra; Schwarz, Kathleen A.; ...

2017-11-14

Density-functional theory (DFT) has revolutionized computational prediction of atomic-scale properties from first principles in physics, chemistry and materials science. Continuing development of new methods is necessary for accurate predictions of new classes of materials and properties, and for connecting to nano- and mesoscale properties using coarse-grained theories. JDFTx is a fully-featured open-source electronic DFT software designed specifically to facilitate rapid development of new theories, models and algorithms. Using an algebraic formulation as an abstraction layer, compact C++11 code automatically performs well on diverse hardware including GPUs (Graphics Processing Units). This code hosts the development of joint density-functional theory (JDFT) thatmore » combines electronic DFT with classical DFT and continuum models of liquids for first-principles calculations of solvated and electrochemical systems. In addition, the modular nature of the code makes it easy to extend and interface with, facilitating the development of multi-scale toolkits that connect to ab initio calculations, e.g. photo-excited carrier dynamics combining electron and phonon calculations with electromagnetic simulations.« less

JDFTx: Software for joint density-functional theory

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

Sundararaman, Ravishankar; Letchworth-Weaver, Kendra; Schwarz, Kathleen A.

Density-functional theory (DFT) has revolutionized computational prediction of atomic-scale properties from first principles in physics, chemistry and materials science. Continuing development of new methods is necessary for accurate predictions of new classes of materials and properties, and for connecting to nano- and mesoscale properties using coarse-grained theories. JDFTx is a fully-featured open-source electronic DFT software designed specifically to facilitate rapid development of new theories, models and algorithms. Using an algebraic formulation as an abstraction layer, compact C++11 code automatically performs well on diverse hardware including GPUs (Graphics Processing Units). This code hosts the development of joint density-functional theory (JDFT) thatmore » combines electronic DFT with classical DFT and continuum models of liquids for first-principles calculations of solvated and electrochemical systems. In addition, the modular nature of the code makes it easy to extend and interface with, facilitating the development of multi-scale toolkits that connect to ab initio calculations, e.g. photo-excited carrier dynamics combining electron and phonon calculations with electromagnetic simulations.« less

Single- and multiple-pulse noncoherent detection statistics associated with partially developed speckle.

PubMed

Osche, G R

2000-08-20

Single- and multiple-pulse detection statistics are presented for aperture-averaged direct detection optical receivers operating against partially developed speckle fields. A partially developed speckle field arises when the probability density function of the received intensity does not follow negative exponential statistics. The case of interest here is the target surface that exhibits diffuse as well as specular components in the scattered radiation. An approximate expression is derived for the integrated intensity at the aperture, which leads to single- and multiple-pulse discrete probability density functions for the case of a Poisson signal in Poisson noise with an additive coherent component. In the absence of noise, the single-pulse discrete density function is shown to reduce to a generalized negative binomial distribution. The radar concept of integration loss is discussed in the context of direct detection optical systems where it is shown that, given an appropriate set of system parameters, multiple-pulse processing can be more efficient than single-pulse processing over a finite range of the integration parameter n.

The nature of three-body interactions in DFT: Exchange and polarization effects

NASA Astrophysics Data System (ADS)

Hapka, Michał; Rajchel, Łukasz; Modrzejewski, Marcin; Schäffer, Rainer; Chałasiński, Grzegorz; Szcześniak, Małgorzata M.

2017-08-01

We propose a physically motivated decomposition of density functional theory (DFT) 3-body nonadditive interaction energies into the exchange and density-deformation (polarization) components. The exchange component represents the effect of the Pauli exclusion in the wave function of the trimer and is found to be challenging for density functional approximations (DFAs). The remaining density-deformation nonadditivity is less dependent upon the DFAs. Numerical demonstration is carried out for rare gas atom trimers, Ar2-HX (X = F, Cl) complexes, and small hydrogen-bonded and van der Waals molecular systems. None of the tested semilocal, hybrid, and range-separated DFAs properly accounts for the nonadditive exchange in dispersion-bonded trimers. By contrast, for hydrogen-bonded systems, range-separated DFAs achieve a qualitative agreement to within 20% of the reference exchange energy. A reliable performance for all systems is obtained only when the monomers interact through the Hartree-Fock potential in the dispersion-free Pauli blockade scheme. Additionally, we identify the nonadditive second-order exchange-dispersion energy as an important but overlooked contribution in force-field-like dispersion corrections. Our results suggest that range-separated functionals do not include this component, although semilocal and global hybrid DFAs appear to imitate it in the short range.

First TILLING Platform in Cucurbita pepo: A New Mutant Resource for Gene Function and Crop Improvement

PubMed Central

Vicente-Dólera, Nelly; Troadec, Christelle; Moya, Manuel; del Río-Celestino, Mercedes; Pomares-Viciana, Teresa; Bendahmane, Abdelhafid; Picó, Belén; Román, Belén; Gómez, Pedro

2014-01-01

Although the availability of genetic and genomic resources for Cucurbita pepo has increased significantly, functional genomic resources are still limited for this crop. In this direction, we have developed a high throughput reverse genetic tool: the first TILLING (Targeting Induced Local Lesions IN Genomes) resource for this species. Additionally, we have used this resource to demonstrate that the previous EMS mutant population we developed has the highest mutation density compared with other cucurbits mutant populations. The overall mutation density in this first C. pepo TILLING platform was estimated to be 1/133 Kb by screening five additional genes. In total, 58 mutations confirmed by sequencing were identified in the five targeted genes, thirteen of which were predicted to have an impact on the function of the protein. The genotype/phenotype correlation was studied in a peroxidase gene, revealing that the phenotype of seedling homozygous for one of the isolated mutant alleles was albino. These results indicate that the TILLING approach in this species was successful at providing new mutations and can address the major challenge of linking sequence information to biological function and also the identification of novel variation for crop breeding. PMID:25386735

Optical properties of an indium doped CdSe nanocrystal: A density functional approach

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

Salini, K.; Mathew, Vincent, E-mail: vincent@cukerala.ac.in; Mathew, Thomas

2016-05-06

We have studied the electronic and optical properties of a CdSe nanocrystal doped with n-type impurity atom. First principle calculations of the CdSe nanocrystal based on the density functional theory (DFT), as implemented in the Vienna Ab Initio Simulation Package (VASP) was used in the calculations. We have introduced a single Indium impurity atom into CdSe nanocrystal with 1.3 nm diameter. Nanocrystal surface dangling bonds are passivated with hydrogen atom. The band-structure, density of states and absorption spectra of the doped and undopted nanocrystals were discussed. Inclusion of the n-type impurity atom introduces an additional electron in conduction band, and significantlymore » alters the electronic and optical properties of undoped CdSe nanocrystal. Indium doped CdSe nannocrystal have potential applications in optoelectronic devices.« less

Laser collisional induced fluorescence electron density measurements as a function of ring bias and the onset of anode spot formation in a ring cusp magnetic field

NASA Astrophysics Data System (ADS)

Arthur, N. A.; Foster, J. E.; Barnat, E. V.

2018-05-01

Two-dimensional electron density measurements are made in a magnetic ring cusp discharge using laser collisional induced fluorescence. The magnet rings are isolated from the anode structure such that they can be biased independently in order to modulate electron flows through the magnetic cusps. Electron density images are captured as a function of bias voltage in order to assess the effects of current flow through the cusp on the spatial extent of the cusp. We anticipated that for a fixed current density being funneled through the magnetic cusp, the leak width would necessarily increase. Unexpectedly, the leak width, as measured by LCIF images, does not increase. This suggests that the current density is not constant, and that possibly either electrons are being heated or additional ionization events are occurring within the cusp. Spatially resolving electron temperature would be needed to determine if electrons are being heated within the cusp. We also observe breakdown of the anode magnetosheath and formation of anode spots at high bias voltage.

Calculation of nuclear spin-spin coupling constants using frozen density embedding

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

Götz, Andreas W., E-mail: agoetz@sdsc.edu; Autschbach, Jochen; Visscher, Lucas, E-mail: visscher@chem.vu.nl

2014-03-14

We present a method for a subsystem-based calculation of indirect nuclear spin-spin coupling tensors within the framework of current-spin-density-functional theory. Our approach is based on the frozen-density embedding scheme within density-functional theory and extends a previously reported subsystem-based approach for the calculation of nuclear magnetic resonance shielding tensors to magnetic fields which couple not only to orbital but also spin degrees of freedom. This leads to a formulation in which the electron density, the induced paramagnetic current, and the induced spin-magnetization density are calculated separately for the individual subsystems. This is particularly useful for the inclusion of environmental effects inmore » the calculation of nuclear spin-spin coupling constants. Neglecting the induced paramagnetic current and spin-magnetization density in the environment due to the magnetic moments of the coupled nuclei leads to a very efficient method in which the computationally expensive response calculation has to be performed only for the subsystem of interest. We show that this approach leads to very good results for the calculation of solvent-induced shifts of nuclear spin-spin coupling constants in hydrogen-bonded systems. Also for systems with stronger interactions, frozen-density embedding performs remarkably well, given the approximate nature of currently available functionals for the non-additive kinetic energy. As an example we show results for methylmercury halides which exhibit an exceptionally large shift of the one-bond coupling constants between {sup 199}Hg and {sup 13}C upon coordination of dimethylsulfoxide solvent molecules.« less

Residual Defect Density in Random Disks Deposits.

PubMed

Topic, Nikola; Pöschel, Thorsten; Gallas, Jason A C

2015-08-03

We investigate the residual distribution of structural defects in very tall packings of disks deposited randomly in large channels. By performing simulations involving the sedimentation of up to 50 × 10(9) particles we find all deposits to consistently show a non-zero residual density of defects obeying a characteristic power-law as a function of the channel width. This remarkable finding corrects the widespread belief that the density of defects should vanish algebraically with growing height. A non-zero residual density of defects implies a type of long-range spatial order in the packing, as opposed to only local ordering. In addition, we find deposits of particles to involve considerably less randomness than generally presumed.

Theoretical analysis of the electronic properties of the sex pheromone and its analogue derivatives in the female processionary moth Thaumetopoea pytiocampa.

PubMed

Chamorro, Ester R; Sequeira, Alfredo F; Zalazar, M Fernanda; Peruchena, Nélida M

2008-09-15

In the present work, the distribution of the electronic charge density of the natural sex pheromone, the (Z)-13-hexadecen-11-ynyl acetate, in the female processionary moth, Thaumetopoea pytiocampa, and its nine analogue derivatives was studied within the framework of the Density Functional Theory and the Atoms in Molecules (AIM) Theory at B3LYP/6-31G *//B3LYP/6-31++G * * level. Additionally, molecular electrostatic potential (MEP) maps of the previously mentioned compounds were computed and compared. Furthermore, the substitution of hydrogen atoms from the methyl group in the acetate group by electron withdrawing substituents (i.e., halogen atoms) as well as the replacement effect of hydrogen by electron donor substituents (+I effect) as methyl group, were explored. The key feature of the topological distribution of the charge density in analogue compounds, such as the variations of the topological properties encountered in the region formed by neighbouring atoms from the substitution site were presented and discussed. Using topological parameters, such as electronic charge density, Laplacian, kinetic energy density, and potential energy density evaluated at bond critical points (BCP), we provide here a detailed analysis of the nature of the chemical bonding of these molecules. In addition, the atomic properties (population, charge, energy, volume, and dipole moment) were determined on selected atoms. These properties were analyzed at the substitution site (with respect to the natural sex pheromone) and related to the biological activity and to the possible binding site with the pheromone binding protein, (PBP). Moreover, the Laplacian function of the electronic density was used to locate electrophilic regions susceptible to be attacked (by deficient electron atoms or donor hydrogen). Our results indicate that the change in the atomic properties, such as electronic population and atomic volume, are sensitive indicators of the loss of the biological activity in the analogues studied here. The crucial interaction between the acetate group of the natural sex pheromone and the PBP is most likely to be a hydrogen bonding and the substitution of hydrogen atoms by electronegative atoms in the pheromone molecule reduces the hydrogen acceptor capacity. This situation is mirrored by the diminish of the electronic population on carbon and oxygen atoms at the carbonylic group in the halo-acetate group. Additionally, the modified acetate group (with electronegative atoms) shows new charge concentration critical points or regions of concentration of charge density in which an electrophilic attack can also occur. Finally, the use of the topological analysis based in the charge density distribution and its Laplacian function, in conjunction with MEP maps provides valuable information about the steric volume and electronic requirement of the sex pheromone for binding to the PBP.

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

Seljak, Uroš; McDonald, Patrick, E-mail: useljak@berkeley.edu, E-mail: pvmcdonald@lbl.gov

We develop a phase space distribution function approach to redshift space distortions (RSD), in which the redshift space density can be written as a sum over velocity moments of the distribution function. These moments are density weighted and have well defined physical interpretation: their lowest orders are density, momentum density, and stress energy density. The series expansion is convergent if kμu/aH < 1, where k is the wavevector, H the Hubble parameter, u the typical gravitational velocity and μ = cos θ, with θ being the angle between the Fourier mode and the line of sight. We perform an expansionmore » of these velocity moments into helicity modes, which are eigenmodes under rotation around the axis of Fourier mode direction, generalizing the scalar, vector, tensor decomposition of perturbations to an arbitrary order. We show that only equal helicity moments correlate and derive the angular dependence of the individual contributions to the redshift space power spectrum. We show that the dominant term of μ{sup 2} dependence on large scales is the cross-correlation between the density and scalar part of momentum density, which can be related to the time derivative of the matter power spectrum. Additional terms contributing to μ{sup 2} and dominating on small scales are the vector part of momentum density-momentum density correlations, the energy density-density correlations, and the scalar part of anisotropic stress density-density correlations. The second term is what is usually associated with the small scale Fingers-of-God damping and always suppresses power, but the first term comes with the opposite sign and always adds power. Similarly, we identify 7 terms contributing to μ{sup 4} dependence. Some of the advantages of the distribution function approach are that the series expansion converges on large scales and remains valid in multi-stream situations. We finish with a brief discussion of implications for RSD in galaxies relative to dark matter, highlighting the issue of scale dependent bias of velocity moments correlators.« less

Co-altered functional networks and brain structure in unmedicated patients with bipolar and major depressive disorders.

PubMed

He, Hao; Sui, Jing; Du, Yuhui; Yu, Qingbao; Lin, Dongdong; Drevets, Wayne C; Savitz, Jonathan B; Yang, Jian; Victor, Teresa A; Calhoun, Vince D

2017-12-01

Bipolar disorder (BD) and major depressive disorder (MDD) share similar clinical characteristics that often obscure the diagnostic distinctions between their depressive conditions. Both functional and structural brain abnormalities have been reported in these two disorders. However, the direct link between altered functioning and structure in these two diseases is unknown. To elucidate this relationship, we conducted a multimodal fusion analysis on the functional network connectivity (FNC) and gray matter density from MRI data from 13 BD, 40 MDD, and 33 matched healthy controls (HC). A data-driven fusion method called mCCA+jICA was used to identify the co-altered FNC and gray matter components. Comparing to HC, BD exhibited reduced gray matter density in the parietal and occipital cortices, which correlated with attenuated functional connectivity within sensory and motor networks, as well as hyper-connectivity in regions that are putatively engaged in cognitive control. In addition, lower gray matter density was found in MDD in the amygdala and cerebellum. High accuracy in discriminating across groups was also achieved by trained classification models, implying that features extracted from the fusion analysis hold the potential to ultimately serve as diagnostic biomarkers for mood disorders.

Dual descriptors within the framework of spin-polarized density functional theory.

PubMed

Chamorro, E; Pérez, P; Duque, M; De Proft, F; Geerlings, P

2008-08-14

Spin-polarized density functional theory (SP-DFT) allows both the analysis of charge-transfer (e.g., electrophilic and nucleophilic reactivity) and of spin-polarization processes (e.g., photophysical changes arising from electron transitions). In analogy with the dual descriptor introduced by Morell et al. [J. Phys. Chem. A 109, 205 (2005)], we introduce new dual descriptors intended to simultaneously give information of the molecular regions where the spin-polarization process linking states of different multiplicity will drive electron density and spin density changes. The electronic charge and spin rearrangement in the spin forbidden radiative transitions S(0)-->T(n,pi(*)) and S(0)-->T(pi,pi(*)) in formaldehyde and ethylene, respectively, have been used as benchmark examples illustrating the usefulness of the new spin-polarization dual descriptors. These quantities indicate those regions where spin-orbit coupling effects are at work in such processes. Additionally, the qualitative relationship between the topology of the spin-polarization dual descriptors and the vertical singlet triplet energy gap in simple substituted carbene series has been also discussed. It is shown that the electron density and spin density rearrangements arise in agreement with spectroscopic experimental evidence and other theoretical results on the selected target systems.

Fluids density functional theory and initializing molecular dynamics simulations of block copolymers

NASA Astrophysics Data System (ADS)

Brown, Jonathan R.; Seo, Youngmi; Maula, Tiara Ann D.; Hall, Lisa M.

2016-03-01

Classical, fluids density functional theory (fDFT), which can predict the equilibrium density profiles of polymeric systems, and coarse-grained molecular dynamics (MD) simulations, which are often used to show both structure and dynamics of soft materials, can be implemented using very similar bead-based polymer models. We aim to use fDFT and MD in tandem to examine the same system from these two points of view and take advantage of the different features of each methodology. Additionally, the density profiles resulting from fDFT calculations can be used to initialize the MD simulations in a close to equilibrated structure, speeding up the simulations. Here, we show how this method can be applied to study microphase separated states of both typical diblock and tapered diblock copolymers in which there is a region with a gradient in composition placed between the pure blocks. Both methods, applied at constant pressure, predict a decrease in total density as segregation strength or the length of the tapered region is increased. The predictions for the density profiles from fDFT and MD are similar across materials with a wide range of interfacial widths.

On the v-representability of ensemble densities of electron systems

NASA Astrophysics Data System (ADS)

Gonis, A.; Däne, M.

2018-05-01

Analogously to the case at zero temperature, where the density of the ground state of an interacting many-particle system determines uniquely (within an arbitrary additive constant) the external potential acting on the system, the thermal average of the density over an ensemble defined by the Boltzmann distribution at the minimum of the thermodynamic potential, or the free energy, determines the external potential uniquely (and not just modulo a constant) acting on a system described by this thermodynamic potential or free energy. The paper describes a formal procedure that generates the domain of a constrained search over general ensembles (at zero or elevated temperatures) that lead to a given density, including as a special case a density thermally averaged at a given temperature, and in the case of a v-representable density determines the external potential leading to the ensemble density. As an immediate consequence of the general formalism, the concept of v-representability is extended beyond the hitherto discussed case of ground state densities to encompass excited states as well. Specific application to thermally averaged densities solves the v-representability problem in connection with the Mermin functional in a manner analogous to that in which this problem was recently settled with respect to the Hohenberg and Kohn functional. The main formalism is illustrated with numerical results for ensembles of one-dimensional, non-interacting systems of particles under a harmonic potential.

On the v-representability of ensemble densities of electron systems

DOE PAGES

Gonis, A.; Dane, M.

2017-12-30

Analogously to the case at zero temperature, where the density of the ground state of an interacting many-particle system determines uniquely (within an arbitrary additive constant) the external potential acting on the system, the thermal average of the density over an ensemble defined by the Boltzmann distribution at the minimum of the thermodynamic potential, or the free energy, determines the external potential uniquely (and not just modulo a constant) acting on a system described by this thermodynamic potential or free energy. The study describes a formal procedure that generates the domain of a constrained search over general ensembles (at zeromore » or elevated temperatures) that lead to a given density, including as a special case a density thermally averaged at a given temperature, and in the case of a v-representable density determines the external potential leading to the ensemble density. As an immediate consequence of the general formalism, the concept of v-representability is extended beyond the hitherto discussed case of ground state densities to encompass excited states as well. Specific application to thermally averaged densities solves the v-representability problem in connection with the Mermin functional in a manner analogous to that in which this problem was recently settled with respect to the Hohenberg and Kohn functional. Finally, the main formalism is illustrated with numerical results for ensembles of one-dimensional, non-interacting systems of particles under a harmonic potential.« less

Parametric dependence of ion temperature and relative density in the NASA Lewis SUMMA facility. [superconducting magnetic mirror

NASA Technical Reports Server (NTRS)

Snyder, A.; Lauver, M. R.; Patch, R. W.

1976-01-01

Further hot-ion plasma experiments were conducted in the SUMMA superconducting magnetic mirror facility. A steady-state ExB plasma was formed by applying a strong radially inward dc electric field between cylindrical anodes and hollow cathodes located near the magnetic mirror maxima. Extending the use of water cooling to the hollow cathodes, in addition to the anodes, resulted in higher maximum power input to the plasma. Steady-state hydrogen plasmas with ion kinetic temperatures as high as 830 eV were produced. Functional relations were obtained empirically among the plasma current, voltage, magnetic flux density, ion temperature, and relative ion density. The functional relations were deduced by use of a multiple correlation analysis. Data were obtained for midplane magnetic fields from 0.5 to 3.37 tesla and input power up to 45 kW. Also, initial absolute electron density measurements are reported from a 90 deg Thomson scattering laser system.

A marked correlation function for constraining modified gravity models

NASA Astrophysics Data System (ADS)

White, Martin

2016-11-01

Future large scale structure surveys will provide increasingly tight constraints on our cosmological model. These surveys will report results on the distance scale and growth rate of perturbations through measurements of Baryon Acoustic Oscillations and Redshift-Space Distortions. It is interesting to ask: what further analyses should become routine, so as to test as-yet-unknown models of cosmic acceleration? Models which aim to explain the accelerated expansion rate of the Universe by modifications to General Relativity often invoke screening mechanisms which can imprint a non-standard density dependence on their predictions. This suggests density-dependent clustering as a `generic' constraint. This paper argues that a density-marked correlation function provides a density-dependent statistic which is easy to compute and report and requires minimal additional infrastructure beyond what is routinely available to such survey analyses. We give one realization of this idea and study it using low order perturbation theory. We encourage groups developing modified gravity theories to see whether such statistics provide discriminatory power for their models.

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

PubMed

Cioslowski, Jerzy

2015-03-21

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

Decoupling the Effects of Mass Density and Hydrogen-, Oxygen-, and Aluminum-Based Defects on Optoelectronic Properties of Realistic Amorphous Alumina.

PubMed

Riffet, Vanessa; Vidal, Julien

2017-06-01

The search for functional materials is currently hindered by the difficulty to find significant correlation between constitutive properties of a material and its functional properties. In the case of amorphous materials, the diversity of local structures, chemical composition, impurities and mass densities makes such a connection difficult to be addressed. In this Letter, the relation between refractive index and composition has been investigated for amorphous AlO x materials, including nonstoichiometric AlO x , emphasizing the role of structural defects and the absence of effect of the band gap variation. It is found that the Newton-Drude (ND) relation predicts the refractive index from mass density with a rather high level of precision apart from some structures displaying structural defects. Our results show especially that O- and Al-based defects act as additive local disturbance in the vicinity of band gap, allowing us to decouple the mass density effects from defect effects (n = n[ND] + Δn defect ).

Density reconstruction in multiparameter elastic full-waveform inversion

NASA Astrophysics Data System (ADS)

Sun, Min'ao; Yang, Jizhong; Dong, Liangguo; Liu, Yuzhu; Huang, Chao

2017-12-01

Elastic full-waveform inversion (EFWI) is a quantitative data fitting procedure that recovers multiple subsurface parameters from multicomponent seismic data. As density is involved in addition to P- and S-wave velocities, the multiparameter EFWI suffers from more serious tradeoffs. In addition, compared with P- and S-wave velocities, the misfit function is less sensitive to density perturbation. Thus, a robust density reconstruction remains a difficult problem in multiparameter EFWI. In this paper, we develop an improved scattering-integral-based truncated Gauss-Newton method to simultaneously recover P- and S-wave velocities and density in EFWI. In this method, the inverse Gauss-Newton Hessian has been estimated by iteratively solving the Gauss-Newton equation with a matrix-free conjugate gradient algorithm. Therefore, it is able to properly handle the parameter tradeoffs. To give a detailed illustration of the tradeoffs between P- and S-wave velocities and density in EFWI, wavefield-separated sensitivity kernels and the Gauss-Newton Hessian are numerically computed, and their distribution characteristics are analyzed. Numerical experiments on a canonical inclusion model and a modified SEG/EAGE Overthrust model have demonstrated that the proposed method can effectively mitigate the tradeoff effects, and improve multiparameter gradients. Thus, a high convergence rate and an accurate density reconstruction can be achieved.

Density Functional Investigation of the Adsorption of Isooctane, Ethanol, and Acetic Acid on a Water-Covered Fe(100) Surface

PubMed Central

2014-01-01

The presence of water in biofuels poses the question of how it affects the frictional performance of additives in fuels containing organic substances. To investigate the effect of water on the adsorption of molecules present in fuel and its additives we simulated within the framework of density functional theory the adsorption of ethanol, isooctane (2,2,4-trimethylpentane), and acetic acid on a bare and a water-covered Fe(100) surface. Van der Waals interactions are taken into account in our computations. In those molecules, where dispersion forces contribute significantly to the binding mechanism, the water layer has a stronger screening effect. Additionally, this effect can be enhanced by the presence of polar functional groups in the molecule. Thus, with the introduction of a water layer, the adsorption energy of isooctane and ethanol is reduced but it is increased in the case of the acetic acid. The adsorption configuration of ethanol is changed, while the one of acetic acid is moderately, and for isooctane only very slightly altered. Therefore, the effect of a water layer in the adsorption of organic molecules on an Fe(100) surface strongly depends on the type of bond and consequently, so do the tribological properties. PMID:25243045

How Accurate Are the Minnesota Density Functionals for Noncovalent Interactions, Isomerization Energies, Thermochemistry, and Barrier Heights Involving Molecules Composed of Main-Group Elements?

DOE PAGES

Mardirossian, Narbe; Head-Gordon, Martin

2016-08-18

The 14 Minnesota density functionals published between the years 2005 and early 2016 are benchmarked on a comprehensive database of 4986 data points (84 data sets) involving molecules composed of main-group elements. The database includes noncovalent interactions, isomerization energies, thermochemistry, and barrier heights, as well as equilibrium bond lengths and equilibrium binding energies of noncovalent dimers. Additionally, the sensitivity of the Minnesota density functionals to the choice of basis set and integration grid is explored for both noncovalent interactions and thermochemistry. By and large, the main strength of the hybrid Minnesota density functionals is that the best ones provide verymore » good performance for thermochemistry (e.g., M06-2X), barrier heights (e.g., M08-HX, M08-SO, MN15), and systems heavily characterized by self-interaction error (e.g., M06-2X, M08-HX, M08-SO, MN15), while the main weakness is that none of them are state-of-the-art for the full spectrum of noncovalent interactions and isomerization energies (although M06-2X is recommended from the 10 hybrid Minnesota functionals). Similarly, the main strength of the local Minnesota density functionals is that the best ones provide very good performance for thermochemistry (e.g., MN15-L), barrier heights (e.g., MN12-L), and systems heavily characterized by self-interaction error (e.g., MN12-L and MN15-L), while the main weakness is that none of them are state-of-the-art for the full spectrum of noncovalent interactions and isomerization energies (although M06-L is clearly the best from the four local Minnesota functionals). Finally, as an overall guide, M06-2X and MN15 are perhaps the most broadly useful hybrid Minnesota functionals, while M06-L and MN15-L are perhaps the most broadly useful local Minnesota functionals, although each has different strengths and weaknesses.« less

Next-generation biomedical implants using additive manufacturing of complex, cellular and functional mesh arrays.

PubMed

Murr, L E; Gaytan, S M; Medina, F; Lopez, H; Martinez, E; Machado, B I; Hernandez, D H; Martinez, L; Lopez, M I; Wicker, R B; Bracke, J

2010-04-28

In this paper, we examine prospects for the manufacture of patient-specific biomedical implants replacing hard tissues (bone), particularly knee and hip stems and large bone (femoral) intramedullary rods, using additive manufacturing (AM) by electron beam melting (EBM). Of particular interest is the fabrication of complex functional (biocompatible) mesh arrays. Mesh elements or unit cells can be divided into different regions in order to use different cell designs in different areas of the component to produce various or continually varying (functionally graded) mesh densities. Numerous design elements have been used to fabricate prototypes by AM using EBM of Ti-6Al-4V powders, where the densities have been compared with the elastic (Young) moduli determined by resonant frequency and damping analysis. Density optimization at the bone-implant interface can allow for bone ingrowth and cementless implant components. Computerized tomography (CT) scans of metal (aluminium alloy) foam have also allowed for the building of Ti-6Al-4V foams by embedding the digital-layered scans in computer-aided design or software models for EBM. Variations in mesh complexity and especially strut (or truss) dimensions alter the cooling and solidification rate, which alters the alpha-phase (hexagonal close-packed) microstructure by creating mixtures of alpha/alpha' (martensite) observed by optical and electron metallography. Microindentation hardness measurements are characteristic of these microstructures and microstructure mixtures (alpha/alpha') and sizes.

Jacob's Ladder as Sketched by Escher: Assessing the Performance of Broadly Used Density Functionals on Transition Metal Surface Properties.

PubMed

Vega, Lorena; Ruvireta, Judit; Viñes, Francesc; Illas, Francesc

2018-01-09

The present work surveys the performance of various widely used density functional theory exchange-correlation (xc) functionals in describing observable surface properties of a total of 27 transition metals with face-centered cubic (fcc), body-centered cubic (bcc), or hexagonal close-packed (hcp) crystallographic structures. A total of 81 low Miller index surfaces were considered employing slab models. Exemplary xc functionals within the three first rungs of Jacob's ladder were considered, including the Vosko-Wilk-Nusair xc functional within the local density approximation, the Perdew-Burke-Ernzerhof (PBE) functional within the generalized gradient approximation (GGA), and the Tao-Perdew-Staroverov-Scuseria functional as a meta-GGA functional. Hybrids were excluded in the survey because they are known to fail in properly describing metallic systems. In addition, two variants of PBE were considered, PBE adapted for solids (PBEsol) and revised PBE (RPBE), aimed at improving adsorption energies. Interlayer atomic distances, surface energies, and surface work functions were chosen as the scrutinized properties. A comparison with available experimental data, including single-crystal and polycrystalline values, shows that no xc functional is best at describing all of the surface properties. However, in statistical mean terms the PBEsol xc functional is advised, while PBE is recommended when considering both bulk and surface properties. On the basis of the present results, a discussion of adapting GGA functionals to the treatment of metallic surfaces in an alternative way to meta-GGA or hybrids is provided.

Covalent addition of chitosan to graphene sheets: Density functional theory explorations of quadrupole coupling constants

NASA Astrophysics Data System (ADS)

Mokhtari, Ali; Harismah, Kun; Mirzaei, Mahmoud

2015-12-01

Density functional theory (DFT) calculations have been performed to detect the stabilities and properties of chitosan-functionalized graphene and graphene-oxide structures (G-Chit and GO-Chit). The model systems with two different sizes of sheets have been optimized and the molecular and atomic properties have been evaluated for them. The results indicated that investigated G-Chit and GO-Chit structures could be considered as stable structures but with different properties. The properties for GO and GO-Chit structures are almost similar; however, they are different from the original G and G-Chit structures. The results also indicated that the properties could be also size-dependent, in which different molecular and atomic properties have been observed for the investigate G sheets.

Rates of Space Weathering in Lunar Regolith Grains

NASA Technical Reports Server (NTRS)

Zhang, S.; Keller, L. P.

2012-01-01

While the processes and products of lunar space weathering are reasonably well-studied, their accumulation rates in lunar soils are poorly constrained. Previously, we showed that the thickness of solar wind irradiated rims on soil grains is a smooth function of their solar flare particle track density, whereas the thickness of vapor-deposited rims was largely independent of track density [1]. Here, we have extended these preliminary results with data on additional grains from other mature soils.

Towards a Density Functional Theory Exchange-Correlation Functional able to describe localization/delocalization

NASA Astrophysics Data System (ADS)

Mattsson, Ann E.; Wills, John M.

2013-03-01

The inability to computationally describe the physics governing the properties of actinides and their alloys is the poster child of failure of existing Density Functional Theory exchange-correlation functionals. The intricate competition between localization and delocalization of the electrons, present in these materials, exposes the limitations of functionals only designed to properly describe one or the other situation. We will discuss the manifestation of this competition in real materials and propositions on how to construct a functional able to accurately describe properties of these materials. I addition we will discuss both the importance of using the Dirac equation to describe the relativistic effects in these materials, and the connection to the physics of transition metal oxides. 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.

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

PubMed

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

2015-09-08

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

Physical evaluations of Co-Cr-Mo parts processed using different additive manufacturing techniques

NASA Astrophysics Data System (ADS)

Ghani, Saiful Anwar Che; Mohamed, Siti Rohaida; Harun, Wan Sharuzi Wan; Noar, Nor Aida Zuraimi Md

2017-12-01

In recent years, additive manufacturing with highly design customization has gained an important technique for fabrication in aerospace and medical fields. Despite the ability of the process to produce complex components with highly controlled architecture geometrical features, maintaining the part's accuracy, ability to fabricate fully functional high density components and inferior surfaces quality are the major obstacles in producing final parts using additive manufacturing for any selected application. This study aims to evaluate the physical properties of cobalt chrome molybdenum (Co-Cr-Mo) alloys parts fabricated by different additive manufacturing techniques. The full dense Co-Cr-Mo parts were produced by Selective Laser Melting (SLM) and Direct Metal Laser Sintering (DMLS) with default process parameters. The density and relative density of samples were calculated using Archimedes' principle while the surface roughness on the top and side surface was measured using surface profiler. The roughness average (Ra) for top surface for SLM produced parts is 3.4 µm while 2.83 µm for DMLS produced parts. The Ra for side surfaces for SLM produced parts is 4.57 µm while 9.0 µm for DMLS produced parts. The higher Ra values on side surfaces compared to the top faces for both manufacturing techniques was due to the balling effect phenomenon. The yield relative density for both Co-Cr-Mo parts produced by SLM and DMLS are 99.3%. Higher energy density has influence the higher density of produced samples by SLM and DMLS processes. The findings of this work demonstrated that SLM and DMLS process with default process parameters have effectively produced full dense parts of Co-Cr-Mo with high density, good agreement of geometrical accuracy and better surface finish. Despite of both manufacturing process yield that produced components with higher density, the current finding shows that SLM technique could produce components with smoother surface quality compared to DMLS process with default parameters.

Local electric dipole moments for periodic systems via density functional theory embedding.

PubMed

Luber, Sandra

2014-12-21

We describe a novel approach for the calculation of local electric dipole moments for periodic systems. Since the position operator is ill-defined in periodic systems, maximally localized Wannier functions based on the Berry-phase approach are usually employed for the evaluation of local contributions to the total electric dipole moment of the system. We propose an alternative approach: within a subsystem-density functional theory based embedding scheme, subset electric dipole moments are derived without any additional localization procedure, both for hybrid and non-hybrid exchange-correlation functionals. This opens the way to a computationally efficient evaluation of local electric dipole moments in (molecular) periodic systems as well as their rigorous splitting into atomic electric dipole moments. As examples, Infrared spectra of liquid ethylene carbonate and dimethyl carbonate are presented, which are commonly employed as solvents in Lithium ion batteries.

Accurate density functional prediction of molecular electron affinity with the scaling corrected Kohn–Sham frontier orbital energies

NASA Astrophysics Data System (ADS)

Zhang, DaDi; Yang, Xiaolong; Zheng, Xiao; Yang, Weitao

2018-04-01

Electron affinity (EA) is the energy released when an additional electron is attached to an atom or a molecule. EA is a fundamental thermochemical property, and it is closely pertinent to other important properties such as electronegativity and hardness. However, accurate prediction of EA is difficult with density functional theory methods. The somewhat large error of the calculated EAs originates mainly from the intrinsic delocalisation error associated with the approximate exchange-correlation functional. In this work, we employ a previously developed non-empirical global scaling correction approach, which explicitly imposes the Perdew-Parr-Levy-Balduz condition to the approximate functional, and achieve a substantially improved accuracy for the calculated EAs. In our approach, the EA is given by the scaling corrected Kohn-Sham lowest unoccupied molecular orbital energy of the neutral molecule, without the need to carry out the self-consistent-field calculation for the anion.

Ab-initio investigation of Rb substitution in KTP single crystal

NASA Astrophysics Data System (ADS)

Ghoohestani, Marzieh; Arab, Ali; Hashemifar, S. Javad; Sadeghi, Hossein

2018-01-01

The effects of rubidium doping on the structural, electronic, and optical properties of KTiOPO4 (KTP) are investigated in the framework of density functional theory. The equilibrium structural parameters of KTP and RbTiOPO4 (RTP) are calculated within the local density and Perdew-Burke-Ernzerhof (PBE), Wu-Cohen, and PBEsol formulation of generalized gradient approximations. We discuss that PBEsol predicts better equilibrium parameters for the KTP alloy. In addition, the variation of lattice constants and Ti-O-Ti bond angles are evaluated as a function of rubidium concentration. The modern modified Becke-Johnson functional is applied for more accurate band gap determination in the pure and alloyed KTP/RTP compounds. The phenomenological pseudoinversion parameter is calculated for a qualitative understanding of the effect of impurity on a non-linear optical response of KTP. We also analyze the behavior of the dielectric function, dispersive refractive indices, and birefringence of KTP/RTP alloys.

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

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

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

Analytic Expressions for the Gravity Gradient Tensor of 3D Prisms with Depth-Dependent Density

NASA Astrophysics Data System (ADS)

Jiang, Li; Liu, Jie; Zhang, Jianzhong; Feng, Zhibing

2017-12-01

Variable-density sources have been paid more attention in gravity modeling. We conduct the computation of gravity gradient tensor of given mass sources with variable density in this paper. 3D rectangular prisms, as simple building blocks, can be used to approximate well 3D irregular-shaped sources. A polynomial function of depth can represent flexibly the complicated density variations in each prism. Hence, we derive the analytic expressions in closed form for computing all components of the gravity gradient tensor due to a 3D right rectangular prism with an arbitrary-order polynomial density function of depth. The singularity of the expressions is analyzed. The singular points distribute at the corners of the prism or on some of the lines through the edges of the prism in the lower semi-space containing the prism. The expressions are validated, and their numerical stability is also evaluated through numerical tests. The numerical examples with variable-density prism and basin models show that the expressions within their range of numerical stability are superior in computational accuracy and efficiency to the common solution that sums up the effects of a collection of uniform subprisms, and provide an effective method for computing gravity gradient tensor of 3D irregular-shaped sources with complicated density variation. In addition, the tensor computed with variable density is different in magnitude from that with constant density. It demonstrates the importance of the gravity gradient tensor modeling with variable density.

Structure and characteristics of functional powder composite materials obtained by spark plasma sintering

NASA Astrophysics Data System (ADS)

Oglezneva, S. A.; Kachenyuk, M. N.; Kulmeteva, V. B.; Ogleznev, N. B.

2017-07-01

The article describes the results of spark plasma sintering of ceramic materials based on titanium carbide, titanium carbosilicide, ceramic composite materials based on zirconium oxide, strengthened by carbon nanostructures and composite materials of electrotechnical purpose based on copper with addition of carbon structures and titanium carbosilicide. The research shows that the spark plasma sintering can achieve relative density of the material up to 98%. The effect of sintering temperature on the phase composition, density and porosity of the final product has been studied. It was found that with addition of carbon nanostructures the relative density and hardness decrease, but the fracture strength of ZrO2 increases up to times 2. The relative erosion resistance of the electrodes made of composite copper-based powder materials, obtained by spark plasma sintering during electroerosion treatment of tool steel exceeds that parameter of pure copper up to times 15.

Self-consistent implementation of meta-GGA functionals for the ONETEP linear-scaling electronic structure package.

PubMed

Womack, James C; Mardirossian, Narbe; Head-Gordon, Martin; Skylaris, Chris-Kriton

2016-11-28

Accurate and computationally efficient exchange-correlation functionals are critical to the successful application of linear-scaling density functional theory (DFT). Local and semi-local functionals of the density are naturally compatible with linear-scaling approaches, having a general form which assumes the locality of electronic interactions and which can be efficiently evaluated by numerical quadrature. Presently, the most sophisticated and flexible semi-local functionals are members of the meta-generalized-gradient approximation (meta-GGA) family, and depend upon the kinetic energy density, τ, in addition to the charge density and its gradient. In order to extend the theoretical and computational advantages of τ-dependent meta-GGA functionals to large-scale DFT calculations on thousands of atoms, we have implemented support for τ-dependent meta-GGA functionals in the ONETEP program. In this paper we lay out the theoretical innovations necessary to implement τ-dependent meta-GGA functionals within ONETEP's linear-scaling formalism. We present expressions for the gradient of the τ-dependent exchange-correlation energy, necessary for direct energy minimization. We also derive the forms of the τ-dependent exchange-correlation potential and kinetic energy density in terms of the strictly localized, self-consistently optimized orbitals used by ONETEP. To validate the numerical accuracy of our self-consistent meta-GGA implementation, we performed calculations using the B97M-V and PKZB meta-GGAs on a variety of small molecules. Using only a minimal basis set of self-consistently optimized local orbitals, we obtain energies in excellent agreement with large basis set calculations performed using other codes. Finally, to establish the linear-scaling computational cost and applicability of our approach to large-scale calculations, we present the outcome of self-consistent meta-GGA calculations on amyloid fibrils of increasing size, up to tens of thousands of atoms.

Self-consistent implementation of meta-GGA functionals for the ONETEP linear-scaling electronic structure package

NASA Astrophysics Data System (ADS)

Womack, James C.; Mardirossian, Narbe; Head-Gordon, Martin; Skylaris, Chris-Kriton

2016-11-01

Accurate and computationally efficient exchange-correlation functionals are critical to the successful application of linear-scaling density functional theory (DFT). Local and semi-local functionals of the density are naturally compatible with linear-scaling approaches, having a general form which assumes the locality of electronic interactions and which can be efficiently evaluated by numerical quadrature. Presently, the most sophisticated and flexible semi-local functionals are members of the meta-generalized-gradient approximation (meta-GGA) family, and depend upon the kinetic energy density, τ, in addition to the charge density and its gradient. In order to extend the theoretical and computational advantages of τ-dependent meta-GGA functionals to large-scale DFT calculations on thousands of atoms, we have implemented support for τ-dependent meta-GGA functionals in the ONETEP program. In this paper we lay out the theoretical innovations necessary to implement τ-dependent meta-GGA functionals within ONETEP's linear-scaling formalism. We present expressions for the gradient of the τ-dependent exchange-correlation energy, necessary for direct energy minimization. We also derive the forms of the τ-dependent exchange-correlation potential and kinetic energy density in terms of the strictly localized, self-consistently optimized orbitals used by ONETEP. To validate the numerical accuracy of our self-consistent meta-GGA implementation, we performed calculations using the B97M-V and PKZB meta-GGAs on a variety of small molecules. Using only a minimal basis set of self-consistently optimized local orbitals, we obtain energies in excellent agreement with large basis set calculations performed using other codes. Finally, to establish the linear-scaling computational cost and applicability of our approach to large-scale calculations, we present the outcome of self-consistent meta-GGA calculations on amyloid fibrils of increasing size, up to tens of thousands of atoms.

Investigation of ground state charge transfer complex between paracetamol and p-chloranil through DFT and UV-visible studies

NASA Astrophysics Data System (ADS)

Shukla, Madhulata; Srivastava, Nitin; Saha, Satyen

2012-08-01

The present report deals with the theoretical investigation on ground state structure and charge transfer (CT) transitions in paracetamol (PA)/p-chloranil (CA) complex using Density Functional Theory (DFT) and Time Dependent Density Functional Theory (TD-DFT) method. It is found that Cdbnd O bond length of p-chloranil increases on complexation with paracetamol along with considerable amount of charge transfer from PA to CA. TD-DFT calculations have been performed to analyse the observed UV-visible spectrum of PA-CA charge transferred complex. Interestingly, in addition to expected CT transition, a weak symmetry relieved π-π* transition in the chloranil is also observed.

Orbital relaxation effects on Kohn–Sham frontier orbital energies in density functional theory

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

Zhang, DaDi; Zheng, Xiao, E-mail: xz58@ustc.edu.cn; Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026

2015-04-21

We explore effects of orbital relaxation on Kohn–Sham frontier orbital energies in density functional theory by using a nonempirical scaling correction approach developed in Zheng et al. [J. Chem. Phys. 138, 174105 (2013)]. Relaxation of Kohn–Sham orbitals upon addition/removal of a fractional number of electrons to/from a finite system is determined by a systematic perturbative treatment. The information of orbital relaxation is then used to improve the accuracy of predicted Kohn–Sham frontier orbital energies by Hartree–Fock, local density approximation, and generalized gradient approximation methods. The results clearly highlight the significance of capturing the orbital relaxation effects. Moreover, the proposed scalingmore » correction approach provides a useful way of computing derivative gaps and Fukui quantities of N-electron finite systems (N is an integer), without the need to perform self-consistent-field calculations for (N ± 1)-electron systems.« less

Collision dynamics of H+ + N2 at low energies based on time-dependent density-functional theory

NASA Astrophysics Data System (ADS)

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

2018-02-01

Using time-dependent density-functional theory at the level of local density approximation augmented by a self-interaction correction and coupled non-adiabatically to molecular dynamics, we study, from a theoretical perspective, scattering dynamics of the proton in collisions with the N2 molecule at 30 eV. Nine different collision configurations are employed to analyze the proton energy loss spectra, electron depletion, scattering angles and self-interaction effects. Our results agree qualitatively with the experimental data and previous theoretical calculations. The discrepancies are ascribed to the limitation of the theoretical models in use. We find that self-interaction effects can significantly influence the electron capture and the excited diatomic vibrational motion, which is in consistent with other calculations. In addition, it is found that the molecular structure can be readily retrieved from the proton energy loss spectra due to a significant momentum transfer in head-on collisions.

Theoretical study of porous surfaces derived from graphene and boron nitride

NASA Astrophysics Data System (ADS)

Fabris, G. S. L.; Marana, N. L.; Longo, E.; Sambrano, J. R.

2018-02-01

Porous graphene (PG), graphenylene (GP), inorganic graphenylene (IGP-BN), and porous boron nitride (PBN) single-layer have been studied via periodic density functional theory with a modified B3LYP functional and an all-electron Gaussian basis set. The structural, elastic, electronic, vibrational, and topological properties of the surfaces were investigated. The analysis showed that all porous structures had a nonzero band gap, and only PG exhibited a non-planar shape. All porous structures seem to be more susceptible to longitudinal deformation than their pristine counterparts, and GP exhibits a higher strength than graphene in the transversal direction. In addition, the electron densities of GP and IGP-BN are localized closer to the atoms, in contrast with PG and PBN, whose charge density is shifted towards the pore center; this property could find application in various fields, such as gas adsorption.

Study on the effect of hydrogen addition on the variation of plasma parameters of argon-oxygen magnetron glow discharge for synthesis of TiO{sub 2} films

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

Saikia, Partha, E-mail: partha.008@gmail.com; Institute of Physics, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Santiago; Saikia, Bipul Kumar

2016-04-15

We report the effect of hydrogen addition on plasma parameters of argon-oxygen magnetron glow discharge plasma in the synthesis of H-doped TiO{sub 2} films. The parameters of the hydrogen-added Ar/O{sub 2} plasma influence the properties and the structural phases of the deposited TiO{sub 2} film. Therefore, the variation of plasma parameters such as electron temperature (T{sub e}), electron density (n{sub e}), ion density (n{sub i}), degree of ionization of Ar and degree of dissociation of H{sub 2} as a function of hydrogen content in the discharge is studied. Langmuir probe and Optical emission spectroscopy are used to characterize the plasma.more » On the basis of the different reactions in the gas phase of the magnetron discharge, the variation of plasma parameters and sputtering rate are explained. It is observed that the electron and heavy ion density decline with gradual addition of hydrogen in the discharge. Hydrogen addition significantly changes the degree of ionization of Ar which influences the structural phases of the TiO{sub 2} film.« less

Cumulants and large deviations of the current through non-equilibrium steady states

NASA Astrophysics Data System (ADS)

Bodineau, Thierry; Derrida, Bernard

2007-06-01

Using a generalisation of detailed balance for systems maintained out of equilibrium by contact with 2 reservoirs at unequal temperatures or at unequal densities, one can recover the fluctuation theorem for the large deviation function of the current. For large diffusive systems, we show how the large deviation function of the current can be computed using a simple additivity principle. The validity of this additivity principle and the occurrence of phase transitions are discussed in the framework of the macroscopic fluctuation theory. To cite this article: T. Bodineau, B. Derrida, C. R. Physique 8 (2007).

Low bone mineral density in ambulatory persons with cerebral palsy? A systematic review.

