density functional vdw-df: Topics by Science.gov

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Signatures of van der Waals binding: A coupling-constant scaling analysis

NASA Astrophysics Data System (ADS)

Jiao, Yang; Schröder, Elsebeth; Hyldgaard, Per

2018-02-01

The van der Waals (vdW) density functional (vdW-DF) method [Rep. Prog. Phys. 78, 066501 (2015), 10.1088/0034-4885/78/6/066501] describes dispersion or vdW binding by tracking the effects of an electrodynamic coupling among pairs of electrons and their associated exchange-correlation holes. This is done in a nonlocal-correlation energy term Ecnl, which permits density functional theory calculation in the Kohn-Sham scheme. However, to map the nature of vdW forces in a fully interacting materials system, it is necessary to also account for associated kinetic-correlation energy effects. Here, we present a coupling-constant scaling analysis, which permits us to compute the kinetic-correlation energy Tcnl that is specific to the vdW-DF account of nonlocal correlations. We thus provide a more complete spatially resolved analysis of the electrodynamical-coupling nature of nonlocal-correlation binding, including vdW attraction, in both covalently and noncovalently bonded systems. We find that kinetic-correlation energy effects play a significant role in the account of vdW or dispersion interactions among molecules. Furthermore, our mapping shows that the total nonlocal-correlation binding is concentrated to pockets in the sparse electron distribution located between the material fragments.
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.
Ab-initio study of structural and electronic properties of WS2/h-BN van der Waals heterostructure

NASA Astrophysics Data System (ADS)

Ghasemi majd, Zahra; Amiri, Peiman; Taghizadeh, Seyed Fardin

2018-06-01

First-principle calculations with different exchange-correlation functionals, including LDA, GGA, semi-empirical and ab-initio van der Waals in the forms of vdW-DF2B86R and vdW-DF2 were performed to evaluate the performance of different functionals in describing the bonding mechanism, adsorption energy and interlayer distance of WS2 monolayer on and between h-BN layers. The finding was that the vdW-DF2B86R seems to be the approach best lending itself to this purpose. In order to include the van der Waals (vdW) interactions in our calculations, we used the DFT-D2 and vdW methods, which gave rise to a physical adsorption with no net charge transfer between the WS2 layer and the corresponding substrates. In addition, we investigated the electronic and structural properties of WS2 and h-BN heterolayers, using vdW-DF2B86R functional. Based on density functional theory calculations, WS2 on and between h-BN layers showed a direct band gap at the K-point, which was experimentally observed.
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
Dispersion interactions in Density Functional Theory

NASA Astrophysics Data System (ADS)

Andrinopoulos, Lampros; Hine, Nicholas; Mostofi, Arash

2012-02-01

Semilocal functionals in Density Functional Theory (DFT) achieve high accuracy simulating a wide range of systems, but miss the effect of dispersion (vdW) interactions, important in weakly bound systems. We study two different methods to include vdW in DFT: First, we investigate a recent approach [1] to evaluate the vdW contribution to the total energy using maximally-localized Wannier functions. Using a set of simple dimers, we show that it has a number of shortcomings that hamper its predictive power; we then develop and implement a series of improvements [2] and obtain binding energies and equilibrium geometries in closer agreement to quantum-chemical coupled-cluster calculations. Second, we implement the vdW-DF functional [3], using Soler's method [4], within ONETEP [5], a linear-scaling DFT code, and apply it to a range of systems. This method within a linear-scaling DFT code allows the simulation of weakly bound systems of larger scale, such as organic/inorganic interfaces, biological systems and implicit solvation models. [1] P. Silvestrelli, JPC A 113, 5224 (2009). [2] L. Andrinopoulos et al, JCP 135, 154105 (2011). [3] M. Dion et al, PRL 92, 246401 (2004). [4] G. Rom'an-P'erez, J.M. Soler, PRL 103, 096102 (2009). [5] C. Skylaris et al, JCP 122, 084119 (2005).
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.
Origin of the size-dependence of the equilibrium van der Waals binding between nanostructures

NASA Astrophysics Data System (ADS)

Tao, Jianmin; Perdew, John P.; Tang, Hong; Shahi, Chandra

2018-02-01

Nanostructures can be bound together at equilibrium by the van der Waals (vdW) effect, a small but ubiquitous many-body attraction that presents challenges to density functional theory. How does the binding energy depend upon the size or number of atoms in one of a pair of identical nanostructures? To answer this question, we treat each nanostructure as a whole object, not as a collection of atoms. Our calculations start from an accurate static dipole polarizability for each considered nanostructure, and an accurate equilibrium center-to-center distance for the pair (the latter from experiment or from the vdW-DF-cx functional). We consider the competition in each term -C2k/d2k (k = 3, 4, 5) of the long-range vdW series for the interaction energy, between the size dependence of the vdW coefficient C2k and that of the 2kth power of the center-to-center distance d. The damping of these vdW terms can be negligible, but in any case, it does not affect the size dependence for a given term in the absence of non-vdW binding. To our surprise, the vdW energy can be size-independent for quasi-spherical nanoclusters bound to one another by vdW interaction, even with strong nonadditivity of the vdW coefficient, as demonstrated for fullerenes. We also show that, for low-dimensional systems, the vdW interaction yields the strongest size-dependence, in stark contrast to that of fullerenes. We illustrate this with parallel planar polycyclic aromatic hydrocarbons. The size dependences of other morphologies or bonding types lie between, as shown by sodium clusters.
Origin of the size-dependence of the equilibrium van der Waals binding between nanostructures

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

Tao, Jianmin

Nanostructures can be bound together at equilibrium by the van der Waals (vdW) effect, a small but ubiquitous many-body attraction that presents challenges to density functional theory. How does the binding energy depend upon the size or number of atoms in one of a pair of identical nanostructures? To answer this question, we treat each nanostructure properly as a whole object, not as a collection of atoms. Our calculations start from an accurate static dipole polarizability for each considered nanostructure, and an accurate equilibrium center-to-center distance for the pair (the latter from experiment, or from the vdW-DF-cx functional). We consider the competition in each termmore » $$-C_{2k}/d^{2k}$$ ($k=3, 4, 5$) of the long-range vdW series for the interaction energy, between the size dependence of the vdW coefficient $$C_{2k}$$ and that of the $2k$-th power of the center-to-center distance $d$. The damping of these vdW terms can be negligible, but in any case it does not affect the size dependence for a given term in the absence of non-vdW binding. To our surprise, the vdW energy can be size-independent for quasi-spherical nanoclusters bound to one another by vdW interaction, even with strong nonadditivity of the vdW coefficient, as demonstrated for fullerenes. We also show that, for low-dimensional systems, the vdW interaction yields the strongest size-dependence, in stark contrast to that of fullerenes. We illustrate this with parallel planar polycyclic aromatic hydrocarbons. Other cases are between, as shown by sodium clusters.« less
Origin of the size-dependence of the equilibrium van der Waals binding between nanostructures

DOE PAGES

Tao, Jianmin

2018-02-21

Nanostructures can be bound together at equilibrium by the van der Waals (vdW) effect, a small but ubiquitous many-body attraction that presents challenges to density functional theory. How does the binding energy depend upon the size or number of atoms in one of a pair of identical nanostructures? To answer this question, we treat each nanostructure properly as a whole object, not as a collection of atoms. Our calculations start from an accurate static dipole polarizability for each considered nanostructure, and an accurate equilibrium center-to-center distance for the pair (the latter from experiment, or from the vdW-DF-cx functional). We consider the competition in each termmore » $$-C_{2k}/d^{2k}$$ ($k=3, 4, 5$) of the long-range vdW series for the interaction energy, between the size dependence of the vdW coefficient $$C_{2k}$$ and that of the $2k$-th power of the center-to-center distance $d$. The damping of these vdW terms can be negligible, but in any case it does not affect the size dependence for a given term in the absence of non-vdW binding. To our surprise, the vdW energy can be size-independent for quasi-spherical nanoclusters bound to one another by vdW interaction, even with strong nonadditivity of the vdW coefficient, as demonstrated for fullerenes. We also show that, for low-dimensional systems, the vdW interaction yields the strongest size-dependence, in stark contrast to that of fullerenes. We illustrate this with parallel planar polycyclic aromatic hydrocarbons. Other cases are between, as shown by sodium clusters.« less
Van der Waals Interactions of Organic Molecules on Semiconductor and Metal Surfaces: a Comparative Study

NASA Astrophysics Data System (ADS)

Li, Guo; Cooper, Valentino; Cho, Jun-Hyung; Tamblyn, Isaac; Du, Shixuan; Neaton, Jeffrey; Gao, Hong-Jun; Zhang, Zhenyu

2012-02-01

We present a comparative investigation of vdW interactions of the organic molecules on semiconductor and metal surfaces using the DFT method implemented with vdW-DF. For styrene/H-Si(100), the vdW interactions reverse the effective intermolecular interaction from repulsive to attractive, ensuring preferred growth of long wires as observed experimentally. We further propose that an external E field and the selective creation of Si dangling bonds can drastically improve the ordered arrangement of the molecular nanowires [1]. For BDA/Au(111), the vdW interactions not only dramatically enhances the adsorption energies, but also significantly changes the molecular configurations. In the azobenzene/Ag(111) system, vdW-DF produces superior predictions for the adsorption energy than those obtained with other vdW corrected DFT approaches, providing evidence for the applicability of the vdW-DF method [2].
Including screening in van der Waals corrected density functional theory calculations: the case of atoms and small molecules physisorbed on graphene.

PubMed

Silvestrelli, Pier Luigi; Ambrosetti, Alberto

2014-03-28

The Density Functional Theory (DFT)/van der Waals-Quantum Harmonic Oscillator-Wannier function (vdW-QHO-WF) method, recently developed to include the vdW interactions in approximated DFT by combining the quantum harmonic oscillator model with the maximally localized Wannier function technique, is applied to the cases of atoms and small molecules (X=Ar, CO, H2, H2O) weakly interacting with benzene and with the ideal planar graphene surface. Comparison is also presented with the results obtained by other DFT vdW-corrected schemes, including PBE+D, vdW-DF, vdW-DF2, rVV10, and by the simpler Local Density Approximation (LDA) and semilocal generalized gradient approximation approaches. While for the X-benzene systems all the considered vdW-corrected schemes perform reasonably well, it turns out that an accurate description of the X-graphene interaction requires a proper treatment of many-body contributions and of short-range screening effects, as demonstrated by adopting an improved version of the DFT/vdW-QHO-WF method. We also comment on the widespread attitude of relying on LDA to get a rough description of weakly interacting systems.
EDITORIAL: Van der Waals interactions in advanced materials, in memory of David C Langreth Van der Waals interactions in advanced materials, in memory of David C Langreth

NASA Astrophysics Data System (ADS)

Hyldgaard, Per; Rahman, Talat S.

2012-10-01

The past decade has seen a dramatic rise in interest in exploring the role that van der Waals (vdW) or dispersion forces play in materials and in material behavior. Part of this stems from the obvious fact that vdW interactions (and other weak forces, such as Casimir) underpin molecular recognition, i.e., nature's approach to search for a match between genes and anti-genes and hence enable biological function. Less obvious is the recognition that vdW interactions affect a multitude of properties of a vast variety of materials in general, some of which also have strong technological applications. While for two atom- or orbital-sized material fragments the dispersive contributions to binding are small compared to those from the better known forms (ionic, covalent, metallic), those between sparse materials (spread over extended areas) can be of paramount importance. For example, an understanding of binding in graphite cannot arise solely from a study of the graphene layers individually, but also requires insight from inter-sheet graphene vdW bonding. It is the extended-area vdW bonding that provides sufficient cohesion to make graphite a robust, naturally occurring material. In fact, it is the vdW-bonded graphite, and not the all-covalently bonded diamond, that is the preferred form of pure carbon under ambient conditions. Also important is the understanding that vdW attraction can attain a dramatic relevance even if the material fragments, the building blocks, are not necessarily parallel from the outset or smooth when viewed in isolation (such as a graphene sheet or a carbon nanotube). This can happen if the building blocks have some softness and flexibility and allow an internal relative alignment to emerge. The vdW forces can then cause increasingly larger parts of the interacting fragments to line up at sub-nanometer separations and thus beget more areas with a sizable vdW bonding contribution. The gecko can scale a wall because it can bring its flexible hairs sufficiently close to any corrugated—and/or any smooth—surface and thus enforce a strong vdW-type adhesion; it exploits what is then essentially a contact force (dominated by the attraction exerted in the near-surface regions) to defy the pull of gravity on its own bulk. This Journal of Physics: Condensed Matter special issue is dedicated to the memory of David C Langreth. David is a dearly missed friend and mentor who inspired many of us. He was an outstanding condensed matter theorist and a scholar who greatly influenced us through his many-particle-physics based insights into density functional theory (DFT), surface science and related areas. His seminal works range from conserving formulations of interacting nonequilibrium transport [1] and formal-scattering theory [2] to an explicit formulation [3] of the exact DFT exchange-correlation energy in the adiabatic connection formula (ACF), the latter also being derived independently by Gunnarsson and Lundqvist [4]. David's portfolio also includes an analysis [5] that helped catalyze and guide the development of DFT from the local-density approximation (LDA) to the formulations of generalized gradient approximations (GGAs). Another salient contribution of David's is in the area of vdW interactions in materials. He was a key architect of the vdW density functional (vdW-DF) method [6, 7]. This method was developed in a long-standing Rutgers-Chalmers collaboration between David's group and that of Bengt I Lundqvist, later extending to a wider group of researchers on both sides of the Atlantic. Plasmons are collective excitations that depend on electron-density variation. The plasmon response can be seen as defining the nature of the LDA [4] and their description can thus also be seen as contributing to the success of GGA. The vdW-DF method is a regular constraint-based density functional (for ground-state DFT) which is derived within the ACF framework and which emphasizes the electrodynamical nature of the coupling between these collective plasmon excitations. The vdW-DF method thus seeks to utilise the implicit plasmon nature of the LDA/GGA success to also provide a nonempirical account of the fully nonlocal correlations that underpin the vdW bond [8]. The method retains a seamless integration [6] with the semilocal density functional components. We know that David was pleased to see how this quantitative, material-specific theory helped address problems in a broad class of materials that are sparse, i.e., that contain low electron density regions which are of significant consequence in determining material characteristics [9]. In a DFT framework, the vdW-DF method supplements other nonlocal functional descriptions [10] and the DFT-dispersion class of methods, extending GGA-DFT with an atom-based asymptotic description which relies on the vdW interaction coefficients [11]. The recent quest to understand the role of vdW forces in materials has certainly been facilitated and intensified by the set of recent developments in DFT itself. This is because these vdW-aware methods provide an opportunity to deliver a computationally effective account of the quantum-physical behavior even when the materials are sparse. It is the expectation that with such new-found theoretical capability, one may further extend the immense progress already attained by traditional (GGA) DFT calculations in reliably predicting the characteristics of materials and phenomena in materials, nanoscience, chemistry and other related fields [12]. This special issue contains a wealth of exciting contributions, mostly on vdW forces in materials. The special issue was suggested following the well-attended first focused vdW and materials session arranged by the Division of Materials Physics (DMP) of the American Physical Society (APS) at the March Meeting in 2011. The sad and unexpected passing of David in the spring of 2011 caused some rethinking and at the memorial symposium, held by David's colleagues at Rutgers in November 2011, we proposed to dedicate this special issue to David's contributions to the field. We are delighted with the overwhelmingly positive reaction that we received in response to our call for papers. We are also delighted to now be able to bring so many exciting contributions to you. The papers included in this special issue focus, in general, either through experiments or through theoretical characterization, on material properties in which vdW forces represent a central component. These articles contain arguments for and against a broader usage of DFT with vdW to account for material description, as well as establishing benchmarks which measure progress in the field. This special issue also includes fundamental theoretical analysis and suggestions for sensitive experiments that can resolve outstanding issues underlying the nature and role of the interaction. We believe that these papers will help stimulate further material-theory developments and, even more importantly, more discussions and feedback between theory and experiment. Physisorption is important to enable lubrication. This is because physisorption keeps the lubricating molecules at the interface at which a pair of internal surfaces must be free to move relative to each other. In turn, physisorbed (or perhaps weakly chemisorbed) lubricants prevent, for example, the formation of stronger bonding that will impede mechanical operation. However, it is also important to further characterize the nature and dynamics of the vdW bonding of lubricants: while physisorption means a weak binding further from the surface, there are still important friction effects. Walker et al present an experimental study, along with theoretical analysis, that directly determines the frictional heating of a Kr overlayer on graphene through quartz crystal microbalance measurements. The properties of materials reflect their atomic structure and hence indirectly their bonding nature and character. We can explore the role of dispersion forces by examining the impact their inclusion has on predictions of material properties. On the other hand, the experimental and theoretical study of Casimir forces also plays a vital role in the exploration of material behavior. vdW forces are related to the Casimir force but lack retardation effects. While the vdW bonding depends on additional effects (for example, the multipole contributions that reflect image-plane effects), the study of Casimir forces provides direct (and not indirect) measurements of the nature of interactions. Klimchitskaya et al note that to reconcile explicit measurements of the Casmir forces between semiconductor fragments within the Lifshitz description, it is relevant to question the Drude-like description of the contributions from free carriers and instead proceed with a formulation based only on optical observations of the permittivity. This optical response can be seen as a reflection of a more plasmon-like behavior. The authors suggest an experiment involving the study of the impact on the Casimir forces by a Mott transition in doped semiconductors. Such an experiment would permit explicit testing of the validity of the present model for Casimir forces and hence provide additional perspectives on the nature of dispersive interactions. There is an effort to store energy, e.g. H2 or CO2, inside a range of open cage-like structures, such as metal organics frameworks (MOF) or clathrates. The fact that the internal molecular adhesion is dominated by vdW forces suggests that the storage and retrieval costs could perhaps be lowered as compared to an approach that involves more traditional chemical compounds. Nijem et al have provided spectroscopic characterization of vdW interactions of both hydrogen molecules and CO in a specific MOF. The study includes a vdW-DF calculation of structure and a theoretical prediction of expected infrared activity. The potential applications to energy materials have motivated more theoretical characterizations. Li and Thonhauser use the vdW-DF method to investigate the limitations and hydrogen storage potential of hydrogen-methane compounds in a MOF. Similarly, Ihm et al combine vdW-DF studies with a thermodynamics argument to characterize the potential for molecular hydrogen uptake in expanded graphite, for example, through intercalation. The relevance of vdW-aware DFT calculations and the usefulness of such methods reaches beyond the study of molecules, surfaces and adsorption/absorption problems. Moellmann et al present a dispersion-DFT study of TiO2 bulk and surfaces, which illustrates that vdW forces can also play a prominent role when comparing the energies of different oxide structures. Perdew et al present a spherical-shell model and a simplified classical electrodynamical determination of the vdW interaction coefficients that describes the asymptotic interaction between fullerenes or other nearly spherical nanoclusters. The overall modeling framework also permits a formal expression of multipole contributions. Dappe et al used a combination of DFT and second-order perturbation theory to analyze the interactions between graphene layers, thus also exploring the role of dynamical screening in the vdW binding. The work of Sabatini et al extends the vdW-DF description with accounts of the stress tensor, providing the method with the same versatility as one has grown to expect in traditional LDA/GGA-DFT calculations. The method is illustrated with investigations of amino acid crystals under various pressures. The vdW-DF method was originally perceived as computationally more expensive than other approaches. It has now benefited from the development of efficient algorithms so the computational cost is comparable to that of traditional GGA-DFT calculations. As is also the case for some of the dispersion-DFT methods, there is an overhead when these are implemented self-consistently. Noting that sparse-matter structure determination and relaxations may well employ a sequence of methods, Le et al have suggested a simplified (cost-free relative to GGA) formulation of self-consistent dispersion-DFT calculations that is cost-free in the evaluation of forces and yet adapts the atom-centered pair-wise interaction coefficients through the change in local electron distributions. There is a need for continued testing of accuracy in the description of material properties and of the robustness and transferability of predictions across systems and length scales. This need is widely appreciated and is also reflected in the fact that many of the contributions touch on, suggest, or pursue a systematic benchmarking. There is an interest in careful analysis of detailed experiments on the physisorption of inert atoms, light molecules and organic molecules on smooth surfaces. Chen et al investigated the role of vdW forces in noble gas adsorption on various metal surfaces. Londero et al analyzed a set of experimental results for the desorption of n-alkanes from graphene in a program that had undergraduate participation. Lee et al benchmarked the performance of the vdW-DF2 functional and other methods against the physisorption potential curve that can be established from a rich data set of resonant backscattering of hydrogen molecules on various facets of Cu crystals. A few of the investigations included here noted that the vdW-DF method permits a more detailed analysis of the nature of strong physisorption and/or weak chemisorption cases than do DFT-dispersion methods and discussed the ramifications of the fact that GGA-DFT often, and vdW-aware DFT sometimes, pose difficulties for systems with a partial vdW component in the binding. Caciuc et al thus present a combined ab initio and semi-empirical vdW study comparing benzene/triazine/broazine adsorption on graphene and on boron-nitride sheets. On a more strategic note, Lazic et al broadened the discussion of a graphene/Ir(111) system and used the documented limitation of a GGA description to discuss a rationale for considering a more general switch to nonlocal functionals. Graziano et al note that the accuracy in the description of some soft layered systems like graphene and boron-nitride can be increased by changing the exchange description away from what was suggested in the original vdW-DF method. Hanke et al focused on the weak chemisorption of ethene on the various Cu facets that have an increasing degree of openness and provide a method for benchmarking through comparison with experimental observations. Finally, Björkman et al raise the question 'Are we van der Waals ready?' and proceed to test our readiness by benchmarking the performance of a range of vdW-aware methods for the group of 96 known layered structures. We have also included in this special issue one study of nonequilibrium transport which is linked to David's work in formal scattering theory [1, 2] and which observes that vdW forces (and possible generalizations to nonequilibrium transport conditions) will be of central importance in a richer computational characterization of molecular electronics under operational conditions. David was always keen to spearhead the development of tools that improved descriptions of nature and addressed actual experiments. We know that he was happy that DMP started the focused session on vdW and materials in 2011. We know that he would have thoroughly appreciated the articles in this special issue. He would have hoped, as we do, that materials theory may continue to learn how to tackle even more exciting experimental problems and that we may continue to deepen our understanding of materials and their functionality. Bibliography [1]Langreth D C 1976 1975 Nato Advanced Study Institute on Linear and Nonlinear Transport in Solids, Antwerben vol B17 (New York: Plenum) pp 3-32 [2]Langreth D C 1966 Friedel sum rule for Anderson's model of localized impurity states Phys. Rev. 150 516 [3]Langreth D C and Perdew J P 1975 The exchange-correlation energy of a metallic surface Solid State Commun. 17 1425 [4]Gunnarsson O and Lundqvist B I 1976 Exchange and correlation in atoms, molecules, and solids by the spin-density-functional formalism Phys. Rev. B 13 4274 [5]Langreth D C and Mehl M J 1981 Beyond the local-density approximation in calculations of ground-state electronic properties Phys. Rev. B 47 446 [6]Dion M, Rydberg H, Schröder E, Langreth D C and Lundqvist B I 2004 Van der Waals density functional for general geometries Phys. Rev. Lett. 92 246401 Thonhauser T, Cooper V R, Li S, Puzder A, Hyldgaard P and Langreth D C 2007 Van der Waals density functional: self-consistent potential and the nature of the van der Waals bond Phys. Rev. B 76 125112 [7]Lee K, Murray E D, Kong L, Lundqvist B I and Langreth D C 2010 A higher-accuracy van der Waals density functional Phys. Rev. B 82 081101 [8]Rapcewicz K and Ashcroft N W 1991 Fluctuation attraction in condensed matter: a nonlocal functional approach Phys. Rev. B 44 4032 Lundqvist B I, Andersson Y, Shao H, Chan S and Langreth D C 1995 Density functional theory including van der Waals forces Int. J. Quant. Chem. 56 247 [9]Langreth D C et al 2009 A density functional for sparse matter J. Phys.: Condens. Matter 21 084203 [10]For example, Kohn W, Meir Y and Makarov D E 1998 The exchange-correlation energy of a metallic surface Phys. Rev. Lett. 80 4153 Kurth S and Perdew J P 1999 Phys. Rev. B 59 10461 Dobson J F and Wang J 1999 Phys. Rev. Lett. 82 2123 Pitarke J M and Perdew J P 2003 Phys. Rev. B 67 045101 Vydrov O A and van Voorhi T 2009 Phys. Rev. Lett. 103 063004 [11]For example, Grimme S 2004 J. Comput. Phys. 25 1463 Tkatchenko A and Scheffler M 2009 Phys. Rev. Lett. 102 073005 Grimme S, Antony J, Ehrlich S and Krieg H 2010 J. Chem. Phys. 132 154004 [12]Burke K 2012 Perspectives on density functional theory J. Chem. Phys. 136 150901 Van der Waals interactions in advanced materials contents Van der Waals interactions in advanced materials, in memory of David C LangrethPer Hyldgaard and Talat S Rahman Frictional temperature rise in a sliding physisorbed monolayer of Kr/grapheneM Walker, C Jaye, J Krim and Milton W Cole How to modify the van der Waals and Casimir forces without change of the dielectric permittivityG L Klimchitskaya, U Mohideen and V M Mostepanenko Spectroscopic characterization of van der Waals interactions in a metal organic framework with unsaturated metal centers: MOF-74-MgNour Nijem, Pieremanuele Canepa, Lingzhu Kong, Haohan Wu, Jing Li, Timo Thonhauser and Yves J Chabal A theoretical study of the hydrogen-storage potential of (H2)4CH4 in metal organic framework materials and carbon nanotubesQ Li and T Thonhauser The influence of dispersion interactions on the hydrogen adsorption properties of expanded graphiteYungok Ihm, Valentino R Cooper, Lujian Peng and James R Morris A DFT-D study of structural and energetic properties of TiO2 modificationsJonas Moellmann, Stephan Ehrlich, Ralf Tonner and Stefan Grimme Spherical-shell model for the van der Waals coefficients between fullerenes and/or nearly spherical nanoclustersJohn P Perdew, Jianmin Tao, Pan Hao, Adrienn Ruzsinszky, Gábor I Csonka and J M Pitarke Dynamical screening of the van der Waals interaction between graphene layersY J Dappe, P G Bolcatto, J Ortega and F Flores Structural evolution of amino acid crystals under stress from a non-empirical density functionalRiccardo Sabatini, Emine Küçükbenli, Brian Kolb, T Thonhauser and Stefano de Gironcoli Physisorption of nucleobases on graphene: a comparative van der Waals studyDuy Le, Abdelkader Kara, Elsebeth Schröder, Per Hyldgaard and Talat S Rahman The role of van der Waals interactions in the adsorption of noble gases on metal surfacesDe-Li Chen, W A Al-Saidi and J Karl Johnson Desorption of n-alkanes from graphene: a van der Waals density functional studyElisa Londero, Emma K Karlson, Marcus Landahl, Dimitri Ostrovskii, Jonatan D Rydberg and Elsebeth Schröder Benchmarking van der Waals density functionals with experimental data: potential-energy curves for H2 molecules on Cu(111), (100) and (110) surfacesKyuho Lee, Kristian Berland, Mina Yoon, Stig Andersson, Elsebeth Schröder, Per Hyldgaard and Bengt I Lundqvist Ab initio and semi-empirical van der Waals study of graphene-boron nitride interaction from a molecular point of viewVasile Caciuc, Nicolae Atodiresei, Martin Callsen, Predrag Lazić and Stefan Blügel Rationale for switching to nonlocal functionals in density functional theoryP Lazić, N Atodiresei, V Caciuc, R Brako, B Gumhalter and S Blügel Improved description of soft layered materials with van der Waals density functional theoryGabriella Graziano, Jiří Klimeš, Felix Fernandez-Alonso and Angelos Michaelides Structure and stability of weakly chemisorbed ethene adsorbed on low-index Cu surfaces: performance of density functionals with van der Waals interactionsFelix Hanke, Matthew S Dyer, Jonas Björk and Mats Persson Are we van der Waals ready?T Björkman, A Gulans, A V Krasheninnikov and R M Nieminen Nonequilibrium thermodynamics of interacting tunneling transport: variational grand potential, density functional formulation and nature of steady-state forcesP Hyldgaard
Changes in the reflectivity of a lithium niobate crystal decorated with a graphene layer