PubMed

Mus-Peters, Cindy T R; Huisstede, Bionka M A; Noten, Suzie; Hitters, Minou W M G C; van der Slot, Wilma M A; van den Berg-Emons, Rita J G

2018-05-22

Non-ambulatory persons with cerebral palsy are prone to low bone mineral density. In ambulatory persons with cerebral palsy, bone mineral density deficits are expected to be small or absent, but a consensus conclusion is lacking. In this systematic review bone mineral density in ambulatory persons with cerebral palsy (Gross Motor Function Classification Scales I-III) was studied. Medline, Embase, and Web of Science were searched. According to international guidelines, low bone mineral density was defined as Z-score ≤ -2.0. In addition, we focused on Z-score ≤ -1.0 because this may indicate a tendency towards low bone mineral density. We included 16 studies, comprising 465 patients aged 1-65 years. Moderate and conflicting evidence for low bone mineral density (Z-score ≤ -2.0) was found for several body parts (total proximal femur, total body, distal femur, lumbar spine) in children with Gross Motor Function Classification Scales II and III. We found no evidence for low bone mineral density in children with Gross Motor Function Classification Scale I or adults, although there was a tendency towards low bone mineral density (Z-score ≤ -1.0) for several body parts. Although more high-quality research is needed, results indicate that deficits in bone mineral density are not restricted to non-ambulatory people with cerebral palsy. Implications for Rehabilitation Although more high-quality research is needed, including adults and fracture risk assessment, the current study indicates that deficits in bone mineral density are not restricted to non-ambulatory people with CP. Health care professionals should be aware that optimal nutrition, supplements on indication, and an active lifestyle, preferably with weight-bearing activities, are important in ambulatory people with CP, also from a bone quality point-of-view. If indicated, medication and fall prevention training should be prescribed.

Density functional theory and experimental study of the electronic structure and transport properties of La, V, Nb, and Ta doped SrTiO3

NASA Astrophysics Data System (ADS)

Baniecki, J. D.; Ishii, M.; Aso, H.; Kurihara, K.; Ricinschi, Dan

2013-01-01

The electronic structure and transport properties of donor doped SrTiO3 are studied using density functional theory with spin-orbit coupling and conductivity, Hall, and Seebeck effect measurements over a wide temperature range (100 K to 600 K). Split-off energies ΔSO are tunable through the dopant SO interaction strength and concentration varying from 28.1 meV for pure STO to 70.93 meV for SrTi0.5Nb0.5O3. At lower carrier concentrations and temperatures, SO coupling has a marked effect on both the filling dependence of the density-of-states mass as well as the temperature dependence of the Seebeck coefficient, with quantitative theoretical predictions based on DFT calculations that include the SO interaction in closer agreement to the experimental data. Moreover, the results suggest that the predictive power of the current theory is not unlimited, with less accuracy for the calculated S predicting the magnitude of the experimental S data at lower dopant concentrations than for degenerately doped systems. A concentration dependent mass enhancement of ˜2-5, relative to the density-of-states mass in the local density approximation, possibly due to the influence of electronic screening of the electron-phonon interaction, would bring the theoretical S in accord with the experimental S data. This additional carrier-dependent enhancement mechanism for S may give an additional degree of freedom in terms of designing new higher efficiency thermoelectric energy materials.

Density-induced suppression of the {alpha}-particle condensate in nuclear matter and the structure of {alpha}-cluster states in nuclei

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

Funaki, Y.; Horiuchi, H.; International Institute for Advanced Studies, Kizugawa 619-0225

2008-06-15

At low densities, with decreasing temperatures, in symmetric nuclear matter {alpha} particles are formed, which eventually give raise to a quantum condensate with four-nucleon {alpha}-like correlations (quartetting). Starting with a model of {alpha} matter, where undistorted {alpha} particles interact via an effective interaction such as the Ali-Bodmer potential, the suppression of the condensate fraction at zero temperature with increasing density is considered. Using a Jastrow-Feenberg approach, it is found that the condensate fraction vanishes near saturation density. Additionally, the modification of the internal state of the {alpha} particle due to medium effects will further reduce the condensate. In finite systems,more » an enhancement of the S-state wave function of the center-of-mass orbital of {alpha}-particle motion is considered as the correspondence to the condensate. Wave functions have been constructed for self-conjugate 4n nuclei that describe the condensate state but are fully antisymmetrized on the nucleonic level. These condensate-like cluster wave functions have been successfully applied to describe properties of low-density states near the n{alpha} threshold. Comparison with orthogonality condition model calculations in {sup 12}C and {sup 16}O shows strong enhancement of the occupation of the S-state center-of-mass orbital of the {alpha} particles. This enhancement is decreasing if the baryon density increases, similar to the density-induced suppression of the condensate fraction in {alpha} matter. The ground states of {sup 12}C and {sup 16}O show no enhancement at all, thus a quartetting condensate cannot be formed at saturation densities.« less

Topological entanglement Rényi entropy and reduced density matrix structure.

PubMed

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

2009-12-31

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

Topological Entanglement Rényi Entropy and Reduced Density Matrix Structure

NASA Astrophysics Data System (ADS)

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

2009-12-01

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

Ionic Asymmetry and Solvent Excluded Volume Effects on Spherical Electric Double Layers: A Density Functional Approach

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

Medasani, Bharat; Ovanesyan, Zaven; Thomas, Dennis G.

In this article we present a classical density functional theory for electrical double layers of spherical macroions that extends the capabilities of conventional approaches by accounting for electrostatic ion correlations, size asymmetry and excluded volume effects. The approach is based on a recent approximation introduced by Hansen-Goos and Roth for the hard sphere excess free energy of inhomogeneous fluids (J. Chem. Phys. 124, 154506). It accounts for the proper and efficient description of the effects of ionic asymmetry and solvent excluded volume, especially at high ion concentrations and size asymmetry ratios including those observed in experimental studies. Additionally, we utilizemore » a leading functional Taylor expansion approximation of the ion density profiles. In addition, we use the Mean Spherical Approximation for multi-component charged hard sphere fluids to account for the electrostatic ion correlation effects. These approximations are implemented in our theoretical formulation into a suitable decomposition of the excess free energy which plays a key role in capturing the complex interplay between charge correlations and excluded volume effects. We perform Monte Carlo simulations in various scenarios to validate the proposed approach, obtaining a good compromise between accuracy and computational cost. We use the proposed computational approach to study the effects of ion size, ion size asymmetry and solvent excluded volume on the ion profiles, integrated charge, mean electrostatic potential, and ionic coordination number around spherical macroions in various electrolyte mixtures. Our results show that both solvent hard sphere diameter and density play a dominant role in the distribution of ions around spherical macroions, mainly for experimental water molarity and size values where the counterion distribution is characterized by a tight binding to the macroion, similar to that predicted by the Stern model.« less

Thermodynamically consistent relations involving plasticity, internal energy and thermal effects.

PubMed

Schreyer, H L; Maudlin, P J

2005-11-15

Experimental data associated with plastic deformations indicate that the temperature is less than that predicted from dissipation based on plastic work. To obtain reasonable correlation between theoretical and experimental results, the plastic work is often multiplied by a constant beta. This paper provides an alternative thermodynamic framework in which it is proposed that there is an additional internal energy associated with dislocation pile-up or increase in dislocation density. The form of this internal energy follows from experimental data that relates flow stress to dislocation density and to equivalent plastic strain. The result is that beta is not a constant but a derived function. Representative results for beta and temperature as functions of effective plastic strain are provided for both an uncoupled and a coupled thermoplastic theory. In addition to providing features that are believed to be representative of many metals, the formulation can be used as a basis for more advanced theories such as those needed for large deformations and general forms of internal energy.

Accuracy of lung nodule density on HRCT: analysis by PSF-based image simulation.

PubMed

Ohno, Ken; Ohkubo, Masaki; Marasinghe, Janaka C; Murao, Kohei; Matsumoto, Toru; Wada, Shinichi

2012-11-08

A computed tomography (CT) image simulation technique based on the point spread function (PSF) was applied to analyze the accuracy of CT-based clinical evaluations of lung nodule density. The PSF of the CT system was measured and used to perform the lung nodule image simulation. Then, the simulated image was resampled at intervals equal to the pixel size and the slice interval found in clinical high-resolution CT (HRCT) images. On those images, the nodule density was measured by placing a region of interest (ROI) commonly used for routine clinical practice, and comparing the measured value with the true value (a known density of object function used in the image simulation). It was quantitatively determined that the measured nodule density depended on the nodule diameter and the image reconstruction parameters (kernel and slice thickness). In addition, the measured density fluctuated, depending on the offset between the nodule center and the image voxel center. This fluctuation was reduced by decreasing the slice interval (i.e., with the use of overlapping reconstruction), leading to a stable density evaluation. Our proposed method of PSF-based image simulation accompanied with resampling enables a quantitative analysis of the accuracy of CT-based evaluations of lung nodule density. These results could potentially reveal clinical misreadings in diagnosis, and lead to more accurate and precise density evaluations. They would also be of value for determining the optimum scan and reconstruction parameters, such as image reconstruction kernels and slice thicknesses/intervals.

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

PubMed

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

2014-10-28

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

Preliminary scaling laws for plasma current, ion kinetic temperature, and plasma number density in the NASA Lewis bumpy torus plasma

NASA Technical Reports Server (NTRS)

Roth, J. R.

1976-01-01

Parametric variation of independent variables which may affect the characteristics of bumpy torus plasma have identified those which have a significant effect on the plasma current, ion kinetic temperature, and plasma number density, and those which do not. Empirical power law correlations of the plasma current, and the ion kinetic temperature and number density were obtained as functions of potential applied to the midplane electrode rings, the background neutral gas pressure, and the magnetic field strength. Additional parameters studied included the type of gas, the polarity of the midplane electrode rings, the mode of plasma operation, and the method of measuring the plasma number density. No significant departures from the scaling laws appear to occur at the highest ion kinetic temperatures or number densities obtained to date.

Internal wave energy flux from density perturbations in nonlinear stratifications

NASA Astrophysics Data System (ADS)

Lee, Frank M.; Allshouse, Michael R.; Swinney, Harry L.; Morrison, P. J.

2017-11-01

Tidal flow over the topography at the bottom of the ocean, whose density varies with depth, generates internal gravity waves that have a significant impact on the energy budget of the ocean. Thus, understanding the energy flux (J = p v) is important, but it is difficult to measure simultaneously the pressure and velocity perturbation fields, p and v . In a previous work, a Green's-function-based method was developed to calculate the instantaneous p, v , and thus J , given a density perturbation field for a constant buoyancy frequency N. Here we extend the previous analytic Green's function work to include nonuniform N profiles, namely the tanh-shaped and linear cases, because background density stratifications that occur in the ocean and some experiments are nonlinear. In addition, we present a finite-difference method for the general case where N has an arbitrary profile. Each method is validated against numerical simulations. The methods we present can be applied to measured density perturbation data by using our MATLAB graphical user interface EnergyFlux. PJM was supported by the U.S. Department of Energy Contract DE-FG05-80ET-53088. HLS and MRA were supported by ONR Grant No. N000141110701.

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.

Cetacean population density estimation from single fixed sensors using passive acoustics.

PubMed

Küsel, Elizabeth T; Mellinger, David K; Thomas, Len; Marques, Tiago A; Moretti, David; Ward, Jessica

2011-06-01

Passive acoustic methods are increasingly being used to estimate animal population density. Most density estimation methods are based on estimates of the probability of detecting calls as functions of distance. Typically these are obtained using receivers capable of localizing calls or from studies of tagged animals. However, both approaches are expensive to implement. The approach described here uses a MonteCarlo model to estimate the probability of detecting calls from single sensors. The passive sonar equation is used to predict signal-to-noise ratios (SNRs) of received clicks, which are then combined with a detector characterization that predicts probability of detection as a function of SNR. Input distributions for source level, beam pattern, and whale depth are obtained from the literature. Acoustic propagation modeling is used to estimate transmission loss. Other inputs for density estimation are call rate, obtained from the literature, and false positive rate, obtained from manual analysis of a data sample. The method is applied to estimate density of Blainville's beaked whales over a 6-day period around a single hydrophone located in the Tongue of the Ocean, Bahamas. Results are consistent with those from previous analyses, which use additional tag data. © 2011 Acoustical Society of America

Optical diagnostics with radiation trapping effect in low density and low temperature helium plasma

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

Lee, Wonwook, E-mail: wwlee@kaeri.re.kr; Kwon, Duck-Hee; Park, Kyungdeuk

2016-06-15

Low density (n{sub e} < 10{sup 11 }cm{sup −3}) and low temperature (T{sub e} < 10 eV) helium plasma was generated by hot filament discharge. Electron temperature and density of neutral helium plasma were measured by Langmuir probe and were determined by line intensity ratio method using optical emission spectroscopy with population modelings. Simple corona model and collisional-radiative (CR) model without consideration for radiation trapping effect are applied. In addition, CR model taking into account the radiation trapping effect (RTE) is adopted. The change of single line intensity ratio as a function of electron temperature and density were investigated when the RTE is included and excluded.more » The changes of multi line intensity ratios as a function of electron temperature were scanned for various radiative-excitation rate coefficients from the ground state and the helium gas pressures related with the RTE. Our CR modeling with RTE results in fairly better agreement of the spectroscopic diagnostics for the plasma temperature or density with the Langmuir probe measurements for various helium gas pressures than corona modeling and CR modeling without RTE.« less

Spatial distribution and optimal harvesting of an age-structured population in a fluctuating environment.

PubMed

Engen, Steinar; Lee, Aline Magdalena; Sæther, Bernt-Erik

2018-02-01

We analyze a spatial age-structured model with density regulation, age specific dispersal, stochasticity in vital rates and proportional harvesting. We include two age classes, juveniles and adults, where juveniles are subject to logistic density dependence. There are environmental stochastic effects with arbitrary spatial scales on all birth and death rates, and individuals of both age classes are subject to density independent dispersal with given rates and specified distributions of dispersal distances. We show how to simulate the joint density fields of the age classes and derive results for the spatial scales of all spatial autocovariance functions for densities. A general result is that the squared scale has an additive term equal to the squared scale of the environmental noise, corresponding to the Moran effect, as well as additive terms proportional to the dispersal rate and variance of dispersal distance for the age classes and approximately inversely proportional to the strength of density regulation. We show that the optimal harvesting strategy in the deterministic case is to harvest only juveniles when their relative value (e.g. financial) is large, and otherwise only adults. With increasing environmental stochasticity there is an interval of increasing length of values of juveniles relative to adults where both age classes should be harvested. Harvesting generally tends to increase all spatial scales of the autocovariances of densities. Copyright © 2017. Published by Elsevier Inc.

Ion transport and selectivity in biomimetic nanopores with pH-tunable zwitterionic polyelectrolyte brushes.

PubMed

Zeng, Zhenping; Yeh, Li-Hsien; Zhang, Mingkan; Qian, Shizhi

2015-10-28

Inspired by nature, functionalized nanopores with biomimetic structures have attracted growing interests in using them as novel platforms for applications of regulating ion and nanoparticle transport. To improve these emerging applications, we study theoretically for the first time the ion transport and selectivity in short nanopores functionalized with pH tunable, zwitterionic polyelectrolyte (PE) brushes. In addition to background salt ions, the study takes into account the presence of H(+) and OH(-) ions along with the chemistry reactions between functional groups on PE chains and protons. Due to ion concentration polarization, the charge density of PE layers is not homogeneously distributed and depends significantly on the background salt concentration, pH, grafting density of PE chains, and applied voltage bias, thereby resulting in many interesting and unexpected ion transport phenomena in the nanopore. For example, the ion selectivity of the biomimetic nanopore can be regulated from anion-selective (cation-selective) to cation-selective (anion-selective) by diminishing (raising) the solution pH when a sufficiently small grafting density of PE chains, large voltage bias, and low background salt concentration are applied.

Derivation of force field parameters for SnO2-H2O surface systems from plane-wave density functional theory calculations.

PubMed

Bandura, A V; Sofo, J O; Kubicki, J D

2006-04-27

Plane-wave density functional theory (DFT-PW) calculations were performed on bulk SnO2 (cassiterite) and the (100), (110), (001), and (101) surfaces with and without H2O present. A classical interatomic force field has been developed to describe bulk SnO2 and SnO2-H2O surface interactions. Periodic density functional theory calculations using the program VASP (Kresse et al., 1996) and molecular cluster calculations using Gaussian 03 (Frisch et al., 2003) were used to derive the parametrization of the force field. The program GULP (Gale, 1997) was used to optimize parameters to reproduce experimental and ab initio results. The experimental crystal structure and elastic constants of SnO2 are reproduced reasonably well with the force field. Furthermore, surface atom relaxations and structures of adsorbed H2O molecules agree well between the ab initio and force field predictions. H2O addition above that required to form a monolayer results in consistent structures between the DFT-PW and classical force field results as well.

Restoring Ecological Function to a Submerged Salt Marsh

USGS Publications Warehouse

Stagg, C.L.; Mendelssohn, I.A.

2010-01-01

Impacts of global climate change, such as sea level rise and severe drought, have altered the hydrology of coastal salt marshes resulting in submergence and subsequent degradation of ecosystem function. A potential method of rehabilitating these systems is the addition of sediment-slurries to increase marsh surface elevation, thus ameliorating effects of excessive inundation. Although this technique is growing in popularity, the restoration of ecological function after sediment addition has received little attention. To determine if sediment subsidized salt marshes are functionally equivalent to natural marshes, we examined above- and belowground primary production in replicated restored marshes receiving four levels of sediment addition (29-42 cm North American Vertical Datum of 1988 [NAVD 88]) and in degraded and natural ambient marshes (4-22 cm NAVD 88). Moderate intensities of sediment-slurry addition, resulting in elevations at the mid to high intertidal zone (29-36 cm NAVD 88), restored ecological function to degraded salt marshes. Sediment additions significantly decreased flood duration and frequency and increased bulk density, resulting in greater soil drainage and redox potential and significantly lower phytotoxic sulfide concentrations. However, ecological function in the restored salt marsh showed a sediment addition threshold that was characterized by a decline in primary productivity in areas of excessive sediment addition and high elevation (>36 cm NAVD 88). Hence, the addition of intermediate levels of sediment to submerging salt marshes increased marsh surface elevation, ameliorated impacts of prolonged inundation, and increased primary productivity. However, too much sediment resulted in diminished ecological function that was equivalent to the submerged or degraded system. ?? 2010 Society for Ecological Restoration International.

General framework for fluctuating dynamic density functional theory

NASA Astrophysics Data System (ADS)

Durán-Olivencia, Miguel A.; Yatsyshin, Peter; Goddard, Benjamin D.; Kalliadasis, Serafim

2017-12-01

We introduce a versatile bottom-up derivation of a formal theoretical framework to describe (passive) soft-matter systems out of equilibrium subject to fluctuations. We provide a unique connection between the constituent-particle dynamics of real systems and the time evolution equation of their measurable (coarse-grained) quantities, such as local density and velocity. The starting point is the full Hamiltonian description of a system of colloidal particles immersed in a fluid of identical bath particles. Then, we average out the bath via Zwanzig’s projection-operator techniques and obtain the stochastic Langevin equations governing the colloidal-particle dynamics. Introducing the appropriate definition of the local number and momentum density fields yields a generalisation of the Dean-Kawasaki (DK) model, which resembles the stochastic Navier-Stokes description of a fluid. Nevertheless, the DK equation still contains all the microscopic information and, for that reason, does not represent the dynamical law of observable quantities. We address this controversial feature of the DK description by carrying out a nonequilibrium ensemble average. Adopting a natural decomposition into local-equilibrium and nonequilibrium contribution, where the former is related to a generalised version of the canonical distribution, we finally obtain the fluctuating-hydrodynamic equation governing the time-evolution of the mesoscopic density and momentum fields. Along the way, we outline the connection between the ad hoc energy functional introduced in previous DK derivations and the free-energy functional from classical density-functional theory. The resultant equation has the structure of a dynamical density-functional theory (DDFT) with an additional fluctuating force coming from the random interactions with the bath. We show that our fluctuating DDFT formalism corresponds to a particular version of the fluctuating Navier-Stokes equations, originally derived by Landau and Lifshitz. Our framework thus provides the formal apparatus for ab initio derivations of fluctuating DDFT equations capable of describing the dynamics of soft-matter systems in and out of equilibrium.

Effects of Acids, Bases, and Heteroatoms on Proximal Radial Distribution Functions for Proteins.

PubMed

Nguyen, Bao Linh; Pettitt, B Montgomery

2015-04-14

The proximal distribution of water around proteins is a convenient method of quantifying solvation. We consider the effect of charged and sulfur-containing amino acid side-chain atoms on the proximal radial distribution function (pRDF) of water molecules around proteins using side-chain analogs. The pRDF represents the relative probability of finding any solvent molecule at a distance from the closest or surface perpendicular protein atom. We consider the near-neighbor distribution. Previously, pRDFs were shown to be universal descriptors of the water molecules around C, N, and O atom types across hundreds of globular proteins. Using averaged pRDFs, a solvent density around any globular protein can be reconstructed with controllable relative error. Solvent reconstruction using the additional information from charged amino acid side-chain atom types from both small models and protein averages reveals the effects of surface charge distribution on solvent density and improves the reconstruction errors relative to simulation. Solvent density reconstructions from the small-molecule models are as effective and less computationally demanding than reconstructions from full macromolecular models in reproducing preferred hydration sites and solvent density fluctuations.

Holographic entanglement entropy of a 1 + 1 dimensional p-wave superconductor

NASA Astrophysics Data System (ADS)

Das, Sumit R.; Fujita, Mitsutoshi; Kim, Bom Soo

2017-09-01

We examine the behavior of entanglement entropy S A EE of a subsystem A in a fully backreacted holographic model of a 1 + 1 dimensional p wave superconductor across the phase transition. For a given temperature, the system goes to a superconducting phase beyond a critical value of the charge density. The entanglement entropy, considered as a function of the charge density at a given temperature, has a cusp at the critical point. In addition, we find that there are three different behaviors in the condensed phase, depending on the subsystem size. For a subsystem size l smaller than a critical size l c1, S A EE continues to increase as a function of the charge density as we cross the phase transition. When l lies between l c1 and another critical size l c2 the entanglement entropy displays a non-monotonic behavior, while for l > l c2 it decreases monotonically. At large charge densities S A EE appears to saturate. The non-monotonic behavior leads to a novel phase diagram for this system.

Influence of predator density on nonindependent effects of multiple predator species.

PubMed

Griffen, Blaine D; Williamson, Tucker

2008-02-01

Interactions between multiple predator species are frequent in natural communities and can have important implications for shared prey survival. Predator density may be an important component of these interactions between predator species, as the frequency of interactions between species is largely determined by species density. Here we experimentally examine the importance of predator density for interactions between predator species and subsequent impacts on prey. We show that aggressive interactions between the predatory shore crabs Carcinus maenas and Hemigrapsus sanguineus increased with predator density, yet did not increase as fast as negative interactions between conspecifics. At low density, interactions between conspecific and heterospecific predators had similar inhibitory impacts on predator function, whereas conspecific interference was greater than interference from heterospecifics at high predator density. Thus the impact of conspecific interference at high predator density was sufficient in itself that interactions with a second predator species had no additional impact on per capita predation. Spatial and temporal variability in predator density is a ubiquitous characteristic of natural systems that should be considered in studies of multiple predator species.

Sum-over-states density functional perturbation theory: Prediction of reliable 13C, 15N, and 17O nuclear magnetic resonance chemical shifts

NASA Astrophysics Data System (ADS)

Olsson, Lars; Cremer, Dieter

1996-11-01

Sum-over-states density functional perturbation theory (SOS-DFPT) has been used to calculate 13C, 15N, and 17O NMR chemical shifts of 20 molecules, for which accurate experimental gas-phase values are available. Compared to Hartree-Fock (HF), SOS-DFPT leads to improved chemical shift values and approaches the degree of accuracy obtained with second order Møller-Plesset perturbation theory (MP2). This is particularly true in the case of 15N chemical shifts where SOS-DFPT performs even better than MP2. Additional improvements of SOS-DFPT chemical shifts can be obtained by empirically correcting diamagnetic and paramagnetic contributions to compensate for deficiencies which are typical of DFT.

Temperature dependence of the symmetry energy and neutron skins in Ni, Sn, and Pb isotopic chains

NASA Astrophysics Data System (ADS)

Antonov, A. N.; Kadrev, D. N.; Gaidarov, M. K.; Sarriguren, P.; de Guerra, E. Moya

2017-02-01

The temperature dependence of the symmetry energy for isotopic chains of even-even Ni, Sn, and Pb nuclei is investigated in the framework of the local density approximation (LDA). The Skyrme energy density functional with two Skyrme-class effective interactions, SkM* and SLy4, is used in the calculations. The temperature-dependent proton and neutron densities are calculated through the hfbtho code that solves the nuclear Skyrme-Hartree-Fock-Bogoliubov problem by using the cylindrical transformed deformed harmonic-oscillator basis. In addition, two other density distributions of 208Pb, namely the Fermi-type density determined within the extended Thomas-Fermi (TF) method and symmetrized-Fermi local density obtained within the rigorous density functional approach, are used. The kinetic energy densities are calculated either by the hfbtho code or, for a comparison, by the extended TF method up to second order in temperature (with T2 term). Alternative ways to calculate the symmetry energy coefficient within the LDA are proposed. The results for the thermal evolution of the symmetry energy coefficient in the interval T =0 -4 MeV show that its values decrease with temperature. The temperature dependence of the neutron and proton root-mean-square radii and corresponding neutron skin thickness is also investigated, showing that the effect of temperature leads mainly to a substantial increase of the neutron radii and skins, especially in the more neutron-rich nuclei, a feature that may have consequences on astrophysical processes and neutron stars.

Inductively coupled Cl2/Ar plasma: Experimental investigation and modeling

NASA Astrophysics Data System (ADS)

Efremov, A. M.; Kim, Dong-Pyo; Kim, Chang-Il

2003-07-01

Electrophysical and kinetic characteristics of Cl2/Ar plasma were investigated to understand the influence of the addition of Ar on the volume densities and fluxes of active particles, both neutral and charged. Our analysis combined both experimental methods and plasma modeling. It was found that addition of Ar to Cl2 leads to deformation of the electron energy distribution function and an increase of the electron mean energy due to the ``transparency'' effect. Direct electron impact dissociation of Cl2 molecules represents the main source of chlorine atoms in the plasma volume. The contributions of stepwise dissociation and ionization involving Ar metastable atoms were found to be negligible. Addition of Ar to Cl2 causes the decrease of both electron and ion densities due to a decrease in the total ionization rate and the acceleration of heterogeneous decay of charged particles.

DCMDN: Deep Convolutional Mixture Density Network

NASA Astrophysics Data System (ADS)

D'Isanto, Antonio; Polsterer, Kai Lars

2017-09-01

Deep Convolutional Mixture Density Network (DCMDN) estimates probabilistic photometric redshift directly from multi-band imaging data by combining a version of a deep convolutional network with a mixture density network. The estimates are expressed as Gaussian mixture models representing the probability density functions (PDFs) in the redshift space. In addition to the traditional scores, the continuous ranked probability score (CRPS) and the probability integral transform (PIT) are applied as performance criteria. DCMDN is able to predict redshift PDFs independently from the type of source, e.g. galaxies, quasars or stars and renders pre-classification of objects and feature extraction unnecessary; the method is extremely general and allows the solving of any kind of probabilistic regression problems based on imaging data, such as estimating metallicity or star formation rate in galaxies.

Density implications of shift compensation postprocessing in holographic storage systems

NASA Astrophysics Data System (ADS)

Menetrier, Laure; Burr, Geoffrey W.

2003-02-01

We investigate the effect of data page misregistration, and its subsequent correction in postprocessing, on the storage density of holographic data storage systems. A numerical simulation is used to obtain the bit-error rate as a function of hologram aperture, page misregistration, pixel fill factors, and Gaussian additive intensity noise. Postprocessing of simulated data pages is performed by a nonlinear pixel shift compensation algorithm [Opt. Lett. 26, 542 (2001)]. The performance of this algorithm is analyzed in the presence of noise by determining the achievable areal density. The impact of inaccurate measurements of page misregistration is also investigated. Results show that the shift-compensation algorithm can provide almost complete immunity to page misregistration, although at some penalty to the baseline areal density offered by a system with zero tolerance to misalignment.

The structural, electronic and optical properties of Au-ZnO interface structure from the first-principles calculation

NASA Astrophysics Data System (ADS)

Huo, Jin-Rong; Li, Lu; Cheng, Hai-Xia; Wang, Xiao-Xu; Zhang, Guo-Hua; Qian, Ping

2018-03-01

The interface structure, electronic and optical properties of Au-ZnO are studied using the first-principles calculation based on density functional theory (DFT). Given the interfacial distance, bonding configurations and terminated surface, we built the optimal interface structure and calculated the electronic and optical properties of the interface. The total density of states, partial electronic density of states, electric charge density and atomic populations (Mulliken) are also displayed. The results show that the electrons converge at O atoms at the interface, leading to a stronger binding of interfaces and thereby affecting the optical properties of interface structures. In addition, we present the binding energies of different interface structures. When the interface structure of Au-ZnO gets changed, furthermore, varying optical properties are exhibited.

Free Energy Calculations of Crystalline Hard Sphere Complexes Using Density Functional Theory

DOE PAGES

Gunawardana, K. G.S.H.; Song, Xueyu

2014-12-22

Recently developed fundamental measure density functional theory (FMT) is used to study binary hard sphere (HS) complexes in crystalline phases. By comparing the excess free energy, pressure and phase diagram, we show that the fundamental measure functional yields good agreements to the available simulation results of AB, AB 2 and AB 13 crystals. Additionally, we use this functional to study the HS models of five binary crystals, Cu 5Zr(C15 b), Cu 51Zr 14(β), Cu 10Zr 7(φ), CuZr(B2) and CuZr 2 (C11 b), which are observed in the Cu-Zr system. The FMT functional gives well behaved minimum for most of themore » hard sphere crystal complexes in the two dimensional Gaussian space, namely a crystalline phase. However, the current version of FMT functional (white Bear) fails to give a stable minimum for the structure Cu 10Zr 7(φ). We argue that the observed solid phases for the HS models of the Cu-Zr system are true thermodynamic stable phases and can be used as a reference system in perturbation calculations.« less

Classical density functional theory and the phase-field crystal method using a rational function to describe the two-body direct correlation function.

PubMed

Pisutha-Arnond, N; Chan, V W L; Iyer, M; Gavini, V; Thornton, K

2013-01-01

We introduce a new approach to represent a two-body direct correlation function (DCF) in order to alleviate the computational demand of classical density functional theory (CDFT) and enhance the predictive capability of the phase-field crystal (PFC) method. The approach utilizes a rational function fit (RFF) to approximate the two-body DCF in Fourier space. We use the RFF to show that short-wavelength contributions of the two-body DCF play an important role in determining the thermodynamic properties of materials. We further show that using the RFF to empirically parametrize the two-body DCF allows us to obtain the thermodynamic properties of solids and liquids that agree with the results of CDFT simulations with the full two-body DCF without incurring significant computational costs. In addition, the RFF can also be used to improve the representation of the two-body DCF in the PFC method. Last, the RFF allows for a real-space reformulation of the CDFT and PFC method, which enables descriptions of nonperiodic systems and the use of nonuniform and adaptive grids.

On the Relation Between Soft Electron Precipitations in the Cusp Region and Solar Wind Coupling Functions

NASA Astrophysics Data System (ADS)

Dang, Tong; Zhang, Binzheng; Wiltberge, Michael; Wang, Wenbin; Varney, Roger; Dou, Xiankang; Wan, Weixing; Lei, Jiuhou

2018-01-01

In this study, the correlations between the fluxes of precipitating soft electrons in the cusp region and solar wind coupling functions are investigated utilizing the Lyon-Fedder-Mobarry global magnetosphere model simulations. We conduct two simulation runs during periods from 20 March 2008 to 16 April 2008 and from 15 to 24 December 2014, which are referred as "Equinox Case" and "Solstice Case," respectively. The simulation results of Equinox Case show that the plasma number density in the high-latitude cusp region scales well with the solar wind number density (ncusp/nsw=0.78), which agrees well with the statistical results from the Polar spacecraft measurements. For the Solstice Case, the plasma number density of high-latitude cusp in both hemispheres increases approximately linearly with upstream solar wind number density with prominent hemispheric asymmetry. Due to the dipole tilt effect, the average number density ratio ncusp/nsw in the Southern (summer) Hemisphere is nearly 3 times that in the Northern (winter) Hemisphere. In addition to the solar wind number density, 20 solar wind coupling functions are tested for the linear correlation with the fluxes of precipitating cusp soft electrons. The statistical results indicate that the solar wind dynamic pressure p exhibits the highest linear correlation with the cusp electron fluxes for both equinox and solstice conditions, with correlation coefficients greater than 0.75. The linear regression relations for equinox and solstice cases may provide an empirical calculation for the fluxes of cusp soft electron precipitation based on the upstream solar wind driving conditions.

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.

Barrierless Reactions with Loose Transition States Govern the Yields and Lifetimes of Organic Nitrates Derived from Isoprene

EPA Science Inventory

The chemical reaction mechanism of NO addition to two β and δ isoprene hydroxy–peroxy radical isomers is examined in detail using density functional theory, coupled cluster methods, and the energy resolved master equation formalism to provide estimates of rate co...

Density-based regulation of ascr#2 and ascr#4 expression in Caenorhabditis elegans

USDA-ARS?s Scientific Manuscript database

The ascarosides are a family of nematode small molecules, many of which induce formation of long-lived and highly stress resistant dauer larvae. More recent studies have shown that ascarosides serve additional functions as social signals and mating pheromones. For example, the male attracting pherom...

Preliminary scaling laws for plasma current, ion kinetic temperature, and plasma number density in the NASA Lewis Bumpy Torus plasma

NASA Technical Reports Server (NTRS)

Roth, J. R.

1976-01-01

Parametric variation of independent variables which may affect the characteristics of the NASA Lewis Bumpy Torus plasma have identified those which have a significant effect on the plasma current, ion kinetic temperature, and plasma number density, and those which do not. Empirical power-law correlations of the plasma current, and the ion kinetic temperature and number density were obtained as functions of the potential applied to the midplane electrode rings, the background neutral gas pressure, and the magnetic field strength. Additional parameters studied include the type of gas, the polarity of the midplane electrode rings (and hence the direction of the radial electric field), the mode of plasma operation, and the method of measuring the plasma number density. No significant departures from the scaling laws appear to occur at the highest ion kinetic temperatures or number densities obtained to date.

Observation of a Charge Density Wave Incommensuration Near the Superconducting Dome in Cu x TiSe 2

DOE PAGES

Kogar, A.; de la Pena, G. A.; Lee, Sangjun; ...

2017-01-11

X-ray diffraction was employed to study the evolution of the charge density wave (CDW) in Cu xTiSe 2 as a function of copper intercalation in order to clarify the relationship between the CDW and superconductivity. In this paper, the results show a CDW incommensuration arising at an intercalation value coincident with the onset of superconductivity at around x = 0.055(5) . Additionally, it was found that the charge density wave persists to higher intercalant concentrations than previously assumed, demonstrating that the CDW does not terminate inside the superconducting dome. A charge density wave peak was observed in samples up tomore » x = 0.091(6) , the highest copper concentration examined in this study. Lastly, the phase diagram established in this work suggests that charge density wave incommensuration may play a role in the formation of the superconducting state.« less

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

Van Vleet, Mary J.; Misquitta, Alston J.; Stone, Anthony J.

Short-range repulsion within inter-molecular force fields is conventionally described by either Lennard-Jones or Born-Mayer forms. Despite their widespread use, these simple functional forms are often unable to describe the interaction energy accurately over a broad range of inter-molecular distances, thus creating challenges in the development of ab initio force fields and potentially leading to decreased accuracy and transferability. Herein, we derive a novel short-range functional form based on a simple Slater-like model of overlapping atomic densities and an iterated stockholder atom (ISA) partitioning of the molecular electron density. We demonstrate that this Slater-ISA methodology yields a more accurate, transferable, andmore » robust description of the short-range interactions at minimal additional computational cost compared to standard Lennard-Jones or Born-Mayer approaches. Lastly, we show how this methodology can be adapted to yield the standard Born-Mayer functional form while still retaining many of the advantages of the Slater-ISA approach.« less

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

PubMed

Wang, Xuefeng; Andrews, Lester

2009-08-06

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

Influence of the local-spin-density correlation functional on the stability of bcc ferromagnetic iron

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

Singh, D.; Clougherty, D.P.; MacLaren, J.M.

1991-10-01

The influence of local-spin-dependent correlation effects on the predicted stable ground-state phase of iron is reexamined with use of general-potential linearized augmented-plane-wave calculations. Differences in the form of the Vosko-Wilk-Nusair (VWN) local-spin-density functional used in previous studies are noted, since in previous studies significant additional approximations were made with respect to those of Vosko, Wilk, and Nusan (Can. J. Phys. 58, 1200 (1980)) and of MacLaren, Clougherty, and Albers (Phys. Rev. B 42, 3205 (1990)). While the results of previous linear muffin-tin orbital calculations using the VWN functional predict a bcc ferromagnetic ground state, the present calculations show that themore » VWN spin-correlation effects fail to stabilize a bcc ground state. Considerable sensitivity to the form of the spin interpolation is found.« less

Ab initio approach to the ion stopping power at the plasma-solid interface

NASA Astrophysics Data System (ADS)

Bonitz, Michael; Schlünzen, Niclas; Wulff, Lasse; Joost, Jan-Philip; Balzer, Karsten

2016-10-01

The energy loss of ions in solids is of key relevance for many applications of plasmas, ranging from plasma technology to fusion. Standard approaches are based on density functional theory or SRIM simulations, however, the applicability range and accuracy of these results are difficult to assess, in particular, for low energies. Here we present an independent approach that is based on ab initio nonequilibrium Green functions theory, e.g. that allows to incorporate electronic correlations effects of the solid. We present the first application of this method to low-temperature plasmas, concentrating on proton and alpha-particle stopping in a graphene layer. In addition to the stopping power we present time-dependent results for the local electron density, the spectral function and the photoemission spectrum that is directly accessible in optical, UV or x-ray diagnostics. http://www.itap.uni-kiel.de/theo-physik/bonitz/.

Determination of the absolute configurations of synthetic daunorubicin analogues using vibrational circular dichroism spectroscopy and density functional theory.

PubMed

Yang, Guochun; Tran, Ha; Fan, Eric; Shi, Wei; Lowary, Todd L; Xu, Yunjie

2010-08-01

The absolute configurations of three synthesized anthracycline analogues have been determined using vibrational circular dichroism (VCD) spectroscopy and the density functional theory (DFT) calculations. The experimental VCD spectra of the three compounds have been measured for the first time in the film state, prepared from their CDCl(3) solutions. Conformational searches for the monomers and some dimers of the three compounds have been performed at the DFT level using the B3LYP functional and the 6-311G** and 6-311++G** basis sets. The corresponding vibrational absorption and VCD spectra have been calculated. The good agreement between the experimental and the calculated spectra allows one to assign the absolute configurations of the three compounds with high confidence. In addition, the dominant conformers of the three compounds have also been identified. Copyright 2010 Wiley-Liss, Inc.

Uncertainty quantification of voice signal production mechanical model and experimental updating

NASA Astrophysics Data System (ADS)

Cataldo, E.; Soize, C.; Sampaio, R.

2013-11-01

The aim of this paper is to analyze the uncertainty quantification in a voice production mechanical model and update the probability density function corresponding to the tension parameter using the Bayes method and experimental data. Three parameters are considered uncertain in the voice production mechanical model used: the tension parameter, the neutral glottal area and the subglottal pressure. The tension parameter of the vocal folds is mainly responsible for the changing of the fundamental frequency of a voice signal, generated by a mechanical/mathematical model for producing voiced sounds. The three uncertain parameters are modeled by random variables. The probability density function related to the tension parameter is considered uniform and the probability density functions related to the neutral glottal area and the subglottal pressure are constructed using the Maximum Entropy Principle. The output of the stochastic computational model is the random voice signal and the Monte Carlo method is used to solve the stochastic equations allowing realizations of the random voice signals to be generated. For each realization of the random voice signal, the corresponding realization of the random fundamental frequency is calculated and the prior pdf of this random fundamental frequency is then estimated. Experimental data are available for the fundamental frequency and the posterior probability density function of the random tension parameter is then estimated using the Bayes method. In addition, an application is performed considering a case with a pathology in the vocal folds. The strategy developed here is important mainly due to two things. The first one is related to the possibility of updating the probability density function of a parameter, the tension parameter of the vocal folds, which cannot be measured direct and the second one is related to the construction of the likelihood function. In general, it is predefined using the known pdf. Here, it is constructed in a new and different manner, using the own system considered.

Ionic fluids with r-6 pair interactions have power-law electrostatic screening

NASA Astrophysics Data System (ADS)

Kjellander, Roland; Forsberg, Björn

2005-06-01

The decay behaviour of radial distribution functions for large distances r is investigated for classical Coulomb fluids where the ions interact with an r-6 potential (e.g. a dispersion interaction) in addition to the Coulombic and the short-range repulsive potentials (e.g. a hard core). The pair distributions and the density-density (NN), charge-density (QN) and charge-charge (QQ) correlation functions are investigated analytically and by Monte Carlo simulations. It is found that the NN correlation function ultimately decays like r-6 for large r, just as it does for fluids of electroneutral particles interacting with an r-6 potential. The prefactor is proportional to the squared compressibility in both cases. The QN correlations decay in general like r-8 and the QQ correlations like r-10 in the ionic fluid. The average charge density around an ion decays generally like r-8 and the average electrostatic potential like r-6. This behaviour is in stark contrast to the decay behaviour for classical Coulomb fluids in the absence of the r-6 potential, where all these functions decay exponentially for large r. The power-law decays are, however, the same as for quantum Coulomb fluids. This indicates that the inclusion of the dispersion interaction as an effective r-6 interaction potential in classical systems yields the same decay behaviour for the pair correlations as in quantum ionic systems. An exceptional case is the completely symmetric binary electrolyte for which only the NN correlation has a power-law decay but not the QQ correlations. These features are shown by an analysis of the bridge function.

Functional traits determine tree growth and ecosystem productivity of a tropical montane forest: Insights from a long-term nutrient manipulation experiment.

PubMed

Báez, Selene; Homeier, Jürgen

2018-01-01

Trait-response effects are critical to forecast community structure and biomass production in highly diverse tropical forests. Ecological theory and few observation studies indicate that trees with acquisitive functional traits would respond more strongly to higher resource availability than those with conservative traits. We assessed how long-term tree growth in experimental nutrient addition plots (N, P, and N + P) varied as a function of morphological traits, tree size, and species identity. We also evaluated how trait-based responses affected stand scale biomass production considering the community structure. We found that tree growth depended on interactions between functional traits and the type or combination of nutrients added. Common species with acquisitive functional traits responded more strongly to nutrient addition, mainly to N + P. Phosphorous enhanced the growth rates of species with acquisitive and conservative traits, had mostly positive effects on common species and neutral or negative effects in rare species. Moreover, trees receiving N + P grew faster irrespective of their initial size relative to trees in control or to trees in other treatment plots. Finally, species responses were highly idiosyncratic suggesting that community processes including competition and niche dimensionality may be altered under increased resource availability. We found no statistically significant effects of nutrient additions on aboveground biomass productivity because acquisitive species had a limited potential to increase their biomass, possibly due to their generally lower wood density. In contrast, P addition increased the growth rates of species characterized by more conservative resource strategies (with higher wood density) that were poorly represented in the plant community. We provide the first long-term experimental evidence that trait-based responses, community structure, and community processes modulate the effects of increased nutrient availability on biomass productivity in a tropical forest. © 2017 John Wiley & Sons Ltd.

Density functional theory of gas-liquid phase separation in dilute binary mixtures

NASA Astrophysics Data System (ADS)

Okamoto, Ryuichi; Onuki, Akira

2016-06-01

We examine statics and dynamics of phase-separated states of dilute binary mixtures using density functional theory. In our systems, the difference of the solvation chemical potential between liquid and gas Δ {μ\\text{s}} (the Gibbs energy of transfer) is considerably larger than the thermal energy {{k}\\text{B}}T for each solute particle and the attractive interaction among the solute particles is weaker than that among the solvent particles. In these conditions, the saturated vapor pressure increases by {{k}\\text{B}}Tn2\\ell\\exp ≤ft(Δ {μ\\text{s}}/{{k}\\text{B}}T\\right) , where n2\\ell is the solute density added in liquid. For \\exp ≤ft(Δ {μ\\text{s}}/{{k}\\text{B}}T\\right)\\gg 1 , phase separation is induced at low solute densities in liquid and the new phase remains in gaseous states, even when the liquid pressure is outside the coexistence curve of the solvent. This explains the widely observed formation of stable nanobubbles in ambient water with a dissolved gas. We calculate the density and stress profiles across planar and spherical interfaces, where the surface tension decreases with increasing interfacial solute adsorption. We realize stable solute-rich bubbles with radius about 30 nm, which minimize the free energy functional. We then study dynamics around such a bubble after a decompression of the surrounding liquid, where the bubble undergoes a damped oscillation. In addition, we present some exact and approximate expressions for the surface tension and the interfacial stress tensor.

The effects of visitor density and intensity on the behavior of two captive jaguars (Panthera onca).

PubMed

Sellinger, Rebecca L; Ha, James C

2005-01-01

Several researchers have reported significant effects of visitor density and intensity on captive animal behavior. This study determined whether this was the case for 2 captive jaguars housed at the Woodland Park Zoo, Seattle, WA. Subjects were monitored for changes in behavior as a function of visitor density and intensity. The jaguars were observed for 8 hr per week for 29 weeks--March 31 until October 11, 1998--for a total of 230 hr. Continuous frequency sampling was used, and visitor density and intensity were recorded every minute. Parametric statistics were used to test for correlations between behavior and density, intensity, or a combination of the two. Both density and intensity were significant for time spent non-visible for both cats, and intensity showed a significant effect on the female's pacing behavior. In addition, the male cat exhibited a trend for increased aggression based on both visitor density and intensity and a trend of intensity affecting his social behavior. In conclusion, both density and intensity had a significant effect on behavior, with intensity showing a larger effect.

Atom-scale covalent electrochemical modification of single-layer graphene on SiC substrates by diaryliodonium salts

DOE PAGES

Gearba, Raluca I.; Mueller, Kory M.; Veneman, Peter A.; ...

2015-05-09

Owing to its high conductivity, graphene holds promise as an electrode for energy devices such as batteries and photovoltaics. However, to this end, the work function and doping levels in graphene need to be precisely tuned. One promising route for modifying graphene’s electronic properties is via controlled covalent electrochemical grafting of molecules. We show that by employing diaryliodonium salts instead of the commonly used diazonium salts, spontaneous functionalization is avoided. This then allows for precise tuning of the grafting density. Moreover, by employing bis(4-nitrophenyl)iodonium(III) tetrafluoroborate (DNP) salt calibration curves, the surface functionalization density (coverage) of glassy carbon was controlled usingmore » cyclic voltammetry in varying salt concentrations. These electro-grafting conditions and calibration curves translated directly over to modifying single layer epitaxial graphene substrates (grown on insulating 6H-SiC (0 0 0 1)). In addition to quantifying the functionalization densities using electrochemical methods, samples with low grafting densities were characterized by low-temperature scanning tunneling microscopy (LT-STM). We show that the use of buffer-layer free graphene substrates is required for clear observation of the nitrophenyl modifications. Furthermore, atomically-resolved STM images of single site modifications were obtained, showing no preferential grafting at defect sites or SiC step edges as supposed previously in the literature. Most of the grafts exhibit threefold symmetry, but occasional extended modifications (larger than 4 nm) were observed as well.« less

Density functional theory study the effects of oxygen-containing functional groups on oxygen molecules and oxygen atoms adsorbed on carbonaceous materials.

PubMed

Qi, Xuejun; Song, Wenwu; Shi, Jianwei

2017-01-01

Density functional theory was used to study the effects of different types of oxygen-containing functional groups on the adsorption of oxygen molecules and single active oxygen atoms on carbonaceous materials. During gasification or combustion reactions of carbonaceous materials, oxygen-containing functional groups such as hydroxyl(-OH), carbonyl(-CO), quinone(-O), and carboxyl(-COOH) are often present on the edge of graphite and can affect graphite's chemical properties. When oxygen-containing functional groups appear on a graphite surface, the oxygen molecules are strongly adsorbed onto the surface to form a four-member ring structure. At the same time, the O-O bond is greatly weakened and easily broken. The adsorption energy value indicates that the adsorption of oxygen molecules changes from physisorption to chemisorption for oxygen-containing functional groups on the edge of a graphite surface. In addition, our results indicate that the adsorption energy depends on the type of oxygen-containing functional group. When a single active oxygen atom is adsorbed on the bridge site of graphite, it gives rise to a stable epoxy structure. Epoxy can cause deformation of the graphite lattice due to the transition of graphite from sp2 to sp3 after the addition of an oxygen atom. For quinone group on the edge of graphite, oxygen atoms react with carbon atoms to form the precursor of CO2. Similarly, the single active oxygen atoms of carbonyl groups can interact with edge carbon atoms to form the precursor of CO2. The results show that oxygen-containing functional groups on graphite surfaces enhance the activity of graphite, which promotes adsorption on the graphite surface.

Density functional theory study the effects of oxygen-containing functional groups on oxygen molecules and oxygen atoms adsorbed on carbonaceous materials

PubMed Central

Song, Wenwu; Shi, Jianwei

2017-01-01

Density functional theory was used to study the effects of different types of oxygen-containing functional groups on the adsorption of oxygen molecules and single active oxygen atoms on carbonaceous materials. During gasification or combustion reactions of carbonaceous materials, oxygen-containing functional groups such as hydroxyl(-OH), carbonyl(-CO), quinone(-O), and carboxyl(-COOH) are often present on the edge of graphite and can affect graphite’s chemical properties. When oxygen-containing functional groups appear on a graphite surface, the oxygen molecules are strongly adsorbed onto the surface to form a four-member ring structure. At the same time, the O-O bond is greatly weakened and easily broken. The adsorption energy value indicates that the adsorption of oxygen molecules changes from physisorption to chemisorption for oxygen-containing functional groups on the edge of a graphite surface. In addition, our results indicate that the adsorption energy depends on the type of oxygen-containing functional group. When a single active oxygen atom is adsorbed on the bridge site of graphite, it gives rise to a stable epoxy structure. Epoxy can cause deformation of the graphite lattice due to the transition of graphite from sp2 to sp3 after the addition of an oxygen atom. For quinone group on the edge of graphite, oxygen atoms react with carbon atoms to form the precursor of CO2. Similarly, the single active oxygen atoms of carbonyl groups can interact with edge carbon atoms to form the precursor of CO2. The results show that oxygen-containing functional groups on graphite surfaces enhance the activity of graphite, which promotes adsorption on the graphite surface. PMID:28301544

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.

More Than Cholesterol Transporters: Lipoprotein Receptors in CNS Function and Neurodegeneration

PubMed Central

Lane-Donovan, Courtney E.; Philips, Gary T.; Herz, Joachim

2014-01-01

Members of the low-density lipoprotein (LDL) receptor gene family have a diverse set of biological functions that transcend lipid metabolism. Lipoprotein receptors have broad effects in both the developing and adult brain and participate in synapse development, cargo trafficking, and signal transduction. In addition, several family members play key roles in Alzheimer's disease pathogenesis and neurodegeneration. This review summarizes our current understanding of the role lipoprotein receptors play in CNS function and AD pathology, with a special emphasis on amyloid-independent roles in endocytosis and synaptic dysfunction. PMID:25144875

Ambipolar zinc-polyiodide electrolyte for a high-energy density aqueous redox flow battery

PubMed Central

Li, Bin; Nie, Zimin; Vijayakumar, M.; Li, Guosheng; Liu, Jun; Sprenkle, Vincent; Wang, Wei

2015-01-01

Redox flow batteries are receiving wide attention for electrochemical energy storage due to their unique architecture and advantages, but progress has so far been limited by their low energy density (~25 Wh l−1). Here we report a high-energy density aqueous zinc-polyiodide flow battery. Using the highly soluble iodide/triiodide redox couple, a discharge energy density of 167 Wh l−1 is demonstrated with a near-neutral 5.0 M ZnI2 electrolyte. Nuclear magnetic resonance study and density functional theory-based simulation along with flow test data indicate that the addition of an alcohol (ethanol) induces ligand formation between oxygen on the hydroxyl group and the zinc ions, which expands the stable electrolyte temperature window to from −20 to 50 °C, while ameliorating the zinc dendrite. With the high-energy density and its benign nature free from strong acids and corrosive components, zinc-polyiodide flow battery is a promising candidate for various energy storage applications. PMID:25709083

Experimental Research on Selective Laser Melting AlSi10Mg Alloys: Process, Densification and Performance

NASA Astrophysics Data System (ADS)

Chen, Zhen; Wei, Zhengying; Wei, Pei; Chen, Shenggui; Lu, Bingheng; Du, Jun; Li, Junfeng; Zhang, Shuzhe

2017-12-01

In this work, a set of experiments was designed to investigate the effect of process parameters on the relative density of the AlSi10Mg parts manufactured by SLM. The influence of laser scan speed v, laser power P and hatch space H, which were considered as the dominant parameters, on the powder melting and densification behavior was also studied experimentally. In addition, the laser energy density was introduced to evaluate the combined effect of the above dominant parameters, so as to control the SLM process integrally. As a result, a high relative density (> 97%) was obtained by SLM at an optimized laser energy density of 3.5-5.5 J/mm2. Moreover, a parameter-densification map was established to visually select the optimum process parameters for the SLM-processed AlSi10Mg parts with elevated density and required mechanical properties. The results provide an important experimental guidance for obtaining AlSi10Mg components with full density and gradient functional porosity by SLM.

Ambipolar zinc-polyiodide electrolyte for a high-energy density aqueous redox flow battery.

PubMed

Li, Bin; Nie, Zimin; Vijayakumar, M; Li, Guosheng; Liu, Jun; Sprenkle, Vincent; Wang, Wei

2015-02-24

Redox flow batteries are receiving wide attention for electrochemical energy storage due to their unique architecture and advantages, but progress has so far been limited by their low energy density (~25 Wh l(-1)). Here we report a high-energy density aqueous zinc-polyiodide flow battery. Using the highly soluble iodide/triiodide redox couple, a discharge energy density of 167 Wh l(-1) is demonstrated with a near-neutral 5.0 M ZnI2 electrolyte. Nuclear magnetic resonance study and density functional theory-based simulation along with flow test data indicate that the addition of an alcohol (ethanol) induces ligand formation between oxygen on the hydroxyl group and the zinc ions, which expands the stable electrolyte temperature window to from -20 to 50 °C, while ameliorating the zinc dendrite. With the high-energy density and its benign nature free from strong acids and corrosive components, zinc-polyiodide flow battery is a promising candidate for various energy storage applications.

Tuning the density profile of surface-grafted hyaluronan and the effect of counter-ions.

PubMed

Berts, Ida; Fragneto, Giovanna; Hilborn, Jöns; Rennie, Adrian R

2013-07-01

The present paper investigates the structure and composition of grafted sodium hyaluronan at a solid-liquid interface using neutron reflection. The solvated polymer at the surface could be described with a density profile that decays exponentially towards the bulk solution. The density profile of the polymer varied depending on the deposition protocol. A single-stage deposition resulted in denser polymer layers, while layers created with a two-stage deposition process were more diffuse and had an overall lower density. Despite the diffuse density profile, two-stage deposition leads to a higher surface excess. Addition of calcium ions causes a strong collapse of the sodium hyaluronan chains, increasing the polymer density near the surface. This effect is more pronounced on the sample prepared by two-stage deposition due to the initial less dense profile. This study provides an understanding at a molecular level of how surface functionalization alters the structure and how surface layers respond to changes in calcium ions in the solvent.

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

NASA Astrophysics Data System (ADS)

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

2017-01-01

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

Ab initio studies of 1,3,5,7-tetranitro-1,3,5,7-tetrazocine/1,3-dimethyl-2-imidazolidinone cocrystal under high pressure using dispersion corrected density functional theory

NASA Astrophysics Data System (ADS)

Gu, Bang-Ming; Lin, He; Zhu, Shun-Guan

2014-04-01

A detailed study of structural, electronic, and thermodynamic properties of 1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX)/1,3-dimethyl-2-imidazolidinone (DMI) cocrystal under the hydrostatic pressure of 0-100 GPa was performed by using dispersion-corrected density functional theory (DFT-D) method. The calculated crystal structure is in reasonable agreement with the experimental data at the ambient pressure. Based on the analysis of lattice constants, bond lengths, bond angles, and dihedral angles under compression, it is found that HMX molecules in HMX/DMI cocrystal are seriously distorted. In addition, as the pressure increases, the band gap decreases gradually, which suggests that HMX/DMI cocrystal is becoming more metallic. Some important intermolecular interactions between HMX and DMI are also observed in the density of states spectrum. Finally, its thermodynamic properties were characterized, and the results show that HMX/DMI cocrystal is more easily formed in the low pressure.

Electronic structure and partial charge distribution of Doxorubicin in different molecular environments.

PubMed

Poudel, Lokendra; Wen, Amy M; French, Roger H; Parsegian, V Adrian; Podgornik, Rudolf; Steinmetz, Nicole F; Ching, Wai-Yim

2015-05-18

The electronic structure and partial charge of doxorubicin (DOX) in three different molecular environments-isolated, solvated, and intercalated in a DNA complex-are studied by first-principles density functional methods. It is shown that the addition of solvating water molecules to DOX, together with the proximity to and interaction with DNA, has a significant impact on the electronic structure as well as on the partial charge distribution. Significant improvement in estimating the DOX-DNA interaction energy is achieved. The results are further elucidated by resolving the total density of states and surface charge density into different functional groups. It is concluded that the presence of the solvent and the details of the interaction geometry matter greatly in determining the stability of DOX complexation. Ab initio calculations on realistic models are an important step toward a more accurate description of the long-range interactions in biomolecular systems. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

An atomic orbital based real-time time-dependent density functional theory for computing electronic circular dichroism band spectra

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

Goings, Joshua J.; Li, Xiaosong, E-mail: xsli@uw.edu

2016-06-21

One of the challenges of interpreting electronic circular dichroism (ECD) band spectra is that different states may have different rotatory strength signs, determined by their absolute configuration. If the states are closely spaced and opposite in sign, observed transitions may be washed out by nearby states, unlike absorption spectra where transitions are always positive additive. To accurately compute ECD bands, it is necessary to compute a large number of excited states, which may be prohibitively costly if one uses the linear-response time-dependent density functional theory (TDDFT) framework. Here we implement a real-time, atomic-orbital based TDDFT method for computing the entiremore » ECD spectrum simultaneously. The method is advantageous for large systems with a high density of states. In contrast to previous implementations based on real-space grids, the method is variational, independent of nuclear orientation, and does not rely on pseudopotential approximations, making it suitable for computation of chiroptical properties well into the X-ray regime.« less

Ill-posedness of Dynamic Equations of Compressible Granular Flow

NASA Astrophysics Data System (ADS)

Shearer, Michael; Gray, Nico

2017-11-01

We introduce models for 2-dimensional time-dependent compressible flow of granular materials and suspensions, based on the rheology of Pouliquen and Forterre. The models include density dependence through a constitutive equation in which the density or volume fraction of solid particles with material density ρ* is taken as a function of an inertial number I: ρ = ρ * Φ(I), in which Φ(I) is a decreasing function of I. This modelling has different implications from models relying on critical state soil mechanics, in which ρ is treated as a variable in the equations, contributing to a flow rule. The analysis of the system of equations builds on recent work of Barker et al in the incompressible case. The main result is the identification of a criterion for well-posedness of the equations. We additionally analyze a modification that applies to suspensions, for which the rheology takes a different form and the inertial number reflects the role of the fluid viscosity.

Sound waves and flexural mode dynamics in two-dimensional crystals

NASA Astrophysics Data System (ADS)

Michel, K. H.; Scuracchio, P.; Peeters, F. M.

2017-09-01

Starting from a Hamiltonian with anharmonic coupling between in-plane acoustic displacements and out-of-plane (flexural) modes, we derived coupled equations of motion for in-plane displacements correlations and flexural mode density fluctuations. Linear response theory and time-dependent thermal Green's functions techniques are applied in order to obtain different response functions. As external perturbations we allow for stresses and thermal heat sources. The displacement correlations are described by a Dyson equation where the flexural density distribution enters as an additional perturbation. The flexural density distribution satisfies a kinetic equation where the in-plane lattice displacements act as a perturbation. In the hydrodynamic limit this system of coupled equations is at the basis of a unified description of elastic and thermal phenomena, such as isothermal versus adiabatic sound motion and thermal conductivity versus second sound. The general theory is formulated in view of application to graphene, two-dimensional h-BN, and 2H-transition metal dichalcogenides and oxides.

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

Lindgren, Ingvar; Salomonson, Sten

The locality theorem in density-functional theory (DFT) states that the functional derivative of the Hohenberg-Kohn universal functional can be expressed as a local multiplicative potential function, and this is the basis of DFT and of the successful Kohn-Sham model. Nesbet has in several papers [Phys. Rev. A 58, R12 (1998); ibid.65, 010502 (2001); Adv. Quant. Chem, 43, 1 (2003)] claimed that this theorem is in conflict with fundamental quantum physics, and as a consequence that the Hohenberg-Kohn theory cannot be generally valid. We have commented upon these works [Comment, Phys. Rev. A 67, 056501 (2003)] and recently extended the argumentsmore » [Adv. Quantum Chem. 43, 95 (2003)]. We have shown that there is no such conflict and that the locality theorem is inherently exact. In the present work we have furthermore verified this numerically by constructing a local Kohn-Sham potential for the 1s2s{sup 3}S state of helium that generates the many-body electron density and shown that the corresponding 2s Kohn-Sham orbital eigenvalue agrees with the ionization energy to nine digits. Similar result is obtained with the Hartree-Fock density. Therefore, in addition to verifying the locality theorem, this result also confirms the so-called ionization-potential theorem.« less

Differences in ecological structure, function, and native species abundance between native and invaded Hawaiian streams.

PubMed

Holitzki, Tara M; MacKenzie, Richard A; Wiegner, Tracy N; McDermid, Karla J

2013-09-01

Poeciliids, one of the most invasive species worldwide, are found on almost every continent and have been identified as an "invasive species of concern" in the United States, New Zealand, and Australia. Despite their global prevalence, few studies have quantified their impacts on tropical stream ecosystem structure, function, and biodiversity. Utilizing Hawaiian streams as model ecosystems, we documented how ecological structure, function, and native species abundance differed between poeciliid-free and poeciliid-invaded tropical streams. Stream nutrient yields, benthic biofilm biomass, densities of macroinvertebrates and fish, and community structures of benthic algae, macroinvertebrates, and fish were compared between streams with and without established poeciliid populations on the island of Hawai'i, Hawaii, USA. Sum nitrate (sigmaNO3(-) = NO3(-) + NO2(-)), total nitrogen, and total organic carbon yields were eight times, six times, and five times higher, respectively, in poeciliid streams than in poeciliid-free streams. Benthic biofilm ash-free dry mass was 1.5x higher in poeciliid streams than in poeciliid-free streams. Percentage contributions of chironomids and hydroptilid caddisflies to macroinvertebrate densities were lower in poeciliid streams compared to poeciliid-free streams, while percentage contributions of Cheumatopsyche analis caddisflies, Dugesia sp. flatworms, and oligochaetes were higher. Additionally, mean densities of native gobies were two times lower in poeciliid streams than in poeciliid-free ones, with poeciliid densities being approximately eight times higher than native fish densities. Our results, coupled with the wide distribution of invasive poeciliids across Hawaii and elsewhere in the tropics, suggest that poeciliids may negatively impact the ecosystem structure, function, and native species abundance of tropical streams they invade. This underscores the need for increased public awareness to prevent future introductions and for developing and implementing effective eradication and restoration strategies.

The Effective Correlation Theory for Liquid 3He

NASA Astrophysics Data System (ADS)

Puoskari, M.; Kallio, A.

1981-09-01

We show that when the antisymmetry of liquid 3He is treated with the effective correlation theory of Lado, the optimal HNC solution gives very good agreement with the optimal FHNC theory when in the latter the long wave length properties due to Fermi cancellations are treated properly. When in addition elementary diagrams are calculated with the Pade approximation, we obtain ground state energies that agree quite well with the Monte-Carlo results of Ceperley, Chester and Kalos and Levesque, especially at low densities. In addition we calculate the contribution of the three-body factors in the variational wave function. For the expectation value of the ground state energy we obtain altogether - 1.62 ± 0.15 K at a saturation density 0.015 ± 0.001 Å-3.

Variational principles for relativistic smoothed particle hydrodynamics

NASA Astrophysics Data System (ADS)

Monaghan, J. J.; Price, D. J.

2001-12-01

In this paper we show how the equations of motion for the smoothed particle hydrodynamics (SPH) method may be derived from a variational principle for both non-relativistic and relativistic motion when there is no dissipation. Because the SPH density is a function of the coordinates the derivation of the equations of motion through variational principles is simpler than in the continuum case where the density is defined through the continuity equation. In particular, the derivation of the general relativistic equations is more direct and simpler than that of Fock. The symmetry properties of the Lagrangian lead immediately to the familiar additive conservation laws of linear and angular momentum and energy. In addition, we show that there is an approximately conserved quantity which, in the continuum limit, is the circulation.

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

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.

The returns and risks of investment portfolio in stock market crashes

NASA Astrophysics Data System (ADS)

Li, Jiang-Cheng; Long, Chao; Chen, Xiao-Dan

2015-06-01

The returns and risks of investment portfolio in stock market crashes are investigated by considering a theoretical model, based on a modified Heston model with a cubic nonlinearity, proposed by Spagnolo and Valenti. Through numerically simulating probability density function of returns and the mean escape time of the model, the results indicate that: (i) the maximum stability of returns is associated with the maximum dispersion of investment portfolio and an optimal stop-loss position; (ii) the maximum risks are related with a worst dispersion of investment portfolio and the risks of investment portfolio are enhanced by increasing stop-loss position. In addition, the good agreements between the theoretical result and real market data are found in the behaviors of the probability density function and the mean escape time.

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

Motevaselian, M. H.; Mashayak, S. Y.; Aluru, N. R., E-mail: aluru@illinois.edu

Empirical potential-based quasi-continuum theory (EQT) provides a route to incorporate atomistic detail into continuum framework such as the Nernst-Planck equation. EQT can also be used to construct a grand potential functional for classical density functional theory (cDFT). The combination of EQT and cDFT provides a simple and fast approach to predict the inhomogeneous density, potential profiles, and thermodynamic properties of confined fluids. We extend the EQT-cDFT approach to confined fluid mixtures and demonstrate it by simulating a mixture of methane and hydrogen inside slit-like channels of graphene. We show that the EQT-cDFT predictions for the structure of the confined fluidmore » mixture compare well with the molecular dynamics simulation results. In addition, our results show that graphene slit nanopores exhibit a selective adsorption of methane over hydrogen.« less

Charge transport in nanostructured materials: Implementation and verification of constrained density functional theory

DOE PAGES

Goldey, Matthew B.; Brawand, Nicholas P.; Voros, Marton; ...

2017-04-20

The in silico design of novel complex materials for energy conversion requires accurate, ab initio simulation of charge transport. In this work, we present an implementation of constrained density functional theory (CDFT) for the calculation of parameters for charge transport in the hopping regime. We verify our implementation against literature results for molecular systems, and we discuss the dependence of results on numerical parameters and the choice of localization potentials. In addition, we compare CDFT results with those of other commonly used methods for simulating charge transport between nanoscale building blocks. As a result, we show that some of thesemore » methods give unphysical results for thermally disordered configurations, while CDFT proves to be a viable and robust approach.« less

Discharge Characterization of 40 cm-Microwave ECR Ion Source and Neutralizer

NASA Technical Reports Server (NTRS)

Foster, John E.; Patterson, Michael J.; Britton, Melissa

2003-01-01

Discharge characteristics of a 40 cm, 2.45 GHz Electron Cyclotron Resonance (ECR) ion thruster discharge chamber and neutralizer were acquired. Thruster bulk discharge plasma characteristics were assessed using a single Langmuir probe. Total extractable ion current was measured as a function of input microwave power and flow rate. Additionally, radial ion current density profiles at the thruster.s exit plane were characterized using five equally spaced Faraday probes. Distinct low and high density operating modes were observed as discharge input power was varied from 0 to 200 W. In the high mode, extractable ion currents as high as 0.82 A were measured. Neutralizer emission current was characterized as a function of flow rate and microwave power. Neutralizer extraction currents as high as 0.6 A were measured.

Molecular structure and vibrational spectra of three substituted 4-thioflavones by density functional theory and ab initio Hartree-Fock calculations

NASA Astrophysics Data System (ADS)

Li, Xiao-Hong; Liu, Xiang-Ru; Zhang, Xian-Zhou

2011-01-01

The vibrational frequencies of three substituted 4-thioflavones in the ground state have been calculated using the Hartree-Fock and density functional method (B3LYP) with 6-31G* and 6-31+G** basis sets. The structural analysis shows that there exists H-bonding in the selected compounds and the hydrogen bond lengths increase with the augment of the conjugate parameters of the substituent group on the benzene ring. A complete vibrational assignment aided by the theoretical harmonic wavenumber analysis was proposed. The theoretical spectrograms for FT-IR spectra of the title compounds have been constructed. In addition, it is noted that the selected compounds show significant activity against Shigella flexniri. Several electronic properties and thermodynamic parameters were also calculated.

Accurate structure, thermodynamics and spectroscopy of medium-sized radicals by hybrid Coupled Cluster/Density Functional Theory approaches: the case of phenyl radical

PubMed Central

Barone, Vincenzo; Biczysko, Malgorzata; Bloino, Julien; Egidi, Franco; Puzzarini, Cristina

2015-01-01

The CCSD(T) model coupled with extrapolation to the complete basis-set limit and additive approaches represents the “golden standard” for the structural and spectroscopic characterization of building blocks of biomolecules and nanosystems. However, when open-shell systems are considered, additional problems related to both specific computational difficulties and the need of obtaining spin-dependent properties appear. In this contribution, we present a comprehensive study of the molecular structure and spectroscopic (IR, Raman, EPR) properties of the phenyl radical with the aim of validating an accurate computational protocol able to deal with conjugated open-shell species. We succeeded in obtaining reliable and accurate results, thus confirming and, partly, extending the available experimental data. The main issue to be pointed out is the need of going beyond the CCSD(T) level by including a full treatment of triple excitations in order to fulfil the accuracy requirements. On the other hand, the reliability of density functional theory in properly treating open-shell systems has been further confirmed. PMID:23802956

Non-Transition-Metal Catalytic System for N 2 Reduction to NH 3: A Density Functional Theory Study of Al-Doped Graphene

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

Tian, Yong-Hui; Hu, Shuangli; Sheng, Xiaolan

The prevalent catalysts for natural and artificial N 2 fixation are known to hinge upon transition-metal (TM) elements. In this paper, we demonstrate by density functional theory that Al-doped graphene is a potential non-TM catalyst to convert N 2 to NH 3 in the presence of relatively mild proton/electron sources. In the integrated structure of the catalyst, the Al atom serves as a binding site and catalytic center while the graphene framework serves as an electron buffer during the successive proton/electron additions to N 2 and its various downstream N xH y intermediates. The initial hydrogenation of N 2 canmore » readily take place via an internal H-transfer process with the assistance of a Li + ion as an additive. Finally, in view of the recurrence of H transfer in the first step of N 2 reduction observed in biological nitrogenases and other synthetic catalysts, this finding highlights the significance of heteroatom-assisted H transfer in the design of synthetic catalysts for N 2 fixation.« less

Structure of cold nuclear matter at subnuclear densities by quantum molecular dynamics

NASA Astrophysics Data System (ADS)

Watanabe, Gentaro; Sato, Katsuhiko; Yasuoka, Kenji; Ebisuzaki, Toshikazu

2003-09-01

Structure of cold nuclear matter at subnuclear densities for the proton fraction x=0.5, 0.3, and 0.1 is investigated by quantum molecular dynamics (QMD) simulations. We demonstrate that the phases with slablike and rodlike nuclei, etc. can be formed dynamically from hot uniform nuclear matter without any assumptions on nuclear shape, and also systematically analyze the structure of cold matter using two-point correlation functions and Minkowski functionals. In our simulations, we also observe intermediate phases, which have complicated nuclear shapes. It has been found out that these phases can be characterized as those with negative Euler characteristic. Our result implies the existence of these kinds of phases in addition to the simple “pasta” phases in neutron star crusts and supernova inner cores. In addition, we investigate the properties of the effective QMD interaction used in the present work to examine the validity of our results. The resultant energy per nucleon ɛn of the pure neutron matter, the proton chemical μ(0)p in pure neutron matter and the nuclear surface tension Esurf are generally reasonable in comparison with other nuclear interactions.

Non-Transition-Metal Catalytic System for N 2 Reduction to NH 3: A Density Functional Theory Study of Al-Doped Graphene

DOE PAGES

Tian, Yong-Hui; Hu, Shuangli; Sheng, Xiaolan; ...

2018-01-16

The prevalent catalysts for natural and artificial N 2 fixation are known to hinge upon transition-metal (TM) elements. In this paper, we demonstrate by density functional theory that Al-doped graphene is a potential non-TM catalyst to convert N 2 to NH 3 in the presence of relatively mild proton/electron sources. In the integrated structure of the catalyst, the Al atom serves as a binding site and catalytic center while the graphene framework serves as an electron buffer during the successive proton/electron additions to N 2 and its various downstream N xH y intermediates. The initial hydrogenation of N 2 canmore » readily take place via an internal H-transfer process with the assistance of a Li + ion as an additive. Finally, in view of the recurrence of H transfer in the first step of N 2 reduction observed in biological nitrogenases and other synthetic catalysts, this finding highlights the significance of heteroatom-assisted H transfer in the design of synthetic catalysts for N 2 fixation.« less

Surface chemistry of oxygen on aluminum--Performance of the density functionals: PBE, PBE0, M06, and M06-L.

PubMed

Lousada, Cláudio M; Korzhavyi, Pavel A

2016-04-05

We investigated the performance of the density functional theory (DFT) functionals PBE, PBE0, M06, and M06-L for describing the molecular and dissociative adsorption of O2 onto pure and doped Al(111) surfaces. Adsorption of O2 was studied at the perfect Al(111) surface and compared with the case where an additional Al atom was present as an adatom. Additionally, we studied how these functionals perform when different dopants are present at the Al(111) surface in two distinct geometries: as an adatom or as a substitutional atom replacing an Al atom. The performance of the different functionals is greatly affected by the surface geometry. The inclusion of Hartree-Fock exchange in the functional leads to slight differences in adsorption energies for molecular adsorption of O2 . These differences become very pronounced for dissociative adsorption, with the hybrids PBE0 and M06 predicting more exergonic adsorption than PBE and M06-L. Furthermore, PBE0 and M06 predicted trends in adsorption energies for defective and perfect surfaces which are in line with the experimental knowledge of the effects of surface defects in adsorption energies. The predictions of the non-hybrids PBE and M06-L point in the opposite direction. The analysis of the contributions of the van der Waals (vdW) forces to the adsorption energies reveals that the PBE and PBE0 functionals have similar difficulties in describing vdW interactions for molecular adsorption of O2 while the M06 functional can give a description of these forces with an accuracy which is at least similar to that of the correction of the D3 type. © 2015 Wiley Periodicals, Inc.

Scaled Quantum Mechanical scale factors for vibrational calculations using alternate polarized and augmented basis sets with the B3LYP density functional calculation model

NASA Astrophysics Data System (ADS)

Legler, C. R.; Brown, N. R.; Dunbar, R. A.; Harness, M. D.; Nguyen, K.; Oyewole, O.; Collier, W. B.

2015-06-01

The Scaled Quantum Mechanical (SQM) method of scaling calculated force constants to predict theoretically calculated vibrational frequencies is expanded to include a broad array of polarized and augmented basis sets based on the split valence 6-31G and 6-311G basis sets with the B3LYP density functional. Pulay's original choice of a single polarized 6-31G(d) basis coupled with a B3LYP functional remains the most computationally economical choice for scaled frequency calculations. But it can be improved upon with additional polarization functions and added diffuse functions for complex molecular systems. The new scale factors for the B3LYP density functional and the 6-31G, 6-31G(d), 6-31G(d,p), 6-31G+(d,p), 6-31G++(d,p), 6-311G, 6-311G(d), 6-311G(d,p), 6-311G+(d,p), 6-311G++(d,p), 6-311G(2d,p), 6-311G++(2d,p), 6-311G++(df,p) basis sets are shown. The double d polarized models did not perform as well and the source of the decreased accuracy was investigated. An alternate system of generating internal coordinates that uses the out-of plane wagging coordinate whenever it is possible; makes vibrational assignments via potential energy distributions more meaningful. Automated software to produce SQM scaled vibrational calculations from different molecular orbital packages is presented.

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

Boosting the Performance of Ionic-Liquid-Based Supercapacitors with Polar Additives

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

Liu, Kun; Wu, Jianzhong

Recent years have witnessed growing interests in both the fundamentals and applications of electric double layer capacitors (EDLCs), also known as supercapacitors. A number of strategies have been explored to optimize the device performance in terms of both the energy and power densities. Because the properties of electric double layers (EDL) are sensitive to ion distributions in the close vicinity of the electrode surfaces, the supercapacitor performance is sensitive to both the electrode pore structure and the electrolyte composition. In this paper, we study the effects of polar additives on EDLC capacitance using the classical density functional theory within themore » framework of a coarse-grained model for the microscopic structure of the porous electrodes and room-temperature ionic liquids. The theoretical results indicate that a highly polar, low-molecular-weight additive is able to drastically increase the EDLC capacitance at low bulk concentration. Additionally, the additive is able to dampen the oscillatory dependence of the capacitance on the pore size, thereby boosting the performance of amorphous electrode materials. Finally, the theoretical predictions are directly testable with experiments and provide new insights into the additive effects on EDL properties.« less

A Mechanistic Investigation of the Gold(III)-Catalyzed Hydrofurylation of C-C Multiple Bonds.

PubMed

Hossein Bagi, Amin; Khaledi, Yousef; Ghari, Hossein; Arndt, Sebastian; Hashmi, A Stephen K; Yates, Brian F; Ariafard, Alireza

2016-11-09

The gold-catalyzed direct functionalization of aromatic C-H bonds has attracted interest for constructing organic compounds which have application in pharmaceuticals, agrochemicals, and other important fields. In the literature, two major mechanisms have been proposed for these catalytic reactions: inner-sphere syn-addition and outer-sphere anti-addition (Friedel-Crafts-type mechanism). In this article, the AuCl 3 -catalyzed hydrofurylation of allenyl ketone, vinyl ketone, ketone, and alcohol substrates is investigated with the aid of density functional theory calculations, and it is found that the corresponding functionalizations are best rationalized in terms of a novel mechanism called "concerted electrophilic ipso-substitution" (CEIS) in which the gold(III)-furyl σ-bond produced by furan auration acts as a nucleophile and attacks the protonated substrate via an outer-sphere mechanism. This unprecedented mechanism needs to be considered as an alternative plausible pathway for gold(III)-catalyzed arene functionalization reactions in future studies.

Using Wannier functions to improve solid band gap predictions in density functional theory

DOE PAGES

Ma, Jie; Wang, Lin-Wang

2016-04-26

Enforcing a straight-line condition of the total energy upon removal/addition of fractional electrons on eigen states has been successfully applied to atoms and molecules for calculating ionization potentials and electron affinities, but fails for solids due to the extended nature of the eigen orbitals. Here we have extended the straight-line condition to the removal/addition of fractional electrons on Wannier functions constructed within the occupied/unoccupied subspaces. It removes the self-interaction energies of those Wannier functions, and yields accurate band gaps for solids compared to experiments. It does not have any adjustable parameters and the computational cost is at the DFT level.more » This method can also work for molecules, providing eigen energies in good agreement with experimental ionization potentials and electron affinities. Our approach can be viewed as an alternative approach of the standard LDA+U procedure.« less

Relative importance of impervious area, drainage density, width function, and subsurface storm drainage on flood runoff from an urbanized catchment

NASA Astrophysics Data System (ADS)

Ogden, Fred L.; Raj Pradhan, Nawa; Downer, Charles W.; Zahner, Jon A.

2011-12-01

The literature contains contradictory conclusions regarding the relative effects of urbanization on peak flood flows due to increases in impervious area, drainage density and width function, and the addition of subsurface storm drains. We used data from an urbanized catchment, the 14.3 km2 Dead Run watershed near Baltimore, Maryland, USA, and the physics-based gridded surface/subsurface hydrologic analysis (GSSHA) model to examine the relative effect of each of these factors on flood peaks, runoff volumes, and runoff production efficiencies. GSSHA was used because the model explicitly includes the spatial variability of land-surface and hydrodynamic parameters, including subsurface storm drains. Results indicate that increases in drainage density, particularly increases in density from low values, produce significant increases in the flood peaks. For a fixed land-use and rainfall input, the flood magnitude approaches an upper limit regardless of the increase in the channel drainage density. Changes in imperviousness can have a significant effect on flood peaks for both moderately extreme and extreme storms. For an extreme rainfall event with a recurrence interval in excess of 100 years, imperviousness is relatively unimportant in terms of runoff efficiency and volume, but can affect the peak flow depending on rainfall rate. Changes to the width function affect flood peaks much more than runoff efficiency, primarily in the case of lower density drainage networks with less impermeable area. Storm drains increase flood peaks, but are overwhelmed during extreme rainfall events when they have a negligible effect. Runoff in urbanized watersheds with considerable impervious area shows a marked sensitivity to rainfall rate. This sensitivity explains some of the contradictory findings in the literature.

Molcas 8: New capabilities for multiconfigurational quantum chemical calculations across the periodic table.

PubMed

Aquilante, Francesco; Autschbach, Jochen; Carlson, Rebecca K; Chibotaru, Liviu F; Delcey, Mickaël G; De Vico, Luca; Fdez Galván, Ignacio; Ferré, Nicolas; Frutos, Luis Manuel; Gagliardi, Laura; Garavelli, Marco; Giussani, Angelo; Hoyer, Chad E; Li Manni, Giovanni; Lischka, Hans; Ma, Dongxia; Malmqvist, Per Åke; Müller, Thomas; Nenov, Artur; Olivucci, Massimo; Pedersen, Thomas Bondo; Peng, Daoling; Plasser, Felix; Pritchard, Ben; Reiher, Markus; Rivalta, Ivan; Schapiro, Igor; Segarra-Martí, Javier; Stenrup, Michael; Truhlar, Donald G; Ungur, Liviu; Valentini, Alessio; Vancoillie, Steven; Veryazov, Valera; Vysotskiy, Victor P; Weingart, Oliver; Zapata, Felipe; Lindh, Roland

2016-02-15

In this report, we summarize and describe the recent unique updates and additions to the Molcas quantum chemistry program suite as contained in release version 8. These updates include natural and spin orbitals for studies of magnetic properties, local and linear scaling methods for the Douglas-Kroll-Hess transformation, the generalized active space concept in MCSCF methods, a combination of multiconfigurational wave functions with density functional theory in the MC-PDFT method, additional methods for computation of magnetic properties, methods for diabatization, analytical gradients of state average complete active space SCF in association with density fitting, methods for constrained fragment optimization, large-scale parallel multireference configuration interaction including analytic gradients via the interface to the Columbus package, and approximations of the CASPT2 method to be used for computations of large systems. In addition, the report includes the description of a computational machinery for nonlinear optical spectroscopy through an interface to the QM/MM package Cobramm. Further, a module to run molecular dynamics simulations is added, two surface hopping algorithms are included to enable nonadiabatic calculations, and the DQ method for diabatization is added. Finally, we report on the subject of improvements with respects to alternative file options and parallelization. © 2015 Wiley Periodicals, Inc.

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

Conceptual design of new polychromator on Thomson scattering system to measure Zeff.

PubMed

Lee, Jongha; Oh, Seungtae; Wi, Hanmin; Oh, Youngkook; Yamada, I; Narihara, K; Kawahata, K; Jeon, Jongsu

2012-10-01

To measure the Z(eff) with electron temperature (T(e)) and electron density (n(e)) profiles at the same time and the same position in the KSTAR tokamak, we design a new polychromator for Thomson scattering system that has additional function. The additional function is measuring bremsstrahlung intensity to calculate Z(eff) independent of Thomson signals. For this new polychromator, we design and fabricate a collimation lens set, and interference filter that has center wavelength of 523 nm and 2 nm FWHM. Finally, we change the lenses, detector diodes, and add the bremsstrahlung filter on the KSTAR edge Thomson scattering polychromator. Then this new polychromator was tested by Tungsten light and monochromator.

A hybrid pareto mixture for conditional asymmetric fat-tailed distributions.

PubMed

Carreau, Julie; Bengio, Yoshua

2009-07-01

In many cases, we observe some variables X that contain predictive information over a scalar variable of interest Y , with (X,Y) pairs observed in a training set. We can take advantage of this information to estimate the conditional density p(Y|X = x). In this paper, we propose a conditional mixture model with hybrid Pareto components to estimate p(Y|X = x). The hybrid Pareto is a Gaussian whose upper tail has been replaced by a generalized Pareto tail. A third parameter, in addition to the location and spread parameters of the Gaussian, controls the heaviness of the upper tail. Using the hybrid Pareto in a mixture model results in a nonparametric estimator that can adapt to multimodality, asymmetry, and heavy tails. A conditional density estimator is built by modeling the parameters of the mixture estimator as functions of X. We use a neural network to implement these functions. Such conditional density estimators have important applications in many domains such as finance and insurance. We show experimentally that this novel approach better models the conditional density in terms of likelihood, compared to competing algorithms: conditional mixture models with other types of components and a classical kernel-based nonparametric model.

Stochastic density functional theory at finite temperatures

NASA Astrophysics Data System (ADS)

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

2018-03-01

Simulations in the warm dense matter regime using finite temperature Kohn-Sham density functional theory (FT-KS-DFT), while frequently used, are computationally expensive due to the partial occupation of a very large number of high-energy KS eigenstates which are obtained from subspace diagonalization. We have developed a stochastic method for applying FT-KS-DFT, that overcomes the bottleneck of calculating the occupied KS orbitals by directly obtaining the density from the KS Hamiltonian. The proposed algorithm scales as O (" close=")N3T3)">N T-1 and is compared with the high-temperature limit scaling O Effects of Acids, Bases, and Heteroatoms on Proximal Radial Distribution Functions for Proteins

PubMed Central

Nguyen, Bao Linh; Pettitt, B. Montgomery

2015-01-01

The proximal distribution of water around proteins is a convenient method of quantifying solvation. We consider the effect of charged and sulfur-containing amino acid side-chain atoms on the proximal radial distribution function (pRDF) of water molecules around proteins using side-chain analogs. The pRDF represents the relative probability of finding any solvent molecule at a distance from the closest or surface perpendicular protein atom. We consider the near-neighbor distribution. Previously, pRDFs were shown to be universal descriptors of the water molecules around C, N, and O atom types across hundreds of globular proteins. Using averaged pRDFs, a solvent density around any globular protein can be reconstructed with controllable relative error. Solvent reconstruction using the additional information from charged amino acid side-chain atom types from both small models and protein averages reveals the effects of surface charge distribution on solvent density and improves the reconstruction errors relative to simulation. Solvent density reconstructions from the small-molecule models are as effective and less computationally demanding than reconstructions from full macromolecular models in reproducing preferred hydration sites and solvent density fluctuations. PMID:26388706

A density functional theory model of mechanically activated silyl ester hydrolysis

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

Pill, Michael F.; Schmidt, Sebastian W.; Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Olshausenstraße 40, 24098 Kiel

2014-01-28

To elucidate the mechanism of the mechanically activated dissociation of chemical bonds between carboxymethylated amylose (CMA) and silane functionalized silicon dioxide, we have investigated the dissociation kinetics of the bonds connecting CMA to silicon oxide surfaces with density functional calculations including the effects of force, solvent polarizability, and pH. We have determined the activation energies, the pre-exponential factors, and the reaction rate constants of candidate reactions. The weakest bond was found to be the silyl ester bond between the silicon and the alkoxy oxygen atom. Under acidic conditions, spontaneous proton addition occurs close to the silyl ester such that neutralmore » reactions become insignificant. Upon proton addition at the most favored position, the activation energy for bond hydrolysis becomes 31 kJ mol{sup −1}, which agrees very well with experimental observation. Heterolytic bond scission in the protonated molecule has a much higher activation energy. The experimentally observed bi-exponential rupture kinetics can be explained by different side groups attached to the silicon atom of the silyl ester. The fact that different side groups lead to different dissociation kinetics provides an opportunity to deliberately modify and tune the kinetic parameters of mechanically activated bond dissociation of silyl esters.« less

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.

Dietary antioxidants preserve endothelium-dependent vessel relaxation in cholesterol-fed rabbits.

PubMed Central

Keaney, J F; Gaziano, J M; Xu, A; Frei, B; Curran-Celentano, J; Shwaery, G T; Loscalzo, J; Vita, J A

1993-01-01

Recent evidence suggests that dietary therapy with lipid-soluble antioxidants may be beneficial for patients with atherosclerotic vascular disease but the potential mechanism(s) for these observations remain obscure. Abnormalities in endothelium-dependent control of vascular tone develop early in the course of atherosclerosis and may result from oxidative modification of low density lipoproteins. We examined the role of dietary antioxidants in preserving normal endothelial cell vasodilator function in cholesterol-fed rabbits with particular attention to possible effects on serum lipoproteins, low density lipoprotein oxidation, and atherogenesis. Male New Zealand White rabbits were fed diets containing no additive (controls), 1% cholesterol (cholesterol group), or 1% cholesterol chow supplemented with either beta-carotene (0.6 g/kg of chow) or alpha-tocopherol (1000 international units/kg of chow) for a 28-day period. After dietary therapy, thoracic aortae were harvested for assay of vascular function and for pathologic examination and tissue antioxidant levels. Compared to controls, acetylcholine- and A23187-mediated endothelium-dependent relaxations were significantly impaired in vessels from the cholesterol group (P < 0.001), whereas vessels from animals treated with beta-carotene or alpha-tocopherol demonstrated normal endothelium-dependent arterial relaxation. Preservation of endothelial function was associated with vascular incorporation of alpha-tocopherol and beta-carotene but was unrelated to plasma lipoprotein levels, smooth muscle cell function, or the extent of atherosclerosis. Increased low density lipoprotein resistance to ex vivo copper-mediated oxidation was observed only in the alpha-tocopherol group. Our results suggest that dietary antioxidants may benefit patients with atherosclerosis by preserving endothelial vasodilator function through a mechanism related to vascular tissue antioxidant content and not reflected by assay of low density lipoprotein resistance to ex vivo oxidation. PMID:8265642

Distribution function approach to redshift space distortions. Part IV: perturbation theory applied to dark matter

NASA Astrophysics Data System (ADS)

Vlah, Zvonimir; Seljak, Uroš; McDonald, Patrick; Okumura, Teppei; Baldauf, Tobias

2012-11-01

We develop a perturbative approach to redshift space distortions (RSD) using the phase space distribution function approach and apply it to the dark matter redshift space power spectrum and its moments. RSD can be written as a sum over density weighted velocity moments correlators, with the lowest order being density, momentum density and stress energy density. We use standard and extended perturbation theory (PT) to determine their auto and cross correlators, comparing them to N-body simulations. We show which of the terms can be modeled well with the standard PT and which need additional terms that include higher order corrections which cannot be modeled in PT. Most of these additional terms are related to the small scale velocity dispersion effects, the so called finger of god (FoG) effects, which affect some, but not all, of the terms in this expansion, and which can be approximately modeled using a simple physically motivated ansatz such as the halo model. We point out that there are several velocity dispersions that enter into the detailed RSD analysis with very different amplitudes, which can be approximately predicted by the halo model. In contrast to previous models our approach systematically includes all of the terms at a given order in PT and provides a physical interpretation for the small scale dispersion values. We investigate RSD power spectrum as a function of μ, the cosine of the angle between the Fourier mode and line of sight, focusing on the lowest order powers of μ and multipole moments which dominate the observable RSD power spectrum. Overall we find considerable success in modeling many, but not all, of the terms in this expansion. This is similar to the situation in real space, but predicting power spectrum in redshift space is more difficult because of the explicit influence of small scale dispersion type effects in RSD, which extend to very large scales.

Gray Matter Loss and Related Functional Connectivity Alterations in A Chinese Family With Benign Adult Familial Myoclonic Epilepsy.

PubMed

Zeng, Ling-Li; Long, Lili; Shen, Hui; Fang, Peng; Song, Yanmin; Zhang, Linlin; Xu, Lin; Gong, Jian; Zhang, Yunci; Zhang, Yong; Xiao, Bo; Hu, Dewen

2015-10-01

Benign adult familial myoclonic epilepsy (BAFME) is a non-progressive monogenic epilepsy syndrome. So far, the structural and functional brain reorganizations in BAFME remain uncharacterized. This study aims to investigate gray matter atrophy and related functional connectivity alterations in patients with BAFME using magnetic resonance imaging (MRI).Eleven BAFME patients from a Chinese pedigree and 15 matched healthy controls were enrolled in the study. Optimized voxel-based morphometric and resting-state functional MRI approaches were performed to measure gray matter atrophy and related functional connectivity, respectively. The Trail-Making Test-part A and part B, Digit Symbol Test (DST), and Verbal Fluency Test (VFT) were carried out to evaluate attention and executive functions.The BAFME patients exhibited significant gray matter loss in the right hippocampus, right temporal pole, left orbitofrontal cortex, and left dorsolateral prefrontal cortex. With these regions selected as seeds, the voxel-wise functional connectivity analysis revealed that the right hippocampus showed significantly enhanced connectivity with the right inferior parietal lobule, bilateral middle cingulate cortex, left precuneus, and left precentral gyrus. Moreover, the BAFME patients showed significant lower scores in DST and VFT tests compared with the healthy controls. The gray matter densities of the right hippocampus, right temporal pole, and left orbitofrontal cortex were significantly positively correlated with the DST scores. In addition, the gray matter density of the right temporal pole was significantly positively correlated with the VFT scores, and the gray matter density of the right hippocampus was significantly negatively correlated with the duration of illness in the patients.The current study demonstrates gray matter loss and related functional connectivity alterations in the BAFME patients, perhaps underlying deficits in attention and executive functions in the BAFME.

Electronic states of aryl radical functionalized graphenes: Density functional theory study

NASA Astrophysics Data System (ADS)

Tachikawa, Hiroto; Kawabata, Hiroshi

2016-06-01

Functionalized graphenes are known as a high-performance molecular device. In the present study, the structures and electronic states of the aryl radical functionalized graphene have been investigated by the density functional theory (DFT) method to elucidate the effects of functionalization on the electronic states of graphene (GR). Also, the mechanism of aryl radical reaction with GR was investigated. The benzene, biphenyl, p-terphenyl, and p-quaterphenyl radicals [denoted by (Bz) n (n = 1-4), where n means numbers of benzene rings in aryl radical] were examined as aryl radicals. The DFT calculation of GR-(Bz) n (n = 1-4) showed that the aryl radical binds to the carbon atom of GR, and a C-C single bond was formed. The binding energies of aryl radicals to GR were calculated to be ca. 6.0 kcal mol-1 at the CAM-B3LYP/6-311G(d,p) level. It was found that the activation barrier exists in the aryl radical addition: the barrier heights were calculated to be 10.0 kcal mol-1. The electronic states of GR-(Bz) n were examined on the basis of theoretical results.

Admitting the Inadmissible: Adjoint Formulation for Incomplete Cost Functionals in Aerodynamic Optimization

NASA Technical Reports Server (NTRS)

Arian, Eyal; Salas, Manuel D.

1997-01-01

We derive the adjoint equations for problems in aerodynamic optimization which are improperly considered as "inadmissible." For example, a cost functional which depends on the density, rather than on the pressure, is considered "inadmissible" for an optimization problem governed by the Euler equations. We show that for such problems additional terms should be included in the Lagrangian functional when deriving the adjoint equations. These terms are obtained from the restriction of the interior PDE to the control surface. Demonstrations of the explicit derivation of the adjoint equations for "inadmissible" cost functionals are given for the potential, Euler, and Navier-Stokes equations.

On statistical properties of traded volume in financial markets

NASA Astrophysics Data System (ADS)

de Souza, J.; Moyano, L. G.; Duarte Queirós, S. M.

2006-03-01

In this article we study the dependence degree of the traded volume of the Dow Jones 30 constituent equities by using a nonextensive generalised form of the Kullback-Leibler information measure. Our results show a slow decay of the dependence degree as a function of the lag. This feature is compatible with the existence of non-linearities in this type time series. In addition, we introduce a dynamical mechanism whose associated stationary probability density function (PDF) presents a good agreement with the empirical results.

Structures, phase stabilities, and electrical potentials of Li-Si battery anode materials

NASA Astrophysics Data System (ADS)

Tipton, William W.; Bealing, Clive R.; Mathew, Kiran; Hennig, Richard G.

2013-05-01

The Li-Si materials system holds promise for use as an anode in Li-ion battery applications. For this system, we determine the charge capacity, voltage profiles, and energy storage density solely by ab initio methods without any experimental input. We determine the energetics of the stable and metastable Li-Si phases likely to form during the charging and discharging of a battery. Ab initio molecular dynamics simulations are used to model the structure of amorphous Li-Si as a function of composition, and a genetic algorithm coupled to density-functional theory searches the Li-Si binary phase diagram for small-cell, metastable crystal structures. Calculations of the phonon densities of states using density-functional perturbation theory for selected structures determine the importance of vibrational, including zero-point, contributions to the free energies. The energetics and local structural motifs of these metastable Li-Si phases closely resemble those of the amorphous phases, making these small unit cell crystal phases good approximants of the amorphous phase for use in further studies. The charge capacity is estimated, and the electrical potential profiles and the energy density of Li-Si anodes are predicted. We find, in good agreement with experimental measurements, that the formation of amorphous Li-Si only slightly increases the anode potential. Additionally, the genetic algorithm identifies a previously unreported member of the Li-Si binary phase diagram with composition Li5Si2 which is stable at 0 K with respect to previously known phases. We discuss its relationship to the partially occupied Li7Si3 phase.