NASA Astrophysics Data System (ADS)

Salas, O.; Garcés, E.; Castillo, F. L.; Magaña, L. F.

2017-01-01

Density functional theory and molecular dynamics were used to study the interaction of a graphene layer with the surface of lithium niobate. The simulations were performed at atmospheric pressure and 300K. We found that the graphene layer is physisorbed with an adsorption energy of -0.8205 eV/C-atom. Subsequently, the optical absorption of the graphene-(lithium niobate) system was calculated and compared with that of graphene solo and lithium niobate alone, respectively. The calculations were performed using the Quantum Espresso code with the GGA approximation and Vdw-DF2 (which includes long-range correlation effects as Van der Waals interactions).
Application of vdW-DF Methods to Hydrogen Adsorptions and an Organic Ferroelectric

NASA Astrophysics Data System (ADS)

Lee, Kyuho

2012-02-01

In recent years, several schemes have been proposed to include van der Waals (vdW) interactions into the framework of density functional theory (DFT). These offer the potential to extend the scope and usefulness of DFT, allowing applications to an entire new class of sparse materials. For finite systems, we validated our non-empirical van der Waals density functionals (vdW-DFs) with respect to very accurate quantum chemical calculations of the potential energy curves (PECs) for small molecular duplexes [1]. For extended systems, however, typical tests focus on comparisons with a few accessible observations, such as binding energy and bond length [1]. In this talk, we present a third approach in which full PECs from accurate experiments are used for the assessment of vdW methods for extended systems [2]. We calculate the PECs of the H2 molecule and light atoms on the (100), (110), and (111) surfaces of Cu. The gas-surface-scattering experiments provide the rich data bank that covers results for the whole shape of the physisorption potentials. We also present an application of vdW-DF2 to an organic ferroelectric, phenazine-chloranilic acid [3]. In spite of extensive experimental efforts to characterize this rare organic material, the origin of the long-range order is unclear and even the ground state structure is not completely determined yet. We study its structure, energetics, ferroelectric properties, structural instability, and the proton-transfer process in it in comparison with PBE results and experiments wherever possible. [4pt]% [1] K. Lee, E. Murray, L. Kong, B. I. Lundqvist, and D. C. Langreth, Phys. Rev. B 82, 081101 (2010). [1pt]% [2] K. Lee, A. K. Kelkkanen, K. Berland, S. Andersson, D. C. Langreth, E. Schr"oder, B. I. Lundqvist, and P. Hyldgaard, Phys. Rev. B 84, 193408 (2011). [1pt]% [3] K. Lee, B. Kolb, T. Thonhauser, D. C. Langreth, and D. Vanderbilt, in preparation.
Effects of van der Waals Interactions in the Adsorption of Isooctane and Ethanol on Fe(100) Surfaces

PubMed Central

2014-01-01

van der Waals (vdW) forces play a fundamental role in the structure and behavior of diverse systems. Because of development of functionals that include nonlocal correlation, it is possible to study the effects of vdW interactions in systems of industrial and tribological interest. Here we simulated within the framework of density functional theory (DFT) the adsorption of isooctane (2,2,4-trimethylpentane) and ethanol on an Fe(100) surface, employing various exchange–correlation functionals to take vdW forces into account. In particular, this paper discusses the effect of vdW forces on the magnitude of adsorption energies, equilibrium geometries, and their role in the binding mechanism. According to our calculations, vdW interactions increase the adsorption energies and reduce the equilibrium distances. Nevertheless, they do not influence the spatial configuration of the adsorbed molecules. Their effect on the electronic density is a nonisotropic, delocalized accumulation of charge between the molecule and the slab. In conclusion, vdW forces are essential for the adsorption of isooctane and ethanol on a bcc Fe(100) surface. PMID:25126156
Versatile van der Waals Density Functional Based on a Meta-Generalized Gradient Approximation

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

Peng, Haowei; Yang, Zeng-Hui; Perdew, John P.

A “best-of-both-worlds” van der Waals (vdW) density functional is constructed, seamlessly supplementing the strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation for short- and intermediate-range interactions with the long-range vdW interaction from r VV 10 , the revised Vydrov–van Voorhis nonlocal correlation functional. The resultant SCAN + r VV 10 is the only vdW density functional to date that yields excellent interlayer binding energies and spacings, as well as intralayer lattice constants in 28 layered materials. Its versatility for various kinds of bonding is further demonstrated by its good performance for 22 interactions between molecules; the cohesive energies andmore » lattice constants of 50 solids; the adsorption energy and distance of a benzene molecule on coinage-metal surfaces; the binding energy curves for graphene on Cu(111), Ni(111), and Co(0001) surfaces; and the rare-gas solids. We argue that a good semilocal approximation should (as SCAN does) capture the intermediate-range vdW through its exchange term. We have found an effective range of the vdW interaction between 8 and 16 Å for systems considered here, suggesting that this interaction is negligibly small at the larger distances where it reaches its asymptotic power-law decay.« less
Versatile van der Waals Density Functional Based on a Meta-Generalized Gradient Approximation

DOE PAGES

Peng, Haowei; Yang, Zeng-Hui; Perdew, John P.; ...

2016-10-12

A “best-of-both-worlds” van der Waals (vdW) density functional is constructed, seamlessly supplementing the strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation for short- and intermediate-range interactions with the long-range vdW interaction from r VV 10 , the revised Vydrov–van Voorhis nonlocal correlation functional. The resultant SCAN + r VV 10 is the only vdW density functional to date that yields excellent interlayer binding energies and spacings, as well as intralayer lattice constants in 28 layered materials. Its versatility for various kinds of bonding is further demonstrated by its good performance for 22 interactions between molecules; the cohesive energies andmore » lattice constants of 50 solids; the adsorption energy and distance of a benzene molecule on coinage-metal surfaces; the binding energy curves for graphene on Cu(111), Ni(111), and Co(0001) surfaces; and the rare-gas solids. We argue that a good semilocal approximation should (as SCAN does) capture the intermediate-range vdW through its exchange term. We have found an effective range of the vdW interaction between 8 and 16 Å for systems considered here, suggesting that this interaction is negligibly small at the larger distances where it reaches its asymptotic power-law decay.« less
Electronic charge rearrangement at metal/organic interfaces induced by weak van der Waals interactions

NASA Astrophysics Data System (ADS)

Ferri, Nicola; Ambrosetti, Alberto; Tkatchenko, Alexandre

2017-07-01

Electronic charge rearrangements at interfaces between organic molecules and solid surfaces play a key role in a wide range of applications in catalysis, light-emitting diodes, single-molecule junctions, molecular sensors and switches, and photovoltaics. It is common to utilize electrostatics and Pauli pushback to control the interface electronic properties, while the ubiquitous van der Waals (vdW) interactions are often considered to have a negligible direct contribution (beyond the obvious structural relaxation). Here, we apply a fully self-consistent Tkatchenko-Scheffler vdW density functional to demonstrate that the weak vdW interactions can induce sizable charge rearrangements at hybrid metal/organic systems (HMOS). The complex vdW correlation potential smears out the interfacial electronic density, thereby reducing the charge transfer in HMOS, changes the interface work functions by up to 0.2 eV, and increases the interface dipole moment by up to 0.3 Debye. Our results suggest that vdW interactions should be considered as an additional control parameter in the design of hybrid interfaces with the desired electronic properties.
The adsorption of CH3 and C6H6 on corundum-type sesquioxides: The role of van der Waals interactions

NASA Astrophysics Data System (ADS)

Dabaghmanesh, Samira; Partoens, Bart; Neyts, Erik

Van der Waals (vdW) interactions play an important role in the adsorption of atoms and molecules on the surface of solids. This role becomes more significant whenever the interaction between the adsorbate and surface is physisorption. Thanks to recent developments in density functional theory (DFT), we are now able to employ different vdW methods that helps us to account for the long-range vdW forces. However, the choice of the most efficient vdW functional for different materials is still an open question. In our study, we examine different vdW approaches to compute bulk and molecular adsorption properties of M2O3 oxides (M: Cr, Fe, and Al) as well-known examples of the corundum family. For the bulk properties, we compare our results for the heat of formation, cohesive energy, lattice parameters and bond distances as obtained using the different vdW functionals and available experimental data. Next we compute the adsorption energies of the benzene molecule (as an example of physisorption) and CH3 (as an example of chemisorption) on top of the (0001) M-terminated and MO-terminated surfaces. Calculating the vdW contributions into the adsorption energies, we find that the vdW functionals play important role not just in the weak adsorptions but even in strong adsorption.
On the accuracy of van der Waals inclusive density-functional theory exchange-correlation functionals for ice at ambient and high pressures.

PubMed

Santra, Biswajit; Klimes, Jirí; Tkatchenko, Alexandre; Alfè, Dario; Slater, Ben; Michaelides, Angelos; Car, Roberto; Scheffler, Matthias

2013-10-21

Density-functional theory (DFT) has been widely used to study water and ice for at least 20 years. However, the reliability of different DFT exchange-correlation (xc) functionals for water remains a matter of considerable debate. This is particularly true in light of the recent development of DFT based methods that account for van der Waals (vdW) dispersion forces. Here, we report a detailed study with several xc functionals (semi-local, hybrid, and vdW inclusive approaches) on ice Ih and six proton ordered phases of ice. Consistent with our previous study [B. Santra, J. Klimeš, D. Alfè, A. Tkatchenko, B. Slater, A. Michaelides, R. Car, and M. Scheffler, Phys. Rev. Lett. 107, 185701 (2011)] which showed that vdW forces become increasingly important at high pressures, we find here that all vdW inclusive methods considered improve the relative energies and transition pressures of the high-pressure ice phases compared to those obtained with semi-local or hybrid xc functionals. However, we also find that significant discrepancies between experiment and the vdW inclusive approaches remain in the cohesive properties of the various phases, causing certain phases to be absent from the phase diagram. Therefore, room for improvement in the description of water at ambient and high pressures remains and we suggest that because of the stern test the high pressure ice phases pose they should be used in future benchmark studies of simulation methods for water.