Measuring the stellar luminosity function and spatial density profile of the inner 0.5 pc of the Milky Way nuclear star cluster

NASA Astrophysics Data System (ADS)

Do, Tuan; Ghez, Andrea; Lu, Jessica R.; Morris, Mark R.; Yelda, Sylvana; Martinez, Gregory D.; Peter, Annika H. G.; Wright, Shelley; Bullock, James; Kaplinghat, Manoj; Matthews, K.

2012-07-01

We report on measurements of the luminosity function of early (young) and late-type (old) stars in the central 0.5 pc of the Milky Way nuclear star cluster as well as the density profiles of both components. The young (~ 6 Myr) and old stars (> 1 Gyr) in this region provide different physical probes of the environment around a supermassive black hole; the luminosity function of the young stars offers us a way to measure the initial mass function from star formation in an extreme environment, while the density profile of the old stars offers us a probe of the dynamical interaction of a star cluster with a massive black hole. The two stellar populations are separated through a near-infrared spectroscopic survey using the integral-field spectrograph OSIRIS on Keck II behind the laser guide star adaptive optics system. This spectroscopic survey is able to separate early-type (young) and late-type (old) stars with a completeness of 50% at K' = 15.5. We describe our method of completeness correction using a combination of star planting simulations and Bayesian inference. The completeness corrected luminosity function of the early-type stars contains significantly more young stars at faint magnitudes compared to previous surveys with similar depth. In addition, by using proper motion and radial velocity measurements along with anisotropic spherical Jeans modeling of the cluster, it is possible to measure the spatial density profile of the old stars, which has been difficult to constrain with number counts alone. The most probable model shows that the spatial density profile, n(r) propto r-γ, to be shallow with γ = 0.4 ± 0.2, which is much flatter than the dynamically relaxed case of γ = 3/2 to 7/4, but does rule out a 'hole' in the distribution of old stars. We show, for the first time, that the spatial density profile, the black hole mass, and velocity anisotropy can be fit simultaneously to obtain a black hole mass that is consistent with that derived from individual orbits of stars at distances < 1000 AU from the Galactic center.

Empirical temperature-dependent intermolecular potentials determined by data mining from crystal data

NASA Astrophysics Data System (ADS)

Hofmann, D. W. M.; Kuleshova, L. N.

2018-05-01

Modern force fields are accurate enough to describe thermal effects in molecular crystals. Here, we have extended our earlier approach to discrete force fields for various temperatures to a force field with a continuous function. For the parametrisation of the force field, we used data mining on experimental structures with the temperature as an additional descriptor. The obtained force field can be used to minimise energy at a finite temperature and for molecular dynamics with zero-K potentials. The applicability of the method has been demonstrated for the prediction of crystal density, temperature density gradients and transition temperature.

The any particle molecular orbital grid-based Hartree-Fock (APMO-GBHF) approach

NASA Astrophysics Data System (ADS)

Posada, Edwin; Moncada, Félix; Reyes, Andrés

2018-02-01

The any particle molecular orbital grid-based Hartree-Fock approach (APMO-GBHF) is proposed as an initial step to perform multi-component post-Hartree-Fock, explicitly correlated, and density functional theory methods without basis set errors. The method has been applied to a number of electronic and multi-species molecular systems. Results of these calculations show that the APMO-GBHF total energies are comparable with those obtained at the APMO-HF complete basis set limit. In addition, results reveal a considerable improvement in the description of the nuclear cusps of electronic and non-electronic densities.

Altered auditory and vestibular functioning in individuals with low bone mineral density: a systematic review.

PubMed

Singh, Niraj Kumar; Jha, Raghav Hira; Gargeshwari, Aditi; Kumar, Prawin

2018-01-01

Alteration in the process of bone remodelling is associated with falls and fractures due to increased bone fragility and altered calcium functioning. The auditory system consists of skeletal structures and is, therefore, prone to getting affected by altered bone remodelling. In addition, the vestibule consists of huge volumes of calcium (CaCO3) in the form of otoconia crystals and alteration in functioning calcium levels could, therefore, result in vestibular symptoms. Thus, the present study aimed at compiling information from various studies on assessment of auditory or vestibular systems in individuals with reduced bone mineral density (BMD). A total of 1977 articles were searched using various databases and 19 full-length articles which reported auditory and vestibular outcomes in persons with low BMD were reviewed. An intricate relationship between altered BMD and audio-vestibular function was evident from the studies; nonetheless, how one aspect of hearing or balance affects the other is not clear. Significant effect of reduced bone mineral density could probably be due to the metabolic changes at the level of cochlea, secondary to alterations in BMD. One could also conclude that sympathetic remodelling is associated with vestibular problems in individual; however, whether vestibular problems lead to altered BMD cannot be ascertained with confidence. The studies reviewed in the article provide an evidence of possible involvement of hearing and vestibular system abnormalities in individuals with reduced bone mineral density. Hence, the assessment protocol for these individuals must include hearing and balance evaluation as mandatory for planning appropriate management.

Quasiparticle and hybrid density functional methods in defect studies: An application to the nitrogen vacancy in GaN

NASA Astrophysics Data System (ADS)

Lewis, D. K.; Matsubara, M.; Bellotti, E.; Sharifzadeh, S.

2017-12-01

Defects in semiconductors can play a vital role in the performance of electronic devices, with native defects often dominating the electronic properties of the semiconductor. Understanding the relationship between structural defects and electronic function will be central to the design of new high-performance materials. In particular, it is necessary to quantitatively understand the energy and lifetime of electronic states associated with the defect. Here, we apply first-principles density functional theory (DFT) and many-body perturbation theory within the GW approximation to understand the nature and energy of the defect states associated with a charged nitrogen vacancy on the electronic properties of gallium nitride (GaN), as a model of a well-studied and important wide gap semiconductor grown with defects. We systematically investigate the sources of error associated with the GW approximation and the role of the underlying atomic structure on the predicted defect state energies. Additionally, analysis of the computed electronic density of states (DOS) reveals that there is one occupied defect state 0.2 eV below the valence band maximum and three unoccupied defect states at energy of 0.2-0.4 eV above the conduction band minimum, suggesting that this defect in the +1 charge state will not behave as a carrier trap. Furthermore, we compare the character and energy of the defect state obtained from GW and DFT using the HSE approximate density functional and find excellent agreement. This systematic study provides a more complete understanding of how to obtain quantitative defect energy states in bulk semiconductors.

Kinetics of the addition of olefins to Si-centered radicals: the critical role of dispersion interactions revealed by theory and experiment.

PubMed

Johnson, Erin R; Clarkin, Owen J; Dale, Stephen G; DiLabio, Gino A

2015-06-04

Solution-phase rate constants for the addition of selected olefins to the triethylsilyl and tris(trimethylsilyl)silyl radicals are measured using laser-flash photolysis and competition kinetics. The results are compared with predictions from density functional theory (DFT) calculations, both with and without dispersion corrections obtained from the exchange-hole dipole moment (XDM) model. Without a dispersion correction, the rate constants are consistently underestimated; the errors increase with system size, up to 10(6) s(-1) for the largest system considered. Dispersion interactions preferentially stabilize the transition states relative to the separated reactants and bring the DFT-calculated rate constants into excellent agreement with experiment. Thus, dispersion interactions are found to play a key role in determining the kinetics for addition reactions, particularly those involving sterically bulky functional groups.

Seed viability detection using computerized false-color radiographic image enhancement

NASA Technical Reports Server (NTRS)

Vozzo, J. A.; Marko, Michael

1994-01-01

Seed radiographs are divided into density zones which are related to seed germination. The seeds which germinate have densities relating to false-color red. In turn, a seed sorter may be designed which rejects those seeds not having sufficient red to activate a gate along a moving belt containing the seed source. This results in separating only seeds with the preselected densities representing biological viability lending to germination. These selected seeds demand a higher market value. Actual false-coloring isn't required for a computer to distinguish the significant gray-zone range. This range can be predetermined and screened without the necessity of red imaging. Applying false-color enhancement is a means of emphasizing differences in densities of gray within any subject from photographic, radiographic, or video imaging. Within the 0-255 range of gray levels, colors can be assigned to any single level or group of gray levels. Densitometric values then become easily recognized colors which relate to the image density. Choosing a color to identify any given density allows separation by morphology or composition (form or function). Additionally, relative areas of each color are readily available for determining distribution of that density by comparison with other densities within the image.

A theoretical-electron-density databank using a model of real and virtual spherical atoms.

PubMed

Nassour, Ayoub; Domagala, Slawomir; Guillot, Benoit; Leduc, Theo; Lecomte, Claude; Jelsch, Christian

2017-08-01

A database describing the electron density of common chemical groups using combinations of real and virtual spherical atoms is proposed, as an alternative to the multipolar atom modelling of the molecular charge density. Theoretical structure factors were computed from periodic density functional theory calculations on 38 crystal structures of small molecules and the charge density was subsequently refined using a density model based on real spherical atoms and additional dummy charges on the covalent bonds and on electron lone-pair sites. The electron-density parameters of real and dummy atoms present in a similar chemical environment were averaged on all the molecules studied to build a database of transferable spherical atoms. Compared with the now-popular databases of transferable multipolar parameters, the spherical charge modelling needs fewer parameters to describe the molecular electron density and can be more easily incorporated in molecular modelling software for the computation of electrostatic properties. The construction method of the database is described. In order to analyse to what extent this modelling method can be used to derive meaningful molecular properties, it has been applied to the urea molecule and to biotin/streptavidin, a protein/ligand complex.

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.

Nonparametric entropy estimation using kernel densities.

PubMed

Lake, Douglas E

2009-01-01

The entropy of experimental data from the biological and medical sciences provides additional information over summary statistics. Calculating entropy involves estimates of probability density functions, which can be effectively accomplished using kernel density methods. Kernel density estimation has been widely studied and a univariate implementation is readily available in MATLAB. The traditional definition of Shannon entropy is part of a larger family of statistics, called Renyi entropy, which are useful in applications that require a measure of the Gaussianity of data. Of particular note is the quadratic entropy which is related to the Friedman-Tukey (FT) index, a widely used measure in the statistical community. One application where quadratic entropy is very useful is the detection of abnormal cardiac rhythms, such as atrial fibrillation (AF). Asymptotic and exact small-sample results for optimal bandwidth and kernel selection to estimate the FT index are presented and lead to improved methods for entropy estimation.

Charge density wave order in 1D mirror twin boundaries of single-layer MoSe 2

DOE PAGES

Barja, Sara; Wickenburg, Sebastian; Liu, Zhen-Fei; ...

2016-04-18

Here, We provide direct evidence for the existence of isolated, one-dimensional charge density waves at mirror twin boundaries (MTBs) of single-layer semiconducting MoSe 2. Such MTBs have been previously observed by transmission electron microscopy and have been predicted to be metallic in MoSe 2 and MoS 2. Our low-temperature scanning tunnelling microscopy/spectroscopy measurements revealed a substantial bandgap of 100 meV opening at the Fermi energy in the otherwise metallic one-dimensional structures. We found a periodic modulation in the density of states along the MTB, with a wavelength of approximately three lattice constants. In addition to mapping the energy-dependent densitymore » of states, we determined the atomic structure and bonding of the MTB through simultaneous high-resolution non-contact atomic force microscopy. Density functional theory calculations based on the observed structure reproduced both the gap opening and the spatially resolved density of states.« less

Reference models for thermospheric NO

NASA Technical Reports Server (NTRS)

Barth, C. A.

1989-01-01

Nitric oxide has been measured with an ultraviolet spectrometer on the polar-orbiting satellite Solar Mesosphere Explorer (SME) for the period January 1982 to August 1986. The nitric oxide database contains densities at all latitudes sorted into 5 degree bins and at altitudes between 100 and 140 km sorted into 3.3 km-bins. The largest densities occur at latitudes in the auroral zones where the density varies as a function of geomagnetic activity. Variations of a factor of 10 occur between times of intense activity and quiet times. At low latitudes, the nitric oxide density at 110 km varies from a mean value of 3 times 10(exp 7) molecules per cubic cm in January 1982 to a mean value of 4 times 10(exp 6) molecules per cubic cm during solar minimum conditions in 1986. In addition, the low-latitude nitric oxide density varies plus or minus 50 percent with a period of 27 days during times of high solar activity.

Dependence of Excited State Potential Energy Surfaces on the Spatial Overlap of the Kohn-Sham Orbitals and the Amount of Nonlocal Hartree-Fock Exchange in Time-Dependent Density Functional Theory.

PubMed

Plötner, Jürgen; Tozer, David J; Dreuw, Andreas

2010-08-10

Time-dependent density functional theory (TDDFT) with standard GGA or hybrid exchange-correlation functionals is not capable of describing the potential energy surface of the S1 state of Pigment Yellow 101 correctly; an additional local minimum is observed at a twisted geometry with substantial charge transfer (CT) character. To investigate the influence of nonlocal exact orbital (Hartree-Fock) exchange on the shape of the potential energy surface of the S1 state in detail, it has been computed along the twisting coordinate employing the standard BP86, B3LYP, and BHLYP xc-functionals as well as the long-range separated (LRS) exchange-correlation (xc)-functionals LC-BOP, ωB97X, ωPBE, and CAM-B3LYP and compared to RI-CC2 benchmark results. Additionally, a recently suggested Λ-parameter has been employed that measures the amount of CT in an excited state by calculating the spatial overlap of the occupied and virtual molecular orbitals involved in the transition. Here, the error in the calculated S1 potential energy curves at BP86, B3LYP, and BHLYP can be clearly related to the Λ-parameter, i.e., to the extent of charge transfer. Additionally, it is demonstrated that the CT problem is largely alleviated when the BHLYP xc-functional is employed, although it still exhibits a weak tendency to underestimate the energy of CT states. The situation improves drastically when LRS-functionals are employed within TDDFT excited state calculations. All tested LRS-functionals give qualitatively the correct potential energy curves of the energetically lowest excited states of P. Y. 101 along the twisting coordinate. While LC-BOP and ωB97X overcorrect the CT problem and now tend to give too large excitation energies compared to other non-CT states, ωPBE and CAM-B3LYP are in excellent agreement with the RI-CC2 results, with respect to both the correct shape of the potential energy curve as well as the absolute values of the calculated excitation energies.

Investigation of Structure and Reactivity Relationship in M-N-C Type Catalysts using Density Functional Tight Binding

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

Negre, Christian Francisco Andres; Gonzales, Ivana

Catalysts inhibition studies were performed to indisputably confirm the role of various metal, carbon, and nitrogen moieties in the individual steps of oxygen reduction reaction (ORR) on M-N-C catalysts. ORR activity was studied at University of New Mexico by rotating ring disk electrode method in the acidic electrolyte with the addition of Tris (tris(hydroxymethyl)-aminomethane) as inhibiting agent. To understand the interaction of Tris with different defects that exist in Fe-N-C materials and provide the support for the experimental data, we used density functional theory (DFT) and modeled the interaction of protonated Tris (TrisH) with Fe containingcenters (Fe-N 4 and Fe-Nmore » 2C 2), pyridinic nitrogen, graphitic nitrogen, and pyrrolic nitrogen both as in plane and edge defects.« less

Application of Raman spectroscopy, surface-enhanced Raman scattering (SERS), and density functional theory for the identification of phenethylamines.

PubMed

Taplin, Francis; O'Donnell, Deanna; Kubic, Thomas; Leona, Marco; Lombardi, John

2013-10-01

We evaluated the normal Raman (NR) and the surface-enhanced Raman scattering (SERS) of three sympathomimetic amines: phenethylamine, ephedrine, and 3,4-methylenedioxymethamphetamine (MDMA). In addition, quantum mechanical calculations-geometry optimization and calculations of the harmonic vibrational frequencies-were performed using the density functional theory (DFT) approach. Vibrational assignments were made by comparing the experimental and calculated spectra. The study found that both NR and SERS provided excellent spectra for the drugs tested. Certain conditions, such as response to various laser wavelengths and background fluorescence of the analyte, could be easily managed using SERS techniques. The DFT-calculated spectra could be correlated with the experimental spectra without the aid of a scaling factor. We also present a set of discriminant bands, useful for distinguishing the three compounds, despite their structural similarities.

Addition of simultaneous heat and solute transport and variable fluid viscosity to SEAWAT

USGS Publications Warehouse

Thorne, D.; Langevin, C.D.; Sukop, M.C.

2006-01-01

SEAWAT is a finite-difference computer code designed to simulate coupled variable-density ground water flow and solute transport. This paper describes a new version of SEAWAT that adds the ability to simultaneously model energy and solute transport. This is necessary for simulating the transport of heat and salinity in coastal aquifers for example. This work extends the equation of state for fluid density to vary as a function of temperature and/or solute concentration. The program has also been modified to represent the effects of variable fluid viscosity as a function of temperature and/or concentration. The viscosity mechanism is verified against an analytical solution, and a test of temperature-dependent viscosity is provided. Finally, the classic Henry-Hilleke problem is solved with the new code. ?? 2006 Elsevier Ltd. All rights reserved.

Low cost estimation of the contribution of post-CCSD excitations to the total atomization energy using density functional theory calculations

NASA Astrophysics Data System (ADS)

Sánchez, H. R.; Pis Diez, R.

2016-04-01

Based on the Aλ diagnostic for multireference effects recently proposed [U.R. Fogueri, S. Kozuch, A. Karton, J.M. Martin, Theor. Chem. Acc. 132 (2013) 1], a simple method for improving total atomization energies and reaction energies calculated at the CCSD level of theory is proposed. The method requires a CCSD calculation and two additional density functional theory calculations for the molecule. Two sets containing 139 and 51 molecules are used as training and validation sets, respectively, for total atomization energies. An appreciable decrease in the mean absolute error from 7-10 kcal mol-1 for CCSD to about 2 kcal mol-1 for the present method is observed. The present method provides atomization energies and reaction energies that compare favorably with relatively recent scaled CCSD methods.

Synthesis, crystal structure, vibrational spectra and theoretical calculations of quantum chemistry of a potential antimicrobial Meldrum's acid derivative

NASA Astrophysics Data System (ADS)

Campelo, M. J. M.; Freire, P. T. C.; Mendes Filho, J.; de Toledo, T. A.; Teixeira, A. M. R.; da Silva, L. E.; Bento, R. R. F.; Faria, J. L. B.; Pizani, P. S.; Gusmão, G. O. M.; Coutinho, H. D. M.; Oliveira, M. T. A.

2017-10-01

A new derivative of Meldrum's acid 5-((5-chloropyridin-2-ylamino)methylene)-2,2-dimethyl-1,3-dioxane-4,6-dione (CYMM) of molecular formula C12H11ClN2O4 was synthesized and structurally characterized using single crystal X-ray diffraction technique. The vibrational properties of the crystal were studied by Fourier Transform infrared (FT-IR), Fourier Transform Raman (FT-Raman) techniques and theoretical calculations of quantum chemistry using Density functional theory (DFT) and Density functional perturbation theory (DFPT). A comparison with experimental spectra allowed the assignment of all the normal modes. The descriptions of the normal modes were carried by means of potential energy distribution (PED). Additionally, analysis of the antimicrobial activity and antibiotic resistance modulatory activity was carried out to evaluate the antibacterial potential of the CYMM.

Electronic properties of CdWO{sub 4}: Use of hybrid exchange and correlation functionals

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

Meena, B. S., E-mail: bsmphysics@gmail.com; Mund, H. S.; Ahuja, B. L.

Energy bands, density of states (DOS), Mulliken population (MP) and electron momentum densities (EMDs) of CdWO{sub 4} are presented using hybrid exchange and correlation functionals namely B3LYP, B3PW and PBE0. To validate the present hybrid potentials, theoretical EMDs have been compared with the experimental Compton profile. It is found that LCAO-B3LYP based Compton profile gives a better agreement with experiment than other theoretical profiles. The energy bands and DOS show a wide band gap semiconducting nature of CdWO{sub 4}. The theoretical band gap obtained using B3LYP scheme reconciles well with the available experimental data. In addition, we have also presentedmore » the anisotropies in EMDs along [100], [110] and [001] directions and the bonding effects using the MP data.« less

Molecular design and theoretical characterization of benzodithiophene based organic photovoltaic materials

NASA Astrophysics Data System (ADS)

Bhattacharya, Labanya; Sahu, Sridhar

2018-05-01

Two different oligomers, containing methyl substituted Benzodithiophene (BDT) as donor unit, fluorinated thiophene as the π-bridge unit and two different kinds of acceptors based on fluorinated benzothiadiazole, fluorinated benzoselenadiazole units are designed for bulk heterojunction (BHJ) organic solar cell (OSC). The ground and excited state properties of those donor-π-acceptor-π-donor (D-π-A-π-D) oligomeric configurations are characterized via density functional (DFT) and time dependent density functional theory (TD-DFT). The parameters such as dipole moment (ρ), chemical potential (µ), electronegativity (χ), frontier molecular orbital (FMO) analysis, HOMO-LUMO gap, open circuit voltage (Voc) and driving force (ΔE) are calculated to analyze geometrical, electronic structural, quantum chemical and photovoltaic properties of the compounds. In addition, optical absorption spectra are also presented for the optical characterization of the compounds.

Thermal Analysis of Low Layer Density Multilayer Insulation Test Results

NASA Technical Reports Server (NTRS)

Johnson, Wesley L.

2011-01-01

Investigation of the thermal performance of low layer density multilayer insulations is important for designing long-duration space exploration missions involving the storage of cryogenic propellants. Theoretical calculations show an analytical optimal layer density, as widely reported in the literature. However, the appropriate test data by which to evaluate these calculations have been only recently obtained. As part of a recent research project, NASA procured several multilayer insulation test coupons for calorimeter testing. These coupons were configured to allow for the layer density to be varied from 0.5 to 2.6 layer/mm. The coupon testing was completed using the cylindrical Cryostat-l00 apparatus by the Cryogenics Test Laboratory at Kennedy Space Center. The results show the properties of the insulation as a function of layer density for multiple points. Overlaying these new results with data from the literature reveals a minimum layer density; however, the value is higher than predicted. Additionally, the data show that the transition region between high vacuum and no vacuum is dependent on the spacing of the reflective layers. Historically this spacing has not been taken into account as thermal performance was calculated as a function of pressure and temperature only; however the recent testing shows that the data is dependent on the Knudsen number which takes into account pressure, temperature, and layer spacing. These results aid in the understanding of the performance parameters of MLI and help to complete the body of literature on the topic.

Density Functional Theory Study of the Reaction between d0 Tungsten Alkylidyne Complexes and H2O: Addition versus Hydrolysis.

PubMed

Chen, Ping; Zhang, Linxing; Xue, Zi-Ling; Wu, Yun-Dong; Zhang, Xinhao

2017-06-19

The reactions of early-transition-metal complexes with H 2 O have been investigated. An understanding of these elementary steps promotes the design of precursors for the preparation of metal oxide materials or supported heterogeneous catalysts. Density functional theory (DFT) calculations have been conducted to investigate two elementary steps of the reactions between tungsten alkylidyne complexes and H 2 O, i.e., the addition of H 2 O to the W≡C bond and ligand hydrolysis. Four tungsten alkylidyne complexes, W(≡CSiMe 3 )(CH 2 SiMe 3 ) 3 (A-1), W(≡CSiMe 3 )(CH 2 t Bu) 3 (B-1), W(≡C t Bu)(CH 2 t Bu) 3 (C-1), and W(≡C t Bu)(O t Bu) 3 (D-1), have been compared. The DFT studies provide an energy profile of the two competing pathways. An additional H 2 O molecule can serve as a proton shuttle, accelerating the H 2 O addition reaction. The effect of atoms at the α and β positions has also been examined. Because the lone-pair electrons of an O atom at the α position can interact with the orbital of the proton, the barrier of the ligand-hydrolysis reaction for D-1 is dramatically reduced. Both the electronic and steric effects of the silyl group at the β position lower the barriers of both the H 2 O addition and ligand-hydrolysis reactions. These new mechanistic findings may lead to the further development of metal complex precursors.

Localized overlap algorithm for unexpanded dispersion energies

NASA Astrophysics Data System (ADS)

Rob, Fazle; Misquitta, Alston J.; Podeszwa, Rafał; Szalewicz, Krzysztof

2014-03-01

First-principles-based, linearly scaling algorithm has been developed for calculations of dispersion energies from frequency-dependent density susceptibility (FDDS) functions with account of charge-overlap effects. The transition densities in FDDSs are fitted by a set of auxiliary atom-centered functions. The terms in the dispersion energy expression involving products of such functions are computed using either the unexpanded (exact) formula or from inexpensive asymptotic expansions, depending on the location of these functions relative to the dimer configuration. This approach leads to significant savings of computational resources. In particular, for a dimer consisting of two elongated monomers with 81 atoms each in a head-to-head configuration, the most favorable case for our algorithm, a 43-fold speedup has been achieved while the approximate dispersion energy differs by less than 1% from that computed using the standard unexpanded approach. In contrast, the dispersion energy computed from the distributed asymptotic expansion differs by dozens of percent in the van der Waals minimum region. A further increase of the size of each monomer would result in only small increased costs since all the additional terms would be computed from the asymptotic expansion.

Structural brain and neuropsychometric changes associated with pediatric bipolar disorder with psychosis.

PubMed

James, Anthony; Hough, Morgan; James, Susan; Burge, Linda; Winmill, Louise; Nijhawan, Sunita; Matthews, Paul M; Zarei, Mojtaba

2011-02-01

To identify neuropsychological and structural brain changes using a combination of high-resolution structural and diffusion tensor imaging in pediatric bipolar disorder (PBD) with psychosis (presence of delusions and or hallucinations). We recruited 15 patients and 20 euthymic age- and gender-matched healthy controls. All subjects underwent high-resolution structural and diffusion tensor imaging. Voxel-based morphometry (VBM), tract-based spatial statistics (TBSS), and probabilistic tractography were used to analyse magnetic resonance imaging data. The PBD subjects had normal overall intelligence with specific impairments in working memory, executive function, language function, and verbal memory. Reduced gray matter (GM) density was found in the left orbitofrontal cortex, left pars triangularis, right premotor cortex, occipital cortex, right occipital fusiform gyrus, and right crus of the cerebellum. TBSS analysis showed reduced fractional anisotropy (FA) in the anterior corpus callosum. Probabilistic tractography from this cluster showed that this region of the corpus callosum is connected with the prefrontal cortices, including those regions whose density is decreased in PBD. In addition, FA change was correlated with verbal memory and working memory, while more widespread reductions in GM density correlated with working memory, executive function, language function, and verbal memory. The findings suggest widespread cortical changes as well as specific involvement of interhemispheric prefrontal tracts in PBD, which may reflect delayed myelination in these tracts. © 2011 John Wiley and Sons A/S.

A first-principles examination of the asymmetric induction model in the binap/Rh(I)-catalysed 1,4-addition of phenylboronic acid to cyclic enones by density functional theory calculations.

PubMed

Qin, Hua-Li; Chen, Xiao-Qing; Huang, Yi-Zhen; Kantchev, Eric Assen B

2014-09-26

First-principles modelling of the diastereomeric transition states in the enantiodiscrimination stage of the catalytic cycle can reveal intimate details about the mechanism of enantioselection. This information can be invaluable for further improvement of the catalytic protocols by rational design. Herein, we present a density functional theory (IEFPCM/PBE0/DGDZVP level of theory) modelling of the carborhodation step for the asymmetric 1,4-arylation of cyclic α,β-unsaturated ketones mediated by a [(binap)Rh(I)] catalyst. The calculations completely support the older, qualitative, pictorial model predicting the sense of the asymmetric induction for both the chelating diphosphane (binap) and the more recent chiral diene (Phbod) ligands, while also permitting quantification of the enantiomeric excess (ee). The effect of dispersion interaction correction and basis sets has been also investigated. Dispersion-corrected functionals and solvation models significantly improve the predicted ee values. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Beyond Born-Mayer: Improved models for short-range repulsion in ab initio force fields

DOE PAGES

Van Vleet, Mary J.; Misquitta, Alston J.; Stone, Anthony J.; ...

2016-06-23

Short-range repulsion within inter-molecular force fields is conventionally described by either Lennard-Jones or Born-Mayer forms. Despite their widespread use, these simple functional forms are often unable to describe the interaction energy accurately over a broad range of inter-molecular distances, thus creating challenges in the development of ab initio force fields and potentially leading to decreased accuracy and transferability. Herein, we derive a novel short-range functional form based on a simple Slater-like model of overlapping atomic densities and an iterated stockholder atom (ISA) partitioning of the molecular electron density. We demonstrate that this Slater-ISA methodology yields a more accurate, transferable, andmore » robust description of the short-range interactions at minimal additional computational cost compared to standard Lennard-Jones or Born-Mayer approaches. Lastly, we show how this methodology can be adapted to yield the standard Born-Mayer functional form while still retaining many of the advantages of the Slater-ISA approach.« less

The excited-state intramolecular proton transfer in Nsbnd H-type dye molecules with a seven-membered-ring intramolecular hydrogen bond: A theoretical insight

NASA Astrophysics Data System (ADS)

Yuan, Huijuan; Feng, Songyan; Wen, Keke; Guo, Xugeng; Zhang, Jinglai

2018-02-01

Excited-state intramolecular proton transfer (ESIPT) reactions of a series of N(R)sbnd H ⋯ N-type seven-membered-ring hydrogen-bonding compounds were explored by employing density functional theory/time-dependent density functional theory calculations with the PBE0 functional. Our results indicate that the absorption and emission spectra predicted theoretically match very well the experimental findings. Additionally, as the electron-withdrawing strength of R increases, the intramolecular H-bond of the Nsbnd S1 form gradually enhances, and the forward energy barrier along the ESIPT reaction gradually decreases. For compound 4, its ESIPT reaction is found to be a barrierless process due to the involvement of a strong electron-withdrawing COCF3 group. It is therefore a reasonable presumption that the ESIPT efficiency of these N(R)sbnd H ⋯ N-type seven-membered-ring H-bonding systems can be improved when a strong electron-withdrawing group in R is introduced.

A magnetic and electronic circular dichroism study of azurin, plastocyanin, cucumber basic protein, and nitrite reductase based on time-dependent density functional theory calculations.

PubMed

Zhekova, Hristina R; Seth, Michael; Ziegler, Tom

2010-06-03

The excitation, circular dichroism, magnetic circular dichroism (MCD) and electron paramagnetic resonance (EPR) spectra of small models of four blue copper proteins are simulated on the TDDFT/BP86 level. X-Ray diffraction geometries are used for the modeling of the blue copper sites in azurin, plastocyanin, cucumber basic protein, and nitrite reductase. Comparison with experimental data reveals that the calculations reproduce most of the qualitative trends of the observed experimental spectra with some discrepancies in the orbital decompositions and the values of the excitation energies, the g( parallel) components of the g tensor, and the components of the A tensor. These discrepancies are discussed relative to deficiencies in the time-dependent density functional theory (TDDFT) methodology, as opposed to previous studies which address them as a result of insufficient model size or poor performance of the BP86 functional. In addition, attempts are made to elucidate the correlation between the MCD and EPR signals.

Verification of Anderson Superexchange in MnO via Magnetic Pair Distribution Function Analysis and ab initio Theory

NASA Astrophysics Data System (ADS)

Frandsen, Benjamin A.; Brunelli, Michela; Page, Katharine; Uemura, Yasutomo J.; Staunton, Julie B.; Billinge, Simon J. L.

2016-05-01

We present a temperature-dependent atomic and magnetic pair distribution function (PDF) analysis of neutron total scattering measurements of antiferromagnetic MnO, an archetypal strongly correlated transition-metal oxide. The known antiferromagnetic ground-state structure fits the low-temperature data closely with refined parameters that agree with conventional techniques, confirming the reliability of the newly developed magnetic PDF method. The measurements performed in the paramagnetic phase reveal significant short-range magnetic correlations on a ˜1 nm length scale that differ substantially from the low-temperature long-range spin arrangement. Ab initio calculations using a self-interaction-corrected local spin density approximation of density functional theory predict magnetic interactions dominated by Anderson superexchange and reproduce the measured short-range magnetic correlations to a high degree of accuracy. Further calculations simulating an additional contribution from a direct exchange interaction show much worse agreement with the data. The Anderson superexchange model for MnO is thus verified by experimentation and confirmed by ab initio theory.

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.

Trophic cascades: linking ungulates to shrub-dependent birds and butterflies.

PubMed

J Teichman, Kristine; Nielsen, Scott E; Roland, Jens

2013-11-01

1. Studies demonstrating trophic cascades through the loss of top-down regulatory processes in productive and biologically diverse terrestrial ecosystems are limited. 2. Elk Island National Park, Alberta and surrounding protected areas have a wide range of ungulate density due to the functional loss of top predators, management for high ungulate numbers and variable hunting pressure. This provides an ideal setting for studying the effects of hyper-abundant ungulates on vegetation and shrub-dependent bird and butterfly species. 3. To examine the cascading effects of high ungulate density, we quantified vegetation characteristics and abundances of yellow warbler Dendroica petechia and Canadian tiger swallowtail Papilio canadensis under different ungulate density in and around Elk Island National Park. 4. Using Structural Equation Models we found that ungulate density was inversely related to shrub cover, whereas shrub cover was positively related to yellow warbler abundance. In addition, chokecherry Prunus virginiana abundance was inversely related to browse impact but positively related to P. canadensis abundance. 5. These results demonstrate a cascade resulting from hyper-abundant ungulates on yellow warblers and Canadian tiger swallowtails through reductions in shrub cover and larval host plant density. The combined effect of the functional loss of top predators and management strategies that maintain high ungulate numbers can decouple top-down regulation of productive temperate ecosystems. © 2013 The Authors. Journal of Animal Ecology © 2013 British Ecological Society.

Equation of state for dense nucleonic matter from metamodeling. I. Foundational aspects

NASA Astrophysics Data System (ADS)

Margueron, Jérôme; Hoffmann Casali, Rudiney; Gulminelli, Francesca

2018-02-01

Metamodeling for the nucleonic equation of state (EOS), inspired from a Taylor expansion around the saturation density of symmetric nuclear matter, is proposed and parameterized in terms of the empirical parameters. The present knowledge of nuclear empirical parameters is first reviewed in order to estimate their average values and associated uncertainties, and thus defining the parameter space of the metamodeling. They are divided into isoscalar and isovector types, and ordered according to their power in the density expansion. The goodness of the metamodeling is analyzed against the predictions of the original models. In addition, since no correlation among the empirical parameters is assumed a priori, all arbitrary density dependences can be explored, which might not be accessible in existing functionals. Spurious correlations due to the assumed functional form are also removed. This meta-EOS allows direct relations between the uncertainties on the empirical parameters and the density dependence of the nuclear equation of state and its derivatives, and the mapping between the two can be done with standard Bayesian techniques. A sensitivity analysis shows that the more influential empirical parameters are the isovector parameters Lsym and Ksym, and that laboratory constraints at supersaturation densities are essential to reduce the present uncertainties. The present metamodeling for the EOS for nuclear matter is proposed for further applications in neutron stars and supernova matter.

Evaluating interaction energies of weakly bonded systems using the Buckingham-Hirshfeld method

NASA Astrophysics Data System (ADS)

Krishtal, A.; Van Alsenoy, C.; Geerlings, P.

2014-05-01

We present the finalized Buckingham-Hirshfeld method (BHD-DFT) for the evaluation of interaction energies of non-bonded dimers with Density Functional Theory (DFT). In the method, dispersion energies are evaluated from static multipole polarizabilities, obtained on-the-fly from Coupled Perturbed Kohn-Sham calculations and partitioned into diatomic contributions using the iterative Hirshfeld partitioning method. The dispersion energy expression is distributed over four atoms and has therefore a higher delocalized character compared to the standard pairwise expressions. Additionally, full multipolar polarizability tensors are used as opposed to effective polarizabilities, allowing to retain the anisotropic character at no additional computational cost. A density dependent damping function for the BLYP, PBE, BP86, B3LYP, and PBE0 functionals has been implemented, containing two global parameters which were fitted to interaction energies and geometries of a selected number of dimers using a bi-variate RMS fit. The method is benchmarked against the S22 and S66 data sets for equilibrium geometries and the S22x5 and S66x8 data sets for interaction energies around the equilibrium geometry. Best results are achieved using the B3LYP functional with mean average deviation values of 0.30 and 0.24 kcal/mol for the S22 and S66 data sets, respectively. This situates the BHD-DFT method among the best performing dispersion inclusive DFT methods. Effect of counterpoise correction on DFT energies is discussed.

Structural Evolution of Electrochemically Lithiated MoS2 Nanosheets and the Role of Carbon Additive in Li-Ion Batteries

PubMed Central

2016-01-01

Understanding the structure and phase changes associated with conversion-type materials is key to optimizing their electrochemical performance in Li-ion batteries. For example, molybdenum disulfide (MoS2) offers a capacity up to 3-fold higher (∼1 Ah/g) than the currently used graphite anodes, but they suffer from limited Coulombic efficiency and capacity fading. The lack of insights into the structural dynamics induced by electrochemical conversion of MoS2 still hampers its implementation in high energy-density batteries. Here, by combining ab initio density-functional theory (DFT) simulation with electrochemical analysis, we found new sulfur-enriched intermediates that progressively insulate MoS2 electrodes and cause instability from the first discharge cycle. Because of this, the choice of conductive additives is critical for the battery performance. We investigate the mechanistic role of carbon additive by comparing equal loading of standard Super P carbon powder and carbon nanotubes (CNTs). The latter offer a nearly 2-fold increase in capacity and a 45% reduction in resistance along with Coulombic efficiency of over 90%. These insights into the phase changes during MoS2 conversion reactions and stabilization methods provide new solutions for implementing cost-effective metal sulfide electrodes, including Li–S systems in high energy-density batteries. PMID:27818575

Electronic properties of Fe3O4: LCAO calculations and Compton spectroscopy

NASA Astrophysics Data System (ADS)

Panwar, Kalpana; Tiwari, Shailja; Heda, N. L.

2018-04-01

We report the Compton profile (CP) measurements of Fe3O4 using 100 mCi241Am Compton spectrometer at momentum resolution of 0.55 a.u. The experimental CP has been compared with the linear combination of atomic orbitals (LCAO) data within density functional theory (DFT). The local density and generalized gradient approximation (LDA and GGA, respectively) have been used under the framework of DFT scheme. It is found that the DFT-GGA scheme gives the better agreement than to DFT-LDA. In addition, we have also computed the M ulliken's population (M P) and density of states (DOS) using the DFT scheme. M P data predicts the charge transfer from Fe to O atoms while DOS have confirmed the half metallic character of the compound.

Addition and hydrogen abstraction reactions of an OH radical with 8-oxoguanine

NASA Astrophysics Data System (ADS)

Jena, N. R.; Mishra, P. C.

2006-05-01

Addition reaction of an OH radical at the C2, C4, C5 or C8 position of 8-oxoguanine (8OG) and abstraction of its H9 atom by an OH radical were studied using density functional theory (B3LYP) employing 6-31G ∗∗, 6-311++G ∗∗ and AUG-cc-pVDZ basis sets. Solvent effects of aqueous media were treated using the PCM model. It is found that the addition of an OH radical at the C4 position of 8OG would be most favored in both gas phase and aqueous media. These addition and abstraction reactions in aqueous media are both found to be barrierless.

Pairwise additivity of energy components in protein-ligand binding: The HIV II protease-Indinavir case

NASA Astrophysics Data System (ADS)

Ucisik, Melek N.; Dashti, Danial S.; Faver, John C.; Merz, Kenneth M.

2011-08-01

An energy expansion (binding energy decomposition into n-body interaction terms for n ≥ 2) to express the receptor-ligand binding energy for the fragmented HIV II protease-Indinavir system is described to address the role of cooperativity in ligand binding. The outcome of this energy expansion is compared to the total receptor-ligand binding energy at the Hartree-Fock, density functional theory, and semiempirical levels of theory. We find that the sum of the pairwise interaction energies approximates the total binding energy to ˜82% for HF and to >95% for both the M06-L density functional and PM6-DH2 semiempirical method. The contribution of the three-body interactions amounts to 18.7%, 3.8%, and 1.4% for HF, M06-L, and PM6-DH2, respectively. We find that the expansion can be safely truncated after n = 3. That is, the contribution of the interactions involving more than three parties to the total binding energy of Indinavir to the HIV II protease receptor is negligible. Overall, we find that the two-body terms represent a good approximation to the total binding energy of the system, which points to pairwise additivity in the present case. This basic principle of pairwise additivity is utilized in fragment-based drug design approaches and our results support its continued use. The present results can also aid in the validation of non-bonded terms contained within common force fields and in the correction of systematic errors in physics-based score functions.

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.

Density of Electronic States in Impurity-Doped Quantum Well Wires

NASA Astrophysics Data System (ADS)

Sierra-Ortega, J.; Mikhailov, I. D.

2003-03-01

We analyze the electronic states in a cylindrical quantum well-wire (QWW) with randomly distributed neutral, D^0 and negatively charged D^- donors. In order to calculate the ground state energies of the off-center donors D^0 and D^- as a function of the distance from the axis of the QWW, we use the recently developed fractal dimension method [1]. There the problems are reduced to those similar for a hydrogen-like atom and a negative-hydrogen-like ion respectively, in an isotropic effective space with variable fractional dimension. The numerical trigonometric sweep method [2] and the three-parameter Hylleraas-type trial function are used to solve these problems. Novel curves for the density of impurity states in cylindrical QWWs with square-well, parabolic and soft-edge barrier potentials are present. Additionally we analyze the effect of the repulsive core on the density of the impurity states. [1] I.D. Mikhailov, F. J. Betancur, R. Escorcia and J. Sierra-Ortega, Phys. Stat. Sol., 234(b), 590 (2002) [2] F. J. Betancur, I. D. Mikhailov and L. E. Oliveira, J. Appl. Phys. D, 31, 3391(1998)

Spatial Distribution of Oxygen Chemical Potential under Potential Gradients and Theoretical Maximum Power Density with 8YSZ Electrolyte

NASA Astrophysics Data System (ADS)

Lim, Dae-Kwang; Im, Ha-Ni; Song, Sun-Ju

2016-01-01

The maximum power density of SOFC with 8YSZ electrolyte as the function of thickness was calculated by integrating partial conductivities of charge carriers under various DC bias conditions at a fixed oxygen chemical potential gradient at both sides of the electrolyte. The partial conductivities were successfully taken using the Hebb-Wagner polarization method as a function of temperature and oxygen partial pressure, and the spatial distribution of oxygen partial pressure across the electrolyte was calculated based on Choudhury and Patterson’s model by considering zero electrode polarization. At positive voltage conditions corresponding to SOFC and SOEC, the high conductivity region was expanded, but at negative cell voltage condition, the low conductivity region near n-type to p-type transition was expanded. In addition, the maximum power density calculated from the current-voltage characteristic showed approximately 5.76 W/cm2 at 700 oC with 10 μm thick-8YSZ, while the oxygen partial pressure of the cathode and anode sides maintained ≈0.21 and 10-22 atm.

Ab initio studies of 1,3,5,7-tetranitro-1,3,5,7-tetrazocine/1,3-dimethyl-2-imidazolidinone cocrystal under high pressure using dispersion corrected density functional theory

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

Gu, Bang-Ming; Lin, He; Zhu, Shun-Guan, E-mail: zhusguan@yahoo.com

A detailed study of structural, electronic, and thermodynamic properties of 1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX)/1,3-dimethyl-2-imidazolidinone (DMI) cocrystal under the hydrostatic pressure of 0–100 GPa was performed by using dispersion-corrected density functional theory (DFT-D) method. The calculated crystal structure is in reasonable agreement with the experimental data at the ambient pressure. Based on the analysis of lattice constants, bond lengths, bond angles, and dihedral angles under compression, it is found that HMX molecules in HMX/DMI cocrystal are seriously distorted. In addition, as the pressure increases, the band gap decreases gradually, which suggests that HMX/DMI cocrystal is becoming more metallic. Some important intermolecular interactions between HMXmore » and DMI are also observed in the density of states spectrum. Finally, its thermodynamic properties were characterized, and the results show that HMX/DMI cocrystal is more easily formed in the low pressure.« less

Birds and insects as radar targets - A review

NASA Technical Reports Server (NTRS)

Vaughn, C. R.

1985-01-01

A review of radar cross-section measurements of birds and insects is presented. A brief discussion of some possible theoretical models is also given and comparisons made with the measurements. The comparisons suggest that most targets are, at present, better modeled by a prolate spheroid having a length-to-width ratio between 3 and 10 than by the often used equivalent weight water sphere. In addition, many targets observed with linear horizontal polarization have maximum cross sections much better estimated by a resonant half-wave dipole than by a water sphere. Also considered are birds and insects in the aggregate as a local radar 'clutter' source. Order-of-magnitude estimates are given for many reasonable target number densities. These estimates are then used to predict X-band volume reflectivities. Other topics that are of interest to the radar engineer are discussed, including the doppler bandwidth due to the internal motions of a single bird, the radar cross-section probability densities of single birds and insects, the variability of the functional form of the probability density functions, and the Fourier spectra of single birds and insects.

Electron—phonon Coupling and the Superconducting Phase Diagram of the LaAlO3—SrTiO3 Interface

PubMed Central

Boschker, Hans; Richter, Christoph; Fillis-Tsirakis, Evangelos; Schneider, Christof W.; Mannhart, Jochen

2015-01-01

The superconductor at the LaAlO3—SrTiO3 interface provides a model system for the study of two-dimensional superconductivity in the dilute carrier density limit. Here we experimentally address the pairing mechanism in this superconductor. We extract the electron—phonon spectral function from tunneling spectra and conclude, without ruling out contributions of further pairing channels, that electron—phonon mediated pairing is strong enough to account for the superconducting critical temperatures. Furthermore, we discuss the electron—phonon coupling in relation to the superconducting phase diagram. The electron—phonon spectral function is independent of the carrier density, except for a small part of the phase diagram in the underdoped region. The tunneling measurements reveal that the increase of the chemical potential with increasing carrier density levels off and is zero in the overdoped region of the phase diagram. This indicates that the additionally induced carriers do not populate the band that hosts the superconducting state and that the superconducting order parameter therefore is weakened by the presence of charge carriers in another band. PMID:26169351

Enhanced von Weizsäcker Wang-Govind-Carter kinetic energy density functional for semiconductors

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

Shin, Ilgyou; Carter, Emily A., E-mail: eac@princeton.edu

2014-05-14

We propose a new form of orbital-free (OF) kinetic energy density functional (KEDF) for semiconductors that is based on the Wang-Govind-Carter (WGC99) nonlocal KEDF. We enhance within the latter the semi-local von Weizsäcker KEDF term, which is exact for a single orbital. The enhancement factor we introduce is related to the extent to which the electron density is localized. The accuracy of the new KEDF is benchmarked against Kohn-Sham density functional theory (KSDFT) by comparing predicted energy differences between phases, equilibrium volumes, and bulk moduli for various semiconductors, along with metal-insulator phase transition pressures. We also compare point defect andmore » (100) surface energies in silicon for a broad test of its applicability. This new KEDF accurately reproduces the exact non-interacting kinetic energy of KSDFT with only one additional adjustable parameter beyond the three parameters in the WGC99 KEDF; it exhibits good transferability between semiconducting to metallic silicon phases and between various III-V semiconductors without parameter adjustment. Overall, this KEDF is more accurate than previously proposed OF KEDFs (e.g., the Huang-Carter (HC) KEDF) for semiconductors, while the computational efficiency remains at the level of the WGC99 KEDF (several hundred times faster than the HC KEDF). This accurate, fast, and transferable new KEDF holds considerable promise for large-scale OFDFT simulations of metallic through semiconducting materials.« less

Quantification of breast density with spectral mammography based on a scanned multi-slit photon-counting detector: a feasibility study.

PubMed

Ding, Huanjun; Molloi, Sabee

2012-08-07

A simple and accurate measurement of breast density is crucial for the understanding of its impact in breast cancer risk models. The feasibility to quantify volumetric breast density with a photon-counting spectral mammography system has been investigated using both computer simulations and physical phantom studies. A computer simulation model involved polyenergetic spectra from a tungsten anode x-ray tube and a Si-based photon-counting detector has been evaluated for breast density quantification. The figure-of-merit (FOM), which was defined as the signal-to-noise ratio of the dual energy image with respect to the square root of mean glandular dose, was chosen to optimize the imaging protocols, in terms of tube voltage and splitting energy. A scanning multi-slit photon-counting spectral mammography system has been employed in the experimental study to quantitatively measure breast density using dual energy decomposition with glandular and adipose equivalent phantoms of uniform thickness. Four different phantom studies were designed to evaluate the accuracy of the technique, each of which addressed one specific variable in the phantom configurations, including thickness, density, area and shape. In addition to the standard calibration fitting function used for dual energy decomposition, a modified fitting function has been proposed, which brought the tube voltages used in the imaging tasks as the third variable in dual energy decomposition. For an average sized 4.5 cm thick breast, the FOM was maximized with a tube voltage of 46 kVp and a splitting energy of 24 keV. To be consistent with the tube voltage used in current clinical screening exam (∼32 kVp), the optimal splitting energy was proposed to be 22 keV, which offered a FOM greater than 90% of the optimal value. In the experimental investigation, the root-mean-square (RMS) error in breast density quantification for all four phantom studies was estimated to be approximately 1.54% using standard calibration function. The results from the modified fitting function, which integrated the tube voltage as a variable in the calibration, indicated a RMS error of approximately 1.35% for all four studies. The results of the current study suggest that photon-counting spectral mammography systems may potentially be implemented for an accurate quantification of volumetric breast density, with an RMS error of less than 2%, using the proposed dual energy imaging technique.

Stellar mass and velocity functions of galaxies. Backward evolution and the fate of Milky Way siblings

NASA Astrophysics Data System (ADS)

Boissier, S.; Buat, V.; Ilbert, O.

2010-11-01

Context. In recent years, stellar mass functions of both star-forming and quiescent galaxies have been observed at different redshifts in various fields. In addition, star formation rate (SFR) distributions (e.g. in the form of far infrared luminosity functions) were also obtained. Taken together, they offer complementary pieces of information concerning the evolution of galaxies. Aims: We attempt in this paper to check the consistency of the observed stellar mass functions, SFR functions, and the cosmic SFR density with simple backward evolutionary models. Methods: Starting from observed stellar mass functions for star-forming galaxies, we use backwards models to predict the evolution of a number of quantities, such as the SFR function, the cosmic SFR density and the velocity function. Because the velocity is a parameter attached to a galaxy during its history (contrary to the stellar mass), this approach allows us to quantify the number density evolution of galaxies of a given velocity, e.g. of the Milky Way siblings. Results: Observations suggest that the stellar mass function of star-forming galaxies is constant between redshift 0 and 1. To reproduce this result, we must quench star formation in a number of star-forming galaxies. The stellar mass function of these “quenched” galaxies is consistent with available data concerning the increase in the population of quiescent galaxies in the same redshift interval. The stellar mass function of quiescent galaxies is then mainly determined by the distribution of active galaxies that must stop star formation, with a modest mass redistribution during mergers. The cosmic SFR density and the evolution of the SFR functions are recovered relatively well, although they provide some clues to a minor evolution of the stellar mass function of star forming galaxies at the lowest redshifts. We thus consider that we have obtained in a simple way a relatively consistent picture of the evolution of galaxies at intermediate redshifts. If this picture is correct, 50% of the Milky-Way sisters (galaxies with the same velocity as our Galaxy, i.e. 220 km s-1) have quenched their star formation since redshift 1 (and an even higher fraction for higher velocities). We discuss the processes that might be responsible for this transformation.

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

Influence of Chemical Composition and Structure in Silicon Dielectric Materials on Passivation of Thin Crystalline Silicon on Glass.

PubMed

Calnan, Sonya; Gabriel, Onno; Rothert, Inga; Werth, Matteo; Ring, Sven; Stannowski, Bernd; Schlatmann, Rutger

2015-09-02

In this study, various silicon dielectric films, namely, a-SiOx:H, a-SiNx:H, and a-SiOxNy:H, grown by plasma enhanced chemical vapor deposition (PECVD) were evaluated for use as interlayers (ILs) between crystalline silicon and glass. Chemical bonding analysis using Fourier transform infrared spectroscopy showed that high values of oxidant gases (CO2 and/or N2), added to SiH4 during PECVD, reduced the Si-H and N-H bond density in the silicon dielectrics. Various three layer stacks combining the silicon dielectric materials were designed to minimize optical losses between silicon and glass in rear side contacted heterojunction pn test cells. The PECVD grown silicon dielectrics retained their functionality despite being subjected to harsh subsequent processing such as crystallization of the silicon at 1414 °C or above. High values of short circuit current density (Jsc; without additional hydrogen passivation) required a high density of Si-H bonds and for the nitrogen containing films, additionally, a high N-H bond density. Concurrently high values of both Jsc and open circuit voltage Voc were only observed when [Si-H] was equal to or exceeded [N-H]. Generally, Voc correlated with a high density of [Si-H] bonds in the silicon dielectric; otherwise, additional hydrogen passivation using an active plasma process was required. The highest Voc ∼ 560 mV, for a silicon acceptor concentration of about 10(16) cm(-3), was observed for stacks where an a-SiOxNy:H film was adjacent to the silicon. Regardless of the cell absorber thickness, field effect passivation of the buried silicon surface by the silicon dielectric was mandatory for efficient collection of carriers generated from short wavelength light (in the vicinity of the glass-Si interface). However, additional hydrogen passivation was obligatory for an increased diffusion length of the photogenerated carriers and thus Jsc in solar cells with thicker absorbers.

Coordination between leaf and stem traits related to leaf carbon gain and hydraulics across 32 drought-tolerant angiosperms.

PubMed

Ishida, Atsushi; Nakano, Takashi; Yazaki, Kenichi; Matsuki, Sawako; Koike, Nobuya; Lauenstein, Diego L; Shimizu, Michiru; Yamashita, Naoko

2008-05-01

We examined 15 traits in leaves and stems related to leaf C economy and water use for 32 co-existing angiosperms at ridge sites with shallow soil in the Bonin Islands. Across species, stem density was positively correlated to leaf mass per area (LMA), leaf lifespan (LLS), and total phenolics and condensed tannins per unit leaf N (N-based), and negatively correlated to leaf osmotic potential and saturated water content in leaves. LMA and LLS were negatively correlated to photosynthetic parameters, such as area-, mass-, and N-based assimilation rates. Although stem density and leaf osmotic potential were not associated with photosynthetic parameters, they were associated with some parameters of the leaf C economy, such as LMA and LLS. In the principal component (PCA) analysis, the first three axes accounted for 74.4% of total variation. Axis 1, which explained 41.8% of the total variation, was well associated with parameters for leaf C and N economy. Similarly, axis 2, which explained 22.3% of the total variation, was associated with parameters for water use. Axis 3, which explained 10.3% of the total variation, was associated with chemical defense within leaves. Axes 1 and 2 separated functional types relatively well, i.e., creeping trees, ruderal trees, other woody plants, C(3) shrubs and forbs, palms, and CAM plants, indicating that plant functional types were characterized by similar attributes of traits related to leaf C and N economy and water use. In addition, when the plot was extended by two unrelated traits, leaf mass-based assimilation rates and stem density, it also separated these functional types. These data indicate that differences in the functional types with contrasting plant strategies can be attributed to functional integration among leaf C economy, hydraulics, and leaf longevity, and that both leaf mass-based assimilation rates and stem density are key factors reflecting the different functions of plant species.

VEGF induces sensory and motor peripheral plasticity, alters bladder function, and promotes visceral sensitivity

PubMed Central

2012-01-01

Background This work tests the hypothesis that bladder instillation with vascular endothelial growth factor (VEGF) modulates sensory and motor nerve plasticity, and, consequently, bladder function and visceral sensitivity. In addition to C57BL/6J, ChAT-cre mice were used for visualization of bladder cholinergic nerves. The direct effect of VEGF on the density of sensory nerves expressing the transient receptor potential vanilloid subfamily 1 (TRPV1) and cholinergic nerves (ChAT) was studied one week after one or two intravesical instillations of the growth factor. To study the effects of VEGF on bladder function, mice were intravesically instilled with VEGF and urodynamic evaluation was assessed. VEGF-induced alteration in bladder dorsal root ganglion (DRG) neurons was performed on retrogradly labeled urinary bladder afferents by patch-clamp recording of voltage gated Na+ currents. Determination of VEGF-induced changes in sensitivity to abdominal mechanostimulation was performed by application of von Frey filaments. Results In addition to an overwhelming increase in TRPV1 immunoreactivity, VEGF instillation resulted in an increase in ChAT-directed expression of a fluorescent protein in several layers of the urinary bladder. Intravesical VEGF caused a profound change in the function of the urinary bladder: acute VEGF (1 week post VEGF treatment) reduced micturition pressure and longer treatment (2 weeks post-VEGF instillation) caused a substantial reduction in inter-micturition interval. In addition, intravesical VEGF resulted in an up-regulation of voltage gated Na+ channels (VGSC) in bladder DRG neurons and enhanced abdominal sensitivity to mechanical stimulation. Conclusions For the first time, evidence is presented indicating that VEGF instillation into the mouse bladder promotes a significant increase in peripheral nerve density together with alterations in bladder function and visceral sensitivity. The VEGF pathway is being proposed as a key modulator of neural plasticity in the pelvis and enhanced VEGF content may be associated with visceral hyperalgesia, abdominal discomfort, and/or pelvic pain. PMID:23249422

Exercise training improves obesity‐related lymphatic dysfunction

PubMed Central

Hespe, Geoffrey E.; Kataru, Raghu P.; Savetsky, Ira L.; García Nores, Gabriela D.; Torrisi, Jeremy S.; Nitti, Matthew D.; Gardenier, Jason C.; Zhou, Jie; Yu, Jessie Z.; Jones, Lee W.

2016-01-01

Key points Obesity results in perilymphatic inflammation and lymphatic dysfunction.Lymphatic dysfunction in obesity is characterized by decreased lymphatic vessel density, decreased collecting lymphatic vessel pumping frequency, decreased lymphatic trafficking of immune cells, increased lymphatic vessel leakiness and changes in the gene expression patterns of lymphatic endothelial cells.Aerobic exercise, independent of weight loss, decreases perilymphatic inflammatory cell accumulation, improves lymphatic function and reverses pathological changes in gene expression in lymphatic endothelial cells. Abstract Although previous studies have shown that obesity markedly decreases lymphatic function, the cellular mechanisms that regulate this response remain unknown. In addition, it is unclear whether the pathological effects of obesity on the lymphatic system are reversible with behavioural modifications. The purpose of this study, therefore, was to analyse lymphatic vascular changes in obese mice and to determine whether these pathological effects are reversible with aerobic exercise. We randomized obese mice to either aerobic exercise (treadmill running for 30 min per day, 5 days a week, for 6 weeks) or a sedentary group that was not exercised and analysed lymphatic function using a variety of outcomes. We found that sedentary obese mice had markedly decreased collecting lymphatic vessel pumping capacity, decreased lymphatic vessel density, decreased lymphatic migration of immune cells, increased lymphatic vessel leakiness and decreased expression of lymphatic specific markers compared with lean mice (all P < 0.01). Aerobic exercise did not cause weight loss but markedly improved lymphatic function compared with sedentary obese mice. Exercise had a significant anti‐inflammatory effect, resulting in decreased perilymphatic accumulation of inflammatory cells and inducible nitric oxide synthase expression. In addition, exercise normalized isolated lymphatic endothelial cell gene expression of lymphatic specific genes, including VEGFR‐3 and Prox1. Taken together, our findings suggest that obesity impairs lymphatic function via multiple mechanisms and that these pathological changes can be reversed, in part, with aerobic exercise, independent of weight loss. In addition, our study shows that obesity‐induced lymphatic endothelial cell gene expression changes are reversible with behavioural modifications. PMID:26931178

Kinetic-scale fluctuations resolved with the Fast Plasma Investigation on NASA's Magnetospheric Multiscale mission.

NASA Astrophysics Data System (ADS)

Gershman, D. J.; Figueroa-Vinas, A.; Dorelli, J.; Goldstein, M. L.; Shuster, J. R.; Avanov, L. A.; Boardsen, S. A.; Stawarz, J. E.; Schwartz, S. J.; Schiff, C.; Lavraud, B.; Saito, Y.; Paterson, W. R.; Giles, B. L.; Pollock, C. J.; Strangeway, R. J.; Russell, C. T.; Torbert, R. B.; Moore, T. E.; Burch, J. L.

2017-12-01

Measurements from the Fast Plasma Investigation (FPI) on NASA's Magnetospheric Multiscale (MMS) mission have enabled unprecedented analyses of kinetic-scale plasma physics. FPI regularly provides estimates of current density and pressure gradients of sufficient accuracy to evaluate the relative contribution of terms in plasma equations of motion. In addition, high-resolution three-dimensional velocity distribution functions of both ions and electrons provide new insights into kinetic-scale processes. As an example, for a monochromatic kinetic Alfven wave (KAW) we find non-zero, but out-of-phase parallel current density and electric field fluctuations, providing direct confirmation of the conservative energy exchange between the wave field and particles. In addition, we use fluctuations in current density and magnetic field to calculate the perpendicular and parallel wavelengths of the KAW. Furthermore, examination of the electron velocity distribution inside the KAW reveals a population of electrons non-linearly trapped in the kinetic-scale magnetic mirror formed between successive wave peaks. These electrons not only contribute to the wave's parallel electric field but also account for over half of the density fluctuations within the wave, supplying an unexpected mechanism for maintaining quasi-neutrality in a KAW. Finally, we demonstrate that the employed wave vector determination technique is also applicable to broadband fluctuations found in Earth's turbulent magnetosheath.

Path integral approach to the Wigner representation of canonical density operators for discrete systems coupled to harmonic baths.

PubMed

Montoya-Castillo, Andrés; Reichman, David R

2017-01-14

We derive a semi-analytical form for the Wigner transform for the canonical density operator of a discrete system coupled to a harmonic bath based on the path integral expansion of the Boltzmann factor. The introduction of this simple and controllable approach allows for the exact rendering of the canonical distribution and permits systematic convergence of static properties with respect to the number of path integral steps. In addition, the expressions derived here provide an exact and facile interface with quasi- and semi-classical dynamical methods, which enables the direct calculation of equilibrium time correlation functions within a wide array of approaches. We demonstrate that the present method represents a practical path for the calculation of thermodynamic data for the spin-boson and related systems. We illustrate the power of the present approach by detailing the improvement of the quality of Ehrenfest theory for the correlation function C zz (t)=Re⟨σ z (0)σ z (t)⟩ for the spin-boson model with systematic convergence to the exact sampling function. Importantly, the numerically exact nature of the scheme presented here and its compatibility with semiclassical methods allows for the systematic testing of commonly used approximations for the Wigner-transformed canonical density.

Intramolecularly Protein-Crosslinked DNA Gels: New Biohybrid Nanomaterials with Controllable Size and Catalytic Activity.

PubMed

Zhou, Li; Morel, Mathieu; Rudiuk, Sergii; Baigl, Damien

2017-07-01

DNA micro- and nanogels-small-sized hydrogels made of a crosslinked DNA backbone-constitute new promising materials, but their functions have mainly been limited to those brought by DNA. Here a new way is described to prepare sub-micrometer-sized DNA gels of controllable crosslinking density that are able to embed novel functions, such as an enzymatic activity. It consists of using proteins, instead of traditional base-pairing assembly or covalent approaches, to form crosslinks inside individual DNA molecules, resulting in structures referred to as intramolecularly protein-crosslinked DNA gels (IPDGs). It is first shown that the addition of streptavidin to biotinylated T4DNA results in the successful formation of thermally stable IPDGs with a controllable crosslinking density, forming structures ranging from elongated to raspberry-shaped and pearl-necklace-like morphologies. Using reversible DNA condensation strategies, this paper shows that the gels can be reversibly actuated at a low crosslinking density, or further stabilized when they are highly crosslinked. Finally, by using streptavidin-protein conjugates, IPDGs with various enzymes are successfully functionalized. It is demonstrated that the enzymes keep their catalytic activity upon their incorporation into the gels, opening perspectives ranging from biotechnologies (e.g., enzyme manipulation) to nanomedicine (e.g., vectorization). © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Pressure induced structural phase transition in solid oxidizer KClO3: A first-principles study

NASA Astrophysics Data System (ADS)

Yedukondalu, N.; Ghule, Vikas D.; Vaitheeswaran, G.

2013-05-01

High pressure behavior of potassium chlorate (KClO3) has been investigated from 0 to 10 GPa by means of first principles density functional theory calculations. The calculated ground state parameters, transition pressure, and phonon frequencies using semiempirical dispersion correction scheme are in excellent agreement with experiment. It is found that KClO3 undergoes a pressure induced first order phase transition with an associated volume collapse of 6.4% from monoclinic (P21/m) → rhombohedral (R3m) structure at 2.26 GPa, which is in good accord with experimental observation. However, the transition pressure was found to underestimate (0.11 GPa) and overestimate (3.57 GPa) using local density approximation and generalized gradient approximation functionals, respectively. Mechanical stability of both the phases is explained from the calculated single crystal elastic constants. In addition, the zone center phonon frequencies have been calculated using density functional perturbation theory at ambient as well as at high pressure and the lattice modes are found to soften under pressure between 0.6 and 1.2 GPa. The present study reveals that the observed structural phase transition leads to changes in the decomposition mechanism of KClO3 which corroborates with the experimental results.

Pressure induced structural phase transition in solid oxidizer KClO3: a first-principles study.

PubMed

Yedukondalu, N; Ghule, Vikas D; Vaitheeswaran, G

2013-05-07

High pressure behavior of potassium chlorate (KClO3) has been investigated from 0 to 10 GPa by means of first principles density functional theory calculations. The calculated ground state parameters, transition pressure, and phonon frequencies using semiempirical dispersion correction scheme are in excellent agreement with experiment. It is found that KClO3 undergoes a pressure induced first order phase transition with an associated volume collapse of 6.4% from monoclinic (P2(1)/m) → rhombohedral (R3m) structure at 2.26 GPa, which is in good accord with experimental observation. However, the transition pressure was found to underestimate (0.11 GPa) and overestimate (3.57 GPa) using local density approximation and generalized gradient approximation functionals, respectively. Mechanical stability of both the phases is explained from the calculated single crystal elastic constants. In addition, the zone center phonon frequencies have been calculated using density functional perturbation theory at ambient as well as at high pressure and the lattice modes are found to soften under pressure between 0.6 and 1.2 GPa. The present study reveals that the observed structural phase transition leads to changes in the decomposition mechanism of KClO3 which corroborates with the experimental results.

Density functional study of the electronic structure of dye-functionalized fullerenes and their model donor-acceptor complexes containing P3HT

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

Baruah, Tunna; Garnica, Amanda; Paggen, Marina

2016-04-14

We study the electronic structure of C{sub 60} fullerenes functionalized with a thiophene-diketo-pyrrolopyrrole-thiophene based chromophore using density functional theory combined with large polarized basis sets. As the attached chromophore has electron donor character, the functionalization of the fullerene leads to a donor-acceptor (DA) system. We examine in detail the effect of the linker and the addition site on the electronic structure of the functionalized fullerenes. We further study the electronic structure of these DA complexes with a focus on the charge transfer excitations. Finally, we examine the interface of the functionalized fullerenes with the widely used poly(3-hexylthiophene-2,5-diyl) (P3HT) donor. Ourmore » results show that all functionalized fullerenes with an exception of the C{sub 60}-pyrrolidine [6,6], where the pyrrolidine is attached at a [6,6] site, have larger electron affinities relative to the pristine C{sub 60} fullerene. We also estimate the quasi-particle gap, lowest charge transfer excitation energy, and the exciton binding energies of the functionalized fullerene-P3MT model systems. Results show that the exciton binding energies in these model complexes are slightly smaller compared to a similarly prepared phenyl-C{sub 61}-butyric acid methyl ester (PCBM)-P3MT complex.« less

A continued role for signaling functions in the early evolution of feathers.

PubMed

Ruxton, Graeme D; Persons Iv, W Scott; Currie, Philip J

2017-03-01

Persons and Currie (2015) argued against either flight, thermoregulation, or signaling as a functional benefit driving the earliest evolution of feathers; rather, they favored simple feathers having an initial tactile sensory function, which changed to a thermoregulatory function as density increased. Here, we explore the relative merits of early simple feathers that may have originated as tactile sensors progressing instead toward a signaling, rather than (or in addition to) a thermoregulatory function. We suggest that signaling could act in concert with a sensory function more naturally than could thermoregulation. As such, the dismissal of a possible signaling function and the presumption that an initial sensory function led directly to a thermoregulatory function (implicit in the title "bristles before down") are premature. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

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.

Assessment of Methods to Consolidate Iodine-Loaded Silver-Functionalized Silica Aerogel

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

Matyas, Josef; Engler, Robert K.

2013-09-01

The U.S. Department of Energy is currently investigating alternative sorbents for the removal and immobilization of radioiodine from the gas streams in a nuclear fuel reprocessing plant. One of these new sorbents, Ag0-functionalized silica aerogels, shows great promise as a potential replacement for Ag-bearing mordenites because of its high selectivity and sorption capacity for iodine. Moreover, a feasible consolidation of iodine-loaded Ag0-functionalized silica aerogels to a durable SiO2-based waste form makes this aerogel an attractive choice for sequestering radioiodine. This report provides a preliminary assessment of the methods that can be used to consolidate iodine-loaded Ag0-functionalized silica aerogels into amore » final waste form. In particular, it focuses on experimental investigation of densification of as prepared Ag0-functionalized silica aerogels powders, with or without organic moiety and with or without sintering additive (colloidal silica), with three commercially available techniques: 1) hot uniaxial pressing (HUP), 2) hot isostatic pressing (HIP), and 3) spark plasma sintering (SPS). The densified products were evaluated with helium gas pycnometer for apparent density, with the Archimedes method for apparent density and open porosity, and with high-resolution scanning electron microscopy and energy dispersive spectroscopy (SEM-EDS) for the extent of densification and distribution of individual elements. The preliminary investigation of HUP, HIP, and SPS showed that these sintering methods can effectively consolidate powders of Ag0-functionalized silica aerogel into products of near-theoretical density. Also, removal of organic moiety and adding 5.6 mass% of colloidal silica to Ag0-functionalized silica aerogel powders before processing provided denser products. Furthermore, the ram travel data for SPS indicated that rapid consolidation of powders can be performed at temperatures below 950°C.« less

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.

Computational chemistry calculations of stability for bismuth nanotubes, fullerene-like structures and hydrogen-containing nanostructures.

PubMed

Kharissova, Oxana V; Osorio, Mario; Vázquez, Mario Sánchez; Kharisov, Boris I

2012-08-01

Using molecular mechanics (MM+), semi-empirical (PM6) and density functional theory (DFT) (B3LYP) methods we characterized bismuth nanotubes. In addition, we predicted the bismuth clusters {Bi(20)(C(5V)), Bi(24)(C(6v)), Bi(28)(C(1)), B(32)(D(3H)), Bi(60)(C(I))} and calculated their conductor properties.

Photoinduced electron transfer process on emission spectrum of N,N‧-bis(salicylidene)-1,2-phenylenediamine as a Mg2+ cation chemosensor: A first principle DFT and TDDFT study

NASA Astrophysics Data System (ADS)

Taherpour, Avat (Arman); Jamshidi, Morteza; Rezaei, Omid; Belverdi, Ali Rezaei

2018-06-01

The electronic and optical properties of N,N‧-bis(salicylidene)-1,2-phenylenediamine (SPDA) ligand were studied as a chemical sensor of Mg2+ cation in two solvents (water and DMSO) using the ab initio theory through Density Functional Theory (DFT) and Time Dependent Density Functional theory (TDDFT) methods. The results show that the SPDA ligand has a high ability for chemical sensing of Mg2+. The results has also represented that HOMO-LUMO energy gap decreases 0.941 eV after the complex formation between SPDA and Mg2+. In addition, obvious changes are found in the UV-Vis absorption spectrum, optical analyses SPDA ligand and [SPDA.Mg]2+ complex, which it has the capability of detecting Mg2+ via the adsorptive UV-Vis and colorimetric methods. Emission spectrum calculations and photoinduced electron transfer (PET) process in water solution shows different wavelength emission spectrum in amount of 4.6 nm. An analysis of NBO (natural bond orbital) data indicates tangible changes in the electron transfers data from the electron pairs of ligand to the conjugated system, both prior and subsequent to Mg2+addition.

Hypervelocity Impact Test Fragment Modeling: Modifications to the Fragment Rotation Analysis and Lightcurve Code

NASA Technical Reports Server (NTRS)

Gouge, Michael F.

2011-01-01

Hypervelocity impact tests on test satellites are performed by members of the orbital debris scientific community in order to understand and typify the on-orbit collision breakup process. By analysis of these test satellite fragments, the fragment size and mass distributions are derived and incorporated into various orbital debris models. These same fragments are currently being put to new use using emerging technologies. Digital models of these fragments are created using a laser scanner. A group of computer programs referred to as the Fragment Rotation Analysis and Lightcurve code uses these digital representations in a multitude of ways that describe, measure, and model on-orbit fragments and fragment behavior. The Dynamic Rotation subroutine generates all of the possible reflected intensities from a scanned fragment as if it were observed to rotate dynamically while in orbit about the Earth. This calls an additional subroutine that graphically displays the intensities and the resulting frequency of those intensities as a range of solar phase angles in a Probability Density Function plot. This document reports the additions and modifications to the subset of the Fragment Rotation Analysis and Lightcurve concerned with the Dynamic Rotation and Probability Density Function plotting subroutines.

Direct G-code manipulation for 3D material weaving

NASA Astrophysics Data System (ADS)

Koda, S.; Tanaka, H.

2017-04-01

The process of conventional 3D printing begins by first build a 3D model, then convert to the model to G-code via a slicer software, feed the G-code to the printer, and finally start the printing. The most simple and popular 3D printing technique is Fused Deposition Modeling. However, in this method, the printing path that the printer head can take is restricted by the G-code. Therefore the printed 3D models with complex pattern have structural errors like holes or gaps between the printed material lines. In addition, the structural density and the material's position of the printed model are difficult to control. We realized the G-code editing, Fabrix, for making a more precise and functional printed model with both single and multiple material. The models with different stiffness are fabricated by the controlling the printing density of the filament materials with our method. In addition, the multi-material 3D printing has a possibility to expand the physical properties by the material combination and its G-code editing. These results show the new printing method to provide more creative and functional 3D printing techniques.

Structural, thermogravimetric, B3LYP and biological studies on some heterocyclic thiosemicarbazide copper (II) complexes and evaluation of their molecular docking

NASA Astrophysics Data System (ADS)

Gaber, Mohamed; Fayed, Tarek A.; El-Gamil, Mohammed M.; Abu El-Reash, Gaber M.

2018-01-01

Two copper (II) complexes of ligands H2L1 and H2L2 have been prepared and investigated. The ligands were prepared by the individually addition of picolinic acid hydrazide and 2-(2-aminothiazol-4-yl) acetohydrazide into benzoyl isothiocyanate. The results of analytical and spectroscopic equipments revealed that H2L1 act as monobasic bidentate with square planner environment. While H2L2 behaves as monobasic tetradentate with Oh geometry. The geometries of ligands and their complexes being carefully studied using Jaguar 9.1 program based on the density functional theory (DFT) to predict properties of materials performed by the hybrid density functional method B3LYP. Additionally, thermal degradation data were evaluated to determine the kinetic and thermodynamic parameters by different methods. Moreover, the anti-oxidant (using DPPH and SOD methods), and anti-bacterial activities of the compounds have been studied. Furthermore, the docking study of ligands and their complexes were applied against gram-positive S. Aureus, negative E. Coli bacterial and C. Albicans fungal strains by Schrödinger suite program using XP glide protocol.

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.

Seed-predator satiation and Janzen-Connell effects vary with spatial scales for seed-feeding insects.

PubMed

Xiao, Zhishu; Mi, Xiangcheng; Holyoak, Marcel; Xie, Wenhua; Cao, Ke; Yang, Xifu; Huang, Xiaoqun; Krebs, Charles J

2017-01-01

The Janzen-Connell model predicts that common species suffer high seed predation from specialized natural enemies as a function of distance from parent trees, and consequently as a function of conspecific density, whereas the predator satiation hypothesis predicts that seed attack is reduced due to predator satiation at high seed densities. Pre-dispersal predation by insects was studied while seeds are still on parent trees, which represents a frequently overlooked stage in which seed predation occurs. Reproductive tree density and seed production were investigated from ten Quercus serrata populations located in south-west China, quantifying density-dependent pre-dispersal seed predation over two years by three insect groups. Acorn infestation was nearly twice as high in the low-seed year as that in the high-seed year, with considerable spatio-temporal variation in the direction and magnitude of density-dependent pre-dispersal seed predation evident. Across whole populations of trees, a high density of reproductive trees caused predator satiation and reduced insect attack in the high-seed year. Within individual trees, and consistent with the Janzen-Connell model, overall insect seed predation was positively correlated with seed production in the low-seed year. In addition, there was variation among insect taxa, with positive density-dependent seed predation by Curculio weevils in the high-seed year and moths in the low-seed year, but apparent density independence by Cyllorhynchites weevils in both years. The overall trend of negative density-dependent, pre-dispersal seed predation suggests that predator satiation limited the occurrence of Janzen-Connell effects across Q. serrata populations. Such effects may have large impacts on plant population dynamics and tree diversity, depending on the extent to which they are reduced by counteracting positive density-dependent predation for seeds on individual trees and other factors affecting successful recruitment. © The Author 2016. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

A study of factors affecting the human cone photoreceptor density measured by adaptive optics scanning laser ophthalmoscope.

PubMed

Park, Sung Pyo; Chung, Jae Keun; Greenstein, Vivienne; Tsang, Stephen H; Chang, Stanley

2013-03-01

To investigate the variation in human cone photoreceptor packing density with various demographic or clinical factors, cone packing density was measured using a Canon prototype adaptive optics scanning laser ophthalmoscope and compared as a function of retinal eccentricity, refractive error, axial length, age, gender, race/ethnicity and ocular dominance. We enrolled 192 eyes of 192 subjects with no ocular pathology. Cone packing density was measured at three different retinal eccentricities (0.5 mm, 1.0 mm, and 1.5 mm from the foveal center) along four meridians. Cone density decreased from 32,200 to 11,600 cells/mm(2) with retinal eccentricity (0.5 mm to 1.5 mm from the fovea, P < 0.001). A trend towards a slightly negative correlation was observed between age and density (r = -0.117, P = 0.14). There was, however, a statistically significant negative correlation (r = -0.367, P = 0.003) between axial length and cone density. Gender, ocular dominance, and race/ethnicity were not important determinants of cone density (all, P > 0.05). In addition, to assess the spatial arrangement of the cone mosaics, the nearest-neighbor distances (NNDs) and the Voronoi domains were analyzed. The results of NND and Voronoi analysis were significantly correlated with the variation of the cone density. Average NND and Voronoi area were gradually increased (all, P ≤ 0.001) and the degree of regularity of the cone mosaics was decreased (P ≤ 0.001) with increasing retinal eccentricity. In conclusion, we demonstrated cone packing density decreases as a function of retinal eccentricity and axial length and the results of NND and Voronoi analysis is a useful index for cone mosaics arrangements. The results also serve as a reference for further studies designed to detect or monitor cone photoreceptors in patients with retinal diseases. Copyright © 2012 Elsevier Ltd. All rights reserved.

A study of factors affecting the human cone photoreceptor density measured by adaptive optics scanning laser ophthalmoscope

PubMed Central

Park, Sung Pyo; Chung, Jae Keun; Greenstein, Vivienne; Tsang, Stephen H.; Chang, Stanley

2015-01-01

To investigate the variation in human cone photoreceptor packing density with various demographic or clinical factors, cone packing density was measured using a Canon prototype adaptive optics scanning laser ophthalmoscope and compared as a function of retinal eccentricity, refractive error, axial length, age, gender, race/ethnicity and ocular dominance. We enrolled 192 eyes of 192 subjects with no ocular pathology. Cone packing density was measured at three different retinal eccentricities (0.5 mm, 1.0 mm, and 1.5 mm from the foveal center) along four meridians. Cone density decreased from 32,200 to 11,600 cells/mm2 with retinal eccentricity (0.5 mm to 1.5 mm from the fovea, P < 0.001). A trend towards a slightly negative correlation was observed between age and density (r = −0.117, P = 0.14). There was, however, a statistically significant negative correlation (r = −0.367, P = 0.003) between axial length and cone density. Gender, ocular dominance, and race/ethnicity were not important determinants of cone density (all, P > 0.05). In addition, to assess the spatial arrangement of the cone mosaics, the nearest-neighbor distances (NNDs) and the Voronoi domains were analyzed. The results of NND and Voronoi analysis were significantly correlated with the variation of the cone density. Average NND and Voronoi area were gradually increased (all, P ≤ 0.001) and the degree of regularity of the cone mosaics was decreased (P ≤ 0.001) with increasing retinal eccentricity. In conclusion, we demonstrated cone packing density decreases as a function of retinal eccentricity and axial length and the results of NND and Voronoi analysis is a useful index for cone mosaics arrangements. The results also serve as a reference for further studies designed to detect or monitor cone photoreceptors in patients with retinal diseases. PMID:23276813

Affordable and accurate large-scale hybrid-functional calculations on GPU-accelerated supercomputers

NASA Astrophysics Data System (ADS)

Ratcliff, Laura E.; Degomme, A.; Flores-Livas, José A.; Goedecker, Stefan; Genovese, Luigi

2018-03-01

Performing high accuracy hybrid functional calculations for condensed matter systems containing a large number of atoms is at present computationally very demanding or even out of reach if high quality basis sets are used. We present a highly optimized multiple graphics processing unit implementation of the exact exchange operator which allows one to perform fast hybrid functional density-functional theory (DFT) calculations with systematic basis sets without additional approximations for up to a thousand atoms. With this method hybrid DFT calculations of high quality become accessible on state-of-the-art supercomputers within a time-to-solution that is of the same order of magnitude as traditional semilocal-GGA functionals. The method is implemented in a portable open-source library.

Morphometric analysis of primary graft non-function in liver transplantation.

PubMed

Vertemati, M; Sabatella, G; Minola, E; Gambacorta, M; Goffredi, M; Vizzotto, L

2005-04-01

Primary graft non-function (PNF) is a life-threatening condition that is thought to be the consequence of microcirculation injury. The aim of the present study was to assess, with a computerized morphometric model, the morphological changes at reperfusion in liver biopsy specimens from patients who developed PNF after liver transplantation. Biopsy specimens were obtained at maximum ischaemia and at the end of reperfusion. Morphology included many stereological parameters, such as volumes of all parenchymal components, surface density, size distribution and mean diameter of hepatocytes. Other variables examined were intensive care unit stay, degree of steatosis, serum liver function tests and ischaemic time. In the postoperative period, the PNF group showed elevated serum levels of alanine transferase, decreased daily rate of bile production and prothrombin activity. Blood lactates were significantly higher in the PNF group than in a control group. When comparing groups, the volumetric parameters related to hepatocytes and sinusoids and the surface densities of the hepatic cells showed an inverse relationship. At the end of reperfusion, in PNF group the volume fraction of hepatocyte cytoplasm was decreased; in contrast, the volume fraction of sinusoidal lumen was markedly increased. The cell profiles showed the same inverse trend: the surface density of the parenchymal border of hepatocytes was decreased in PNF when compared with the control group, while the surface density of the vascular border was increased. In the PNF group, the surface density of the sinusoidal bed was directly correlated with alanine transferase, daily rate of bile production, prothrombin activity and cold ischaemic time. The alterations in hepatic architecture, as demonstrated by morphometric analysis in liver transplant recipients that developed PNF, provide additional information that may represent useful viability markers of the graft to complement conventional histological analysis.

Assessing the spatial relationship between fixation and foveal specializations.

PubMed

Wilk, Melissa A; Dubis, Adam M; Cooper, Robert F; Summerfelt, Phyllis; Dubra, Alfredo; Carroll, Joseph

2017-03-01

Increased cone photoreceptor density, an avascular zone (FAZ), and the displacement of inner retinal neurons to form a pit are distinct features of the human fovea. As the fovea provides the majority of our vision, appreciating how these anatomical specializations are related is important for understanding foveal development, normal visual function, and retinal disease. Here we evaluated the relationship between these specializations and their location relative to the preferred retinal locus of fixation (PRL). We measured foveal pit volume, FAZ area, peak cone density, and location of the PRL in 22 subjects with normal vision using optical coherence tomography and adaptive optics scanning light ophthalmoscopy. Foveal pit volume was positively correlated with FAZ area; however, peak cone density was not correlated with pit volume. In addition, there was no systematic offset of the location of any of these specializations relative to PRL, and there was no correlation between the magnitude of the offset from PRL and the corresponding foveal specialization measurements (pit volume, FAZ area, peak cone density). The standard deviation of our PRL measurements was consistent with previous measurements of fixational stability. These data provide insight into the sequence of events during foveal development and may have implications for visual function and retinal disease. Copyright © 2016 Elsevier Ltd. All rights reserved.

Electrochemical Implications of Defects in Carbon Nanotubes

NASA Astrophysics Data System (ADS)

Hall, Jonathan Peter

The electrochemical behavior of carbon nanotubes (CNTs) containing both intrinsic and extrinsically introduced defects has been investigated through the study of bamboo and hollow multi-walled CNT morphologies. The controlled addition of argon, hydrogen, and chlorine ions in addition to atomic hydrogen and magnesium vapor was used for varying the charge and type of extrinsic defects. To quantify changes in the CNTs upon treatment, Raman spectroscopy and electrochemical techniques were employed. It was indicated from Raman spectroscopy, cyclic voltammetry, electrochemical impedance spectroscopy, and chronopotentiometric experiments that the electrochemical response of hollow type CNTs could be tailored more significantly compared to bamboo type CNTs, which have innately high reactive site densities and are less amenable to modification. Total defect density and edge-plane-like defect concentrations monitored through Raman spectroscopy were used to correlate changes in the electrochemical response of the CNT electrodes as a function of treatment. The implementation of CNT electrodes in a prototypical electrolytic capacitor device was then explored and characterized. Dependencies on source current and redox couple concentration were evaluated, as well as changes in the total capacitance as a function of treatment. Cyclability studies were also performed as a function of source current magnitude to evaluate the longevity of the faradaic currents which typically decrease over time in other similar capacitors. This thesis then concludes with an overall summary of the themes and findings of the research presented in this work.

Antioxidant Activities of Functional Beverage Concentrates Containing Herbal Medicine Extracts.

PubMed

Park, Seon-Joo; Kim, Mi-Ok; Kim, Jung Hoan; Jeong, Sehyun; Kim, Min Hee; Yang, Su-Jin; Lee, Jongsung; Lee, Hae-Jeung

2017-03-01

This study investigated the antioxidant activity of functional beverage concentrates containing herbal medicine extracts (FBCH) using various antioxidant assays, such as 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging activity, 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid (ABTS) radical scavenging activity, and reducing power assay. The total polyphenolic content of FBCH (81.45 mg/100 g) was higher than Ssanghwa tea (SHT, 37.56 mg/100 g). The antioxidant activities of FBCH showed 52.92% DPPH and 55.18% ABTS radical scavenging activities at 100 mg/mL, respectively. FBCH showed significantly higher antioxidant activities compared to the SHT (DPPH, 23.43%; ABTS, 22.21%; reducing power optical density; 0.23, P <0.05). In addition, intracellular reactive oxygen species generation significantly decreased in a concentration-dependent manner following FBCH treatment. These results suggest that the addition of herbal medicine extract contributes to the improved functionality of beverage concentrates.

Characterizing the Spatial Density Functions of Neural Arbors

NASA Astrophysics Data System (ADS)

Teeter, Corinne Michelle

Recently, it has been proposed that a universal function describes the way in which all arbors (axons and dendrites) spread their branches over space. Data from fish retinal ganglion cells as well as cortical and hippocampal arbors from mouse, rat, cat, monkey and human provide evidence that all arbor density functions (adf) can be described by a Gaussian function truncated at approximately two standard deviations. A Gaussian density function implies that there is a minimal set of parameters needed to describe an adf: two or three standard deviations (depending on the dimensionality of the arbor) and an amplitude. However, the parameters needed to completely describe an adf could be further constrained by a scaling law found between the product of the standard deviations and the amplitude of the function. In the following document, I examine the scaling law relationship in order to determine the minimal set of parameters needed to describe an adf. First, I find that the at, two-dimensional arbors of fish retinal ganglion cells require only two out of the three fundamental parameters to completely describe their density functions. Second, the three-dimensional, volume filling, cortical arbors require four fundamental parameters: three standard deviations and the total length of an arbor (which corresponds to the amplitude of the function). Next, I characterize the shape of arbors in the context of the fundamental parameters. I show that the parameter distributions of the fish retinal ganglion cells are largely homogenous. In general, axons are bigger and less dense than dendrites; however, they are similarly shaped. The parameter distributions of these two arbor types overlap and, therefore, can only be differentiated from one another probabilistically based on their adfs. Despite artifacts in the cortical arbor data, different types of arbors (apical dendrites, non-apical dendrites, and axons) can generally be differentiated based on their adfs. In addition, within arbor type, there is evidence of different neuron classes (such as interneurons and pyramidal cells). How well different types and classes of arbors can be differentiated is quantified using the Random ForestTM supervised learning algorithm.

The structures and electronic properties of zigzag silicene nanoribbons with periodically embedded with four- and eight-membered rings

NASA Astrophysics Data System (ADS)

Tan, Guiping; Lu, Junzhe; Zhu, Hengjiang; Li, Fangfang; Ma, Miaomiao; Wang, Xiaoning

2018-07-01

Using density functional theory (DFT), we have studied the structure of a zigzag silicene nanoribbons (SiNRs) with periodically embedded with four- and eight-membered rings, and studied their electronic properties by calculating its band structures and density of states (DOS). The results showed that the zigzag SiNRs have a sp2 hybridization, in addition, the band gap gradually decreased with the increase of the width by layer, and gradually changed from semiconductor properties to metal properties. The existence of vacancy defects increased the band gap and energies, but their positions could not change the structure and the electronic properties.

Defect-engineered graphene chemical sensors with ultrahigh sensitivity.

PubMed

Lee, Geonyeop; Yang, Gwangseok; Cho, Ara; Han, Jeong Woo; Kim, Jihyun

2016-05-25

We report defect-engineered graphene chemical sensors with ultrahigh sensitivity (e.g., 33% improvement in NO2 sensing and 614% improvement in NH3 sensing). A conventional reactive ion etching system was used to introduce the defects in a controlled manner. The sensitivity of graphene-based chemical sensors increased with increasing defect density until the vacancy-dominant region was reached. In addition, the mechanism of gas sensing was systematically investigated via experiments and density functional theory calculations, which indicated that the vacancy defect is a major contributing factor to the enhanced sensitivity. This study revealed that defect engineering in graphene has significant potential for fabricating ultra-sensitive graphene chemical sensors.

Random packing of regular polygons and star polygons on a flat two-dimensional surface.

PubMed

Cieśla, Michał; Barbasz, Jakub

2014-08-01

Random packing of unoriented regular polygons and star polygons on a two-dimensional flat continuous surface is studied numerically using random sequential adsorption algorithm. Obtained results are analyzed to determine the saturated random packing ratio as well as its density autocorrelation function. Additionally, the kinetics of packing growth and available surface function are measured. In general, stars give lower packing ratios than polygons, but when the number of vertexes is large enough, both shapes approach disks and, therefore, properties of their packing reproduce already known results for disks.

Charge Compensation and Electrostatic Transferability in Three Entropy Stabilized Oxides: Results from Density Functional Theory Calculations

DTIC Science & Technology

2016-09-06

displacements from ideal lattice sites, along with reduction of a few Co and Ni cations. Addition of Li to J14 reduces the lattice constant, consistent...associated with the atoms as well as in displacements of atoms from their ideal lattice sites. II. SYNTHESIS OF THE J141Sc COMPOSITION Berardan et al...Plotted in Figure 6 are the average atom displacements for the three large systems as a function of element type. For J14 (open bars), the dis

Crowd evacuation model based on bacterial foraging algorithm

NASA Astrophysics Data System (ADS)

Shibiao, Mu; Zhijun, Chen

To understand crowd evacuation, a model based on a bacterial foraging algorithm (BFA) is proposed in this paper. Considering dynamic and static factors, the probability of pedestrian movement is established using cellular automata. In addition, given walking and queue times, a target optimization function is built. At the same time, a BFA is used to optimize the objective function. Finally, through real and simulation experiments, the relationship between the parameters of evacuation time, exit width, pedestrian density, and average evacuation speed is analyzed. The results show that the model can effectively describe a real evacuation.

Tunnel magnetoresistance of ferrocene molecules

NASA Astrophysics Data System (ADS)

Matsuura, Yukihito

2018-01-01

The spin transport in ferrocene molecules has been examined by using the nonequilibrium Green's function formalism with density functional theory. The ferrocene molecules were sandwiched between the two nickel electrodes in a parallel magnetic configuration, which enhanced the current in comparison with that in an antiparallel spin state and resulting in tunnel magnetoresistance (TMR). The current, having an opposite spin state to that of the ferromagnetic electrode, was the main channel for electron transport. In addition, it became clear that ferrocenylene molecules, having a fulvalene structure with an extended π-conjugation, enhanced the TMR effect.

Interpretation of scrape-off layer profile evolution and first-wall ion flux statistics on JET using a stochastic framework based on fillamentary motion

NASA Astrophysics Data System (ADS)

Walkden, N. R.; Wynn, A.; Militello, F.; Lipschultz, B.; Matthews, G.; Guillemaut, C.; Harrison, J.; Moulton, D.; Contributors, JET

2017-08-01

This paper presents the use of a novel modelling technique based around intermittent transport due to filament motion, to interpret experimental profile and fluctuation data in the scrape-off layer (SOL) of JET during the onset and evolution of a density profile shoulder. A baseline case is established, prior to shoulder formation, and the stochastic model is shown to be capable of simultaneously matching the time averaged profile measurement as well as the PDF shape and autocorrelation function from the ion-saturation current time series at the outer wall. Aspects of the stochastic model are then varied with the aim of producing a profile shoulder with statistical measurements consistent with experiment. This is achieved through a strong localised reduction in the density sink acting on the filaments within the model. The required reduction of the density sink occurs over a highly localised region with the timescale of the density sink increased by a factor of 25. This alone is found to be insufficient to model the expansion and flattening of the shoulder region as the density increases, which requires additional changes within the stochastic model. An example is found which includes both a reduction in the density sink and filament acceleration and provides a consistent match to the experimental data as the shoulder expands, though the uniqueness of this solution can not be guaranteed. Within the context of the stochastic model, this implies that the localised reduction in the density sink can trigger shoulder formation, but additional physics is required to explain the subsequent evolution of the profile.

Pseudopotential plane-wave calculation of the structural properties of yttrium

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

Wang, Y.; Chou, M.Y.

1991-11-01

The structural properties of hexagonal-close-packed yttrium are studied by using the plane-wave basis within the pseudopotential method and local-density-functional approximation. By employing a soft'' pseudopotential proposed by Troullier and Martins, satisfactory convergence is achieved with a plane-wave energy cutoff of 30--40 Ry for this early-transition-metal element. The overall results for the structural properties are in good agreement with experiment. It is found that the charge overlap between core and valence electrons has a substantial effect on the accuracy of the calculated structural properties. Two different calculations are performed with and without the outer-core 4{ital p} orbital included as a valencemore » state. In addition, as found in some other local-density calculations, the uncertainty in the results due to different exchange-correlation energy functionals may not be negligible in transition metals.« less

Recent Progress in Treating Protein-Ligand Interactions with Quantum-Mechanical Methods.

PubMed

Yilmazer, Nusret Duygu; Korth, Martin

2016-05-16

We review the first successes and failures of a "new wave" of quantum chemistry-based approaches to the treatment of protein/ligand interactions. These approaches share the use of "enhanced", dispersion (D), and/or hydrogen-bond (H) corrected density functional theory (DFT) or semi-empirical quantum mechanical (SQM) methods, in combination with ensemble weighting techniques of some form to capture entropic effects. Benchmark and model system calculations in comparison to high-level theoretical as well as experimental references have shown that both DFT-D (dispersion-corrected density functional theory) and SQM-DH (dispersion and hydrogen bond-corrected semi-empirical quantum mechanical) perform much more accurately than older DFT and SQM approaches and also standard docking methods. In addition, DFT-D might soon become and SQM-DH already is fast enough to compute a large number of binding modes of comparably large protein/ligand complexes, thus allowing for a more accurate assessment of entropic effects.

Atomically thin heterostructures based on single-layer tungsten diselenide and graphene.