Adsorption of pentacene on (100) vicinal surfaces: role of coordination, surface chemistry and vdWs effects

NASA Astrophysics Data System (ADS)

Matos, Jeronimo; Kara, Abdelkader

2015-03-01

In contrast to low miller index surfaces, vicinal surfaces are characterized by steps and step edges that not only present an interesting atomic landscape for the adsorption organic molecules, but also a unique electronic structure resulting in part from the low coordinated atoms at the step edges. The adsorption of pentacene on the stepped (511), (711), (911) surfaces (respectively 3, 4 and 5-atom wide terraces) of Cu and Ag (coinage transition metals); Pt (reactive transition metal); and Ni (reactive, magnetic transition metal) are studied using density functional theory, in order to investigate the support effects arising from differing surface chemistry. We compare the adsorption energy, adsorption geometry and electronic structure predicted by the PBE functional with those obtained from one of the optimized vdW-DF methods: optB88-vdW. Work supported by the U.S. Department of Energy Basic Energy Science under Contract No. DE-FG02-11ER16243.
The role of the van der Waals interactions in the adsorption of anthracene and pentacene on the Ag(111) surface

NASA Astrophysics Data System (ADS)

Morbec, Juliana M.; Kratzer, Peter

2017-01-01

Using first-principles calculations based on density-functional theory (DFT), we investigated the effects of the van der Waals (vdW) interactions on the structural and electronic properties of anthracene and pentacene adsorbed on the Ag(111) surface. We found that the inclusion of vdW corrections strongly affects the binding of both anthracene/Ag(111) and pentacene/Ag(111), yielding adsorption heights and energies more consistent with the experimental results than standard DFT calculations with generalized gradient approximation (GGA). For anthracene/Ag(111) the effect of the vdW interactions is even more dramatic: we found that "pure" DFT-GGA calculations (without including vdW corrections) result in preference for a tilted configuration, in contrast to the experimental observations of flat-lying adsorption; including vdW corrections, on the other hand, alters the binding geometry of anthracene/Ag(111), favoring the flat configuration. The electronic structure obtained using a self-consistent vdW scheme was found to be nearly indistinguishable from the conventional DFT electronic structure once the correct vdW geometry is employed for these physisorbed systems. Moreover, we show that a vdW correction scheme based on a hybrid functional DFT calculation (HSE) results in an improved description of the highest occupied molecular level of the adsorbed molecules.
Modeling the physisorption of graphene on metals

NASA Astrophysics Data System (ADS)

Tao, Jianmin; Tang, Hong; Patra, Abhirup; Bhattarai, Puskar; Perdew, John P.

2018-04-01

Many processes of technological and fundamental importance occur on surfaces. Adsorption is one of these phenomena that has received the most attention. However, it presents a great challenge to conventional density functional theory. Starting with the Lifshitz-Zaremba-Kohn second-order perturbation theory, here we develop a long-range van der Waals (vdW) correction for physisorption of graphene on metals. The model importantly includes quadrupole-surface interaction and screening effects. The results show that, when the vdW correction is combined with the Perdew-Burke-Enzerhof functional, it yields adsorption energies in good agreement with the random-phase approximation, significantly improving upon other vdW methods. We also find that, compared with the leading-order interaction, the higher-order quadrupole-surface correction accounts for about 25 % of the total vdW correction, suggesting the importance of the higher-order term.
Application of Molecular Dynamics Simulations in Molecular Property Prediction I: Density and Heat of Vaporization

PubMed Central

Wang, Junmei; Tingjun, Hou

2011-01-01

Molecular mechanical force field (FF) methods are useful in studying condensed phase properties. They are complementary to experiment and can often go beyond experiment in atomic details. Even a FF is specific for studying structures, dynamics and functions of biomolecules, it is still important for the FF to accurately reproduce the experimental liquid properties of small molecules that represent the chemical moieties of biomolecules. Otherwise, the force field may not describe the structures and energies of macromolecules in aqueous solutions properly. In this work, we have carried out a systematic study to evaluate the General AMBER Force Field (GAFF) in studying densities and heats of vaporization for a large set of organic molecules that covers the most common chemical functional groups. The latest techniques, such as the particle mesh Ewald (PME) for calculating electrostatic energies, and Langevin dynamics for scaling temperatures, have been applied in the molecular dynamics (MD) simulations. For density, the average percent error (APE) of 71 organic compounds is 4.43% when compared to the experimental values. More encouragingly, the APE drops to 3.43% after the exclusion of two outliers and four other compounds for which the experimental densities have been measured with pressures higher than 1.0 atm. For heat of vaporization, several protocols have been investigated and the best one, P4/ntt0, achieves an average unsigned error (AUE) and a root-mean-square error (RMSE) of 0.93 and 1.20 kcal/mol, respectively. How to reduce the prediction errors through proper van der Waals (vdW) parameterization has been discussed. An encouraging finding in vdW parameterization is that both densities and heats of vaporization approach their “ideal” values in a synchronous fashion when vdW parameters are tuned. The following hydration free energy calculation using thermodynamic integration further justifies the vdW refinement. We conclude that simple vdW parameterization can significantly reduce the prediction errors. We believe that GAFF can greatly improve its performance in predicting liquid properties of organic molecules after a systematic vdW parameterization, which will be reported in a separate paper. PMID:21857814
X-ray electron density investigation of chemical bonding in van der Waals materials

NASA Astrophysics Data System (ADS)

Kasai, Hidetaka; Tolborg, Kasper; Sist, Mattia; Zhang, Jiawei; Hathwar, Venkatesha R.; Filsø, Mette Ø.; Cenedese, Simone; Sugimoto, Kunihisa; Overgaard, Jacob; Nishibori, Eiji; Iversen, Bo B.

2018-03-01

Van der Waals (vdW) solids have attracted great attention ever since the discovery of graphene, with the essential feature being the weak chemical bonding across the vdW gap. The nature of these weak interactions is decisive for many extraordinary properties, but it is a strong challenge for current theory to accurately model long-range electron correlations. Here we use synchrotron X-ray diffraction data to precisely determine the electron density in the archetypal vdW solid, TiS2, and compare the results with density functional theory calculations. Quantitative agreement is observed for the chemical bonding description in the covalent TiS2 slabs, but significant differences are identified for the interactions across the gap, with experiment revealing more electron deformation than theory. The present data provide an experimental benchmark for testing theoretical models of weak chemical bonding.
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.
Effect of van der Waals interactions on the stability of SiC polytypes

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

Kawanishi, Sakiko, E-mail: s-kawa@tagen.tohoku.ac.jp; Mizoguchi, Teruyasu

2016-05-07

Density functional theory calculations with a correction of the long-range dispersion force, namely, the van der Waals (vdW) force, are performed for SiC polytypes. The lattice parameters are in good agreement with those obtained from the experiments. Furthermore, the stability of the polytypes in the experiments, which show 3C-SiC as the most stable, is reproduced by the present calculations. The effects of the vdW force on the electronic structure and the stability of polytypes are discussed. We observe that the vdW interaction is more sensitive to the cubic site than the hexagonal site. Thus, the influence of the vdW forcemore » increases with decreasing the hexagonality of the polytype, which results in the confirmation that the most stable polytype is 3C-SiC.« less
DOE Office of Scientific and Technical Information (OSTI.GOV)

Shulenburger, Luke; Baczewski, A. D.; Zhu, Z.

Sensitive dependence of the electronic structure on the number of layers in few-layer phosphorene raises a question about the true nature of the interlayer interaction in so-called van der Waals (vdW) solids . We performed quantum Monte Carlo calculations and found that the interlayer interaction in bulk black phosphorus and related few-layer phosphorene is associated with a significant charge redistribution that is incompatible with purely dispersive forces and not captured by density functional theory calculations with different vdW corrected functionals. Lastly, these findings confirm the necessity of more sophisticated treatment of nonlocal electron correlation in total energy calculations.
Adsorption of thiophene on transition metal surfaces with the inclusion of van der Waals effects

NASA Astrophysics Data System (ADS)

Malone, Walter; Matos, Jeronimo; Kara, Abdelkader

2018-03-01

We use density functional theory with the inclusion of the van der Waals interaction to study the adsorption of thiophene, C4H4S, on Pt, Rh, Pd, Au, and Ag (100) surfaces. The five van der Waals (vdW) inclusive functionals we employ are optB86b-vdW, optB88-vdW, optPBE-vdW, revPBE-vdW, and rPW86-vdW2. For comparison we also run calculations with the GGA- Perdew Burke and Ernzerhof (PBE) functional. We examine several adsorption sites with the plane of the molecule parallel or perpendicular to the surface. The most stable configuration on all metals was the site where the center of the thiophene lies over a 4-fold hollow site with the sulfur atom lying close to a top site. Furthermore, we examine several electronic and geometric properties of the adsorbate including charge transfer, modification of the d-band, adsorption energy, tilt angle, and adsorption height. For the coinage metals PBE gives the lowest adsorption energy. For reactive transition metal substrates, revPBE-vdW and rPW86-vdW2 give lower adsorption energies than PBE.
Electronic structures and enhanced optical properties of blue phosphorene/transition metal dichalcogenides van der Waals heterostructures.

PubMed

Peng, Qiong; Wang, Zhenyu; Sa, Baisheng; Wu, Bo; Sun, Zhimei

2016-08-24

As a fast emerging topic, van der Waals (vdW) heterostructures have been proposed to modify two-dimensional layered materials with desired properties, thus greatly extending the applications of these materials. In this work, the stacking characteristics, electronic structures, band edge alignments, charge density distributions and optical properties of blue phosphorene/transition metal dichalcogenides (BlueP/TMDs) vdW heterostructures were systematically studied based on vdW corrected density functional theory. Interestingly, the valence band maximum and conduction band minimum are located in different parts of BlueP/MoSe2, BlueP/WS2 and BlueP/WSe2 heterostructures. The MoSe2, WS2 or WSe2 layer can be used as the electron donor and the BlueP layer can be used as the electron acceptor. We further found that the optical properties under visible-light irradiation of BlueP/TMDs vdW heterostructures are significantly improved. In particular, the predicted upper limit energy conversion efficiencies of BlueP/MoS2 and BlueP/MoSe2 heterostructures reach as large as 1.16% and 0.98%, respectively, suggesting their potential applications in efficient thin-film solar cells and optoelectronic devices.
van der Waals interactions are critical in Car-Parrinello molecular dynamics simulations of porphyrin-fullerene dyads.

PubMed

Karilainen, Topi; Cramariuc, Oana; Kuisma, Mikael; Tappura, Kirsi; Hukka, Terttu I

2015-04-05

The interplay between electrostatic and van der Waals (vdW) interactions in porphyrin-C60 dyads is still under debate despite its importance in influencing the structural characteristics of such complexes considered for various applications in molecular photovoltaics. In this article, we sample the conformational space of a porphyrin-C60 dyad using Car-Parrinello molecular dynamics simulations with and without empirical vdW corrections. Long-range vdW interactions, which are poorly described by the commonly used density functional theory functionals, prove to be essential for a proper dynamics of the dyad moieties. Inclusion of vdW corrections brings porphyrin and C60 close together in an orientation that is in agreement with experimental observations. The structural differences arising from the vdW corrections are shown to be significant for several properties and potentially less important for others. Additionally, our Mulliken population analysis reveals that contrary to the common belief, porphyrin is not the primary electron donating moiety for C60 . In the considered dyad, fullerene's affinity for electrons is primarily satisfied by charge transfer from the amide group of the linker. However, we show that in the absence of another suitable bound donor, C60 can withdraw electrons from porphyrin if it is sufficiently close. © 2015 Wiley Periodicals, Inc.
Predicting elastic properties of β-HMX from first-principles calculations.

PubMed

Peng, Qing; Rahul; Wang, Guangyu; Liu, Gui-Rong; Grimme, Stefan; De, Suvranu

2015-05-07

We investigate the performance of van der Waals (vdW) functions in predicting the elastic constants of β cyclotetramethylene tetranitramine (HMX) energetic molecular crystals using density functional theory (DFT) calculations. We confirm that the accuracy of the elastic constants is significantly improved using the vdW corrections with environment-dependent C6 together with PBE and revised PBE exchange-correlation functionals. The elastic constants obtained using PBE-D3(0) calculations yield the most accurate mechanical response of β-HMX when compared with experimental stress-strain data. Our results suggest that PBE-D3 calculations are reliable in predicting the elastic constants of this material.
Communication: Accurate higher-order van der Waals coefficients between molecules from a model dynamic multipole polarizability

DOE PAGES

Tao, Jianmin; Rappe, Andrew M.

2016-01-20

Due to the absence of the long-range van der Waals (vdW) interaction, conventional density functional theory (DFT) often fails in the description of molecular complexes and solids. In recent years, considerable progress has been made in the development of the vdW correction. However, the vdW correction based on the leading-order coefficient C 6 alone can only achieve limited accuracy, while accurate modeling of higher-order coefficients remains a formidable task, due to the strong non-additivity effect. Here, we apply a model dynamic multipole polarizability within a modified single-frequency approximation to calculate C 8 and C 10 between small molecules. We findmore » that the higher-order vdW coefficients from this model can achieve remarkable accuracy, with mean absolute relative deviations of 5% for C 8 and 7% for C 10. As a result, inclusion of accurate higher-order contributions in the vdW correction will effectively enhance the predictive power of DFT in condensed matter physics and quantum chemistry.« less
Ab-initio adsorption study of chitosan on functionalized graphene: critical role of van der Waals interactions.

PubMed

Rahman, R; Mazumdar, D

2012-03-01

We investigate the adsorption process of an organic biomolecule (chitosan) on epoxy-functionalized graphene using ab-initio density functional methods incorporating van-der-waals (vdW) interactions. The role of London dispersion force on the cohesive energy and conformal preference of the molecule is quantitatively elucidated. Functionalizing graphene with epoxy leads to weak hydrogen-bond interactions with chitosan. Binding energy values increase by over an order of magnitude after including vdW corrections, implying that dispersive interactions dominate the physisorption process. Conformal study show binding upto 30 kcal/mol when the molecule is oriented with the hydroxyl group approaching the functionalized graphene. Our study advances the promise of functionalized graphene for a variety of applications.
The nature of the interlayer interaction in bulk and few-layer phosphorus

DOE PAGES

Shulenburger, Luke; Baczewski, A. D.; Zhu, Z.; ...

2015-11-02

Sensitive dependence of the electronic structure on the number of layers in few-layer phosphorene raises a question about the true nature of the interlayer interaction in so-called van der Waals (vdW) solids . We performed quantum Monte Carlo calculations and found that the interlayer interaction in bulk black phosphorus and related few-layer phosphorene is associated with a significant charge redistribution that is incompatible with purely dispersive forces and not captured by density functional theory calculations with different vdW corrected functionals. Lastly, these findings confirm the necessity of more sophisticated treatment of nonlocal electron correlation in total energy calculations.
The Nature of the Interlayer Interaction in Bulk and Few-Layer Phosphorus.

PubMed

Shulenburger, L; Baczewski, A D; Zhu, Z; Guan, J; Tománek, D

2015-12-09

Sensitive dependence of the electronic structure on the number of layers in few-layer phosphorene raises a question about the true nature of the interlayer interaction in so-called "van der Waals (vdW) solids". We performed quantum Monte Carlo calculations and found that the interlayer interaction in bulk black phosphorus and related few-layer phosphorene is associated with a significant charge redistribution that is incompatible with purely dispersive forces and not captured by density functional theory calculations with different vdW corrected functionals. These findings confirm the necessity of more sophisticated treatment of nonlocal electron correlation in total energy calculations.
Evaluation of van der Waals density functionals for layered materials

NASA Astrophysics Data System (ADS)

Tawfik, Sherif Abdulkader; Gould, Tim; Stampfl, Catherine; Ford, Michael J.

2018-03-01

In 2012, Björkman et al. posed the question "Are we van der Waals ready?" [T. Björkman et al., J. Phys.: Condens. Matter 24, 424218 (2012), 10.1088/0953-8984/24/42/424218] about the ability of ab initio modeling to reproduce van der Waals (vdW) dispersion forces in layered materials. The answer at that time was no, however. Here we report on a new generation of vdW dispersion models and show that one, i.e., the fractionally ionic atom theory with many-body dispersions, offers close to quantitative predictions for layered structures. Furthermore, it does so from a qualitatively correct picture of dispersion forces. Other methods, such as D3 and optB88vdW, also work well, albeit with some exceptions. We thus argue that we are nearly vdW ready and that some modern dispersion methods are accurate enough to be used for nanomaterial prediction, albeit with some caution required.
A comparison of integral equations and density functional theory versus Monte Carlo for hard dumbbells near a hard wall

NASA Astrophysics Data System (ADS)

Henderson, Douglas; Quintana, Jacqueline; Sokołowski, Stefan

1995-03-01

A comparison of Percus-Yevick-Pynn-Lado model theory and a density functional (DF) theory of nonuniform fluids of nonspherical particles is performed. The DF used is a new generalization of Tarazona's theory. The conclusion is that DF theory provides a preferable route to describe the system under consideration. Its accuracy can be improved with better approximation for the direct correlation function (DCF) for bulk system.
Predicting vapor liquid equilibria using density functional theory: A case study of argon

NASA Astrophysics Data System (ADS)

Goel, Himanshu; Ling, Sanliang; Ellis, Breanna Nicole; Taconi, Anna; Slater, Ben; Rai, Neeraj

2018-06-01

Predicting vapor liquid equilibria (VLE) of molecules governed by weak van der Waals (vdW) interactions using the first principles approach is a significant challenge. Due to the poor scaling of the post Hartree-Fock wave function theory with system size/basis functions, the Kohn-Sham density functional theory (DFT) is preferred for systems with a large number of molecules. However, traditional DFT cannot adequately account for medium to long range correlations which are necessary for modeling vdW interactions. Recent developments in DFT such as dispersion corrected models and nonlocal van der Waals functionals have attempted to address this weakness with a varying degree of success. In this work, we predict the VLE of argon and assess the performance of several density functionals and the second order Møller-Plesset perturbation theory (MP2) by determining critical and structural properties via first principles Monte Carlo simulations. PBE-D3, BLYP-D3, and rVV10 functionals were used to compute vapor liquid coexistence curves, while PBE0-D3, M06-2X-D3, and MP2 were used for computing liquid density at a single state point. The performance of the PBE-D3 functional for VLE is superior to other functionals (BLYP-D3 and rVV10). At T = 85 K and P = 1 bar, MP2 performs well for the density and structural features of the first solvation shell in the liquid phase.
Modulation of band gap by an applied electric field in BN-based heterostructures

NASA Astrophysics Data System (ADS)

Luo, M.; Xu, Y. E.; Zhang, Q. X.

2018-05-01

First-principles density functional theory (DFT) calculations are performed on the structural and electronic properties of the SiC/BN van der Waals (vdW) heterostructures under an external electric field (E-field). Our results reveal that the SiC/BN vdW heterostructure has a direct band gap of 2.41 eV in the raw. The results also imply that electrons are likely to transfer from BN to SiC monolayer due to the deeper potential of BN monolayer. It is also observed that, by applying an E-field, ranging from -0.50 to +0.65 V/Å, the band gap decreases from 2.41 eV to zero, which presents a parabola-like relationship around 0.0 V/Å. Through partial density of states (PDOS) plots, it is revealed that, p orbital of Si, C, B, and N atoms are responsible for the significant variations of band gap. These obtained results predict that, the electric field tunable band gap of the SiC/BN vdW heterostructures carries potential applications for nanoelectronics and spintronic device applications.

Physisorption of three amine terminated molecules (TMBDA, BDA, TFBDA) on the Au(111) Surface: The Role of van der Waals Interaction

NASA Astrophysics Data System (ADS)

Aminpour, Maral; Le, Duy; Rahman, Talat S.

2012-02-01

Recently, the electronic properties and alignment of tetramethyl-1,4-benzenediamine (TMBDA), 1,4-benzenediamine (BDA) and tetrafluro-1,4-benzenediamine (TFBDA) molecules were studied experimentally. Discrepancies were found for both the binding energy and the molecule tilt angle with respect to the surface, when results were compared with density functional theory calculations [1]. We have included the effect of vdW interactions both between the molecules and the Au(111) surface and find binding energies which are in very good agreement with experiments. We also find that at low coverages each of these molecules would adsorb almost parallel to the surface. N-Au bond lengths and charge redistribution on adsorption of the molecules are also analyzed. Our calculations are based on DFT using vdW-DF exchange correlation functionals. For BDA (since we are aware of experimental data), we show that for higher coverage, inclusion of intermolecular van der Waals interaction leads to tilting of the molecules with respect to the surface and formation of line structures. Our results demonstrate the central role played by intermolecular interaction in pattern formation on this surface.[4pt] [1] M. Dell'Angela et al, Nano Lett. 2010, 10, 2470; M. Kamenetska et al, J. Phys. Chem. C, 2011, 115, 12625
Predicting the thermodynamic stability of double-perovskite halides from density functional theory

DOE PAGES

Han, Dan; Zhang, Tao; Huang, Menglin; ...

2018-05-24

Recently, a series of double-perovskite halide compounds such as Cs 2AgBiCl 6 and Cs 2AgBiBr 6 have attracted intensive interest as promising alternatives to the solar absorber material CH 3NH 3PbI 3 because they are Pb-free and may exhibit enhanced stability. The thermodynamic stability of a number of double-perovskite halides has been predicted based on density functional theory (DFT) calculations of compound formation energies. In this paper, we found that the stability prediction can be dependent on the approximations used for the exchange-correlation functionals, e.g., the DFT calculations using the widely used Perdew, Burke, Ernzerhof (PBE) functional predict that Csmore » 2AgBiBr 6 is thermodynamically unstable against phase-separation into the competing phases such as AgBr, Cs 2AgBr 3, Cs 3Bi 2Br 9, etc., obviously inconsistent with the good stability observed experimentally. The incorrect prediction by the PBE calculation results from its failure to predict the correct ground-state structures of AgBr, AgCl, and CsCl. By contrast, the DFT calculations based on local density approximation, optB86b-vdW, and optB88-vdW functionals predict the ground-state structures of these binary halides correctly. Furthermore, the optB88-vdW functional is found to give the most accurate description of the lattice constants of the double-perovskite halides and their competing phases. Given these two aspects, we suggest that the optB88-vdW functional should be used for predicting thermodynamic stability in the future high-throughput computational material design or the construction of the Materials Genome database for new double-perovskite halides. As a result, using different exchange-correlation functionals has little influence on the dispersion of the conduction and the valence bands near the electronic bandgap; however, the calculated bandgap can be affected indirectly by the optimized lattice constant, which varies for different functionals.« less
Predicting the thermodynamic stability of double-perovskite halides from density functional theory

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

Han, Dan; Zhang, Tao; Huang, Menglin

Recently, a series of double-perovskite halide compounds such as Cs 2AgBiCl 6 and Cs 2AgBiBr 6 have attracted intensive interest as promising alternatives to the solar absorber material CH 3NH 3PbI 3 because they are Pb-free and may exhibit enhanced stability. The thermodynamic stability of a number of double-perovskite halides has been predicted based on density functional theory (DFT) calculations of compound formation energies. In this paper, we found that the stability prediction can be dependent on the approximations used for the exchange-correlation functionals, e.g., the DFT calculations using the widely used Perdew, Burke, Ernzerhof (PBE) functional predict that Csmore » 2AgBiBr 6 is thermodynamically unstable against phase-separation into the competing phases such as AgBr, Cs 2AgBr 3, Cs 3Bi 2Br 9, etc., obviously inconsistent with the good stability observed experimentally. The incorrect prediction by the PBE calculation results from its failure to predict the correct ground-state structures of AgBr, AgCl, and CsCl. By contrast, the DFT calculations based on local density approximation, optB86b-vdW, and optB88-vdW functionals predict the ground-state structures of these binary halides correctly. Furthermore, the optB88-vdW functional is found to give the most accurate description of the lattice constants of the double-perovskite halides and their competing phases. Given these two aspects, we suggest that the optB88-vdW functional should be used for predicting thermodynamic stability in the future high-throughput computational material design or the construction of the Materials Genome database for new double-perovskite halides. As a result, using different exchange-correlation functionals has little influence on the dispersion of the conduction and the valence bands near the electronic bandgap; however, the calculated bandgap can be affected indirectly by the optimized lattice constant, which varies for different functionals.« less
The direct-to-indirect band gap crossover in two-dimensional van der Waals Indium Selenide crystals

PubMed Central

Mudd, G. W.; Molas, M. R.; Chen, X.; Zólyomi, V.; Nogajewski, K.; Kudrynskyi, Z. R.; Kovalyuk, Z. D.; Yusa, G.; Makarovsky, O.; Eaves, L.; Potemski, M.; Fal’ko, V. I.; Patanè, A.

2016-01-01

The electronic band structure of van der Waals (vdW) layered crystals has properties that depend on the composition, thickness and stacking of the component layers. Here we use density functional theory and high field magneto-optics to investigate the metal chalcogenide InSe, a recent addition to the family of vdW layered crystals, which transforms from a direct to an indirect band gap semiconductor as the number of layers is reduced. We investigate this direct-to-indirect bandgap crossover, demonstrate a highly tuneable optical response from the near infrared to the visible spectrum with decreasing layer thickness down to 2 layers, and report quantum dot-like optical emissions distributed over a wide range of energy. Our analysis also indicates that electron and exciton effective masses are weakly dependent on the layer thickness and are significantly smaller than in other vdW crystals. These properties are unprecedented within the large family of vdW crystals and demonstrate the potential of InSe for electronic and photonic technologies. PMID:28008964
The direct-to-indirect band gap crossover in two-dimensional van der Waals Indium Selenide crystals.

PubMed

Mudd, G W; Molas, M R; Chen, X; Zólyomi, V; Nogajewski, K; Kudrynskyi, Z R; Kovalyuk, Z D; Yusa, G; Makarovsky, O; Eaves, L; Potemski, M; Fal'ko, V I; Patanè, A

2016-12-23

The electronic band structure of van der Waals (vdW) layered crystals has properties that depend on the composition, thickness and stacking of the component layers. Here we use density functional theory and high field magneto-optics to investigate the metal chalcogenide InSe, a recent addition to the family of vdW layered crystals, which transforms from a direct to an indirect band gap semiconductor as the number of layers is reduced. We investigate this direct-to-indirect bandgap crossover, demonstrate a highly tuneable optical response from the near infrared to the visible spectrum with decreasing layer thickness down to 2 layers, and report quantum dot-like optical emissions distributed over a wide range of energy. Our analysis also indicates that electron and exciton effective masses are weakly dependent on the layer thickness and are significantly smaller than in other vdW crystals. These properties are unprecedented within the large family of vdW crystals and demonstrate the potential of InSe for electronic and photonic technologies.
Vibrational dynamics of aniline(Ar)1 and aniline(CH4)1 clusters

NASA Astrophysics Data System (ADS)

Nimlos, M. R.; Young, M. A.; Bernstein, E. R.; Kelley, D. F.