PubMed

Lin, Yu-Chuan; Chang, Chih-Yuan S; Ghosh, Ram Krishna; Li, Jie; Zhu, Hui; Addou, Rafik; Diaconescu, Bogdan; Ohta, Taisuke; Peng, Xin; Lu, Ning; Kim, Moon J; Robinson, Jeremy T; Wallace, Robert M; Mayer, Theresa S; Datta, Suman; Li, Lain-Jong; Robinson, Joshua A

2014-12-10

Heterogeneous engineering of two-dimensional layered materials, including metallic graphene and semiconducting transition metal dichalcogenides, presents an exciting opportunity to produce highly tunable electronic and optoelectronic systems. In order to engineer pristine layers and their interfaces, epitaxial growth of such heterostructures is required. We report the direct growth of crystalline, monolayer tungsten diselenide (WSe2) on epitaxial graphene (EG) grown from silicon carbide. Raman spectroscopy, photoluminescence, and scanning tunneling microscopy confirm high-quality WSe2 monolayers, whereas transmission electron microscopy shows an atomically sharp interface, and low energy electron diffraction confirms near perfect orientation between WSe2 and EG. Vertical transport measurements across the WSe2/EG heterostructure provides evidence that an additional barrier to carrier transport beyond the expected WSe2/EG band offset exists due to the interlayer gap, which is supported by theoretical local density of states (LDOS) calculations using self-consistent density functional theory (DFT) and nonequilibrium Green's function (NEGF).

Exploring correlations in the CGC wave function: Odd azimuthal anisotropy

DOE PAGES

Kovner, Alex; Lublinsky, Michael; Skokov, Vladimir

2017-07-17

In this paper, we extend the color glass condensate (CGC) approach to a calculation of the double inclusive gluon production by including the high density effect in the CGC wave function of the projectile (proton). Our main result is that these effects lead to the appearance of odd harmonics in the two particle correlation C(k,p). We find that in the high momentum limit, |k|, |p| >> Q s, this results in a positive c 1{2}. Additionally when the magnitudes of the two momenta are approximately equal, |k|/|p| ≈ 1, the density effects also generate a positive third harmonic c 3{2},more » which translates into a nonvanishing v 3 when the momenta of the trigger and an associated particle are in the same momentum bin. Finally, the sign of c 3{2} becomes negative when |k|/|p| > 1.1 suggesting an interesting experimental signature.« less

Theoretical study of the Raman active CDW gap mode in manganites.

PubMed

Rout, G C; Panda, Saswati; Behera, S N

2010-09-22

We report here the microscopic theory of the Raman spectra of the colossal magnetoresistive (CMR) manganite systems. The system is described by a model Hamiltonian consisting of the double exchange interaction in addition to the charge ordering interaction in the e(g) band and spin-spin interaction among the t(2g) core electrons. Further the phonon coupling to the conduction electron density is incorporated in the model for phonons in the harmonic approximation. The spectral density function for the Raman spectra is calculated from the imaginary part of the phonon Green's function. The calculated spectra display the Raman active bare phonon peak along with the charge ordering peak. The magnetic field and temperature dependence of the charge ordering peak agrees with the 480 cm(-1) JT mode observed in the experiments. The evolution of this mode is investigated in the report.

Estimation of vegetation cover at subpixel resolution using LANDSAT data

NASA Technical Reports Server (NTRS)

Jasinski, Michael F.; Eagleson, Peter S.

1986-01-01

The present report summarizes the various approaches relevant to estimating canopy cover at subpixel resolution. The approaches are based on physical models of radiative transfer in non-homogeneous canopies and on empirical methods. The effects of vegetation shadows and topography are examined. Simple versions of the model are tested, using the Taos, New Mexico Study Area database. Emphasis has been placed on using relatively simple models requiring only one or two bands. Although most methods require some degree of ground truth, a two-band method is investigated whereby the percent cover can be estimated without ground truth by examining the limits of the data space. Future work is proposed which will incorporate additional surface parameters into the canopy cover algorithm, such as topography, leaf area, or shadows. The method involves deriving a probability density function for the percent canopy cover based on the joint probability density function of the observed radiances.

Ground-state energies and highest occupied eigenvalues of atoms in exchange-only density-functional theory

NASA Astrophysics Data System (ADS)

Li, Yan; Harbola, Manoj K.; Krieger, J. B.; Sahni, Viraht

1989-11-01

The exchange-correlation potential of the Kohn-Sham density-functional theory has recently been interpreted as the work required to move an electron against the electric field of its Fermi-Coulomb hole charge distribution. In this paper we present self-consistent results for ground-state total energies and highest occupied eigenvalues of closed subshell atoms as obtained by this formalism in the exchange-only approximation. The total energies, which are an upper bound, lie within 50 ppm of Hartree-Fock theory for atoms heavier than Be. The highest occupied eigenvalues, as a consequence of this interpretation, approximate well the experimental ionization potentials. In addition, the self-consistently calculated exchange potentials are very close to those of Talman and co-workers [J. D. Talman and W. F. Shadwick, Phys. Rev. A 14, 36 (1976); K. Aashamar, T. M. Luke, and J. D. Talman, At. Data Nucl. Data Tables 22, 443 (1978)].

Nitric oxide coupling to generate N2O promoted by a single-heme system as examined by density functional theory.

PubMed

Yi, Jun; Campbell, Adam L O; Richter-Addo, George B

2016-11-30

Bacteria utilize a heme/non-heme enzyme system to detoxify nitric oxide (NO) to N 2 O. In order to probe the capacity of a single-heme system to mediate this NO-to-N 2 O transformation, various scenarios for addition of electrons, protons, and a second NO molecule to a heme nitrosyl to generate N 2 O were explored by density functional theory calculations. We describe, utilizing this single-heme system, several stepwise intermediates along pathways that enable the critical N-N bond formation step yielding the desired Fe-N 2 O product. We also report a hitherto unreported directional second protonation that results in either productive N 2 O formation with loss of water, or formation of a non-productive hyponitrous acid adduct Fe{HONNOH}. Copyright © 2016 Elsevier Inc. All rights reserved.

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.

Comparative analysis of quantum cascade laser modeling based on density matrices and non-equilibrium Green's functions

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

Lindskog, M., E-mail: martin.lindskog@teorfys.lu.se; Wacker, A.; Wolf, J. M.

2014-09-08

We study the operation of an 8.5 μm quantum cascade laser based on GaInAs/AlInAs lattice matched to InP using three different simulation models based on density matrix (DM) and non-equilibrium Green's function (NEGF) formulations. The latter advanced scheme serves as a validation for the simpler DM schemes and, at the same time, provides additional insight, such as the temperatures of the sub-band carrier distributions. We find that for the particular quantum cascade laser studied here, the behavior is well described by simple quantum mechanical estimates based on Fermi's golden rule. As a consequence, the DM model, which includes second order currents,more » agrees well with the NEGF results. Both these simulations are in accordance with previously reported data and a second regrown device.« less

Feasibility of generating quantitative composition images in dual energy mammography: a simulation study

NASA Astrophysics Data System (ADS)

Lee, Donghoon; Kim, Ye-seul; Choi, Sunghoon; Lee, Haenghwa; Choi, Seungyeon; Kim, Hee-Joung

2016-03-01

Breast cancer is one of the most common malignancies in women. For years, mammography has been used as the gold standard for localizing breast cancer, despite its limitation in determining cancer composition. Therefore, the purpose of this simulation study is to confirm the feasibility of obtaining tumor composition using dual energy digital mammography. To generate X-ray sources for dual energy mammography, 26 kVp and 39 kVp voltages were generated for low and high energy beams, respectively. Additionally, the energy subtraction and inverse mapping functions were applied to provide compositional images. The resultant images showed that the breast composition obtained by the inverse mapping function with cubic fitting achieved the highest accuracy and least noise. Furthermore, breast density analysis with cubic fitting showed less than 10% error compare to true values. In conclusion, this study demonstrated the feasibility of creating individual compositional images and capability of analyzing breast density effectively.

Competing phases, phase separation, and coexistence in the extended one-dimensional bosonic Hubbard model

DOE PAGES

Batrouni, G. G.; Rousseau, V. G.; Scalettar, R. T.; ...

2014-11-17

Here, we study the phase diagram of the one-dimensional bosonic Hubbard model with contact (U) and near neighbor (V ) interactions focusing on the gapped Haldane insulating (HI) phase which is characterized by an exotic nonlocal order parameter. The parameter regime (U, V and μ) where this phase exists and how it competes with other phases such as the supersolid (SS) phase, is incompletely understood. We use the Stochastic Green Function quantum Monte Carlo algorithm as well as the density matrix renormalization group to map out the phase diagram. The HI exists only at = 1, the SS phase existsmore » for a very wide range of parameters (including commensurate fillings) and displays power law decay in the one body Green function were our main conclusions. Additionally, we show that at fixed integer density, the system exhibits phase separation in the (U, V ) plane.« less

Neurolastin, a dynamin family GTPase, regulates excitatory synapses and spine density

PubMed Central

Madan Lomash, Richa; Gu, Xinglong; Youle, Richard J.; Lu, Wei; Roche, Katherine W.

2015-01-01

SUMMARY Membrane trafficking and spinogenesis contribute significantly to changes in synaptic strength during development and in various paradigms of synaptic plasticity. GTPases of the dynamin family are key players regulating membrane trafficking. Here, we identify a brain-specific dynamin family GTPase, neurolastin (RNF112/Znf179), with closest homology to atlastin. We demonstrate that neurolastin has functional GTPase and RING domains, making it a unique protein identified with this multi-enzymatic domain organization. We also show that neurolastin is a peripheral membrane protein, which localizes to endosomes and affects endosomal membrane dynamics via its RING domain. In addition, neurolastin knockout mice have fewer dendritic spines, and rescue of the wildtype phenotype requires both the GTPase and RING domains. Furthermore, we find fewer functional synapses and reduced paired pulse facilitation in neurolastin knockout mice. Thus, we identify neurolastin as a dynamin family GTPase that affects endosome size and spine density. PMID:26212327

Simplified curve fits for the thermodynamic properties of equilibrium air

NASA Technical Reports Server (NTRS)

Srinivasan, S.; Tannehill, J. C.; Weilmuenster, K. J.

1987-01-01

New, improved curve fits for the thermodynamic properties of equilibrium air have been developed. The curve fits are for pressure, speed of sound, temperature, entropy, enthalpy, density, and internal energy. These curve fits can be readily incorporated into new or existing computational fluid dynamics codes if real gas effects are desired. The curve fits are constructed from Grabau-type transition functions to model the thermodynamic surfaces in a piecewise manner. The accuracies and continuity of these curve fits are substantially improved over those of previous curve fits. These improvements are due to the incorporation of a small number of additional terms in the approximating polynomials and careful choices of the transition functions. The ranges of validity of the new curve fits are temperatures up to 25 000 K and densities from 10 to the -7 to 10 to the 3d power amagats.

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

Vörös, Márton; Brawand, Nicholas P.; Galli, Giulia

Lead chalcogenide (PbX) nanoparticles are promising materials for solar energy conversion. However, the presence of trap states in their electronic gap limits their usability, and developing a universal strategy to remove trap states is a persistent challenge. Using calculations based on density functional theory, we show that hydrogen acts as an amphoteric impurity on PbX nanoparticle surfaces; hydrogen atoms may passivate defects arising from ligand imbalance or off-stoichiometric surface terminations irrespective of whether they originate from cation or anion excess. In addition, we show, using constrained density functional theory calculations, that hydrogen treatment of defective nanoparticles is also beneficial formore » charge transport in films. We also find that hydrogen adsorption on stoichiometric nanoparticles leads to electronic doping, preferentially n-type. Lastly, our findings suggest that postsynthesis hydrogen treatment of lead chalcogenide nanoparticle films is a viable approach to reduce electronic trap states or to dope well-passivated films.« less

Ethane and Xenon mixing: density functional theory (DFT) simulations and experiments on Sandia's Z machine

NASA Astrophysics Data System (ADS)

Magyar, Rudolph; Root, Seth; Mattsson, Thomas; Cochrane, Kyle

2012-02-01

The combination of ethane and xenon is one of the simplest binary mixtures in which bond breaking is expected to play a role under shock conditions. At cryogenic conditions, xenon is often understood to mix with alkanes such as Ethane as if it were also an alkane, but this model is expected to break down at higher temperatures and pressures. To investigate the breakdown, we have performed density functional theory (DFT) calculations on several xenon/ethane mixtures. Additionally, we have performed shock compression experiments on Xenon-Ethane using the Sandia Z - accelerator. The DFT and experimental results are compared to hydrodynamic simulations using different mixing models in the equation of state. Sandia National Laboratories is a multi-program laboratory operated by Sandia Corporation, a wholly owned subsidiary of the Lockheed Martin company, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Probabilistic density function method for nonlinear dynamical systems driven by colored noise

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

Barajas-Solano, David A.; Tartakovsky, Alexandre M.

2016-05-01

We present a probability density function (PDF) method for a system of nonlinear stochastic ordinary differential equations driven by colored noise. The method provides an integro-differential equation for the temporal evolution of the joint PDF of the system's state, which we close by means of a modified Large-Eddy-Diffusivity-type closure. Additionally, we introduce the generalized local linearization (LL) approximation for deriving a computable PDF equation in the form of the second-order partial differential equation (PDE). We demonstrate the proposed closure and localization accurately describe the dynamics of the PDF in phase space for systems driven by noise with arbitrary auto-correlation time.more » We apply the proposed PDF method to the analysis of a set of Kramers equations driven by exponentially auto-correlated Gaussian colored noise to study the dynamics and stability of a power grid.« less

A Well-Tempered Hybrid Method for Solving Challenging Time-Dependent Density Functional Theory (TDDFT) Systems.

PubMed

Kasper, Joseph M; Williams-Young, David B; Vecharynski, Eugene; Yang, Chao; Li, Xiaosong

2018-04-10

The time-dependent Hartree-Fock (TDHF) and time-dependent density functional theory (TDDFT) equations allow one to probe electronic resonances of a system quickly and inexpensively. However, the iterative solution of the eigenvalue problem can be challenging or impossible to converge, using standard methods such as the Davidson algorithm for spectrally dense regions in the interior of the spectrum, as are common in X-ray absorption spectroscopy (XAS). More robust solvers, such as the generalized preconditioned locally harmonic residual (GPLHR) method, can alleviate this problem, but at the expense of higher average computational cost. A hybrid method is proposed which adapts to the problem in order to maximize computational performance while providing the superior convergence of GPLHR. In addition, a modification to the GPLHR algorithm is proposed to adaptively choose the shift parameter to enforce a convergence of states above a predefined energy threshold.

Theoretical investigation of structural, mechanical and electronic properties of GaAs1-xNx alloys under ambient and high pressure

NASA Astrophysics Data System (ADS)

Li, Jian; Han, Xiuxun; Dong, Chen; Fan, Changzeng

2017-12-01

Using first-principles total energy calculations, we have studied the structural, mechanical and electronic properties of GaAs1-xNx ternary semiconductor alloys with the zinc-blende crystal structure over the whole nitrogen concentration range (with x from 0 to 1) within density functional theory (DFT) framework. To obtain the ideal band gap, we employ the semi-empirical approach called local density approximation plus the multi-orbital mean-field Hubbard model (LDA+U). The calculated results illustrate the varying lattice constants and band gap in GaAs1-xNx alloys as functions of the nitrogen concentration x. According to the pressure dependence of the lattice constants and volume, the higher N concentration alloy exhibits the better anti-compressibility. In addition, an increasing band gap is predicted under 20 GPa pressure for GaAs1-xNx alloys.

Exploring the Photovoltaic Properties of Metal Bipyridine Complexes (Metal = Fe, Zn, Cr, and Ru) by Density Functional Theory

NASA Astrophysics Data System (ADS)

Irfan, Ahmad; Abbas, Ghulam

2018-03-01

The synthesis and characterisation of mononuclear Fe complexes were carried out by using bipyridine (Compound 1) at ambient conditions. Additionally, three more derivatives were designed by substituting the central Fe metal with Zn, Cr, and Ru (Compound 2, Compound 3, and Compound 4), respectively. The ground state geometry calculations were carried out by using density functional theory (DFT) at B3LYP/6-31G** (LANL2DZ) level of theory. We shed light on the frontier molecular orbitals, electronic properties, photovoltaic parameters, and structure-property relationship. The open-circuit voltage is a promising parameter that considerably affects the photovoltaic performance; thus, we have estimated its value by considering the complexes as donors whereas TiO2 and/or Si were used as acceptors. The solar cell performance behaviour was also studied by shedding light on the band alignment and energy level offset.

Functional and numerical responses of shrews to competition vary with mouse density.

PubMed

Eckrich, Carolyn A; Flaherty, Elizabeth A; Ben-David, Merav

2018-01-01

For decades, ecologists have debated the importance of biotic interactions (e.g., competition) and abiotic factors in regulating populations. Competition can influence patterns of distribution, abundance, and resource use in many systems but remains difficult to measure. We quantified competition between two sympatric small mammals, Keen's mice (Peromyscus keeni) and dusky shrews (Sorex monticolus), in four habitat types on Prince of Wales Island in Southeast Alaska. We related shrew density to that of mice using standardized regression models while accounting for habitat variables in each year from 2010-2012, during which mice populations peaked (2011) and then crashed (2012). Additionally, we measured dietary overlap and segregation using stable isotope analysis and kernel utilization densities and estimated the change in whole community energy consumption among years. We observed an increase in densities of dusky shrews after mice populations crashed in 2012 as expected under competitive release. In addition, competition coefficients revealed that the influence of Keen's mice was dependent on their density. Also in 2012, shrew diets shifted, indicating that they were able to exploit resources previously used by mice. Nonetheless, increases in shrew numbers only partially compensated for the community energy consumption because, as insectivores, they are unlikely to utilize all food types consumed by their competitors. In pre-commercially thinned stands, which exhibit higher diversity of resources compared to other habitat types, shrew populations were less affected by changes in mice densities. These spatially and temporally variable interactions between unlikely competitors, observed in a relatively simple, high-latitude island ecosystem, highlight the difficulty in assessing the role of biotic factors in structuring communities.

Multiconfigurational short-range density-functional theory for open-shell systems

NASA Astrophysics Data System (ADS)

Hedegârd, Erik Donovan; Toulouse, Julien; Jensen, Hans Jørgen Aagaard

2018-06-01

Many chemical systems cannot be described by quantum chemistry methods based on a single-reference wave function. Accurate predictions of energetic and spectroscopic properties require a delicate balance between describing the most important configurations (static correlation) and obtaining dynamical correlation efficiently. The former is most naturally done through a multiconfigurational (MC) wave function, whereas the latter can be done by, e.g., perturbation theory. We have employed a different strategy, namely, a hybrid between multiconfigurational wave functions and density-functional theory (DFT) based on range separation. The method is denoted by MC short-range DFT (MC-srDFT) and is more efficient than perturbative approaches as it capitalizes on the efficient treatment of the (short-range) dynamical correlation by DFT approximations. In turn, the method also improves DFT with standard approximations through the ability of multiconfigurational wave functions to recover large parts of the static correlation. Until now, our implementation was restricted to closed-shell systems, and to lift this restriction, we present here the generalization of MC-srDFT to open-shell cases. The additional terms required to treat open-shell systems are derived and implemented in the DALTON program. This new method for open-shell systems is illustrated on dioxygen and [Fe(H2O)6]3+.

Blocking PirB up-regulates spines and functional synapses to unlock visual cortical plasticity and facilitate recovery from amblyopia

PubMed Central

Bochner, David N.; Sapp, Richard W.; Adelson, Jaimie D.; Zhang, Siyu; Lee, Hanmi; Djurisic, Maja; Syken, Josh; Dan, Yang; Shatz, Carla J.

2015-01-01

During critical periods of development, the brain easily changes in response to environmental stimuli, but this neural plasticity declines by adulthood. By acutely disrupting paired immunoglobulin-like receptor B(PirB) function at specific ages, we show that PirB actively represses neural plasticity throughout life. We disrupted PirB function either by genetically introducing a conditional PirB allele into mice or by minipump infusion of a soluble PirB ectodomain (sPirB) into mouse visual cortex. We found that neural plasticity, as measured by depriving mice of vision in one eye and testing ocular dominance, was enhanced by this treatment both during the critical period and when PirB function was disrupted in adulthood. Acute blockade of PirB triggered the formation of new functional synapses, as indicated by increases in miniature excitatory postsynaptic current (mEPSC) frequency and spine density on dendrites of layer 5 pyramidal neurons. In addition, recovery from amblyopia— the decline in visual acuity and spine density resulting from long-term monocular deprivation— was possible after a 1-week infusion of sPirB after the deprivation period. Thus, neural plasticity in adult visual cortex is actively repressed and can be enhanced by blocking PirB function. PMID:25320232

Embedding beyond electrostatics-The role of wave function confinement.

PubMed

Nåbo, Lina J; Olsen, Jógvan Magnus Haugaard; Holmgaard List, Nanna; Solanko, Lukasz M; Wüstner, Daniel; Kongsted, Jacob

2016-09-14

We study excited states of cholesterol in solution and show that, in this specific case, solute wave-function confinement is the main effect of the solvent. This is rationalized on the basis of the polarizable density embedding scheme, which in addition to polarizable embedding includes non-electrostatic repulsion that effectively confines the solute wave function to its cavity. We illustrate how the inclusion of non-electrostatic repulsion results in a successful identification of the intense π → π(∗) transition, which was not possible using an embedding method that only includes electrostatics. This underlines the importance of non-electrostatic repulsion in quantum-mechanical embedding-based methods.

Thermal Performance of Cryogenic Multilayer Insulation at Various Layer Spacings

NASA Technical Reports Server (NTRS)

Johnson, Wesley Louis

2010-01-01

Multilayer insulation (MLI) has been shown to be the best performing cryogenic insulation system at high vacuum (less that 10 (exp 3) torr), and is widely used on spaceflight vehicles. Over the past 50 years, many investigations into MLI have yielded a general understanding of the many variables that are associated with MLI. MLI has been shown to be a function of variables such as warm boundary temperature, the number of reflector layers, and the spacer material in between reflectors, the interstitial gas pressure and the interstitial gas. Since the conduction between reflectors increases with the thickness of the spacer material, yet the radiation heat transfer is inversely proportional to the number of layers, it stands to reason that the thermal performance of MLI is a function of the number of layers per thickness, or layer density. Empirical equations that were derived based on some of the early tests showed that the conduction term was proportional to the layer density to a power. This power depended on the material combination and was determined by empirical test data. Many authors have graphically shown such optimal layer density, but none have provided any data at such low densities, or any method of determining this density. Keller, Cunnington, and Glassford showed MLI thermal performance as a function of layer density of high layer densities, but they didn't show a minimal layer density or any data below the supposed optimal layer density. However, it was recently discovered that by manipulating the derived empirical equations and taking a derivative with respect to layer density yields a solution for on optimal layer density. Various manufacturers have begun manufacturing MLI at densities below the optimal density. They began this based on the theory that increasing the distance between layers lowered the conductive heat transfer and they had no limitations on volume. By modifying the circumference of these blankets, the layer density can easily be varied. The simplest method of determining the thermal performance of MLI at cryogenic temperature is by boil-off calorimetry. Several blankets were procured and tested at various layer densities at the Cryogenics Test Laboratory at Kennedy Space Center. The densities that the blankets were tested over covered a wide range of layer densities including the analytical minimum. Several of the blankets were tested at the same insulation thickness while changing the layer density (thus a different number of reflector layers). Optimizing the layer density of multilayer insulation systems for heat transfer would remove a layer density from the complex method of designing such insulation systems. Additional testing was performed at various warm boundary temperatures and pressures. The testing and analysis was performed to simplify the analysis of cryogenic thermal insulation systems. This research was funded by the National Aeronautics and Space Administration's Exploration Technology Development Program's Cryogenic Fluid Management Project

Vapour-liquid interfacial properties of square-well chains from density functional theory and Monte Carlo simulation.

PubMed

Martínez-Ruiz, Francisco José; Blas, Felipe J; Moreno-Ventas Bravo, A Ignacio; Míguez, José Manuel; MacDowell, Luis G

2017-05-17

The statistical associating fluid theory for attractive potentials of variable range (SAFT-VR) density functional theory (DFT) developed by [Gloor et al., J. Chem. Phys., 2004, 121, 12740-12759] is used to predict the interfacial behaviour of molecules modelled as fully-flexible square-well chains formed from tangentially-bonded monomers of diameter σ and potential range λ = 1.5σ. Four different model systems, comprising 4, 8, 12, and 16 monomers per molecule, are considered. In addition to that, we also compute a number of interfacial properties of molecular chains from direct simulation of the vapour-liquid interface. The simulations are performed in the canonical ensemble, and the vapour-liquid interfacial tension is evaluated using the wandering interface (WIM) method, a technique based on the thermodynamic definition of surface tension. Apart from surface tension, we also obtain density profiles, coexistence densities, vapour pressures, and critical temperature and density, paying particular attention to the effect of the chain length on these properties. According to our results, the main effect of increasing the chain length (at fixed temperature) is to sharpen the vapour-liquid interface and to increase the width of the biphasic coexistence region. As a result, the interfacial thickness decreases and the surface tension increases as the molecular chains get longer. The interfacial thickness and surface tension appear to exhibit an asymptotic limiting behaviour for long chains. A similar behaviour is also observed for the coexistence densities and critical properties. Agreement between theory and simulation results indicates that SAFT-VR DFT is only able to predict qualitatively the interfacial properties of the model. Our results are also compared with simulation data taken from the literature, including the vapour-liquid coexistence densities, vapour pressures, and surface tension.

Structure factor of blends of solvent-free nanoparticle-organic hybrid materials: density-functional theory and small angle X-ray scattering.

PubMed

Yu, Hsiu-Yu; Srivastava, Samanvaya; Archer, Lynden A; Koch, Donald L

2014-12-07

We investigate the static structure factor S(q) of solvent-free nanoparticle-organic hybrid materials consisting of silica nanocores and space-filling polyethylene glycol coronas using a density-functional theory and small angle X-ray scattering measurements. The theory considers a bidisperse suspension of hard spheres with different radii and tethered bead-spring oligomers with different grafting densities to approximate the polydispersity effects in experiments. The experimental systems studied include pure samples with different silica core volume fractions and the associated mean corona grafting densities, and blends with different mixing ratios of the pure samples, in order to introduce varying polydispersity of corona grafting density. Our scattering experiments and theory show that, compared to the hard-sphere suspension with the same core volume fraction, S(q) for pure samples exhibit both substantially smaller values at small q and stronger particle correlations corresponding to a larger effective hard core at large q, indicating that the tethered incompressible oligomers enforce a more uniform particle distribution, and the densely grafted brush gives rise to an additional exclusionary effect between the nanoparticles. According to the theory, polydispersity in the oligomer grafting density controls the deviation of S(q) from the monodisperse system at smaller q, and the interplay of the enhanced effective core size and the entropic attraction among the particles is responsible for complex variations in the particle correlations at larger q. The successful comparison between the predictions and the measurements for the blends further suggests that S(q) can be used to assess the uniformity of grafting density in polymer-grafted nanoparticle materials.

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.

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

Adjusting the surface areal density of click-reactive azide groups by kinetic control of the azide substitution reaction on bromine-functional SAMs.

PubMed

Zhang, Shuo; Maidenberg, Yanir; Luo, Kai; Koberstein, Jeffrey T

2014-06-03

Azide-alkyne click chemistry has emerged as an important and versatile means for tethering a wide variety of guest molecules to virtually any substrate. In many of these applications, it is important to exercise control over the areal density of surface functional groups to achieve a desired areal density of the tethered guest molecule of interest. We demonstrate herein that the areal density of surface azide groups on flat germanium surfaces and nanoparticle substrates (silica and iron oxide) can be controlled kinetically by appropriately timed quenching of the S(N)2 substitution reaction of bromo-alkane-silane monolayers induced by the addition of sodium azide. The kinetics of the azide substitution reaction on monolayers formed on flat Ge substrates, determined by attenuated total reflection infrared spectroscopy (ATR-IR), are found to be identical to those for monolayers formed on both silica and iron oxide nanoparticles, the latter determined by transmission infrared spectroscopy. To validate the method, the percentages of surface bromine groups converted to azide groups after various reaction times were measured by quenching the S(N)2 reaction followed by analysis with ATR-IR (for Ge) and thermogravimetric analysis (after a subsequent click reaction with an alkyne-terminal polymer) for the nanoparticle substrates. The conversions found after quenching agree well with those expected from the standard kinetic curves. The latter result suggests that the kinetic method for the control of azide group areal density is a versatile means for functionalizing substrates with a prescribed areal density of azide groups for subsequent click reactions, and that the method is universal for any substrate, flat or nanoparticle, that can be modified with bromo-alkane-silane monolayers. Regardless of the surface geometry, we find that the azide substitution reaction is complete within 2-3 h, in sharp contrast to previous reports that indicate times of 48-60 h required for completion of the reaction.

Systematic investigation of structural, electronic, optical and thermal properties of ternary MoAlB; an ab initio approach

NASA Astrophysics Data System (ADS)

Rajpoot, Priyanka; Rastogi, Anugya; Verma, U. P.

2018-02-01

Structural, electronic, optical and thermal properties of molybdenum aluminum boride (MoAlB) have been analyzed systematically using the full potential linearized augmented plane wave method based on density functional theory at ambient condition as well as high pressure and high temperature. Density of states and band structure calculation reflect the metallic character of MoAlB. In addition to this, the electron charge density calculation reveals the strong covalent bonding, in between ‘B’ atoms as well as ‘Mo’ and ‘B’ atoms. Optical parameters exhibit anisotropic nature and MoAlB become transparent in ultraviolet region for the radiation of energy above 25 eV. The thermal properties were investigated by using the quasi-harmonic Debye model at high temperature and high pressure.

Using the MCNP Taylor series perturbation feature (efficiently) for shielding problems

NASA Astrophysics Data System (ADS)

Favorite, Jeffrey

2017-09-01

The Taylor series or differential operator perturbation method, implemented in MCNP and invoked using the PERT card, can be used for efficient parameter studies in shielding problems. This paper shows how only two PERT cards are needed to generate an entire parameter study, including statistical uncertainty estimates (an additional three PERT cards can be used to give exact statistical uncertainties). One realistic example problem involves a detailed helium-3 neutron detector model and its efficiency as a function of the density of its high-density polyethylene moderator. The MCNP differential operator perturbation capability is extremely accurate for this problem. A second problem involves the density of the polyethylene reflector of the BeRP ball and is an example of first-order sensitivity analysis using the PERT capability. A third problem is an analytic verification of the PERT capability.

Thermalization of oscillator chains with onsite anharmonicity and comparison with kinetic theory

DOE PAGES

Mendl, Christian B.; Lu, Jianfeng; Lukkarinen, Jani

2016-12-02

We perform microscopic molecular dynamics simulations of particle chains with an onsite anharmonicity to study relaxation of spatially homogeneous states to equilibrium, and directly compare the simulations with the corresponding Boltzmann-Peierls kinetic theory. The Wigner function serves as a common interface between the microscopic and kinetic level. We demonstrate quantitative agreement after an initial transient time interval. In particular, besides energy conservation, we observe the additional quasiconservation of the phonon density, defined via an ensemble average of the related microscopic field variables and exactly conserved by the kinetic equations. On superkinetic time scales, density quasiconservation is lost while energy remainsmore » conserved, and we find evidence for eventual relaxation of the density to its canonical ensemble value. Furthermore, the precise mechanism remains unknown and is not captured by the Boltzmann-Peierls equations.« less

Thermalization of oscillator chains with onsite anharmonicity and comparison with kinetic theory

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

Mendl, Christian B.; Lu, Jianfeng; Lukkarinen, Jani

We perform microscopic molecular dynamics simulations of particle chains with an onsite anharmonicity to study relaxation of spatially homogeneous states to equilibrium, and directly compare the simulations with the corresponding Boltzmann-Peierls kinetic theory. The Wigner function serves as a common interface between the microscopic and kinetic level. We demonstrate quantitative agreement after an initial transient time interval. In particular, besides energy conservation, we observe the additional quasiconservation of the phonon density, defined via an ensemble average of the related microscopic field variables and exactly conserved by the kinetic equations. On superkinetic time scales, density quasiconservation is lost while energy remainsmore » conserved, and we find evidence for eventual relaxation of the density to its canonical ensemble value. Furthermore, the precise mechanism remains unknown and is not captured by the Boltzmann-Peierls equations.« less

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.

What Does a Submillimeter Galaxy Selection Actually Select? The Dependence of Submillimeter Flux Density on Star Formation Rate and Dust Mass

NASA Astrophysics Data System (ADS)

Hayward, Christopher C.; Kereš, Dušan; Jonsson, Patrik; Narayanan, Desika; Cox, T. J.; Hernquist, Lars

2011-12-01

We perform three-dimensional dust radiative transfer (RT) calculations on hydrodynamic simulations of isolated and merging disk galaxies in order to quantitatively study the dependence of observed-frame submillimeter (submm) flux density on galaxy properties. We find that submm flux density and star formation rate (SFR) are related in dramatically different ways for quiescently star-forming galaxies and starbursts. Because the stars formed in the merger-induced starburst do not dominate the bolometric luminosity and the rapid drop in dust mass and more compact geometry cause a sharp increase in dust temperature during the burst, starbursts are very inefficient at boosting submm flux density (e.g., a >~ 16 × boost in SFR yields a <~ 2 × boost in submm flux density). Moreover, the ratio of submm flux density to SFR differs significantly between the two modes; thus one cannot assume that the galaxies with highest submm flux density are necessarily those with the highest bolometric luminosity or SFR. These results have important consequences for the bright submillimeter-selected galaxy (SMG) population. Among them are: (1) The SMG population is heterogeneous. In addition to merger-driven starbursts, there is a subpopulation of galaxy pairs, where two disks undergoing a major merger but not yet strongly interacting are blended into one submm source because of the large (gsim 15" or ~130 kpc at z = 2) beam of single-dish submm telescopes. (2) SMGs must be very massive (M sstarf >~ 6 × 1010 M ⊙). (3) The infall phase makes the SMG duty cycle a factor of a few greater than what is expected for a merger-driven starburst. Finally, we provide fitting functions for SCUBA and AzTEC submm flux densities as a function of SFR and dust mass and bolometric luminosity and dust mass; these should be useful for calculating submm flux density in semi-analytic models and cosmological simulations when performing full RT is computationally not feasible.

Dynamic density functional theory with hydrodynamic interactions and fluctuations

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

Donev, Aleksandar, E-mail: donev@courant.nyu.edu; Vanden-Eijnden, Eric, E-mail: eve2@courant.nyu.edu

2014-06-21

We derive a closed equation for the empirical concentration of colloidal particles in the presence of both hydrodynamic and direct interactions. The ensemble average of our functional Langevin equation reproduces known deterministic Dynamic Density Functional Theory (DDFT) [M. Rex and H. Löwen, “Dynamical density functional theory with hydrodynamic interactions and colloids in unstable traps,” Phys. Rev. Lett. 101(14), 148302 (2008)], and, at the same time, it also describes the microscopic fluctuations around the mean behavior. We suggest separating the ideal (non-interacting) contribution from additional corrections due to pairwise interactions. We find that, for an incompressible fluid and in the absencemore » of direct interactions, the mean concentration follows Fick's law just as for uncorrelated walkers. At the same time, the nature of the stochastic terms in fluctuating DDFT is shown to be distinctly different for hydrodynamically-correlated and uncorrelated walkers. This leads to striking differences in the behavior of the fluctuations around Fick's law, even in the absence of pairwise interactions. We connect our own prior work [A. Donev, T. G. Fai, and E. Vanden-Eijnden, “A reversible mesoscopic model of diffusion in liquids: from giant fluctuations to Fick's law,” J. Stat. Mech.: Theory Exp. (2014) P04004] on fluctuating hydrodynamics of diffusion in liquids to the DDFT literature, and demonstrate that the fluid cannot easily be eliminated from consideration if one wants to describe the collective diffusion in colloidal suspensions.« less

Combining the GW formalism with the polarizable continuum model: A state-specific non-equilibrium approach

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

Duchemin, Ivan, E-mail: ivan.duchemin@cea.fr; Jacquemin, Denis; Institut Universitaire de France, 1 rue Descartes, 75005 Paris Cedex 5

We have implemented the polarizable continuum model within the framework of the many-body Green’s function GW formalism for the calculation of electron addition and removal energies in solution. The present formalism includes both ground-state and non-equilibrium polarization effects. In addition, the polarization energies are state-specific, allowing to obtain the bath-induced renormalisation energy of all occupied and virtual energy levels. Our implementation is validated by comparisons with ΔSCF calculations performed at both the density functional theory and coupled-cluster single and double levels for solvated nucleobases. The present study opens the way to GW and Bethe-Salpeter calculations in disordered condensed phases ofmore » interest in organic optoelectronics, wet chemistry, and biology.« less

Simple and Inexpensive Paper-Based Astrocyte Co-culture to Improve Survival of Low-Density Neuronal Networks

PubMed Central

Aebersold, Mathias J.; Thompson-Steckel, Greta; Joutang, Adriane; Schneider, Moritz; Burchert, Conrad; Forró, Csaba; Weydert, Serge; Han, Hana; Vörös, János

2018-01-01

Bottom-up neuroscience aims to engineer well-defined networks of neurons to investigate the functions of the brain. By reducing the complexity of the brain to achievable target questions, such in vitro bioassays better control experimental variables and can serve as a versatile tool for fundamental and pharmacological research. Astrocytes are a cell type critical to neuronal function, and the addition of astrocytes to neuron cultures can improve the quality of in vitro assays. Here, we present cellulose as an astrocyte culture substrate. Astrocytes cultured on the cellulose fiber matrix thrived and formed a dense 3D network. We devised a novel co-culture platform by suspending the easy-to-handle astrocytic paper cultures above neuronal networks of low densities typically needed for bottom-up neuroscience. There was significant improvement in neuronal viability after 5 days in vitro at densities ranging from 50,000 cells/cm2 down to isolated cells at 1,000 cells/cm2. Cultures exhibited spontaneous spiking even at the very low densities, with a significantly greater spike frequency per cell compared to control mono-cultures. Applying the co-culture platform to an engineered network of neurons on a patterned substrate resulted in significantly improved viability and almost doubled the density of live cells. Lastly, the shape of the cellulose substrate can easily be customized to a wide range of culture vessels, making the platform versatile for different applications that will further enable research in bottom-up neuroscience and drug development. PMID:29535595

A density functional study of second-row dicarbides C2X (X = Na-Cl) with carbon monosulfide molecule: molecular structure and bonding mechanism

NASA Astrophysics Data System (ADS)

Parida, Saroj K.; Sahu, Sridhar

2018-05-01

In present work, a systematic study regarding molecular structure, and bonding mechanism of carbon monosulfide (CS) on second-row dicarbides C2X with (X = Na-Cl) has been investigated within the framework of density functional theory (DFT). In presence of carbon monosulfide molecule, the structures of C2Na, C2Mg, C2Al, and C2Si are found be changed from cyclic to linear, whereas geometries of C2P, C2S, and C2Cl clusters are almost remain unchanged. Interestingly, the bare carbon monosulfide molecule is attached with carbon site of bare C2X clusters rather than the second-row elements (X = Na-Cl). Furthermore, the nature of bonding in C2XCS clusters has been studiedthrough Bader's topological analysis of the electron charge density distribution ρ(r), Laplacian ∇2 ρ(r) and total energy density H BCP at the bond critical points (BCPs) of the clusters within the framework of the atoms in molecules theory (AIM). In C2XCS clusters, electron density at the bond critical point ρ(r) > 0.30 a.u. with negative values of Laplacian ∇2 ρ(r) indicates shared-kind of interactions between both the carbon atoms of C2X and CS molecule. In addition, we also analyze IR spectra that could assist for the experimental detection.

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

Chauhan, Aditya; Patel, Satyanarayan; Vaish, Rahul, E-mail: rahul@iitmandi.ac.in

With the advent of modern power electronics, embedded circuits and non-conventional energy harvesting, the need for high performance capacitors is bound to become indispensible. The current state-of-art employs ferroelectric ceramics and linear dielectrics for solid state capacitance. However, lead-free ferroelectric ceramics propose to offer significant improvement in the field of electrical energy storage owing to their high discharge efficiency and energy storage density. In this regards, the authors have investigated the effects of compressive stress as a means of improving the energy storage density of lead-free ferroelectric ceramics. The energy storage density of 0.91(Bi{sub 0.5}Na{sub 0.5})TiO{sub 3}-0.07BaTiO{sub 3}-0.02(K{sub 0.5}Na{sub 0.5})NbO{submore » 3} ferroelectric bulk ceramic was analyzed as a function of varying levels of compressive stress and operational temperature .It was observed that a peak energy density of 387 mJ.cm{sup -3} was obtained at 100 MPa applied stress (25{sup o}C). While a maximum energy density of 568 mJ.cm{sup -3} was obtained for the same stress at 80{sup o}C. These values are indicative of a significant, 25% and 84%, improvement in the value of stored energy compared to an unloaded material. Additionally, material's discharge efficiency has also been discussed as a function of operational parameters. The observed phenomenon has been explained on the basis of field induced structural transition and competitive domain switching theory.« less

Tip-growing cells of the moss Ceratodon purpureus Are gravitropic in high-density media

NASA Technical Reports Server (NTRS)

Schwuchow, Jochen Michael; Kern, Volker Dieter; Sack, Fred David

2002-01-01

Gravity sensing in plants and algae is hypothesized to rely upon either the mass of the entire cell or that of sedimenting organelles (statoliths). Protonemata of the moss Ceratodon purpureus show upward gravitropism and contain amyloplasts that sediment. If moss sensing were whole-cell based, then media denser than the cell should prevent gravitropism or reverse its direction. Cells that were inverted or reoriented to the horizontal displayed distinct negative gravitropism in solutions of iodixanol with densities of 1.052 to 1.320 as well as in bovine serum albumin solutions with densities of 1.037 to 1.184 g cm(-3). Studies using tagged molecules of different sizes and calculations of diffusion times suggest that both types of media penetrate through the apical cell wall. Estimates of the density of the apical cell range from 1.004 to 1.085. Because protonemata grow upward when the cells have a density that is lower than the surrounding medium, gravitropic sensing probably utilizes an intracellular mass in moss protonemata. These data provide additional support for the idea that sedimenting amyloplasts function as statoliths in gravitropism.

Effect of strain rate and dislocation density on the twinning behavior in Tantalum

DOE PAGES

Florando, Jeffrey N.; El-Dasher, Bassem S.; Chen, Changqiang; ...

2016-04-28

The conditions which affect twinning in tantalum have been investigated across a range of strain rates and initial dislocation densities. Tantalum samples were subjected to a range of strain rates, from 10 –4/s to 10 3/s under uniaxial stress conditions, and under laser-induced shock-loading conditions. In this study, twinning was observed at 77K at strain rates from 1/s to 103/s, and during laser-induced shock experiments. The effect of the initial dislocation density, which was imparted by deforming the material to different amounts of pre-strain, was also studied, and it was shown that twinning is suppressed after a given amount ofmore » pre-strain, even as the global stress continues to increase. These results indicate that the conditions for twinning cannot be represented solely by a critical global stress value, but are also dependent on the evolution of the dislocation density. Additionally, the analysis shows that if twinning is initiated, the nucleated twins may continue to grow as a function of strain, even as the dislocation density continues to increase.« less

The interacting effects of temperature and food chain length on trophic abundance and ecosystem function.

PubMed

Beveridge, Oliver S; Humphries, Stuart; Petchey, Owen L

2010-05-01

1. While much is known about the independent effects of trophic structure and temperature on density and ecosystem processes, less is known about the interaction(s) between the two. 2. We manipulated the temperature of laboratory-based bacteria-protist communities that contained communities with one, two, or three trophic levels, and recorded species' densities and bacterial decomposition. 3. Temperature, food chain length and their interaction produced significant responses in microbial density and bacterial decomposition. Prey and resource density expressed different patterns of temperature dependency during different phases of population dynamics. The addition of a predator altered the temperature-density relationship of prey, from a unimodal trend to a negative one. Bacterial decomposition was greatest in the presence of consumers at higher temperatures. 4. These results are qualitatively consistent with a recent model of direct and indirect temperature effects on resource-consumer population dynamics. Results highlight and reinforce the importance of indirect effects of temperature mediated through trophic interactions. Understanding and predicting the consequences of environmental change will require that indirect effects, trophic structure, and individual species' tolerances be incorporated into theory and models.

Design and simulation of stratified probability digital receiver with application to the multipath communication

NASA Technical Reports Server (NTRS)

Deal, J. H.

1975-01-01

One approach to the problem of simplifying complex nonlinear filtering algorithms is through using stratified probability approximations where the continuous probability density functions of certain random variables are represented by discrete mass approximations. This technique is developed in this paper and used to simplify the filtering algorithms developed for the optimum receiver for signals corrupted by both additive and multiplicative noise.

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

Eliminating cubic terms in the pseudopotential lattice Boltzmann model for multiphase flow

NASA Astrophysics Data System (ADS)

Huang, Rongzong; Wu, Huiying; Adams, Nikolaus A.

2018-05-01

It is well recognized that there exist additional cubic terms of velocity in the lattice Boltzmann (LB) model based on the standard lattice. In this work, elimination of these cubic terms in the pseudopotential LB model for multiphase flow is investigated, where the force term and density gradient are considered. By retaining high-order (≥3 ) Hermite terms in the equilibrium distribution function and the discrete force term, as well as introducing correction terms in the LB equation, the additional cubic terms of velocity are entirely eliminated. With this technique, the computational simplicity of the pseudopotential LB model is well maintained. Numerical tests, including stationary and moving flat and circular interface problems, are carried out to show the effects of such cubic terms on the simulation of multiphase flow. It is found that the elimination of additional cubic terms is beneficial to reduce the numerical error, especially when the velocity is relatively large. Numerical results also suggest that these cubic terms mainly take effect in the interfacial region and that the density-gradient-related cubic terms are more important than the other cubic terms for multiphase flow.

SEAWAT Version 4: A Computer Program for Simulation of Multi-Species Solute and Heat Transport

USGS Publications Warehouse

Langevin, Christian D.; Thorne, Daniel T.; Dausman, Alyssa M.; Sukop, Michael C.; Guo, Weixing

2008-01-01

The SEAWAT program is a coupled version of MODFLOW and MT3DMS designed to simulate three-dimensional, variable-density, saturated ground-water flow. Flexible equations were added to the program to allow fluid density to be calculated as a function of one or more MT3DMS species. Fluid density may also be calculated as a function of fluid pressure. The effect of fluid viscosity variations on ground-water flow was included as an option. Fluid viscosity can be calculated as a function of one or more MT3DMS species, and the program includes additional functions for representing the dependence on temperature. Although MT3DMS and SEAWAT are not explicitly designed to simulate heat transport, temperature can be simulated as one of the species by entering appropriate transport coefficients. For example, the process of heat conduction is mathematically analogous to Fickian diffusion. Heat conduction can be represented in SEAWAT by assigning a thermal diffusivity for the temperature species (instead of a molecular diffusion coefficient for a solute species). Heat exchange with the solid matrix can be treated in a similar manner by using the mathematically equivalent process of solute sorption. By combining flexible equations for fluid density and viscosity with multi-species transport, SEAWAT Version 4 represents variable-density ground-water flow coupled with multi-species solute and heat transport. SEAWAT Version 4 is based on MODFLOW-2000 and MT3DMS and retains all of the functionality of SEAWAT-2000. SEAWAT Version 4 also supports new simulation options for coupling flow and transport, and for representing constant-head boundaries. In previous versions of SEAWAT, the flow equation was solved for every transport timestep, regardless of whether or not there was a large change in fluid density. A new option was implemented in SEAWAT Version 4 that allows users to control how often the flow field is updated. New options were also implemented for representing constant-head boundaries with the Time-Variant Constant-Head (CHD) Package. These options allow for increased flexibility when using CHD flow boundaries with the zero-dispersive flux solute boundaries implemented by MT3DMS at constant-head cells. This report contains revised input instructions for the MT3DMS Dispersion (DSP) Package, Variable-Density Flow (VDF) Package, Viscosity (VSC) Package, and CHD Package. The report concludes with seven cases of an example problem designed to highlight many of the new features.

Efficacy of Laser Photobiomodulation on Morphological and Functional Repair of the Facial Nerve.

PubMed

Buchaim, Daniela Vieira; Andreo, Jesus Carlos; Ferreira Junior, Rui Seabra; Barraviera, Benedito; Rodrigues, Antonio de Castro; Macedo, Mariana de Cássia; Rosa Junior, Geraldo Marco; Shinohara, Andre Luis; Santos German, Iris Jasmin; Pomini, Karina Torres; Buchaim, Rogerio Leone

2017-08-01

Evaluate the efficacy of low-level laser therapy (LLLT) on qualitative, quantitative, and functional aspects in the facial nerve regeneration process. Forty-two male Wistar rats were used, randomly divided into a control group (CG; n = 10), in which the facial nerve without lesion was collected, and four experimental groups: (1) suture experimental group (SEG) and (2) fibrin experimental group (FEG), consisting of 16 animals in which the buccal branch of the facial nerve was sectioned on both sides of the face; an end-to-end epineural suture was performed on the right side, and a fibrin sealant was used on the left side for coaptation of the stumps; and (3) laser suture experimental group (LSEG) and (4) laser fibrin experimental group (LFEG), consisting of 16 animals that underwent the same surgical procedures as SEG and FEG with the addition of laser application at three different points along the surgical site (pulsed laser of 830 nm wavelength, optical output power of 30 mW, power density of 0.2586 W/cm 2 , energy density of 6.2 J/cm 2 , beam area of 0.116 cm 2 , exposure time of 24 sec per point, total energy per session of 2.16 J, and cumulative dose of 34.56 J). The animals were submitted to functional analysis (subjective observation of whisker movement) and the data obtained were compared using Fisher's exact test. Euthanasia was performed at 5 and 10 weeks postoperative. The total number and density of regenerated axons were analyzed using the unpaired t-test (p < 0.05). Laser therapy resulted in a significant increase in the number and density of regenerated axons. The LSEG and LFEG presented better scores in functional analysis in comparison with the SEG and FEG. LLLT enhanced axonal regeneration and accelerated functional recovery of the whiskers, and both repair techniques allowed the growth of axons.