1989-11-01

The first excited electronic state (S1) vibrational dynamics of aniline(Ar)1 and aniline(CH4)1 van der Waals (vdW) clusters have been studied using molecular jet and time resolved emission spectroscopic techniques. The rates of intramolecular vibrational energy redistribution (IVR) and vibrational predissociation (VP) as functions of vibrational energy are reported for both clusters. For vibrational energy in excess of the cluster binding energy, both clusters are observed to dissociate. The dispersed emission spectra of these clusters demonstrate that aniline(Ar)1 dissociates to all energetically accessible bare molecule states and that aniline(CH4)1 dissociates selectively to only the bare molecule vibrationless state. The emission kinetics show that in the aniline(Ar)1 case, the initially excited states have nanosecond lifetimes, and intermediate cluster states have very short lifetimes. In contrast, the initially excited aniline(CH4)1 states and other intermediate vibrationally excited cluster states are very short lived (<100 ps), and the intermediate cluster 00 state is observed. These results can be understood semiquantitatively in terms of an overall serial IVR/VP mechanism which consists of the following: (1) the rates of chromophore to vdW mode IVR are given by Fermi's golden rule, and the density of vdW vibrational states is the most important factor in determining the relative [aniline(Ar)1 vs aniline(CH4)1] rates of IVR; (2) IVR among the vdW modes is rapid; and (3) VP rates can be calculated by a restricted vdW mode phase space Rice-Ramsberger-Kassel-Marcus theory. Since the density of vdW states is three orders of magnitude greater for aniline(CH4)1 than aniline(Ar)1 at 700 cm-1, the model predicts that IVR is slow and rate limiting in aniline(Ar)1, whereas VP is slow and rate limiting in aniline(CH4)1. The agreement of these predictions with the experimental results is very good and is discussed in detail.
Accurate van der Waals coefficients from density functional theory

PubMed Central

Tao, Jianmin; Perdew, John P.; Ruzsinszky, Adrienn

2012-01-01

The van der Waals interaction is a weak, long-range correlation, arising from quantum electronic charge fluctuations. This interaction affects many properties of materials. A simple and yet accurate estimate of this effect will facilitate computer simulation of complex molecular materials and drug design. Here we develop a fast approach for accurate evaluation of dynamic multipole polarizabilities and van der Waals (vdW) coefficients of all orders from the electron density and static multipole polarizabilities of each atom or other spherical object, without empirical fitting. Our dynamic polarizabilities (dipole, quadrupole, octupole, etc.) are exact in the zero- and high-frequency limits, and exact at all frequencies for a metallic sphere of uniform density. Our theory predicts dynamic multipole polarizabilities in excellent agreement with more expensive many-body methods, and yields therefrom vdW coefficients C6, C8, C10 for atom pairs with a mean absolute relative error of only 3%. PMID:22205765
Vibrational and thermodynamic properties of β-HMX: a first-principles investigation.

PubMed

Wu, Zhongqing; Kalia, Rajiv K; Nakano, Aiichiro; Vashishta, Priya

2011-05-28

Thermodynamic properties of β-HMX crystal are investigated using the quasi-harmonic approximation and density functional theory within the local density approximation (LDA), generalized gradient approximation (GGA), and GGA + empirical van der Waals (vdW) correction. It is found that GGA well describes the thermal expansion coefficient and heat capacity but fails to produce correct bulk modulus and equilibrium volume. The vdW correction improves the bulk modulus and volume, but worsens the thermal expansion coefficient and heat capacity. In contrast, LDA describes all thermodynamic properties with reasonable accuracy, and overall is a good exchange-correlation functional for β-HMX molecular crystal. The results also demonstrate significant contributions of phonons to the equation of state. The static calculation of equilibrium volume for β-HMX differs from the room-temperature value incorporating lattice vibrations by over 5%. Therefore, for molecular crystals, it is essential to include phonon contributions when calculated equation of state is compared with experimental data at ambient condition. © 2011 American Institute of Physics
Correlational Effects of the Molecular-Tilt Configuration and the Intermolecular van der Waals Interaction on the Charge Transport in the Molecular Junction.

PubMed

Shin, Jaeho; Gu, Kyungyeol; Yang, Seunghoon; Lee, Chul-Ho; Lee, Takhee; Jang, Yun Hee; Wang, Gunuk

2018-06-25

Molecular conformation, intermolecular interaction, and electrode-molecule contacts greatly affect charge transport in molecular junctions and interfacial properties of organic devices by controlling the molecular orbital alignment. Here, we statistically investigated the charge transport in molecular junctions containing self-assembled oligophenylene molecules sandwiched between an Au probe tip and graphene according to various tip-loading forces ( F L ) that can control the molecular-tilt configuration and the van der Waals (vdW) interactions. In particular, the molecular junctions exhibited two distinct transport regimes according to the F L dependence (i.e., F L -dependent and F L -independent tunneling regimes). In addition, the charge-injection tunneling barriers at the junction interfaces are differently changed when the F L ≤ 20 nN. These features are associated to the correlation effects between the asymmetry-coupling factor (η), the molecular-tilt angle (θ), and the repulsive intermolecular vdW force ( F vdW ) on the molecular-tunneling barriers. A more-comprehensive understanding of these charge transport properties was thoroughly developed based on the density functional theory calculations in consideration of the molecular-tilt configuration and the repulsive vdW force between molecules.
Polymorphism and Elastic Response of Molecular Materials from First Principles: How Hard Can it Be?

NASA Astrophysics Data System (ADS)

Reilly, Anthony; Tkatchenko, Alexandre

2014-03-01

Molecular materials are of great fundamental and applied importance in science and industry, with numerous applications in pharmaceuticals, electronics, sensing, and catalysis. A key challenge for theory has been the prediction of their stability, polymorphism and response to perturbations. While pairwise models of van der Waals (vdW) interactions have improved the ability of density functional theory (DFT) to model these systems, substantial quantitative and even qualitative failures remain. In this contribution we show how a many-body description of vdW interactions can dramatically improve the accuracy of DFT for molecular materials, yielding quantitative description of stabilities and polymorphism for these challenging systems. Moreover, the role of many-body vdW interactions goes beyond stabilities to response properties. In particular, we have studied the elastic properties of a series of molecular crystals, finding that many-body vdW interactions can account for up to 30% of the elastic response, leading to quantitative and qualitative changes in elastic behavior. We will illustrate these crucial effects with the challenging case of the polymorphs of aspirin, leading to a better understanding of the conflicting experimental and theoretical studies of this system.
Computational screening of high-performance optoelectronic materials using OptB88vdW and TB-mBJ formalisms.

PubMed

Choudhary, Kamal; Zhang, Qin; Reid, Andrew C E; Chowdhury, Sugata; Van Nguyen, Nhan; Trautt, Zachary; Newrock, Marcus W; Congo, Faical Yannick; Tavazza, Francesca

2018-05-08

We perform high-throughput density functional theory (DFT) calculations for optoelectronic properties (electronic bandgap and frequency dependent dielectric function) using the OptB88vdW functional (OPT) and the Tran-Blaha modified Becke Johnson potential (MBJ). This data is distributed publicly through JARVIS-DFT database. We used this data to evaluate the differences between these two formalisms and quantify their accuracy, comparing to experimental data whenever applicable. At present, we have 17,805 OPT and 7,358 MBJ bandgaps and dielectric functions. MBJ is found to predict better bandgaps and dielectric functions than OPT, so it can be used to improve the well-known bandgap problem of DFT in a relatively inexpensive way. The peak positions in dielectric functions obtained with OPT and MBJ are in comparable agreement with experiments. The data is available on our websites http://www.ctcms.nist.gov/~knc6/JVASP.html and https://jarvis.nist.gov.
Dispersion interactions in room-temperature ionic liquids: Results from a non-empirical density functional

NASA Astrophysics Data System (ADS)

Kohanoff, Jorge; Pinilla, Carlos; Youngs, Tristan G. A.; Artacho, Emilio; Soler, José M.

2011-10-01

The role of dispersion or van de Waals (VDW) interactions in imidazolium-based room-temperature ionic liquids is studied within the framework of density functional theory, using a recently developed non-empirical functional [M. Dion, H. Rydberg, E. Schröder, D. C. Langreth, and B. I. Lundqvist, Phys. Rev. Lett. 92, 246401 (2004), 10.1103/PhysRevLett.92.246401], as efficiently implemented in the SIESTA code [G. Román-Pérez and J. M. Soler, Phys. Rev. Lett. 103, 096102 (2009), 10.1103/PhysRevLett.103.096102]. We present results for the equilibrium structure and lattice parameters of several crystalline phases, finding a general improvement with respect to both the local density (LDA) and the generalized gradient approximations (GGA). Similar to other systems characterized by VDW bonding, such as rare gas and benzene dimers as well as solid argon, equilibrium distances and volumes are consistently overestimated by ≈7%, compared to -11% within LDA and 11% within GGA. The intramolecular geometries are retained, while the intermolecular distances and orientations are significantly improved relative to LDA and GGA. The quality is superior to that achieved with tailor-made empirical VDW corrections ad hoc [M. G. Del Pópolo, C. Pinilla, and P. Ballone, J. Chem. Phys. 126, 144705 (2007), 10.1063/1.2715571]. We also analyse the performance of an optimized version of this non-empirical functional, where the screening properties of the exchange have been tuned to reproduce high-level quantum chemical calculations [J. Klimes, D. Bowler, and A. Michaelides, J. Phys.: Condens. Matter 22, 074203 (2010), 10.1088/0953-8984/22/7/074203]. The results for solids are even better with volumes and geometries reproduced within 2% of experimental data. We provide some insight into the issue of polymorphism of [bmim][Cl] crystals, and we present results for the geometry and energetics of [bmim][Tf] and [mmim][Cl] neutral and charged clusters, which validate the use of empirical force fields.
van der Waals Heterostructures with High Accuracy Rotational Alignment.

PubMed

Kim, Kyounghwan; Yankowitz, Matthew; Fallahazad, Babak; Kang, Sangwoo; Movva, Hema C P; Huang, Shengqiang; Larentis, Stefano; Corbet, Chris M; Taniguchi, Takashi; Watanabe, Kenji; Banerjee, Sanjay K; LeRoy, Brian J; Tutuc, Emanuel

2016-03-09

We describe the realization of van der Waals (vdW) heterostructures with accurate rotational alignment of individual layer crystal axes. We illustrate the approach by demonstrating a Bernal-stacked bilayer graphene formed using successive transfers of monolayer graphene flakes. The Raman spectra of this artificial bilayer graphene possess a wide 2D band, which is best fit by four Lorentzians, consistent with Bernal stacking. Scanning tunneling microscopy reveals no moiré pattern on the artificial bilayer graphene, and tunneling spectroscopy as a function of gate voltage reveals a constant density of states, also in agreement with Bernal stacking. In addition, electron transport probed in dual-gated samples reveals a band gap opening as a function of transverse electric field. To illustrate the applicability of this technique to realize vdW heterostructuctures in which the functionality is critically dependent on rotational alignment, we demonstrate resonant tunneling double bilayer graphene heterostructures separated by hexagonal boron-nitride dielectric.
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.
Two-Dimensional Graphene-Gold Interfaces Serve as Robust Templates for Dielectric Capacitors.

PubMed

Teshome, Tamiru; Datta, Ayan

2017-10-04

The electronic structures of novel heterostructures, namely, graphene-Au van der Waals (vdW) interfaces, have been studied using density functional theory. Dispersion-corrected PBE-D2 functionals are used to describe the phonon spectrum and binding energies. Ab initio molecular dynamics simulations reveal that the vdW framework is preserved till 1200 K. Beyond T = 1200 K, a transition of the quasiplanar Au into the three-dimensional cluster-like structure is observed. A dielectric capacitor is designed by placing 1-4 hexagonal boron nitride (h-BN) monolayers between graphene and Au conductive plates. Charge separation between the Au and graphene plates is carried out under the effect of an external field normal to the graphene-h-BN-Au interface. The gravimetric capacitances are computed as C 1 = 7.6 μF/g and C 2 = 3.2 μF/g for h-BN bilayers with the Au-graphene heterostructures. The capacitive behavior shows strong deviations from the classical charging models and exemplifies the importance of quantum phenomenon at short contacts, which eventually nullifies at large interelectrode distances. The graphene-Au interface is predicted to be an exciting vdW heterostructure with a potential application as a dielectric capacitor.
The role of collective motion in the ultrafast charge transfer in van der Waals heterostructures

DOE PAGES

Wang, Han; Bang, Junhyeok; Sun, Yiyang; ...