K- and L-edge X-ray absorption spectrum calculations of closed-shell carbon, silicon, germanium, and sulfur compounds using damped four-component density functional response theory.

PubMed

Fransson, Thomas; Burdakova, Daria; Norman, Patrick

2016-05-21

X-ray absorption spectra of carbon, silicon, germanium, and sulfur compounds have been investigated by means of damped four-component density functional response theory. It is demonstrated that a reliable description of relativistic effects is obtained at both K- and L-edges. Notably, an excellent agreement with experimental results is obtained for L2,3-spectra-with spin-orbit effects well accounted for-also in cases when the experimental intensity ratio deviates from the statistical one of 2 : 1. The theoretical results are consistent with calculations using standard response theory as well as recently reported real-time propagation methods in time-dependent density functional theory, and the virtues of different approaches are discussed. As compared to silane and silicon tetrachloride, an anomalous error in the absolute energy is reported for the L2,3-spectrum of silicon tetrafluoride, amounting to an additional spectral shift of ∼1 eV. This anomaly is also observed for other exchange-correlation functionals, but it is seen neither at other silicon edges nor at the carbon K-edge of fluorine derivatives of ethene. Considering the series of molecules SiH4-XFX with X = 1, 2, 3, 4, a gradual divergence from interpolated experimental ionization potentials is observed at the level of Kohn-Sham density functional theory (DFT), and to a smaller extent with the use of Hartree-Fock. This anomalous error is thus attributed partly to difficulties in correctly emulating the electronic structure effects imposed by the very electronegative fluorines, and partly due to inconsistencies in the spurious electron self-repulsion in DFT. Substitution with one, or possibly two, fluorine atoms is estimated to yield small enough errors to allow for reliable interpretations and predictions of L2,3-spectra of more complex and extended silicon-based systems.

Synthesis of manganese stearate for high density polyethylene (HDPE) and its biodegradation

NASA Astrophysics Data System (ADS)

Aras, Neny Rasnyanti M.; Arcana, I. Made

2015-09-01

An oxidant additive is one type of additive used for oxo-biodegradable polymers. This additive was prepared by reaction multivalent transition metals and fatty acids to accelerate the degradation process of polymers by providing a thermal treatment or irradiation with light. This study focused on the synthesis of manganese stearate as an additive for application in High Density Polyethylene (HDPE), and the influence of manganese stearate on the characteristics of HDPE including their biodegradability. Manganese stearate was synthesized by the reaction of stearic acid with sodium hydroxide, and sodium stearate formed was reacted with manganese chloride tetrahydrate to form manganese stearate with a melting point of 100-110 °C. Based on the FTIR spectrum showed absorption peak at wave number around 1560 cm-1 which is an asymmetric vibration of CO functional group that binds to the manganese. The films of oxo-biodegradable polymer were prepared by blending HDPE and manganese stearate additives at various concentrations with using the polymer melting method, followed heating at a temperature of 50°C and 70°C for 10 days. The characterizations of the oxo-biodegradable polymers were carried out by analysis the functional groups (FTIR and ATR),thermal properties (TGA), surface properties (SEM), as well as analysis of the biodegradability (the biodegradation test by using activated sludge, % weight loss). Based on COi indicate that the additive of manganese stearate is active in oxidizing polymer by heating treatment. Results of biodegradation by microorganisms from activated sludge showed that the percentage weight loss of polymers increase with the increasing incubation time and the concentration of manganese stearate in HDPE. Biodegradability of HDPE with the addition of manganese stearate and followed by heating at a higher temperature was better observed. The highest percentage weight loss was obtained at the polymer with concentration of 0.2% manganese stearate, and followed by thermal treatment at a temperature of 70 °C and the incubation time for 45 days in the activated sludge.

Galaxy evolution and large-scale structure in the far-infrared. I - IRAS pointed observations

NASA Astrophysics Data System (ADS)

Lonsdale, Carol J.; Hacking, Perry B.

1989-04-01

Redshifts for 66 galaxies were obtained from a sample of 93 60-micron sources detected serendipitously in 22 IRAS deep pointed observations, covering a total area of 18.4 sq deg. The flux density limit of this survey is 150 mJy, 4 times fainter than the IRAS Point Source Catalog (PSC). The luminosity function is similar in shape with those previously published for samples selected from the PSC, with a median redshift of 0.048 for the fainter sample, but shifted to higher space densities. There is evidence that some of the excess number counts in the deeper sample can be explained in terms of a large-scale density enhancement beyond the Pavo-Indus supercluster. In addition, the faintest counts in the new sample confirm the result of Hacking et al. (1989) that faint IRAS 60-micron source counts lie significantly in excess of an extrapolation of the PSC counts assuming no luminosity or density evolution.

Galaxy evolution and large-scale structure in the far-infrared. I. IRAS pointed observations

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

Lonsdale, C.J.; Hacking, P.B.

1989-04-01

Redshifts for 66 galaxies were obtained from a sample of 93 60-micron sources detected serendipitously in 22 IRAS deep pointed observations, covering a total area of 18.4 sq deg. The flux density limit of this survey is 150 mJy, 4 times fainter than the IRAS Point Source Catalog (PSC). The luminosity function is similar in shape with those previously published for samples selected from the PSC, with a median redshift of 0.048 for the fainter sample, but shifted to higher space densities. There is evidence that some of the excess number counts in the deeper sample can be explained inmore » terms of a large-scale density enhancement beyond the Pavo-Indus supercluster. In addition, the faintest counts in the new sample confirm the result of Hacking et al. (1989) that faint IRAS 60-micron source counts lie significantly in excess of an extrapolation of the PSC counts assuming no luminosity or density evolution. 81 refs.« less

Galaxy evolution and large-scale structure in the far-infrared. I - IRAS pointed observations

NASA Technical Reports Server (NTRS)

Lonsdale, Carol J.; Hacking, Perry B.

1989-01-01

Redshifts for 66 galaxies were obtained from a sample of 93 60-micron sources detected serendipitously in 22 IRAS deep pointed observations, covering a total area of 18.4 sq deg. The flux density limit of this survey is 150 mJy, 4 times fainter than the IRAS Point Source Catalog (PSC). The luminosity function is similar in shape with those previously published for samples selected from the PSC, with a median redshift of 0.048 for the fainter sample, but shifted to higher space densities. There is evidence that some of the excess number counts in the deeper sample can be explained in terms of a large-scale density enhancement beyond the Pavo-Indus supercluster. In addition, the faintest counts in the new sample confirm the result of Hacking et al. (1989) that faint IRAS 60-micron source counts lie significantly in excess of an extrapolation of the PSC counts assuming no luminosity or density evolution.

The effect of a periodic absorptive strip arrangement on an interior sound field in a room.

PubMed

Park, Joo-Bae; Grosh, Karl; Kim, Yang-Hann

2005-02-01

In this paper we study the effect of periodically arranged sound absorptive strips on the mean acoustic potential energy density distribution of a room. The strips are assumed to be attached on the room's surface of interest. In order to determine their effect, the mean acoustic potential energy density variation is evaluated as the function of a ratio of the strip's arrangement period to wavelength. The evaluation demonstrates that the mean acoustic potential energy density tends to converge. In addition, a comparison with a case in which absorptive materials completely cover the selected absorptive plane shows that a periodic arrangement that uses only half of the absorptive material can be more efficient than a total covering, unless the frequency of interest does not coincide with the room's resonant frequencies. Consequently, the results prove that the ratio of the arrangement period to the wavelength plays an important role in the effectiveness of a periodic absorptive strip arrangement to minimize a room's mean acoustic potential energy density.

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.

Effect of Thermospheric Neutral Density upon Inner Trapped-belt Proton Flux

NASA Technical Reports Server (NTRS)

Wilson, Thomas L.; Lodhi, M. A. K.; Diaz, Abel B.

2007-01-01

We wish to point out that a secular change in the Earth's atmospheric neutral density alters charged-particle lifetime in the inner trapped radiation belts, in addition to the changes recently reported as produced by greenhouse gases. Heretofore, changes in neutral density have been of interest primarily because of their effect on the orbital drag of satellites. We extend this to include the orbital lifetime of charged particles in the lower radiation belts. It is known that the charged-belt population is coupled to the neutral density of the atmosphere through changes induced by solar activity, an effect produced by multiple scattering off neutral and ionized atoms along with ionization loss in the thermosphere where charged and neutral populations interact. It will be shown here that trapped-belt flux J is bivariant in energy E and thermospheric neutral density , as J(E,rho). One can conclude that proton lifetimes in these belts are also directly affected by secular changes in the neutral species populating the Earth s thermosphere. This result is a consequence of an intrinsic property of charged-particle flux, that flux is not merely a function of E but is dependent upon density rho when a background of neutrals is present.

A general framework for numerical simulation of improvised explosive device (IED)-detection scenarios using density functional theory (DFT) and terahertz (THz) spectra.

PubMed

Shabaev, Andrew; Lambrakos, Samuel G; Bernstein, Noam; Jacobs, Verne L; Finkenstadt, Daniel

2011-04-01

We have developed a general framework for numerical simulation of various types of scenarios that can occur for the detection of improvised explosive devices (IEDs) through the use of excitation using incident electromagnetic waves. A central component model of this framework is an S-matrix representation of a multilayered composite material system. Each layer of the system is characterized by an average thickness and an effective electric permittivity function. The outputs of this component are the reflectivity and the transmissivity as functions of frequency and angle of the incident electromagnetic wave. The input of the component is a parameterized analytic-function representation of the electric permittivity as a function of frequency, which is provided by another component model of the framework. The permittivity function is constructed by fitting response spectra calculated using density functional theory (DFT) and parameter adjustment according to any additional information that may be available, e.g., experimentally measured spectra or theory-based assumptions concerning spectral features. A prototype simulation is described that considers response characteristics for THz excitation of the high explosive β-HMX. This prototype simulation includes a description of a procedure for calculating response spectra using DFT as input to the Smatrix model. For this purpose, the DFT software NRLMOL was adopted. © 2011 Society for Applied Spectroscopy

Influence of cations on noncovalent interactions between 6-propionyl-2-dimethylaminonaphthalene (PRODAN) and dissolved fulvic and humic acids.

PubMed

Gadad, Praveen; Nanny, Mark A

2008-12-01

The influence of cations (Na(+), Ca(2+) and Mg(2+)) on noncovalent interactions between 6-propionyl-2-dimethylaminonaphthalene (PRODAN) and dissolved fulvic acids (FAs) (Norman landfill leachate fulvic acid (NLFA) and Suwannee River fulvic acid (SRFA)) and dissolved humic acids (HAs) (Suwannee River humic acid (SRHA) and Leonardite humic acid (LHA)) was examined using steady-state fluorescence spectroscopy at pH 4, 7 and 10 as a function of cation concentration (up to 25-100mM). Regardless of pH and cation concentration, PRODAN quenching by FA was unaffected by cations. However, interactions between PRODAN and HA decreased in the presence of cations at pH 7 and 10. Cation concentrations below the HA charge density resulted in the greatest decrease of PRODAN quenching, while very little additional decrease in PRODAN quenching occurred at cation concentrations above the HA charge density. This suggests that as the HA carboxylic acid functional groups form inner sphere complexes with divalent cations, intramolecular interactions result in a contraction of the HA molecular structure, thereby preventing PRODAN from associating with the condensed aromatic, electron accepting moieties inherent within HA molecules and responsible for PRODAN quenching. However, once the HA carboxylic acid functional groups are fully titrated with divalent cations, PRODAN quenching is no longer significantly influenced by the further addition of cations, even though these additional cations facilitate intermolecular interactions between the HA molecules to form supramolecular HA aggregates that can continue to increase in size. Regardless of FA and HA type, pH, cation type and concentration, the lack of blue-shifted fluorescence emission spectra indicated that micelle-like hydrophobic regions, amenable to PRODAN partitioning, were not formed by intra- and intermolecular interactions of FA and HA.

The effect of cinnamon extract and long-term aerobic training on heart function, biochemical alterations and lipid profile following exhaustive exercise in male rats.

PubMed

Badalzadeh, Reza; Shaghaghi, Mehrnoush; Mohammadi, Mustafa; Dehghan, Gholamreza; Mohammadi, Zeynab

2014-12-01

Regular training is suggested to offer a host of benefits especially on cardiovascular system. In addition, medicinal plants can attenuate oxidative stress-mediated damages induced by stressor insults. In this study, we investigated the concomitant effect of cinnamon extract and long-term aerobic training on cardiac function, biochemical alterations and lipid profile following exhaustive exercise. Male Wistar rats (250-300 g) were divided into five groups depending on receiving regular training, cinnamon bark extraction, none or both of them, and then encountered with an exhausted exercise in last session. An 8-week endurance training program was designed with a progressive increase in training speed and time. Myocardial hemodynamics was monitored using a balloon-tipped catheter inserted into left ventricles. Blood samples were collected for analyzing biochemical markers, lipid profiles and lipid-peroxidation marker, malondealdehyde (MDA). Trained animals showed an enhanced cardiac force and contractility similar to cinnamon-treated rats. Co-application of regular training and cinnamon had additive effect in cardiac hemodynamic (P<0.05). Both regular training and supplementation with cinnamon significantly decreased serum levels of total cholesterol, low-density lipoprotein (LDL), and increased high-density lipoprotein (HDL) level and HDL/LDL ratio as compared to control group (P<0.01). Furthermore, pre-treatment with cinnamon extract and/or regular training significantly reduced MDA level elevation induced by exhausted exercise (P<0.01). Long-term treatment of rats with cinnamon and regular training improved cardiac hemodynamic through an additive effect. The positive effects of cinnamon and regular training on cardiac function were associated with a reduced serum MDA level and an improved blood lipid profile.

Generalized quantum Fokker-Planck equation for photoinduced nonequilibrium processes with positive definiteness condition

NASA Astrophysics Data System (ADS)

Jang, Seogjoo

2016-06-01

This work provides a detailed derivation of a generalized quantum Fokker-Planck equation (GQFPE) appropriate for photo-induced quantum dynamical processes. The path integral method pioneered by Caldeira and Leggett (CL) [Physica A 121, 587 (1983)] is extended by utilizing a nonequilibrium influence functional applicable to different baths for the ground and the excited electronic states. Both nonequilibrium and non-Markovian effects are accounted for consistently by expanding the paths in the exponents of the influence functional up to the second order with respect to time. This procedure results in approximations involving only single time integrations for the exponents of the influence functional but with additional time dependent boundary terms that have been ignored in previous works. The boundary terms complicate the derivation of a time evolution equation but do not affect position dependent physical observables or the dynamics in the steady state limit. For an effective density operator with the boundary terms factored out, a time evolution equation is derived, through short time expansion of the effective action and Gaussian integration in analytically continued complex domain of space. This leads to a compact form of the GQFPE with time dependent kernels and additional terms, which renders the resulting equation to be in the Dekker form [Phys. Rep. 80, 1 (1981)]. Major terms of the equation are analyzed for the case of Ohmic spectral density with Drude cutoff, which shows that the new GQFPE satisfies the positive definiteness condition in medium to high temperature limit. Steady state limit of the GQFPE is shown to approach the well-known expression derived by CL in the high temperature and Markovian bath limit and also provides additional corrections due to quantum and non-Markovian effects of the bath.

Infection Unit Density as an Index of Infection Potential of Arbuscular Mycorrhizal Fungi.

PubMed

Ohtomo, Ryo; Kobae, Yoshihiro; Morimoto, Sho; Oka, Norikuni

2018-03-29

The effective use of arbuscular mycorrhizal (AM) fungal function to promote host plant phosphate uptake in agricultural practice requires the accurate quantitative evaluation of AM fungal infection potential in field soil or AM fungal inoculation material. The number of infection units (IUs), intraradical fungal structures derived from single root entries formed after a short cultivation period, may reflect the number of propagules in soil when pot soil is completely permeated by the host root. However, the original IU method, in which all AM propagules in a pot are counted, requires the fine tuning of plant growing conditions and is considered to be laborious. The objective of the present study was to test whether IU density, not the total count of IU, but the number of IUs per unit root length, reflects the density of AM fungal propagules in soil. IU density assessed after 12 d of host plant cultivation and 3,3'-diaminobenzidine (DAB) staining showed a stronger linear correlation with propagule density than the mean infection percentage (MIP). In addition, IU density was affected less by the host plant species than MIP. We suggest that IU density provides a more rapid and reliable quantitation of the propagule density of AM fungi than MIP or the original IU method. Thus, IU density may be a more robust index of AM fungal infection potential for research and practical applications.

The electronic and optical properties of Cs adsorbed GaAs nanowires via first-principles study

NASA Astrophysics Data System (ADS)

Diao, Yu; Liu, Lei; Xia, Sihao; Feng, Shu; Lu, Feifei

2018-07-01

In this study, we investigate the Cs adsorption mechanism on (110) surface of zinc-blende GaAs nanowire. The adsorption energy, work function, dipole moment, geometric structure, Mulliken charge distribution, charge transfer index, band structures, density of state and optical properties of Cs adsorption structures are calculated utilizing first-principles method based on density function theory. Total-energy calculations show that all the adsorption energies are negative, indicating that Cs adsorption process is exothermic and Cs covered GaAs nanowires are stable. The work function of nanowire surface has an obvious decrease after Cs adsorption. Besides, the ionization of nanowire surface is enhanced as well. More importantly, Cs adsorption contributes to a lower side shift of bands near Fermi level, and the corresponding band gap disappears. Additionally, the absorption peak and energy loss function after Cs adsorption are far higher than those before adsorption, implying better light absorption characteristic of nanowire surface after Cs adsorption. These theoretical calculations can directly guide the Cs activation experiment for negative electron affinity GaAs nanowire, and also lay a foundation for the further study of Cs/O co-adsorption on the nanowire surface.

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.

Study of Polyurethane Foaming Dynamics Using a Heat Flow Meter

NASA Astrophysics Data System (ADS)

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

2017-05-01

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

Structure and Dynamics of Hydroxyl-Functionalized Protic Ammonium Carboxylate Ionic Liquids.

PubMed

Thummuru, Dhileep Nagi Reddy; Mallik, Bhabani S

2017-10-26

We performed classical molecular dynamics simulations to investigate the structure and dynamics of protic ionic liquids, 2-hydroxy ethylammonium acetate, ethylammonium hydroxyacetate, and 2-hydroxyethylammonium hydroxyacetate at ambient conditions. Structural properties such as density, radial distribution functions, spatial distribution functions, and structure factors have been calculated. Dynamic properties such as mean square displacements, as well as residence and hydrogen bond dynamics have also been calculated. Hydrogen bond lifetimes and residence times change with the addition of hydroxyl groups. We observe that when a hydroxyl group is present on the cation, dynamics become very slow and it forms a strong hydrogen bond with carboxylate oxygen atoms of the anion. The hydroxyl functionalized ILs show more dynamic diversity than structurally similar ILs.

On extending Kohn-Sham density functionals to systems with fractional number of electrons.

PubMed

Li, Chen; Lu, Jianfeng; Yang, Weitao

2017-06-07

We analyze four ways of formulating the Kohn-Sham (KS) density functionals with a fractional number of electrons, through extending the constrained search space from the Kohn-Sham and the generalized Kohn-Sham (GKS) non-interacting v-representable density domain for integer systems to four different sets of densities for fractional systems. In particular, these density sets are (I) ensemble interacting N-representable densities, (II) ensemble non-interacting N-representable densities, (III) non-interacting densities by the Janak construction, and (IV) non-interacting densities whose composing orbitals satisfy the Aufbau occupation principle. By proving the equivalence of the underlying first order reduced density matrices associated with these densities, we show that sets (I), (II), and (III) are equivalent, and all reduce to the Janak construction. Moreover, for functionals with the ensemble v-representable assumption at the minimizer, (III) reduces to (IV) and thus justifies the previous use of the Aufbau protocol within the (G)KS framework in the study of the ground state of fractional electron systems, as defined in the grand canonical ensemble at zero temperature. By further analyzing the Aufbau solution for different density functional approximations (DFAs) in the (G)KS scheme, we rigorously prove that there can be one and only one fractional occupation for the Hartree Fock functional, while there can be multiple fractional occupations for general DFAs in the presence of degeneracy. This has been confirmed by numerical calculations using the local density approximation as a representative of general DFAs. This work thus clarifies important issues on density functional theory calculations for fractional electron systems.

Functional thermo-dynamics: a generalization of dynamic density functional theory to non-isothermal situations.

PubMed

Anero, Jesús G; Español, Pep; Tarazona, Pedro

2013-07-21

We present a generalization of Density Functional Theory (DFT) to non-equilibrium non-isothermal situations. By using the original approach set forth by Gibbs in his consideration of Macroscopic Thermodynamics (MT), we consider a Functional Thermo-Dynamics (FTD) description based on the density field and the energy density field. A crucial ingredient of the theory is an entropy functional, which is a concave functional. Therefore, there is a one to one connection between the density and energy fields with the conjugate thermodynamic fields. The connection between the three levels of description (MT, DFT, FTD) is clarified through a bridge theorem that relates the entropy of different levels of description and that constitutes a generalization of Mermin's theorem to arbitrary levels of description whose relevant variables are connected linearly. Although the FTD level of description does not provide any new information about averages and correlations at equilibrium, it is a crucial ingredient for the dynamics in non-equilibrium states. We obtain with the technique of projection operators the set of dynamic equations that describe the evolution of the density and energy density fields from an initial non-equilibrium state towards equilibrium. These equations generalize time dependent density functional theory to non-isothermal situations. We also present an explicit model for the entropy functional for hard spheres.

Universal functions of nuclear proximity potential for Skyrme nucleus-nucleus interaction in a semiclassical approach

NASA Astrophysics Data System (ADS)

Gupta, Raj K.; Singh, Dalip; Kumar, Raj; Greiner, Walter

2009-07-01

The universal function of the nuclear proximity potential is obtained for the Skyrme nucleus-nucleus interaction in the semiclassical extended Thomas-Fermi (ETF) approach. This is obtained as a sum of the spin-orbit-density-independent and spin-orbit-density-dependent parts of the Hamiltonian density, since the two terms behave differently, the spin-orbit-density-independent part mainly attractive and the spin-orbit-density-dependent part mainly repulsive. The semiclassical expansions of kinetic energy density and spin-orbit density are allowed up to second order, and the two-parameter Fermi density, with its parameters fitted to experiments, is used for the nuclear density. The universal functions or the resulting nuclear proximity potential reproduce the 'exact' Skyrme nucleus-nucleus interaction potential in the semiclassical approach, within less than ~1 MeV of difference, both at the maximum attraction and in the surface region. An application of the resulting interaction potential to fusion excitation functions shows clearly that the parameterized universal functions of nuclear proximity potential substitute completely the 'exact' potential in the Skyrme energy density formalism based on the semiclassical ETF method, including also the modifications of interaction barriers at sub-barrier energies in terms of modifying the constants of the universal functions.

Reexamination of the interaction of atoms with a LiF(001) surface

NASA Astrophysics Data System (ADS)

Miraglia, J. E.; Gravielle, M. S.

2017-02-01

Pairwise additive potentials for multielectronic atoms interacting with a LiF(001) surface are revisited by including an improved description of the electron density associated with the different lattice sites, as well as nonlocal electron density contributions. Within this model, the electron distribution around each ionic site of the crystal is described by means of a so-called "onion" approach that accounts for the influence of the Madelung potential. From such densities, binary interatomic potentials are then derived by using well-known nonlocal functionals. Rumpling and long-range contributions due to projectile polarization and van der Waals forces are also included. We apply this pairwise additive approximation to evaluate the interaction potential between closed-shell (He, Ne, Ar, Kr, and Xe) and open-shell (N, S, and Cl) atoms and the LiF surface, analyzing the relative importance of the different contributions. The performance of the proposed potentials is assessed by contrasting angular positions of rainbow and supernumerary rainbow maxima produced by fast grazing incidence with available experimental data. One important result of our model is that both van der Waals contributions and thermal lattice vibrations play a negligible role for normal energies in the eV range.

Epidemiological Implications of Host Biodiversity and Vector Biology: Key Insights from Simple Models.

PubMed

Dobson, Andrew D M; Auld, Stuart K J R

2016-04-01

Models used to investigate the relationship between biodiversity change and vector-borne disease risk often do not explicitly include the vector; they instead rely on a frequency-dependent transmission function to represent vector dynamics. However, differences between classes of vector (e.g., ticks and insects) can cause discrepancies in epidemiological responses to environmental change. Using a pair of disease models (mosquito- and tick-borne), we simulated substitutive and additive biodiversity change (where noncompetent hosts replaced or were added to competent hosts, respectively), while considering different relationships between vector and host densities. We found important differences between classes of vector, including an increased likelihood of amplified disease risk under additive biodiversity change in mosquito models, driven by higher vector biting rates. We also draw attention to more general phenomena, such as a negative relationship between initial infection prevalence in vectors and likelihood of dilution, and the potential for a rise in density of infected vectors to occur simultaneously with a decline in proportion of infected hosts. This has important implications; the density of infected vectors is the most valid metric for primarily zoonotic infections, while the proportion of infected hosts is more relevant for infections where humans are a primary host.

Double-hybrid density-functional theory with meta-generalized-gradient approximations

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

Souvi, Sidi M. O., E-mail: sidi.souvi@irsn.fr; Sharkas, Kamal; Toulouse, Julien, E-mail: julien.toulouse@upmc.fr

2014-02-28

We extend the previously proposed one-parameter double-hybrid density-functional theory [K. Sharkas, J. Toulouse, and A. Savin, J. Chem. Phys. 134, 064113 (2011)] to meta-generalized-gradient-approximation (meta-GGA) exchange-correlation density functionals. We construct several variants of one-parameter double-hybrid approximations using the Tao-Perdew-Staroverov-Scuseria (TPSS) meta-GGA functional and test them on test sets of atomization energies and reaction barrier heights. The most accurate variant uses the uniform coordinate scaling of the density and of the kinetic energy density in the correlation functional, and improves over both standard Kohn-Sham TPSS and second-order Møller-Plesset calculations.

Verification of Anderson Superexchange in MnO via Magnetic Pair Distribution Function Analysis and ab initio Theory.

PubMed

Frandsen, Benjamin A; Brunelli, Michela; Page, Katharine; Uemura, Yasutomo J; Staunton, Julie B; Billinge, Simon J L

2016-05-13

We present a temperature-dependent atomic and magnetic pair distribution function (PDF) analysis of neutron total scattering measurements of antiferromagnetic MnO, an archetypal strongly correlated transition-metal oxide. The known antiferromagnetic ground-state structure fits the low-temperature data closely with refined parameters that agree with conventional techniques, confirming the reliability of the newly developed magnetic PDF method. The measurements performed in the paramagnetic phase reveal significant short-range magnetic correlations on a ∼1  nm length scale that differ substantially from the low-temperature long-range spin arrangement. Ab initio calculations using a self-interaction-corrected local spin density approximation of density functional theory predict magnetic interactions dominated by Anderson superexchange and reproduce the measured short-range magnetic correlations to a high degree of accuracy. Further calculations simulating an additional contribution from a direct exchange interaction show much worse agreement with the data. The Anderson superexchange model for MnO is thus verified by experimentation and confirmed by ab initio theory.

Verification of Anderson superexchange in MnO via magnetic pair distribution function analysis and ab initio theory

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

Benjamin A. Frandsen; Brunelli, Michela; Page, Katharine

Here, we present a temperature-dependent atomic and magnetic pair distribution function (PDF) analysis of neutron total scattering measurements of antiferromagnetic MnO, an archetypal strongly correlated transition-metal oxide. The known antiferromagnetic ground-state structure fits the low-temperature data closely with refined parameters that agree with conventional techniques, confirming the reliability of the newly developed magnetic PDF method. The measurements performed in the paramagnetic phase reveal significant short-range magnetic correlations on a ~1 nm length scale that differ substantially from the low-temperature long-range spin arrangement. Ab initio calculations using a self-interaction-corrected local spin density approximation of density functional theory predict magnetic interactions dominatedmore » by Anderson superexchange and reproduce the measured short-range magnetic correlations to a high degree of accuracy. Further calculations simulating an additional contribution from a direct exchange interaction show much worse agreement with the data. Furthermore, the Anderson superexchange model for MnO is thus verified by experimentation and confirmed by ab initio theory.« less

Verification of Anderson superexchange in MnO via magnetic pair distribution function analysis and ab initio theory

DOE PAGES

Benjamin A. Frandsen; Brunelli, Michela; Page, Katharine; ...

2016-05-11

Here, we present a temperature-dependent atomic and magnetic pair distribution function (PDF) analysis of neutron total scattering measurements of antiferromagnetic MnO, an archetypal strongly correlated transition-metal oxide. The known antiferromagnetic ground-state structure fits the low-temperature data closely with refined parameters that agree with conventional techniques, confirming the reliability of the newly developed magnetic PDF method. The measurements performed in the paramagnetic phase reveal significant short-range magnetic correlations on a ~1 nm length scale that differ substantially from the low-temperature long-range spin arrangement. Ab initio calculations using a self-interaction-corrected local spin density approximation of density functional theory predict magnetic interactions dominatedmore » by Anderson superexchange and reproduce the measured short-range magnetic correlations to a high degree of accuracy. Further calculations simulating an additional contribution from a direct exchange interaction show much worse agreement with the data. Furthermore, the Anderson superexchange model for MnO is thus verified by experimentation and confirmed by ab initio theory.« less

Quantum Monte Carlo analysis of a charge ordered insulating antiferromagnet: The Ti 4O 7 Magneli phase

DOE PAGES

Benali, Anouar; Shulenburger, Luke; Krogel, Jaron T.; ...

2016-06-07

The Magneli phase Ti 4O 7 is an important transition metal oxide with a wide range of applications because of its interplay between charge, spin, and lattice degrees of freedom. At low temperatures, it has non-trivial magnetic states very close in energy, driven by electronic exchange and correlation interactions. We have examined three low- lying states, one ferromagnetic and two antiferromagnetic, and calculated their energies as well as Ti spin moment distributions using highly accurate Quantum Monte Carlo methods. We compare our results to those obtained from density functional theory- based methods that include approximate corrections for exchange and correlation.more » Our results confirm the nature of the states and their ordering in energy, as compared with density-functional theory methods. However, the energy differences and spin distributions differ. Here, a detailed analysis suggests that non-local exchange-correlation functionals, in addition to other approximations such as LDA+U to account for correlations, are needed to simultaneously obtain better estimates for spin moments, distributions, energy differences and energy gaps.« less

Synthesis of functionalized 3D porous graphene using both ionic liquid and SiO2 spheres as ``spacers'' for high-performance application in supercapacitors

NASA Astrophysics Data System (ADS)

Li, Tingting; Li, Na; Liu, Jiawei; Cai, Kai; Foda, Mohamed F.; Lei, Xiaomin; Han, Heyou

2014-12-01

In this work, a high-capacity supercapacitor material based on functionalized three-dimensional (3D) porous graphene was fabricated by low temperature hydrothermal treatment of graphene oxide (GO) using both ionic liquid (IL) and SiO2 spheres as ``spacers''. In the synthesis, the introduction of dual ``spacers'' effectively enlarged the interspace between graphene sheets and suppressed their re-stacking. In addition, the IL also acted as a structure-directing agent playing a crucial role in inducing the formation of unique 3D architectures. Consequently, fast electron/ion transport channels were successfully constructed and numerous oxygen-containing groups on graphene sheets were effectively reserved, which had unique advantages in decreasing ion diffusion resistance and providing additional pseudocapacitance. As expected, the obtained material exhibited superior specific capacitance and rate capability compared to single ``spacer'' designed electrodes and simultaneously maintained excellent cycling stability. In particular, there was nearly no loss of its initial capacitance after 3000 cycles. In addition, we further assembled a symmetric two-electrode device using the material, which showed outstanding flexibility and low equivalent series resistance (ESR). More importantly, it was capable of yielding a maximum power density of about 13.3 kW kg-1 with an energy density of about 7.0 W h kg-1 at a voltage of 1.0 V in 1 M H2SO4 electrolyte. All these impressive results demonstrate that the material obtained by this approach is greatly promising for application in high-performance supercapacitors.In this work, a high-capacity supercapacitor material based on functionalized three-dimensional (3D) porous graphene was fabricated by low temperature hydrothermal treatment of graphene oxide (GO) using both ionic liquid (IL) and SiO2 spheres as ``spacers''. In the synthesis, the introduction of dual ``spacers'' effectively enlarged the interspace between graphene sheets and suppressed their re-stacking. In addition, the IL also acted as a structure-directing agent playing a crucial role in inducing the formation of unique 3D architectures. Consequently, fast electron/ion transport channels were successfully constructed and numerous oxygen-containing groups on graphene sheets were effectively reserved, which had unique advantages in decreasing ion diffusion resistance and providing additional pseudocapacitance. As expected, the obtained material exhibited superior specific capacitance and rate capability compared to single ``spacer'' designed electrodes and simultaneously maintained excellent cycling stability. In particular, there was nearly no loss of its initial capacitance after 3000 cycles. In addition, we further assembled a symmetric two-electrode device using the material, which showed outstanding flexibility and low equivalent series resistance (ESR). More importantly, it was capable of yielding a maximum power density of about 13.3 kW kg-1 with an energy density of about 7.0 W h kg-1 at a voltage of 1.0 V in 1 M H2SO4 electrolyte. All these impressive results demonstrate that the material obtained by this approach is greatly promising for application in high-performance supercapacitors. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr05473c

Porphinogen Formation from the Co-Oligomerization of Formaldehyde and Pyrrole: Free Energy Pathways.

PubMed

Kua, Jeremy; Loli, Helen

2017-10-26

We have investigated the nonoxidative stepwise co-oligomerization of formaldehyde and pyrrole to form porphinogen using density functional theory calculations that include free energy corrections. While the addition of formaldehyde to the pyrrole nitrogen is kinetically favored, thermodynamics suggest that this reaction is reversible in aqueous solution. The more thermodynamically favorable addition of formaldehyde to the ortho-carbon of pyrrole begins a stepwise process, forming dipyrromethane via an azafulvene intermediate. Subsequent additions of formaldehyde and pyrrole lead to bilanes (linear tetrapyrroles), which favorably cyclize to form porphinogen. Porphinogen is a precursor to porphin, the simplest unsubstituted porphyrin that could have played a role in primitive metabolism at the origin of life.

Influence of xc functional on thermal-elastic properties of Ceria: A DFT-based Debye-Grüneisen model approach

NASA Astrophysics Data System (ADS)

Lee, Ji-Hwan; Tak, Youngjoo; Lee, Taehun; Soon, Aloysius

Ceria (CeO2-x) is widely studied as a choice electrolyte material for intermediate-temperature (~ 800 K) solid oxide fuel cells. At this temperature, maintaining its chemical stability and thermal-mechanical integrity of this oxide are of utmost importance. To understand their thermal-elastic properties, we firstly test the influence of various approximations to the density-functional theory (DFT) xc functionals on specific thermal-elastic properties of both CeO2 and Ce2O3. Namely, we consider the local-density approximation (LDA), the generalized gradient approximation (GGA-PBE) with and without additional Hubbard U as applied to the 4 f electron of Ce, as well as the recently popularized hybrid functional due to Heyd-Scuseria-Ernzehof (HSE06). Next, we then couple this to a volume-dependent Debye-Grüneisen model to determine the thermodynamic quantities of ceria at arbitrary temperatures. We find an explicit description of the strong correlation (e.g. via the DFT + U and hybrid functional approach) is necessary to have a good agreement with experimental values, in contrast to the mean-field treatment in standard xc approximations (such as LDA or GGA-PBE). We acknowledge support from Samsung Research Funding Center of Samsung Electronics (SRFC-MA1501-03).

Changes in microbial community characteristics and soil organic matter with nitrogen additions in two tropical forests.

PubMed

Cusack, Daniela F; Silver, Whendee L; Torn, Margaret S; Burton, Sarah D; Firestone, Mary K

2011-03-01

Microbial communities and their associated enzyme activities affect the amount and chemical quality of carbon (C) in soils. Increasing nitrogen (N) deposition, particularly in N-rich tropical forests, is likely to change the composition and behavior of microbial communities and feed back on ecosystem structure and function. This study presents a novel assessment of mechanistic links between microbial responses to N deposition and shifts in soil organic matter (SOM) quality and quantity. We used phospholipid fatty acid (PLFA) analysis and microbial enzyme assays in soils to assess microbial community responses to long-term N additions in two distinct tropical rain forests. We used soil density fractionation and 13C nuclear magnetic resonance (NMR) spectroscopy to measure related changes in SOM pool sizes and chemical quality. Microbial biomass increased in response to N fertilization in both tropical forests and corresponded to declines in pools of low-density SOM. The chemical quality of this soil C pool reflected ecosystem-specific changes in microbial community composition. In the lower-elevation forest, there was an increase in gram-negative bacteria PLFA biomass, and there were significant losses of labile C chemical groups (O-alkyls). In contrast, the upper-elevation tropical forest had an increase in fungal PLFAs with N additions and declines in C groups associated with increased soil C storage (alkyls). The dynamics of microbial enzymatic activities with N addition provided a functional link between changes in microbial community structure and SOM chemistry. Ecosystem-specific changes in microbial community composition are likely to have far-reaching effects on soil carbon storage and cycling. This study indicates that microbial communities in N-rich tropical forests can be sensitive to added N, but we can expect significant variability in how ecosystem structure and function respond to N deposition among tropical forest types.

The ecological services of plant communities in parks for climate control and recreation-A case study in Shanghai, China.

PubMed

Li, Zhigang; Chen, Dan; Cai, Shize; Che, Shengquan

2018-01-01

Mitigating extreme heat in urban areas is beneficial and sometimes critical to human health. Thriving plant communities in community parks play an important role in mitigating extreme heat through providing cooling effect, while inevitably affecting how people perceive the benefits of using community parks for recreation. Thus, the impacts of plant communities on the thermal environment should be quantified to determine the optimal structure of the plant community. The goal would be to harmonize the functions of improving the thermal environment with the preferences people have related to the recreational benefits of plant communities with various levels of vegetation density. In this paper, the correlations between the structural characteristics of plant communities and their function in mitigating the thermal environment were investigated on calm summer days in Xincheng Central Park, Minhang District, Shanghai, China. In addition to analyzing the plant communities present and their effects on the park microclimate, a questionnaire was employed to determine the plant community preferences of recreational park users. The results showed that plant communities could reduce the air temperature by 1.23-2.42 °C and increase the relative humidity by 2.4-4.2% during the daytime. The microclimate conditions in plant communities with varying vegetation densities were significantly different. The canopy density and leaf area index primarily controlled the temperature reduction, while the canopy density and total canopy cover ratio primarily controlled the increase in humidity; meanwhile, these correlations varied at different times of the day. Moreover, most of the park users preferred a moderately dense plant community which met their environmental perceptions for recreation in parks. Age or education level variables of park users would also predict preferences for different plant community densities. Ultimately, one plant community pattern with appropriate canopy density (60%), leaf area index (≥3) and canopy cover ratio (total 0.80-1.20, with 0.6-0.75 for trees and 0.20-0.45 for shrubs/woodland area) was recommended, which would harmonize the functions of the mitigation of the thermal environment with most people's perception of a desirable vegetation density.

The ecological services of plant communities in parks for climate control and recreation—A case study in Shanghai, China

PubMed Central

Li, Zhigang; Chen, Dan; Cai, Shize; Che, Shengquan

2018-01-01

Mitigating extreme heat in urban areas is beneficial and sometimes critical to human health. Thriving plant communities in community parks play an important role in mitigating extreme heat through providing cooling effect, while inevitably affecting how people perceive the benefits of using community parks for recreation. Thus, the impacts of plant communities on the thermal environment should be quantified to determine the optimal structure of the plant community. The goal would be to harmonize the functions of improving the thermal environment with the preferences people have related to the recreational benefits of plant communities with various levels of vegetation density. In this paper, the correlations between the structural characteristics of plant communities and their function in mitigating the thermal environment were investigated on calm summer days in Xincheng Central Park, Minhang District, Shanghai, China. In addition to analyzing the plant communities present and their effects on the park microclimate, a questionnaire was employed to determine the plant community preferences of recreational park users. The results showed that plant communities could reduce the air temperature by 1.23–2.42 °C and increase the relative humidity by 2.4–4.2% during the daytime. The microclimate conditions in plant communities with varying vegetation densities were significantly different. The canopy density and leaf area index primarily controlled the temperature reduction, while the canopy density and total canopy cover ratio primarily controlled the increase in humidity; meanwhile, these correlations varied at different times of the day. Moreover, most of the park users preferred a moderately dense plant community which met their environmental perceptions for recreation in parks. Age or education level variables of park users would also predict preferences for different plant community densities. Ultimately, one plant community pattern with appropriate canopy density (60%), leaf area index (≥3) and canopy cover ratio (total 0.80–1.20, with 0.6–0.75 for trees and 0.20–0.45 for shrubs/woodland area) was recommended, which would harmonize the functions of the mitigation of the thermal environment with most people’s perception of a desirable vegetation density. PMID:29694401

DAMQT: A package for the analysis of electron density in molecules

NASA Astrophysics Data System (ADS)

López, Rafael; Rico, Jaime Fernández; Ramírez, Guillermo; Ema, Ignacio; Zorrilla, David

2009-09-01

DAMQT is a package for the analysis of the electron density in molecules and the fast computation of the density, density deformations, electrostatic potential and field, and Hellmann-Feynman forces. The method is based on the partition of the electron density into atomic fragments by means of a least deformation criterion. Each atomic fragment of the density is expanded in regular spherical harmonics times radial factors, which are piecewise represented in terms of analytical functions. This representation is used for the fast evaluation of the electrostatic potential and field generated by the electron density and nuclei, as well as for the computation of the Hellmann-Feynman forces on the nuclei. An analysis of the atomic and molecular deformations of the density can be also carried out, yielding a picture that connects with several concepts of the empirical structural chemistry. Program summaryProgram title: DAMQT1.0 Catalogue identifier: AEDL_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDL_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPLv3 No. of lines in distributed program, including test data, etc.: 278 356 No. of bytes in distributed program, including test data, etc.: 31 065 317 Distribution format: tar.gz Programming language: Fortran90 and C++ Computer: Any Operating system: Linux, Windows (Xp, Vista) RAM: 190 Mbytes Classification: 16.1 External routines: Trolltech's Qt (4.3 or higher) ( http://www.qtsoftware.com/products), OpenGL (1.1 or higher) ( http://www.opengl.org/), GLUT 3.7 ( http://www.opengl.org/resources/libraries/glut/). Nature of problem: Analysis of the molecular electron density and density deformations, including fast evaluation of electrostatic potential, electric field and Hellmann-Feynman forces on nuclei. Solution method: The method of Deformed Atoms in Molecules, reported elsewhere [1], is used for partitioning the molecular electron density into atomic fragments, which are further expanded in spherical harmonics times radial factors. The partition is used for defining molecular density deformations and for the fast calculation of several properties associated to density. Restrictions: The current version is limited to 120 atoms, 2000 contracted functions, and l=5 in basis functions. Density must come from a LCAO calculation (any level) with spherical (not Cartesian) Gaussian functions. Unusual features: The program contains an OPEN statement to binary files (stream) in file GOPENMOL.F90. This statement has not a standard syntax in Fortran 90. Two possibilities are considered in conditional compilation: Intel's ifort and Fortran2003 standard. This latter is applied to compilers other than ifort (gfortran uses this one, for instance). Additional comments: The distribution file for this program is over 30 Mbytes and therefore is not delivered directly when download or e-mail is requested. Instead a html file giving details of how the program can be obtained is sent. Running time: Largely dependent on the system size and the module run (from fractions of a second to hours). References: [1] J. Fernández Rico, R. López, I. Ema, G. Ramírez, J. Mol. Struct. (Theochem) 727 (2005) 115.

The force distribution probability function for simple fluids by density functional theory.

PubMed

Rickayzen, G; Heyes, D M

2013-02-28

Classical density functional theory (DFT) is used to derive a formula for the probability density distribution function, P(F), and probability distribution function, W(F), for simple fluids, where F is the net force on a particle. The final formula for P(F) ∝ exp(-AF(2)), where A depends on the fluid density, the temperature, and the Fourier transform of the pair potential. The form of the DFT theory used is only applicable to bounded potential fluids. When combined with the hypernetted chain closure of the Ornstein-Zernike equation, the DFT theory for W(F) agrees with molecular dynamics computer simulations for the Gaussian and bounded soft sphere at high density. The Gaussian form for P(F) is still accurate at lower densities (but not too low density) for the two potentials, but with a smaller value for the constant, A, than that predicted by the DFT theory.

Single-particle energies and density of states in density functional theory

NASA Astrophysics Data System (ADS)

van Aggelen, H.; Chan, G. K.-L.

2015-07-01

Time-dependent density functional theory (TD-DFT) is commonly used as the foundation to obtain neutral excited states and transition weights in DFT, but does not allow direct access to density of states and single-particle energies, i.e. ionisation energies and electron affinities. Here we show that by extending TD-DFT to a superfluid formulation, which involves operators that break particle-number symmetry, we can obtain the density of states and single-particle energies from the poles of an appropriate superfluid response function. The standard Kohn- Sham eigenvalues emerge as the adiabatic limit of the superfluid response under the assumption that the exchange- correlation functional has no dependence on the superfluid density. The Kohn- Sham eigenvalues can thus be interpreted as approximations to the ionisation energies and electron affinities. Beyond this approximation, the formalism provides an incentive for creating a new class of density functionals specifically targeted at accurate single-particle eigenvalues and bandgaps.

Shock Initiation and Equation of State of Ammonium Nitrate

NASA Astrophysics Data System (ADS)

Robbins, David; Sheffield, Steve; Dattelbaum, Dana; Chellappa, Raja; Velisavljevic, Nenad

2013-06-01

Ammonium nitrate (AN) is a widely used fertilizer and mining explosive commonly found in ammonium nitrate-fuel oil. Neat AN is a non-ideal explosive with measured detonation velocities approaching 4 km/s. Previously, we reported a thermodynamically-complete equation of state for AN based on its maximum density, and showed that near-full density AN did not initiate when subjected to shock input conditions up to 22 GPa. In this work, we extend these initial results, by presenting new Hugoniot data for intermediate density neat AN obtained from gas gun-driven plate impact experiments. AN at densities from 1.8 to 1.5 g/cm3 were impacted into LiF windows using a two-stage light gas gun. Dual VISARs were used to measure the interfacial particle velocity wave profile as a function of time following impact. The new Hugoniot data, in addition to updates to thermodynamic parameters derived from structural analysis and vibrational spectroscopy measurements in high pressure diamond anvil cell experiments, are used to refine the unreacted EOS for AN. Furthermore, shock initiation of neat AN was observed as the initial porosity increased (density decreased). Insights into the relationship(s) between initial density and shock initiation sensitivity are also presented, from evidence of shock initiation in the particle velocity profiles obtained for the lower density AN samples.

Effect of lattice defects on the electronic structures and floatability of pyrites

NASA Astrophysics Data System (ADS)

Xian, Yong-jun; Wen, Shu-ming; Chen, Xiu-ming; Deng, Jiu-shuai; Liu, Jian

2012-12-01

The electronic structures of three types of lattice defects in pyrites (i.e., As-substituted, Co-substituted, and intercrystalline Au pyrites) were calculated using the density functional theory (DFT). In addition, their band structures, density of states, and difference charge density were studied. The effect of the three types of lattice defects on the pyrite floatability was explored. The calculated results showed that the band-gaps of pyrites with Co-substitution and intercrystalline Au decreased significantly, which favors the oxidation of xanthate to dixanthogen and the adsorption of dixanthogen during pyrite flotation. The stability of the pyrites increased in the following order: As-substituted < perfect < Co-substituted < intercrystalline Au. Therefore, As-substituted pyrite is easier to be depressed by intensive oxidization compared to perfect pyrite in a strongly alkaline medium. However, Co-substituted and intercrystalline Au pyrites are more difficult to be depressed compared to perfect pyrite. The analysis of the Mulliken bond population and the electron density difference indicates that the covalence characteristic of the S-Fe bond is larger compared to the S-S bond in perfect pyrite. In addition, the presence of the three types of lattice defects in the pyrite bulk results in an increase in the covalence level of the S-Fe bond and a decrease in the covalence level of the S-S bond, which affect the natural floatability of the pyrites.