2016-05-10

Here, the success of van der Waals (vdW) heterostructures, made of graphene, metal dichalcogenides, and other layered materials, hinges on the understanding of charge transfer across the interface as the foundation for new device concepts and applications. In contrast to conventional heterostructures, where a strong interfacial coupling is essential to charge transfer, recent experimental findings indicate that vdW heterostructues can exhibit ultra-fast charge transfer despite the weak binding of the heterostructure. Using time-dependent density functional theory molecular dynamics, we identify a strong dynamic coupling between the vdW layers associated with charge transfer. This dynamic coupling results in rapid nonlinear coherentmore » charge oscillations which constitute a purely electronic phenomenon and are shown to be a general feature of vdW heterostructures provided they have a critical minimum dipole coupling. Application to MoS2/WS2 heterostructure yields good agreement with experiment, indicating near complete charge transfer within a timescale of 100 fs.The success of van der Waals heterostructures made of graphene, metal dichalcogenides and other layered materials, hinges on the understanding of charge transfer across the interface as the foundation for new device concepts and applications. In contrast to conventional heterostructures, where a strong interfacial coupling is essential to charge transfer, recent experimental findings indicate that van der Waals heterostructues can exhibit ultrafast charge transfer despite the weak binding of these heterostructures. Here we find, using time-dependent density functional theory molecular dynamics, that the collective motion of excitons at the interface leads to plasma oscillations associated with optical excitation. By constructing a simple model of the van der Waals heterostructure, we show that there exists an unexpected criticality of the oscillations, yielding rapid charge transfer across the interface. Application to the MoS2/WS2 heterostructure yields good agreement with experiments, indicating near complete charge transfer within a timescale of 100 fs.« less
The role of collective motion in the ultrafast charge transfer in van der Waals heterostructures

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

Wang, Han; Bang, Junhyeok; Sun, Yiyang

Here, the success of van der Waals (vdW) heterostructures, made of graphene, metal dichalcogenides, and other layered materials, hinges on the understanding of charge transfer across the interface as the foundation for new device concepts and applications. In contrast to conventional heterostructures, where a strong interfacial coupling is essential to charge transfer, recent experimental findings indicate that vdW heterostructues can exhibit ultra-fast charge transfer despite the weak binding of the heterostructure. Using time-dependent density functional theory molecular dynamics, we identify a strong dynamic coupling between the vdW layers associated with charge transfer. This dynamic coupling results in rapid nonlinear coherentmore » charge oscillations which constitute a purely electronic phenomenon and are shown to be a general feature of vdW heterostructures provided they have a critical minimum dipole coupling. Application to MoS2/WS2 heterostructure yields good agreement with experiment, indicating near complete charge transfer within a timescale of 100 fs.The success of van der Waals heterostructures made of graphene, metal dichalcogenides and other layered materials, hinges on the understanding of charge transfer across the interface as the foundation for new device concepts and applications. In contrast to conventional heterostructures, where a strong interfacial coupling is essential to charge transfer, recent experimental findings indicate that van der Waals heterostructues can exhibit ultrafast charge transfer despite the weak binding of these heterostructures. Here we find, using time-dependent density functional theory molecular dynamics, that the collective motion of excitons at the interface leads to plasma oscillations associated with optical excitation. By constructing a simple model of the van der Waals heterostructure, we show that there exists an unexpected criticality of the oscillations, yielding rapid charge transfer across the interface. Application to the MoS2/WS2 heterostructure yields good agreement with experiments, indicating near complete charge transfer within a timescale of 100 fs.« less
Nonlocal van der Waals functionals: The case of rare-gas dimers and solids

NASA Astrophysics Data System (ADS)

Tran, Fabien; Hutter, Jürg

2013-05-01

Recently, the nonlocal van der Waals (vdW) density functionals [M. Dion, H. Rydberg, E. Schröder, D. C. Langreth, and B. I. Lundqvist, Phys. Rev. Lett. 92, 246401 (2004), 10.1103/PhysRevLett.92.246401] have attracted considerable attention due to their good performance for systems where weak interactions are important. Since the physics of dispersion is included in these functionals, they are usually more accurate and show less erratic behavior than the semilocal and hybrid methods. In this work, several variants of the vdW functionals have been tested on rare-gas dimers (from He2 to Kr2) and solids (Ne, Ar, and Kr) and their accuracy compared to standard semilocal approximations, supplemented or not by an atom-pairwise dispersion correction [S. Grimme, J. Antony, S. Ehrlich, and H. Krieg, J. Chem. Phys. 132, 154104 (2010), 10.1063/1.3382344]. An analysis of the results in terms of energy decomposition is also provided.
Structural, electronic, and dynamical properties of liquid water by ab initio molecular dynamics based on SCAN functional within the canonical ensemble

NASA Astrophysics Data System (ADS)

Zheng, Lixin; Chen, Mohan; Sun, Zhaoru; Ko, Hsin-Yu; Santra, Biswajit; Dhuvad, Pratikkumar; Wu, Xifan

2018-04-01

We perform ab initio molecular dynamics (AIMD) simulation of liquid water in the canonical ensemble at ambient conditions using the strongly constrained and appropriately normed (SCAN) meta-generalized-gradient approximation (GGA) functional approximation and carry out systematic comparisons with the results obtained from the GGA-level Perdew-Burke-Ernzerhof (PBE) functional and Tkatchenko-Scheffler van der Waals (vdW) dispersion correction inclusive PBE functional. We analyze various properties of liquid water including radial distribution functions, oxygen-oxygen-oxygen triplet angular distribution, tetrahedrality, hydrogen bonds, diffusion coefficients, ring statistics, density of states, band gaps, and dipole moments. We find that the SCAN functional is generally more accurate than the other two functionals for liquid water by not only capturing the intermediate-range vdW interactions but also mitigating the overly strong hydrogen bonds prescribed in PBE simulations. We also compare the results of SCAN-based AIMD simulations in the canonical and isothermal-isobaric ensembles. Our results suggest that SCAN provides a reliable description for most structural, electronic, and dynamical properties in liquid water.
Mechanical Properties of a vdW molecular monolayer at a metal surface: Structural Polymorphism leading to facile compression

NASA Astrophysics Data System (ADS)

Sun, Dezheng; Kim, Daeho; Le, Duy; Borck, Øyvind; Berland, Kristian; Kim, Kwangmoo; Lu, Wenhao; Zhu, Yeming; Luo, Miaomiao; Wyrick, Jon; Cheng, Zhihai; Einstein, T. L.; Rahman, Talat; Hyldgaard, Per; Bartels, Ludwig

2011-03-01

Intermolecular force plays an important role in self-assembly and surface pattern formation. Anthracene and similar unsubstituted arenes attach to a metallic substrate predominantly through van der Waals interaction leading. In this contribution we present images how anthracene on Cu(111) forms a large number of highly ordered patterns that feature a broad array of structural motifs. Density functional theory modeling including vdW interactions allows us to model the energetic of the pattern formation at high fidelity. Moreover, it allows us to deduce the strain energy associated with films of varying coverage. From this work, we obtain the Young's modulus and Poisson Ratio of a molecular monolayer, which resemble properties conventionally found for porous materials. These patterns are in marked contrast to those found after introduction of functional groups in the molecules, such as carbonyls or thiols.

Extent of Fock-exchange mixing for a hybrid van der Waals density functional?

NASA Astrophysics Data System (ADS)

Jiao, Yang; Schröder, Elsebeth; Hyldgaard, Per

2018-05-01

The vdW-DF-cx0 exchange-correlation hybrid design [K. Berland et al., J. Chem. Phys. 146, 234106 (2017)] has a truly nonlocal correlation component and aims to facilitate concurrent descriptions of both covalent and non-covalent molecular interactions. The vdW-DF-cx0 design mixes a fixed ratio, a, of the Fock exchange into the consistent-exchange van der Waals density functional, vdW-DF-cx [K. Berland and P. Hyldgaard, Phys. Rev. B 89, 035412 (2014)]. The mixing value a is sometimes taken as a semi-empirical parameter in hybrid formulations. Here, instead, we assert a plausible optimum average a value for the vdW-DF-cx0 design from a formal analysis; A new, independent determination of the mixing a is necessary since the Becke fit [A. D. Becke, J. Chem. Phys. 98, 5648 (1993)], yielding a' = 0.2, is restricted to semilocal correlation and does not reflect non-covalent interactions. To proceed, we adapt the so-called two-legged hybrid construction [K. Burke et al., Chem. Phys. Lett. 265, 115 (1997)] to a starting point in the vdW-DF-cx functional. For our approach, termed vdW-DF-tlh, we estimate the properties of the adiabatic-connection specification of the exact exchange-correlation functional, by combining calculations of the Fock exchange and of the coupling-constant variation in vdW-DF-cx. We find that such vdW-DF-tlh hybrid constructions yield accurate characterizations of molecular interactions (even if they lack self-consistency). The accuracy motivates trust in the vdW-DF-tlh determination of system-specific values of the Fock-exchange mixing. We find that an average value a' = 0.2 best characterizes the vdW-DF-tlh description of covalent and non-covalent interactions, although there exists some scatter. This finding suggests that the original Becke value, a' = 0.2, also represents an optimal average Fock-exchange mixing for the new, truly nonlocal-correlation hybrids. To enable self-consistent calculations, we furthermore define and test a zero-parameter hybrid functional vdW-DF-cx0p (having fixed mixing a' = 0.2) and document that this truly nonlocal correlation hybrid works for general molecular interactions (at reference and at relaxed geometries). It is encouraging that the vdW-DF-cx0p functional remains useful also for descriptions of some extended systems.
van der Waals Interactions in Hadron Resonance Gas: From Nuclear Matter to Lattice QCD.

PubMed

Vovchenko, Volodymyr; Gorenstein, Mark I; Stoecker, Horst

2017-05-05

An extension of the ideal hadron resonance gas (HRG) model is constructed which includes the attractive and repulsive van der Waals (VDW) interactions between baryons. This VDW-HRG model yields the nuclear liquid-gas transition at low temperatures and high baryon densities. The VDW parameters a and b are fixed by the ground state properties of nuclear matter, and the temperature dependence of various thermodynamic observables at zero chemical potential are calculated within the VDW-HRG model. Compared to the ideal HRG model, the inclusion of VDW interactions between baryons leads to a qualitatively different behavior of second and higher moments of fluctuations of conserved charges, in particular in the so-called crossover region T∼140-190 MeV. For many observables this behavior resembles closely the results obtained from lattice QCD simulations. This hadronic model also predicts nontrivial behavior of net-baryon fluctuations in the region of phase diagram probed by heavy-ion collision experiments. These results imply that VDW interactions play a crucial role in the thermodynamics of hadron gas. Thus, the commonly performed comparisons of the ideal HRG model with the lattice and heavy-ion data may lead to misconceptions and misleading conclusions.
Capillary wave Hamiltonian for the Landau-Ginzburg-Wilson density functional

NASA Astrophysics Data System (ADS)

Chacón, Enrique; Tarazona, Pedro

2016-06-01

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

PubMed

Chacón, Enrique; Tarazona, Pedro

2016-06-22

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

NASA Astrophysics Data System (ADS)

Gieles, Mark; Zocchi, Alice

2017-10-01

LIMEPY solves distribution function (DF) based lowered isothermal models. It solves Poisson's equation used on input parameters and offers fast solutions for isotropic/anisotropic, single/multi-mass models, normalized DF values, density and velocity moments, projected properties, and generates discrete samples.
Computational phase diagrams of noble gas hydrates under pressure

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

Teeratchanan, Pattanasak, E-mail: s1270872@sms.ed.ac.uk; Hermann, Andreas, E-mail: a.hermann@ed.ac.uk

2015-10-21

We present results from a first-principles study on the stability of noble gas-water compounds in the pressure range 0-100 kbar. Filled-ice structures based on the host water networks ice-I{sub h}, ice-I{sub c}, ice-II, and C{sub 0} interacting with guest species He, Ne, and Ar are investigated, using density functional theory (DFT) with four different exchange-correlation functionals that include dispersion effects to various degrees: the non-local density-based optPBE-van der Waals (vdW) and rPW86-vdW2 functionals, the semi-empirical D2 atom pair correction, and the semi-local PBE functional. In the He-water system, the sequence of stable phases closely matches that seen in the hydrogenmore » hydrates, a guest species of comparable size. In the Ne-water system, we predict a novel hydrate structure based on the C{sub 0} water network to be stable or at least competitive at relatively low pressure. In the Ar-water system, as expected, no filled-ice phases are stable; however, a partially occupied Ar-C{sub 0} hydrate structure is metastable with respect to the constituents. The ability of the different DFT functionals to describe the weak host-guest interactions is analysed and compared to coupled cluster results on gas phase systems.« less
Electric field modulation of Schottky barrier height in graphene/MoSe{sub 2} van der Waals heterointerface

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

Sata, Yohta; Moriya, Rai, E-mail: moriyar@iis.u-tokyo.ac.jp, E-mail: tmachida@iis.u-tokyo.ac.jp; Morikawa, Sei

2015-07-13

We demonstrate a vertical field-effect transistor based on a graphene/MoSe{sub 2} van der Waals (vdW) heterostructure. The vdW interface between the graphene and MoSe{sub 2} exhibits a Schottky barrier with an ideality factor of around 1.3, suggesting a high-quality interface. Owing to the low density of states in graphene, the position of the Fermi level in the graphene can be strongly modulated by an external electric field. Therefore, the Schottky barrier height at the graphene/MoSe{sub 2} vdW interface is also modulated. We demonstrate a large current ON-OFF ratio of 10{sup 5}. These results point to the potential high performance ofmore » the graphene/MoSe{sub 2} vdW heterostructure for electronics applications.« less
Valley density-wave (VDW) and Superconductivity in Iron-Pnictides

NASA Astrophysics Data System (ADS)

Cvetkovic, Vladimir; Tesanovic, Zlatko

2009-03-01

One of the experimentally observed features of iron-pnictide superconductors is the structural transition and SDW ordering occurring at almost the same temperature. Starting from a tight-binding model [1], we construct an effective theory for iron-pnictides with the distinctive two hole and two electron Fermi surfaces. This theory is then mapped onto a negative-U Hubbard model with additional orbital and spin flavors [2]. We demonstrate that the superconducting instability of the attractive Hubbard model --- valley density-wave (VDW) --- corresponds to the observed structural and SDW orders. The deviations from perfect nesting between the hole and electron Fermi surfaces are mapped onto the Zeeman field which causes portions of Fermi surface to remain ungapped. The origin of pnictide superconductivity in this model, and its ties to the VDW are discussed. [1] V. Cvetkovic and Z. Tesanovic, http://arxiv.org/abs/0804.4678. [2] V. Cvetkovic and Z. Tesanovic, http://arxiv.org/abs/0808.3742.
Structural evolution of gypsum under high pressure: single-crystal X-ray experiments revisited

NASA Astrophysics Data System (ADS)

Li, Tsung-Lung; Lee, Pei-Lun

2018-05-01

The structures of gypsum at pressures up to approximately 4 GPa are studied with density functional theory (DFT) and thoroughly compared with single-crystal X-ray diffraction experiments reported in the literature [Comodi et al. in (Am Miner 93:1530-1537, 2008)]. It is found that the exchange-correlation density functional revPBE (revised Perdew-Burke-Ernzerhof) in conjunction with a nonlocal van der Waals (vdW) correction is capable of modeling the lattice constants, axial compressibility, and bulk modulus with good accuracy, suggesting that the inclusion of the vdW functional is crucially important for understanding the structure of hydrous minerals. To gain further physical insights, the geometric parameters associated with the constituting components of gypsum (water molecules, SO4 tetrahedra, and CaO8 polyhedra) are analyzed and compared with the experimental values. DFT simulations show that, under pressure, the polyhedral layers remain as nearly planar sheets of interconnecting SO4 tetrahedra and CaO8 polyhedra without further crinkling. DFT analysis on the layer compressibility along the major crystal axis reveals that, in contrast to experimental reports, the hydrous interlayer is less compressible than the polyhedral layer. Squeezed by the lateral pressure, the water molecules in the hydrous interlayer become better affixed along the major axis, making the interlayer harder to compress along this axis.
Many-body van der Waals interactions in molecules and condensed matter.