Thermal island destabilization and the Greenwald limit

DOE PAGES

White, R. B.; Gates, D. A.; Brennan, D. P.

2015-02-24

Magnetic reconnection is ubiquitous in the magnetosphere, the solar corona, and in toroidal fusion research discharges. A magnetic island saturates at a width which produces a minimum in the magnetic energy of the configuration is evident in a fusion device. At saturation, the modified current density profile, a function of the flux in the island, is essentially flat, the growth rate proportional to the difference in the current at the O-point and the X-point. Furthermore, modification of the current density profile in the island interior causes a change in the island stability and additional growth or contraction of the saturatedmore » island. Because field lines in an island are isolated from the outside plasma, an island can heat or cool preferentially depending on the balance of Ohmic heating and radiation loss in the interior, changing the resistivity and hence the current in the island. A simple model of island destabilization due to radiation cooling of the island is constructed, and the effect of modification of the current within an island is calculated. In addition destabilization effect is described, and it is shown that a small imbalance of heating can lead to exponential growth of the island. A destabilized magnetic island near the plasma edge can lead to plasma loss, and because the radiation is proportional to plasma density and charge, this effect can cause an impurity dependent density limit.« less

Thermal island destabilization and the Greenwald limit

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

White, R. B.; Gates, D. A.; Brennan, D. P.

Magnetic reconnection is ubiquitous in the magnetosphere, the solar corona, and in toroidal fusion research discharges. A magnetic island saturates at a width which produces a minimum in the magnetic energy of the configuration is evident in a fusion device. At saturation, the modified current density profile, a function of the flux in the island, is essentially flat, the growth rate proportional to the difference in the current at the O-point and the X-point. Furthermore, modification of the current density profile in the island interior causes a change in the island stability and additional growth or contraction of the saturatedmore » island. Because field lines in an island are isolated from the outside plasma, an island can heat or cool preferentially depending on the balance of Ohmic heating and radiation loss in the interior, changing the resistivity and hence the current in the island. A simple model of island destabilization due to radiation cooling of the island is constructed, and the effect of modification of the current within an island is calculated. In addition destabilization effect is described, and it is shown that a small imbalance of heating can lead to exponential growth of the island. A destabilized magnetic island near the plasma edge can lead to plasma loss, and because the radiation is proportional to plasma density and charge, this effect can cause an impurity dependent density limit.« less

Thermal island destabilization and the Greenwald limit

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

White, R. B.; Gates, D. A.; Brennan, D. P.

Magnetic reconnection is ubiquitous in the magnetosphere, the solar corona, and in toroidal fusion research discharges. In a fusion device, a magnetic island saturates at a width which produces a minimum in the magnetic energy of the configuration. At saturation, the modified current density profile, a function of the flux in the island, is essentially flat, the growth rate proportional to the difference in the current at the O-point and the X-point. Further modification of the current density profile in the island interior causes a change in the island stability and additional growth or contraction of the saturated island. Becausemore » field lines in an island are isolated from the outside plasma, an island can heat or cool preferentially depending on the balance of Ohmic heating and radiation loss in the interior, changing the resistivity and hence the current in the island. A simple model of island destabilization due to radiation cooling of the island is constructed, and the effect of modification of the current within an island is calculated. An additional destabilization effect is described, and it is shown that a small imbalance of heating can lead to exponential growth of the island. A destabilized magnetic island near the plasma edge can lead to plasma loss, and because the radiation is proportional to plasma density and charge, this effect can cause an impurity dependent density limit.« less

Trivial constraints on orbital-free kinetic energy density functionals

NASA Astrophysics Data System (ADS)

Luo, Kai; Trickey, S. B.

2018-03-01

Approximate kinetic energy density functionals (KEDFs) are central to orbital-free density functional theory. Limitations on the spatial derivative dependencies of KEDFs have been claimed from differential virial theorems. We identify a central defect in the argument: the relationships are not true for an arbitrary density but hold only for the minimizing density and corresponding chemical potential. Contrary to the claims therefore, the relationships are not constraints and provide no independent information about the spatial derivative dependencies of approximate KEDFs. A simple argument also shows that validity for arbitrary v-representable densities is not restored by appeal to the density-potential bijection.

Adsorption of hairy particles with mobile ligands: Molecular dynamics and density functional study

NASA Astrophysics Data System (ADS)

Borówko, M.; Sokołowski, S.; Staszewski, T.; Pizio, O.

2018-01-01

We study models of hairy nanoparticles in contact with a hard wall. Each particle is built of a spherical core with a number of ligands attached to it and each ligand is composed of several spherical, tangentially jointed segments. The number of segments is the same for all ligands. Particular models differ by the numbers of ligands and of segments per ligand, but the total number of segments is constant. Moreover, our model assumes that the ligands are tethered to the core in such a manner that they can "slide" over the core surface. Using molecular dynamics simulations we investigate the differences in the structure of a system close to the wall. In order to characterize the distribution of the ligands around the core, we have calculated the end-to-end distances of the ligands and the lengths and orientation of the mass dipoles. Additionally, we also employed a density functional approach to obtain the density profiles. We have found that if the number of ligands is not too high, the proposed version of the theory is capable to predict the structure of the system with a reasonable accuracy.

Wnt-5a/Frizzled9 Receptor Signaling through the Gαo-Gβγ Complex Regulates Dendritic Spine Formation.

PubMed

Ramírez, Valerie T; Ramos-Fernández, Eva; Henríquez, Juan Pablo; Lorenzo, Alfredo; Inestrosa, Nibaldo C

2016-09-02

Wnt ligands play crucial roles in the development and regulation of synapse structure and function. Specifically, Wnt-5a acts as a secreted growth factor that regulates dendritic spine formation in rodent hippocampal neurons, resulting in postsynaptic development that promotes the clustering of the PSD-95 (postsynaptic density protein 95). Here, we focused on the early events occurring after the interaction between Wnt-5a and its Frizzled receptor at the neuronal cell surface. Additionally, we studied the role of heterotrimeric G proteins in Wnt-5a-dependent synaptic development. We report that FZD9 (Frizzled9), a Wnt receptor related to Williams syndrome, is localized in the postsynaptic region, where it interacts with Wnt-5a. Functionally, FZD9 is required for the Wnt-5a-mediated increase in dendritic spine density. FZD9 forms a precoupled complex with Gαo under basal conditions that dissociates after Wnt-5a stimulation. Accordingly, we found that G protein inhibition abrogates the Wnt-5a-dependent pathway in hippocampal neurons. In particular, the activation of Gαo appears to be a key factor controlling the Wnt-5a-induced dendritic spine density. In addition, we found that Gβγ is required for the Wnt-5a-mediated increase in cytosolic calcium levels and spinogenesis. Our findings reveal that FZD9 and heterotrimeric G proteins regulate Wnt-5a signaling and dendritic spines in cultured hippocampal neurons. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Alterations of brain grey matter density and olfactory bulb volume in patients with olfactory loss after traumatic brain injury.

PubMed

Han, Pengfei; Winkler, Nicole; Hummel, Cornelia; Hähner, Antje; Gerber, Johannes; Hummel, Thomas

2018-04-27

Olfactory loss and traumatic brain injury (TBI) both lead to anatomical brain alterations in humans. Little research has been done on the structural brain changes for TBI patients with olfactory loss. Using voxel-based morphometry, the grey matter (GM) density was examined for twenty-two TBI patients with hyposmia, twenty-four TBI patients with anosmia, and twenty-two age-matched controls. Olfactory bulb (OB) volumes were measured by manual segmentation of acquired T2 weighted coronal slices using a standardized protocol. Brain lesions in the olfactory relevant areas were also examined for TBI patients. Results showed that patients with anosmia have more frequent lesions in the OB, orbitofrontal cortex (OFC) and the temporal lobe pole, as compared to patients with hyposmia. GM density in the primary olfactory area was decreased in both groups of patients. In addition, compared to controls, patients with anosmia showed GM density reduction in several secondary olfactory eloquent regions, including the gyrus rectus, medial OFC, anterior cingulate cortex, insula, and cerebellum. However, patients with hyposmia showed a lesser degree of GM reduction compared to healthy controls. Smaller OB volumes were found for patients with olfactory loss as compared to controls. TBI patients with anosmia had the smallest OB volumes which were caused by the lesions for OB. In addition, post-TBI duration was negatively correlated with GM density in the secondary olfactory areas in patients with hyposmia, but was positively correlated with GM density in the frontal and temporal gyrus in patients with anosmia. The GM density and OB volume reduction among TBI patients with olfactory loss was largely depend on the location and severity of brain lesions in olfactory relevant regions. Longer post-TBI duration had an impact on brain GM density changes, which indicate a decreased olfactory function in patients with hyposmia and possible compensatory mechanisms in patients with anosmia.

Quantification of breast density with spectral mammography based on a scanned multi-slit photon-counting detector: A feasibility study

PubMed Central

Ding, Huanjun; Molloi, Sabee

2012-01-01

Purpose A simple and accurate measurement of breast density is crucial for the understanding of its impact in breast cancer risk models. The feasibility to quantify volumetric breast density with a photon-counting spectral mammography system has been investigated using both computer simulations and physical phantom studies. Methods A computer simulation model involved polyenergetic spectra from a tungsten anode x-ray tube and a Si-based photon-counting detector has been evaluated for breast density quantification. The figure-of-merit (FOM), which was defined as the signal-to-noise ratio (SNR) of the dual energy image with respect to the square root of mean glandular dose (MGD), was chosen to optimize the imaging protocols, in terms of tube voltage and splitting energy. A scanning multi-slit photon-counting spectral mammography system has been employed in the experimental study to quantitatively measure breast density using dual energy decomposition with glandular and adipose equivalent phantoms of uniform thickness. Four different phantom studies were designed to evaluate the accuracy of the technique, each of which addressed one specific variable in the phantom configurations, including thickness, density, area and shape. In addition to the standard calibration fitting function used for dual energy decomposition, a modified fitting function has been proposed, which brought the tube voltages used in the imaging tasks as the third variable in dual energy decomposition. Results For an average sized breast of 4.5 cm thick, the FOM was maximized with a tube voltage of 46kVp and a splitting energy of 24 keV. To be consistent with the tube voltage used in current clinical screening exam (~ 32 kVp), the optimal splitting energy was proposed to be 22 keV, which offered a FOM greater than 90% of the optimal value. In the experimental investigation, the root-mean-square (RMS) error in breast density quantification for all four phantom studies was estimated to be approximately 1.54% using standard calibration function. The results from the modified fitting function, which integrated the tube voltage as a variable in the calibration, indicated a RMS error of approximately 1.35% for all four studies. Conclusions The results of the current study suggest that photon-counting spectral mammography systems may potentially be implemented for an accurate quantification of volumetric breast density, with an RMS error of less than 2%, using the proposed dual energy imaging technique. PMID:22771941

Centrality dependence of charged particle multiplicity at midrapidity in Au+Au collisions at (sNN)=130 GeV

NASA Astrophysics Data System (ADS)

Back, B. B.; Baker, M. D.; Barton, D. S.; Betts, R. R.; Bindel, R.; Budzanowski, A.; Busza, W.; Carroll, A.; Decowski, M. P.; Garcia, E.; George, N.; Gulbrandsen, K.; Gushue, S.; Halliwell, C.; Heintzelman, G. A.; Henderson, C.; Hołyński, R.; Hofman, D. J.; Holzman, B.; Johnson, E.; Kane, J. L.; Katzy, J.; Khan, N.; Kucewicz, W.; Kulinich, P.; Lin, W. T.; Manly, S.; McLeod, D.; Michałowski, J.; Mignerey, A. C.; Mülmenstädt, J.; Nouicer, R.; Olszewski, A.; Pak, R.; Park, I. C.; Pernegger, H.; Reed, C.; Remsberg, L. P.; Reuter, M.; Roland, C.; Roland, G.; Rosenberg, L.; Sarin, P.; Sawicki, P.; Skulski, W.; Steadman, S. G.; Stephans, G. S.; Steinberg, P.; Stodulski, M.; Sukhanov, A.; Tang, J.-L.; Teng, R.; Trzupek, A.; Vale, C.; van Nieuwenhuizen, G. J.; Verdier, R.; Wadsworth, B.; Wolfs, F. L.; Wosiek, B.; Woźniak, K.; Wuosmaa, A. H.; Wysłouch, B.

2002-03-01

We present a measurement of the pseudorapidity density of primary charged particles near midrapidity in Au+Au collisions at (sNN)=130 GeV as a function of the number of participating nucleons. The pseudorapidity density, dNch/dη\\|\\|η\\|<1/(1/2), rises from 2.87+/-0.21 in peripheral events (~83) to 3.45+/-0.18 in central events (~353), which is 53+/-8% higher than pp&; collisions at a similar center-of-mass energy. This is consistent with an additional contribution to charged particle production that scales with the number of binary nucleon-nucleon collisions (Ncoll).

STS studies of the surface of Bi2Se3

NASA Astrophysics Data System (ADS)

Romanowich, Megan; Lee, Mal-Soon; Mahanti, S. D.; Tessmer, Stuart; Chung, Duck Young; Song, Jung-Hwan; Kanatzidis, Mercouri

2012-02-01

We apply scanning tunneling spectroscopy to characterize the surface of the topological insulator Bi2Se3. Spectroscopy reveals that the minimum in the local density of states (LDOS) does not actually vanish in the region where Dirac cone states exist. We demonstrate with density functional theory calculations that this can be understood in terms of an asymmetric addition to the LDOS associated with a contribution from the bulk valence band that overlaps in energy with the Dirac point. We will discuss the origin of the fluctuations in the LDOS seen in the experiment near 0.2 eV above the Dirac point, which are associated with tunneling into the lowest conduction band states.

Studies of carbon incorporation on the diamond [100] surface during chemical vapor deposition using density functional theory.

PubMed

Cheesman, Andrew; Harvey, Jeremy N; Ashfold, Michael N R

2008-11-13

Accurate potential energy surface calculations are presented for many of the key steps involved in diamond chemical vapor deposition on the [100] surface (in its 2 x 1 reconstructed and hydrogenated form). The growing diamond surface was described by using a large (approximately 1500 atoms) cluster model, with the key atoms involved in chemical steps being described by using a quantum mechanical (QM, density functional theory, DFT) method and the bulk of the atoms being described by molecular mechanics (MM). The resulting hybrid QM/MM calculations are more systematic and/or at a higher level of theory than previous work on this growth process. The dominant process for carbon addition, in the form of methyl radicals, is predicted to be addition to a surface radical site, opening of the adjacent C-C dimer bond, insertion, and ultimate ring closure. Other steps such as insertion across the trough between rows of dimer bonds or addition to a neighboring dimer leading to formation of a reconstruction on the next layer may also contribute. Etching of carbon can also occur; the most likely mechanism involves loss of a two-carbon moiety in the form of ethene. The present higher-level calculations confirm that migration of inserted carbon along both dimer rows and chains should be relatively facile, with barriers of approximately 150 kJ mol (-1) when starting from suitable diradical species, and that this step should play an important role in establishing growth of smooth surfaces.

Molecular Characterization of a Lysozyme Gene and Its Altered Expression Profile in Crowded Beet Webworm (Loxostege sticticalis)

PubMed Central

Kong, Hailong; Lv, Min; Mao, Nian; Wang, Cheng; Cheng, Yunxia; Zhang, Lei; Jiang, Xingfu; Luo, Lizhi

2016-01-01

There is growing evidence that insects living in high-density populations exhibit an increase in immune function to counter a higher risk of disease. This phenomenon, known as density-dependent prophylaxis, has been experimentally tested in a number of insect species. Although density-dependent prophylaxis is especially prevalent in insects exhibiting density-dependent phase polyphenism, the molecular mechanism remains unclear. Our previous study demonstrated that the antibacterial activity of lysozyme is important for this process in the beet webworm Loxostege sticticalis. In this study, a lysozyme cDNA from L. sticticalis was cloned and characterized. The full-length cDNA is 1078 bp long and contains an open reading frame of 426 bp that encodes 142 amino acids. The deduced protein possesses structural characteristics of a typical c-type lysozyme and clusters with c-type lysozymes from other Lepidoptera. LsLysozyme was found to be expressed throughout all developmental stages, showing the highest level in pupae. LsLysozyme was also highly expressed in the midgut and fat body. Elevated LsLysozyme expression was observed in L. sticticalis larvae infected by Beauveria bassiana and in larvae reared under crowding conditions. In addition, the expression level of LsLysozyme in infected larvae reared at a density of 10 larvae per jar was significantly higher compared to those reared at a density of l or 30 larvae per jar. These results suggest that larval crowding affects the gene expression profile of this lysozyme. This study provides additional insight into the expression of an immune-associated lysozyme gene and helps us to better understand the immune response of L. sticticalis under crowding conditions. PMID:27575006

Atomic kinetic energy, momentum distribution, and structure of solid neon at zero temperature

NASA Astrophysics Data System (ADS)

Cazorla, C.; Boronat, J.

2008-01-01

We report on the calculation of the ground-state atomic kinetic energy Ek and momentum distribution of solid Ne by means of the diffusion Monte Carlo method and Aziz HFD-B pair potential. This approach is shown to perform notably for this crystal since we obtain very good agreement with respect to experimental thermodynamic data. Additionally, we study the structural properties of solid Ne at densities near the equilibrium by estimating the radial pair-distribution function, Lindemann’s ratio, and atomic density profile around the positions of the perfect crystalline lattice. Our value for Ek at the equilibrium density is 41.51(6)K , which agrees perfectly with the recent prediction made by Timms , 41(2)K , based on their deep-inelastic neutron scattering experiments carried out over the temperature range 4-20K , and also with previous path integral Monte Carlo results obtained with the Lennard-Jones and Aziz HFD-C2 atomic pairwise interactions. The one-body density function of solid Ne is calculated accurately and found to fit perfectly, within statistical uncertainty, to a Gaussian curve. Furthermore, we analyze the degree of anharmonicity of solid Ne by calculating some of its microscopic ground-state properties within traditional harmonic approaches. We provide insightful comparison to solid He4 in terms of the Debye model in order to assess the relevance of anharmonic effects in Ne.

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

PubMed

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

2013-09-14

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

Density-functional theory of spherical electric double layers and zeta potentials of colloidal particles in restricted-primitive-model electrolyte solutions.

PubMed

Yu, Yang-Xin; Wu, Jianzhong; Gao, Guang-Hua

2004-04-15

A density-functional theory is proposed to describe the density profiles of small ions around an isolated colloidal particle in the framework of the restricted primitive model where the small ions have uniform size and the solvent is represented by a dielectric continuum. The excess Helmholtz energy functional is derived from a modified fundamental measure theory for the hard-sphere repulsion and a quadratic functional Taylor expansion for the electrostatic interactions. The theoretical predictions are in good agreement with the results from Monte Carlo simulations and from previous investigations using integral-equation theory for the ionic density profiles and the zeta potentials of spherical particles at a variety of solution conditions. Like the integral-equation approaches, the density-functional theory is able to capture the oscillatory density profiles of small ions and the charge inversion (overcharging) phenomena for particles with elevated charge density. In particular, our density-functional theory predicts the formation of a second counterion layer near the surface of highly charged spherical particle. Conversely, the nonlinear Poisson-Boltzmann theory and its variations are unable to represent the oscillatory behavior of small ion distributions and charge inversion. Finally, our density-functional theory predicts charge inversion even in a 1:1 electrolyte solution as long as the salt concentration is sufficiently high. (c) 2004 American Institute of Physics.

Formation and properties of surface-anchored polymer assemblies with tunable physico-chemical characteristics

NASA Astrophysics Data System (ADS)

Wu, Tao

We describe two new methodologies leading to the formation of novel surface-anchored polymer assemblies on solid substrates. While the main goal is to understand the fundamentals pertaining to the preparation and properties of the surface-bound polymer assemblies (including neutral and chargeable polymers), several examples also are mentioned throughout the Thesis that point out to practical applications of such structures. The first method is based on generating assemblies comprising anchored polymers with a gradual variation of grafting densities on solid substrates. These structures are prepared by first covering the substrate with a molecular gradient of the polymerization initiator, followed by polymerization from these substrate-bound initiator centers ("grafting from"). We apply this technique to prepare grafting density gradients of poly(acryl amide) (PAAm) and poly(acrylic acid) (PAA) on silica-covered substrates. We show that using the grafting density gradient geometry, the characteristics of surface-anchored polymers in both the low grafting density ("mushroom") regime as well as the high grafting density ("brush") regime can be accessed conveniently on a single sample. We use a battery of experimental methods, including Fourier transform infrared spectroscopy (FTIR), Near-edge absorption fine structure spectroscopy (NEXAFS), contact angle, ellipsometry, to study the characteristics of the surface-bound polymer layers. We also probe the scaling laws of neutral polymer as a function of grafting density, and for weak polyelectrolyte, in addition to the grafting density, we study the affect of solution ionic strength and pH values. In the second novel method, which we coined as "mechanically assisted polymer assembly" (MAPA), we form surface anchored polymers by "grafting from" polymerization initiators deposited on elastic surfaces that have been previously extended uniaxially by a certain length increment, Deltax. Upon releasing the strain in the substrate after completion of polymerization, we show the grafting density of the polymers grafted to flexible substrates can be tuned as a function of Deltax.

An Efficient Acoustic Density Estimation Method with Human Detectors Applied to Gibbons in Cambodia.

PubMed

Kidney, Darren; Rawson, Benjamin M; Borchers, David L; Stevenson, Ben C; Marques, Tiago A; Thomas, Len

2016-01-01

Some animal species are hard to see but easy to hear. Standard visual methods for estimating population density for such species are often ineffective or inefficient, but methods based on passive acoustics show more promise. We develop spatially explicit capture-recapture (SECR) methods for territorial vocalising species, in which humans act as an acoustic detector array. We use SECR and estimated bearing data from a single-occasion acoustic survey of a gibbon population in northeastern Cambodia to estimate the density of calling groups. The properties of the estimator are assessed using a simulation study, in which a variety of survey designs are also investigated. We then present a new form of the SECR likelihood for multi-occasion data which accounts for the stochastic availability of animals. In the context of gibbon surveys this allows model-based estimation of the proportion of groups that produce territorial vocalisations on a given day, thereby enabling the density of groups, instead of the density of calling groups, to be estimated. We illustrate the performance of this new estimator by simulation. We show that it is possible to estimate density reliably from human acoustic detections of visually cryptic species using SECR methods. For gibbon surveys we also show that incorporating observers' estimates of bearings to detected groups substantially improves estimator performance. Using the new form of the SECR likelihood we demonstrate that estimates of availability, in addition to population density and detection function parameters, can be obtained from multi-occasion data, and that the detection function parameters are not confounded with the availability parameter. This acoustic SECR method provides a means of obtaining reliable density estimates for territorial vocalising species. It is also efficient in terms of data requirements since since it only requires routine survey data. We anticipate that the low-tech field requirements will make this method an attractive option in many situations where populations can be surveyed acoustically by humans.

Evaluating interaction energies of weakly bonded systems using the Buckingham-Hirshfeld method

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

Krishtal, A.; Van Alsenoy, C.; Geerlings, P.

2014-05-14

We present the finalized Buckingham-Hirshfeld method (BHD-DFT) for the evaluation of interaction energies of non-bonded dimers with Density Functional Theory (DFT). In the method, dispersion energies are evaluated from static multipole polarizabilities, obtained on-the-fly from Coupled Perturbed Kohn-Sham calculations and partitioned into diatomic contributions using the iterative Hirshfeld partitioning method. The dispersion energy expression is distributed over four atoms and has therefore a higher delocalized character compared to the standard pairwise expressions. Additionally, full multipolar polarizability tensors are used as opposed to effective polarizabilities, allowing to retain the anisotropic character at no additional computational cost. A density dependent damping functionmore » for the BLYP, PBE, BP86, B3LYP, and PBE0 functionals has been implemented, containing two global parameters which were fitted to interaction energies and geometries of a selected number of dimers using a bi-variate RMS fit. The method is benchmarked against the S22 and S66 data sets for equilibrium geometries and the S22x5 and S66x8 data sets for interaction energies around the equilibrium geometry. Best results are achieved using the B3LYP functional with mean average deviation values of 0.30 and 0.24 kcal/mol for the S22 and S66 data sets, respectively. This situates the BHD-DFT method among the best performing dispersion inclusive DFT methods. Effect of counterpoise correction on DFT energies is discussed.« less

Spatial and Global Sensory Suppression Mapping Encompassing the Central 10° Field in Anisometropic Amblyopia.

PubMed

Li, Jingjing; Li, Jinrong; Chen, Zidong; Liu, Jing; Yuan, Junpeng; Cai, Xiaoxiao; Deng, Daming; Yu, Minbin

2017-01-01

We investigate the efficacy of a novel dichoptic mapping paradigm in evaluating visual function of anisometropic amblyopes. Using standard clinical measures of visual function (visual acuity, stereo acuity, Bagolini lenses, and neutral density filters) and a novel quantitative mapping technique, 26 patients with anisometropic amblyopia (mean age = 19.15 ± 4.42 years) were assessed. Two additional psychophysical interocular suppression measurements were tested with dichoptic global motion coherence and binocular phase combination tasks. Luminance reduction was achieved by placing neutral density filters in front of the normal eye. Our study revealed that suppression changes across the central 10° visual field by mean luminance modulation in amblyopes as well as normal controls. Using simulation and an elimination of interocular suppression, we identified a novel method to effectively reflect the distribution of suppression in anisometropic amblyopia. Additionally, the new quantitative mapping technique was in good agreement with conventional clinical measures, such as interocular acuity difference (P < 0.001) and stereo acuity (P = 0.005). There was a good consistency between the results of interocular suppression with dichoptic mapping paradigm and the results of the other two psychophysical methods (suppression mapping versus binocular phase combination, P < 0.001; suppression mapping versus global motion coherence, P = 0.005). The dichoptic suppression mapping technique is an effective method to represent impaired visual function in patients with anisometropic amblyopia. It offers a potential in "micro-"antisuppression mapping tests and therapies for amblyopia.

The use of additive ceramic hollow spheres on cement slurry to prevent lost circulation in formation `X' having low pressure fracture

NASA Astrophysics Data System (ADS)

Rita, Novia; Mursyidah, Syahindra, Michael

2018-03-01

When drilling, if the hydrostatic pressure is higher than formation pressure (fracture pressure) it will cause lost circulation during cementing process. To solve this problem, hydrostatic pressure of slurry can be decreased by lowering the slurry density by using some additives. Ceramic Hollow Spheres (CHS) is lightweight additive. This additive comes with low specific gravity so it can lowered the slurry density. When the low-density slurry used in cementing process, it can prevent low circulation and fractured formation caused by cement itself. Class G cement is used in this experiment with the standard density of this slurry is 15.8 ppg. With the addition of CHS, slurry density lowered to 12.5 ppg. CHS not only used to lower the slurry density, it also used to make the same properties with the standard slurry even the density has been lowered. Both thickening time and compressive strength have not change if the CHS added to the slurry. With addition of CHS, thickening time at 70 Bc reached in 03 hours 12 minutes. For the compressive strength, 2000 psi reached in 07 hours 07 minutes. Addition of CHS can save more time in cementing process of X formation.

Large Deviations in Weakly Interacting Boundary Driven Lattice Gases

NASA Astrophysics Data System (ADS)

van Wijland, Frédéric; Rácz, Zoltán

2005-01-01

One-dimensional, boundary-driven lattice gases with local interactions are studied in the weakly interacting limit. The density profiles and the correlation functions are calculated to first order in the interaction strength for zero-range and short-range processes differing only in the specifics of the detailed-balance dynamics. Furthermore, the effective free-energy (large-deviation function) and the integrated current distribution are also found to this order. From the former, we find that the boundary drive generates long-range correlations only for the short-range dynamics while the latter provides support to an additivity principle recently proposed by Bodineau and Derrida.

Functional DNA-Containing Nanomaterials: Cellular Applications in Biosensing, Imaging, and Targeted Therapy

PubMed Central

2015-01-01

Conspectus DNA performs a vital function as a carrier of genetic code, but in the field of nanotechnology, DNA molecules can catalyze chemical reactions in the cell, that is, DNAzymes, or bind with target-specific ligands, that is, aptamers. These functional DNAs with different modifications have been developed for sensing, imaging, and therapeutic systems. Thus, functional DNAs hold great promise for future applications in nanotechnology and bioanalysis. However, these functional DNAs face challenges, especially in the field of biomedicine. For example, functional DNAs typically require the use of cationic transfection reagents to realize cellular uptake. Such reagents enter the cells, increasing the difficulty of performing bioassays in vivo and potentially damaging the cell’s nucleus. To address this obstacle, nanomaterials, such as metallic, carbon, silica, or magnetic materials, have been utilized as DNA carriers or assistants. In this Account, we describe selected examples of functional DNA-containing nanomaterials and their applications from our recent research and those of others. As models, we have chosen to highlight DNA/nanomaterial complexes consisting of gold nanoparticles, graphene oxides, and aptamer–micelles, and we illustrate the potential of such complexes in biosensing, imaging, and medical diagnostics. Under proper conditions, multiple ligand–receptor interactions, decreased steric hindrance, and increased surface roughness can be achieved from a high density of DNA that is bound to the surface of nanomaterials, resulting in a higher affinity for complementary DNA and other targets. In addition, this high density of DNA causes a high local salt concentration and negative charge density, which can prevent DNA degradation. For example, DNAzymes assembled on gold nanoparticles can effectively catalyze chemical reactions even in living cells. And it has been confirmed that DNA–nanomaterial complexes can enter cells more easily than free single-stranded DNA. Nanomaterials can be designed and synthesized in needed sizes and shapes, and they possess unique chemical and physical properties, which make them useful as DNA carriers or assistants, excellent signal reporters, transducers, and amplifiers. When nanomaterials are combined with functional DNAs to create novel assay platforms, highly sensitive biosensing and high-resolution imaging result. For example, gold nanoparticles and graphene oxides can quench fluorescence efficiently to achieve low background and effectively increase the signal-to-background ratio. Meanwhile, gold nanoparticles themselves can be colorimetric reporters because of their different optical absorptions between monodispersion and aggregation. DNA self-assembled nanomaterials contain several properties of both DNA and nanomaterials. Compared with DNA–nanomaterial complexes, DNA self-assembled nanomaterials more closely resemble living beings, and therefore they have lower cytotoxicity at high concentrations. Functional DNA self-assemblies also have high density of DNA for multivalent reaction and three-dimensional nanostructures for cell uptake. Now and in the future, we envision the use of DNA bases in making designer molecules for many challenging applications confronting chemists. With the further development of artificial DNA bases using smart organic synthesis, DNA macromolecules based on elegant molecular assembly approaches are expected to achieve great diversity, additional versatility, and advanced functions. PMID:24780000

Functional DNA-containing nanomaterials: cellular applications in biosensing, imaging, and targeted therapy.

PubMed

Liang, Hao; Zhang, Xiao-Bing; Lv, Yifan; Gong, Liang; Wang, Ruowen; Zhu, Xiaoyan; Yang, Ronghua; Tan, Weihong

2014-06-17

CONSPECTUS: DNA performs a vital function as a carrier of genetic code, but in the field of nanotechnology, DNA molecules can catalyze chemical reactions in the cell, that is, DNAzymes, or bind with target-specific ligands, that is, aptamers. These functional DNAs with different modifications have been developed for sensing, imaging, and therapeutic systems. Thus, functional DNAs hold great promise for future applications in nanotechnology and bioanalysis. However, these functional DNAs face challenges, especially in the field of biomedicine. For example, functional DNAs typically require the use of cationic transfection reagents to realize cellular uptake. Such reagents enter the cells, increasing the difficulty of performing bioassays in vivo and potentially damaging the cell's nucleus. To address this obstacle, nanomaterials, such as metallic, carbon, silica, or magnetic materials, have been utilized as DNA carriers or assistants. In this Account, we describe selected examples of functional DNA-containing nanomaterials and their applications from our recent research and those of others. As models, we have chosen to highlight DNA/nanomaterial complexes consisting of gold nanoparticles, graphene oxides, and aptamer-micelles, and we illustrate the potential of such complexes in biosensing, imaging, and medical diagnostics. Under proper conditions, multiple ligand-receptor interactions, decreased steric hindrance, and increased surface roughness can be achieved from a high density of DNA that is bound to the surface of nanomaterials, resulting in a higher affinity for complementary DNA and other targets. In addition, this high density of DNA causes a high local salt concentration and negative charge density, which can prevent DNA degradation. For example, DNAzymes assembled on gold nanoparticles can effectively catalyze chemical reactions even in living cells. And it has been confirmed that DNA-nanomaterial complexes can enter cells more easily than free single-stranded DNA. Nanomaterials can be designed and synthesized in needed sizes and shapes, and they possess unique chemical and physical properties, which make them useful as DNA carriers or assistants, excellent signal reporters, transducers, and amplifiers. When nanomaterials are combined with functional DNAs to create novel assay platforms, highly sensitive biosensing and high-resolution imaging result. For example, gold nanoparticles and graphene oxides can quench fluorescence efficiently to achieve low background and effectively increase the signal-to-background ratio. Meanwhile, gold nanoparticles themselves can be colorimetric reporters because of their different optical absorptions between monodispersion and aggregation. DNA self-assembled nanomaterials contain several properties of both DNA and nanomaterials. Compared with DNA-nanomaterial complexes, DNA self-assembled nanomaterials more closely resemble living beings, and therefore they have lower cytotoxicity at high concentrations. Functional DNA self-assemblies also have high density of DNA for multivalent reaction and three-dimensional nanostructures for cell uptake. Now and in the future, we envision the use of DNA bases in making designer molecules for many challenging applications confronting chemists. With the further development of artificial DNA bases using smart organic synthesis, DNA macromolecules based on elegant molecular assembly approaches are expected to achieve great diversity, additional versatility, and advanced functions.

Fluids Density Functional Theory of Salt-Doped Block Copolymers

NASA Astrophysics Data System (ADS)

Brown, Jonathan R.; Hall, Lisa M.

Block copolymers have attracted a great deal of recent interest as potential non-flammable, solid-state, electrolyte materials for batteries or other charge carrying applications. The microphase separation in block copolymers combines the properties of a conductive (though mechanically soft) polymer with a mechanically robust (though non-conductive) polymer. We use fluids density functional theory (fDFT) to study the phase behavior of salt-doped block copolymers. Because the salt prefers to preferentially solvate into the conductive phase, salt doping effectively enhances the segregation strength between the two polymer types. We consider the effects of this preferential solvation and of charge correlations by separately modeling the ion-rich phase, without bonding, using the Ornstein-Zernike equation and the hypernetted-chain closure. We use the correlations from this subsystem in the inhomogeneous fDFT calculations. Initial addition of salt increases the domain spacing and sharpens the interfacial region, but for high salt loadings the interface can broaden. Addition of salt can also drive a system with a low copolymer segregation strength to order by first passing through a two phase regime with a salt-rich ordered phase and a salt-poor disordered phase. This material is based upon work supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Award Number DE-SC0014209.

A novel model for through-silicon via (TSV) filling process simulation considering three additives and current density effect

NASA Astrophysics Data System (ADS)

Wang, Fuliang; Zhao, Zhipeng; Wang, Feng; Wang, Yan; Nie, Nantian

2017-12-01

Through-silicon via (TSV) filling by electrochemical deposition is still a challenge for 3D IC packaging, and three-component additive systems (accelerator, suppressor, and leveler) were commonly used in the industry to achieve void-free filling. However, models considering three additive systems and the current density effect have not been fully studied. In this paper, a novel three-component model was developed to study the TSV filling mechanism and process, where the interaction behavior of the three additives (accelerator, suppressor, and leveler) were considered, and the adsorption, desorption, and consumption coefficient of the three additives were changed with the current density. Based on this new model, the three filling types (seam void, ‘V’ shape, and key hole) were simulated under different current density conditions, and the filling results were verified by experiments. The effect of the current density on the copper ion concentration, additives surface coverage, and local current density distribution during the TSV filling process were obtained. Based on the simulation and experimental results, the diffusion-adsorption-desorption-consumption competition behavior between the suppressor, the accelerator, and the leveler were discussed. The filling mechanisms under different current densities were also analyzed.

Adaptive focus for deep tissue using diffuse backscatter

NASA Astrophysics Data System (ADS)

Kress, Jeremy; Pourrezaei, Kambiz

2014-02-01

A system integrating high density diffuse optical imaging with adaptive optics using MEMS for deep tissue interaction is presented. In this system, a laser source is scanned over a high density fiber bundle using Digital Micromirror Device (DMD) and channeled to a tissue phantom. Backscatter is then collected from the tissue phantom by a high density fiber array of different fiber type and channeled to CMOS sensor for image acquisition. Intensity focus is directly verified using a second CMOS sensor which measures intensity transmitted though the tissue phantom. A set of training patterns are displayed on the DMD and backscatter is numerically fit to the transmission intensity. After the training patterns are displayed, adaptive focus is performed using only the backscatter and fitting functions. Additionally, tissue reconstruction and prediction of interference focusing by photoacoustic and optical tomographic methods is discussed. Finally, potential NIR applications such as in-vivo adaptive neural photostimulation and cancer targeting are discussed.

Electrochemical Supercapacitor Electrodes from Sponge-like Graphene Nanoarchitectures with Ultrahigh Power Density.

PubMed

Xu, Zhanwei; Li, Zhi; Holt, Chris M B; Tan, Xuehai; Wang, Huanlei; Amirkhiz, Babak Shalchi; Stephenson, Tyler; Mitlin, David

2012-10-18

We employed a microwave synthesis process of cobalt phthalocyanine molecules templated by acid-functionalized multiwalled carbon nanotubes to create three-dimensional sponge-like graphene nanoarchitectures suited for ionic liquid-based electrochemical capacitor electrodes that operate at very high scan rates. The sequential "bottom-up" molecular synthesis and subsequent carbonization process took less than 20 min to complete. The 3D nanoarchitectures are able to deliver an energy density of 7.1 W·h kg(-1) even at an extra high power density of 48 000 W kg(-1). In addition, the ionic liquid supercapacitor based on this material works very well at room temperature due to its fully opened structures, which is ideal for the high-power energy application requiring more tolerance to temperature variation. Moreover, the structures are stable in both ionic liquids and 1 M H2SO4, retaining 90 and 98% capacitance after 10 000 cycles, respectively.

A Density Functional Theory Study of New Boron Nanotubes

NASA Astrophysics Data System (ADS)

Chen, Zhao-Hua; Xie, Zun

2017-11-01

Using first-principles calculations, a series of new boron nanotubes (BNTs), which show various electronic properties, were theoretically predicted. Stable nanotubes with various chiral vectors and diameters can be formed by rolling up the boron sheet with relative stability [H. Tang and S. I. Beigi, Phys. Rev. B 82, 115412 (2010).]. By increasing the diameter for BNT, the stability is enhanced. The calculated density of states and band structures demonstrate that all the predicted BNTs are metallic, regardless of their diameter and chirality. The multicentre chemical bonds of the relatively stable boron sheet and BNTs are analysed using the deformation electron density. Within our study, the BNTs all have metallic conductive characteristics, in addition to having a low effective quality and high carrier concentration, which are very good nanoconductive material properties and could be combined to form high-power electrodes for lithium-ion batteries such as those used in many modern electronics.

Potassium-intercalated H2Pc films: Alkali-induced electronic and geometrical modifications

NASA Astrophysics Data System (ADS)

Nilson, K.; Åhlund, J.; Shariati, M.-N.; Schiessling, J.; Palmgren, P.; Brena, B.; Göthelid, E.; Hennies, F.; Huismans, Y.; Evangelista, F.; Rudolf, P.; Göthelid, M.; Mârtensson, N.; Puglia, C.

2012-07-01

X-ray spectroscopy studies of potassium intercalated metal-free phthalocyanine multilayers adsorbed on Al(110) have been undertaken. Photoelectron spectroscopy measurements show the presence of several charge states of the molecules upon K intercalation, due to a charge transfer from the alkali. In addition, the comparison of valence band photoemission spectra with the density functional theory calculations of the density of states of the H2Pc- anion indicates a filling of the formerly lowest unoccupied molecular orbital by charge transfer from the alkali. This is further confirmed by x-ray absorption spectroscopy (XAS) studies, which show a decreased density of unoccupied states. XAS measurements in different experimental geometries reveal that the molecules in the pristine film are standing upright on the surface or are only slightly tilted away from the surface normal but upon K intercalation, the molecular orientation is changed in that the tilt angle of the molecules increases.

Electronic entanglement in late transition metal oxides.

PubMed

Thunström, Patrik; Di Marco, Igor; Eriksson, Olle

2012-11-02

We present a study of the entanglement in the electronic structure of the late transition metal monoxides--MnO, FeO, CoO, and NiO--obtained by means of density-functional theory in the local density approximation combined with dynamical mean-field theory. The impurity problem is solved through exact diagonalization, which grants full access to the thermally mixed many-body ground state density operator. The quality of the electronic structure is affirmed through a direct comparison between the calculated electronic excitation spectrum and photoemission experiments. Our treatment allows for a quantitative investigation of the entanglement in the electronic structure. Two main sources of entanglement are explicitly resolved through the use of a fidelity based geometrical entanglement measure, and additional information is gained from a complementary entropic entanglement measure. We show that the interplay of crystal field effects and Coulomb interaction causes the entanglement in CoO to take a particularly intricate form.

First-principles investigations on structural, elastic, electronic properties and Debye temperature of orthorhombic Ni3Ta under pressure

NASA Astrophysics Data System (ADS)

Li, Pan; Zhang, Jianxin; Ma, Shiyu; Jin, Huixin; Zhang, Youjian; Zhang, Wenyang

2018-06-01

The structural, elastic, electronic properties and Debye temperature of Ni3Ta under different pressures are investigated using the first-principles method based on density functional theory. Our calculated equilibrium lattice parameters at 0 GPa well agree with the experimental and previous theoretical results. The calculated negative formation enthalpies and elastic constants both indicate that Ni3Ta is stable under different pressures. The bulk modulus B, shear modulus G, Young's modulus E and Poisson's ratio ν are calculated by the Voigt-Reuss-Hill method. The bigger ratio of B/G indicates Ni3Ta is ductile and the pressure can improve the ductility of Ni3Ta. In addition, the results of density of states and the charge density difference show that the stability of Ni3Ta is improved by the increasing pressure. The Debye temperature ΘD calculated from elastic modulus increases along with the pressure.

Locality of correlation in density functional theory.

PubMed

Burke, Kieron; Cancio, Antonio; Gould, Tim; Pittalis, Stefano

2016-08-07

The Hohenberg-Kohn density functional was long ago shown to reduce to the Thomas-Fermi (TF) approximation in the non-relativistic semiclassical (or large-Z) limit for all matter, i.e., the kinetic energy becomes local. Exchange also becomes local in this limit. Numerical data on the correlation energy of atoms support the conjecture that this is also true for correlation, but much less relevant to atoms. We illustrate how expansions around a large particle number are equivalent to local density approximations and their strong relevance to density functional approximations. Analyzing highly accurate atomic correlation energies, we show that EC → -AC ZlnZ + BCZ as Z → ∞, where Z is the atomic number, AC is known, and we estimate BC to be about 37 mhartree. The local density approximation yields AC exactly, but a very incorrect value for BC, showing that the local approximation is less relevant for the correlation alone. This limit is a benchmark for the non-empirical construction of density functional approximations. We conjecture that, beyond atoms, the leading correction to the local density approximation in the large-Z limit generally takes this form, but with BC a functional of the TF density for the system. The implications for the construction of approximate density functionals are discussed.

LINER galaxy properties and the local environment

NASA Astrophysics Data System (ADS)

Coldwell, Georgina V.; Alonso, Sol; Duplancic, Fernanda; Mesa, Valeria

2018-05-01

We analyse the properties of a sample of 5560 low-ionization nuclear emission-line region (LINER) galaxies selected from SDSS-DR12 at low red shift, for a complete range of local density environments. The host LINER galaxies were studied and compared with a well-defined control sample of 5553 non-LINER galaxies matched in red shift, luminosity, morphology and local density. By studying the distributions of galaxy colours and the stellar age population, we find that LINERs are redder and older than the control sample over a wide range of densities. In addition, LINERs are older than the control sample, at a given galaxy colour, indicating that some external process could have accelerated the evolution of the stellar population. The analysis of the host properties shows that the control sample exhibits a strong relation between colours, ages and the local density, while more than 90 per cent of the LINERs are redder and older than the mean values, independently of the neighbourhood density. Furthermore, a detailed study in three local density ranges shows that, while control sample galaxies are redder and older as a function of stellar mass and density, LINER galaxies mismatch the known morphology-density relation of galaxies without low-ionization features. The results support the contribution of hot and old stars to the low-ionization emission although the contribution of nuclear activity is not discarded.

Hybrid density functional study of bandgaps for 27 new proposed half-Heusler semiconductors

NASA Astrophysics Data System (ADS)

Shi, Fangyi; Si, M. S.; Xie, Jiafeng; Mi, Kui; Xiao, Chuntao; Luo, Qiangjun

2017-12-01

Recently, 27 new half-Heusler compounds XYZ (X = Co, Rh, Fe, Ru, Ni; Y = Sc, Ti, V; Z = P, As, Sb, Si, Ge, Sn, Al, Ga, In) with 18 valence electrons are proposed and their bandgaps span a wide range of 0.10-1.39 eV, which have a great potential of applications in varied areas. Note that the bandgaps are predicted on the gradient-corrected Perdew-Burke-Ernzerhof functional, which underestimates the magnitude of bandgap. To obtain the accurate bandgaps, we recalculate them based on the Heyd-Scuseria-Ernzerhof (HSE06) hybrid functional. Our results show that the nonlocal correction from the HSE06 functional mainly acts on the two lowest conduction bands. The variation in energy separation between these two bands dominates the relative increment of bandgap. More importantly, the band ordering is distinguished in the presence of HSE06 functional, where the dz2 orbital exhibits. When the lattice constant varies, such a band ordering can be inverted, similar to the case of topological insulators. In addition, we find an abnormal behavior of the bandgap related to the Pauling electronegativity difference between the X- and Z-sites, which arises from the delocalization of charge on the Y-site. We expect that our work can provide guidance to the study of bandgap based on the hybrid density functional theory in the half-Heusler semiconductors.

Aging and functional brain networks

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

Tomasi D.; Tomasi, D.; Volkow, N.D.

2011-07-11

Aging is associated with changes in human brain anatomy and function and cognitive decline. Recent studies suggest the aging decline of major functional connectivity hubs in the 'default-mode' network (DMN). Aging effects on other networks, however, are largely unknown. We hypothesized that aging would be associated with a decline of short- and long-range functional connectivity density (FCD) hubs in the DMN. To test this hypothesis, we evaluated resting-state data sets corresponding to 913 healthy subjects from a public magnetic resonance imaging database using functional connectivity density mapping (FCDM), a voxelwise and data-driven approach, together with parallel computing. Aging was associatedmore » with pronounced long-range FCD decreases in DMN and dorsal attention network (DAN) and with increases in somatosensory and subcortical networks. Aging effects in these networks were stronger for long-range than for short-range FCD and were also detected at the level of the main functional hubs. Females had higher short- and long-range FCD in DMN and lower FCD in the somatosensory network than males, but the gender by age interaction effects were not significant for any of the networks or hubs. These findings suggest that long-range connections may be more vulnerable to aging effects than short-range connections and that, in addition to the DMN, the DAN is also sensitive to aging effects, which could underlie the deterioration of attention processes that occurs with aging.« less

Phosphorus allotropes: Stability of black versus red phosphorus re-examined by means of the van der Waals inclusive density functional method

NASA Astrophysics Data System (ADS)

Aykol, Muratahan; Doak, Jeff W.; Wolverton, C.

2017-06-01

We evaluate the energetic stabilities of white, red, and black allotropes of phosphorus using density functional theory (DFT) and hybrid functional methods, van der Waals (vdW) corrections (DFT+vdW and hybrid+vdW), vdW density functionals, and random phase approximation (RPA). We find that stability of black phosphorus over red-V (i.e., the violet form) is not ubiquitous among these methods, and the calculated enthalpies for the reaction phosphorus (red-V)→phosphorus (black) are scattered between -20 and 40 meV/atom. With local density and generalized gradient approximations, and hybrid functionals, mean absolute errors (MAEs) in densities of P allotropes relative to experiments are found to be around 10%-25%, whereas with vdW-inclusive methods, MAEs in densities drop below ˜5 %. While the inconsistency among the density functional methods could not shed light on the stability puzzle of black versus red phosphorus, comparison of their accuracy in predicting densities and the supplementary RPA results on relative stabilities indicate that opposite to the common belief, black and red phosphorus are almost degenerate, or the red-V (violet) form of phosphorus might even be the ground state.

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