PubMed

DiStasio, Robert A; Gobre, Vivekanand V; Tkatchenko, Alexandre

2014-05-28

This work reviews the increasing evidence that many-body van der Waals (vdW) or dispersion interactions play a crucial role in the structure, stability and function of a wide variety of systems in biology, chemistry and physics. Starting with the exact expression for the electron correlation energy provided by the adiabatic connection fluctuation-dissipation theorem, we derive both pairwise and many-body interatomic methods for computing the long-range dispersion energy by considering a model system of coupled quantum harmonic oscillators within the random-phase approximation. By coupling this approach to density functional theory, the resulting many-body dispersion (MBD) method provides an accurate and efficient scheme for computing the frequency-dependent polarizability and many-body vdW energy in molecules and materials with a finite electronic gap. A select collection of applications are presented that ascertain the fundamental importance of these non-bonded interactions across the spectrum of intermolecular (the S22 and S66 benchmark databases), intramolecular (conformational energies of alanine tetrapeptide) and supramolecular (binding energy of the 'buckyball catcher') complexes, as well as molecular crystals (cohesive energies in oligoacenes). These applications demonstrate that electrodynamic response screening and beyond-pairwise many-body vdW interactions--both captured at the MBD level of theory--play a quantitative, and sometimes even qualitative, role in describing the properties considered herein. This work is then concluded with an in-depth discussion of the challenges that remain in the future development of reliable (accurate and efficient) methods for treating many-body vdW interactions in complex materials and provides a roadmap for navigating many of the research avenues that are yet to be explored.
All-electron density functional calculation on insulin with quasi-canonical localized orbitals.

PubMed

Inaba, Toru; Tahara, Saisei; Nisikawa, Nobutaka; Kashiwagi, Hiroshi; Sato, Fumitoshi

2005-07-30

An all-electron density functional (DF) calculation on insulin was performed by the Gaussian-based DF program, ProteinDF. Quasi-canonical localized orbitals (QCLOs) were used to improve the initial guess for the self-consistent field (SCF) calculation. All calculations were carried out by parallel computing on eight processors of an Itanium2 cluster (SGI Altix3700) with a theoretical peak performance of 41.6 GFlops. It took 35 h for the whole calculation. Insulin is a protein hormone consisting of two peptide chains linked by three disulfide bonds. The numbers of residues, atoms, electrons, orbitals, and auxiliary functions are 51, 790, 3078, 4439, and 8060, respectively. An all-electron DF calculation on insulin was successfully carried out, starting from connected QCLOs. Regardless of a large molecule with complicated topology, the differences in the total energy and the Mulliken atomic charge between initial and converged wavefunctions were very small. The calculation proceeded smoothly without any trial and error, suggesting that this is a promising method to obtain SCF convergence on large molecules such as proteins.
DFT-based method for more accurate adsorption energies: An adaptive sum of energies from RPBE and vdW density functionals

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

Hensley, Alyssa J. R.; Ghale, Kushal; Rieg, Carolin

In recent years, the popularity of density functional theory with periodic boundary conditions (DFT) has surged for the design and optimization of functional materials. However, no single DFT exchange–correlation functional currently available gives accurate adsorption energies on transition metals both when bonding to the surface is dominated by strong covalent or ionic bonding and when it has strong contributions from van der Waals interactions (i.e., dispersion forces). Here we present a new, simple method for accurately predicting adsorption energies on transition-metal surfaces based on DFT calculations, using an adaptively weighted sum of energies from RPBE and optB86b-vdW (or optB88-vdW) densitymore » functionals. This method has been benchmarked against a set of 39 reliable experimental energies for adsorption reactions. Our results show that this method has a mean absolute error and root mean squared error relative to experiments of 13.4 and 19.3 kJ/mol, respectively, compared to 20.4 and 26.4 kJ/mol for the BEEF-vdW functional. For systems with large van der Waals contributions, this method decreases these errors to 11.6 and 17.5 kJ/mol. Furthermore, this method provides predictions of adsorption energies both for processes dominated by strong covalent or ionic bonding and for those dominated by dispersion forces that are more accurate than those of any current standard DFT functional alone.« less
DFT-based method for more accurate adsorption energies: An adaptive sum of energies from RPBE and vdW density functionals

DOE PAGES

Hensley, Alyssa J. R.; Ghale, Kushal; Rieg, Carolin; ...

2017-01-26

In recent years, the popularity of density functional theory with periodic boundary conditions (DFT) has surged for the design and optimization of functional materials. However, no single DFT exchange–correlation functional currently available gives accurate adsorption energies on transition metals both when bonding to the surface is dominated by strong covalent or ionic bonding and when it has strong contributions from van der Waals interactions (i.e., dispersion forces). Here we present a new, simple method for accurately predicting adsorption energies on transition-metal surfaces based on DFT calculations, using an adaptively weighted sum of energies from RPBE and optB86b-vdW (or optB88-vdW) densitymore » functionals. This method has been benchmarked against a set of 39 reliable experimental energies for adsorption reactions. Our results show that this method has a mean absolute error and root mean squared error relative to experiments of 13.4 and 19.3 kJ/mol, respectively, compared to 20.4 and 26.4 kJ/mol for the BEEF-vdW functional. For systems with large van der Waals contributions, this method decreases these errors to 11.6 and 17.5 kJ/mol. Furthermore, this method provides predictions of adsorption energies both for processes dominated by strong covalent or ionic bonding and for those dominated by dispersion forces that are more accurate than those of any current standard DFT functional alone.« less
The ordering of symmetric diblock copolymers: A comparison of self-consistent-field and density functional approaches

NASA Astrophysics Data System (ADS)

Nath, Shyamal K.; McCoy, John D.; Curro, John G.; Saunders, Randall S.

1997-02-01

Polymer reference interaction site model (PRISM) based density functional (DF) theory is used to evaluate the structure and thermodynamics of structurally symmetric, freely jointed, diblock chains with 0.50 volume fraction. These results are compared to the results of self-consistent-field (SCF) theory. Agreement between the predictions of the SCF and DF theories is found for the lamella spacing well above the order-disorder transition (ODT) and for the qualitative behavior of the interfacial thickness as a function of both chain length and Flory-Huggins χ parameter. Disagreement is found for the magnitude of the interfacial thickness where DF theory indicates that the thickness is 1.7±0.2 times larger than that predicted by SCF theory. It appears that behavior on the monomer length scale is sensitive to system specific details which are neglected by SCF theory.
Molecular adsorption on metal surfaces with van der Waals density functionals

NASA Astrophysics Data System (ADS)

Li, Guo; Tamblyn, Isaac; Cooper, Valentino R.; Gao, Hong-Jun; Neaton, Jeffrey B.

2012-03-01

The adsorption of 1,4-benzenediamine (BDA) on Au(111) and azobenzene on Ag(111) is investigated using density functional theory (DFT) with the nonlocal van der Waals density functional (vdW-DF) and the semilocal Perdew-Burke-Ernzerhof functional. For BDA on Au(111), the inclusion of London dispersion interactions not only dramatically enhances the molecule-substrate binding, resulting in adsorption energies consistent with experimental results, but also significantly alters the BDA binding geometry. For azobenzene on Ag(111), vdW-DFs produce superior adsorption energies compared to those obtained with other dispersion-corrected DFT approaches. These results provide evidence for the applicability of the vdW-DF approach and serve as practical benchmarks for the investigation of molecules adsorbed on noble-metal surfaces.
van der Waals Layered Materials: Opportunities and Challenges.

PubMed

Duong, Dinh Loc; Yun, Seok Joon; Lee, Young Hee

2017-12-26

Since graphene became available by a scotch tape technique, a vast class of two-dimensional (2D) van der Waals (vdW) layered materials has been researched intensively. What is more intriguing is that the well-known physics and chemistry of three-dimensional (3D) bulk materials are often irrelevant, revealing exotic phenomena in 2D vdW materials. By further constructing heterostructures of these materials in the planar and vertical directions, which can be easily achieved via simple exfoliation techniques, numerous quantum mechanical devices have been demonstrated for fundamental research and technological applications. It is, therefore, necessary to review the special features in 2D vdW materials and to discuss the remaining issues and challenges. Here, we review the vdW materials library, technology relevance, and specialties of vdW materials covering the vdW interaction, strong Coulomb interaction, layer dependence, dielectric screening engineering, work function modulation, phase engineering, heterostructures, stability, growth issues, and the remaining challenges.
Diagrams for comprehensive molecular orbital-based chemical reaction analyses: reactive orbital energy diagrams.

PubMed

Tsuneda, Takao; Singh, Raman Kumar; Chattaraj, Pratim Kumar

2018-05-15

Reactive orbital energy diagrams are presented as a tool for comprehensively performing orbital-based reaction analyses. The diagrams rest on the reactive orbital energy theory, which is the expansion of conceptual density functional theory (DFT) to an orbital energy-based theory. The orbital energies on the intrinsic reaction coordinates of fundamental reactions are calculated by long-range corrected DFT, which is confirmed to provide accurate orbital energies of small molecules, combining with a van der Waals (vdW) correlation functional, in order to examine the vdW effect on the orbital energies. By analysing the reactions based on the reactive orbital energy theory using these accurate orbital energies, it is found that vdW interactions significantly affect the orbital energies in the initial reaction processes and that more than 70% of reactions are determined to be initially driven by charge transfer, while the remaining structural deformation (dynamics)-driven reactions are classified into identity, cyclization and ring-opening, unimolecular dissociation, and H2 reactions. The reactive orbital energy diagrams, which are constructed using these results, reveal that reactions progress so as to delocalize the occupied reactive orbitals, which are determined as contributing orbitals and are usually not HOMOs, by hybridizing the unoccupied reactive orbitals, which are usually not LUMOs. These diagrams also raise questions about conventional orbital-based diagrams such as frontier molecular orbital diagrams, even for the well-established interpretation of Diels-Alder reactions.
Towards an accurate description of perovskite ferroelectrics: exchange and correlation effects

DOE PAGES

Yuk, Simuck F.; Pitike, Krishna Chaitanya; Nakhmanson, Serge M.; ...

2017-03-03

Using the van der Waals density functional with C09 exchange (vdW-DF-C09), which has been applied to describing a wide range of dispersion-bound systems, we explore the physical properties of prototypical ABO 3 bulk ferroelectric oxides. Surprisingly, vdW-DF-C09 provides a superior description of experimental values for lattice constants, polarization and bulk moduli, exhibiting similar accuracy to the modified Perdew-Burke-Erzenhoff functional which was designed specifically for bulk solids (PBEsol). The relative performance of vdW-DF-C09 is strongly linked to the form of the exchange enhancement factor which, like PBEsol, tends to behave like the gradient expansion approximation for small reduced gradients. These resultsmore » suggest the general-purpose nature of the class of vdW-DF functionals, with particular consequences for predicting material functionality across dense and sparse matter regimes.« less
Towards an accurate description of perovskite ferroelectrics: exchange and correlation effects

PubMed Central

Yuk, Simuck F.; Pitike, Krishna Chaitanya; Nakhmanson, Serge M.; Eisenbach, Markus; Li, Ying Wai; Cooper, Valentino R.

2017-01-01

Using the van der Waals density functional with C09 exchange (vdW-DF-C09), which has been applied to describing a wide range of dispersion-bound systems, we explore the physical properties of prototypical ABO3 bulk ferroelectric oxides. Surprisingly, vdW-DF-C09 provides a superior description of experimental values for lattice constants, polarization and bulk moduli, exhibiting similar accuracy to the modified Perdew-Burke-Erzenhoff functional which was designed specifically for bulk solids (PBEsol). The relative performance of vdW-DF-C09 is strongly linked to the form of the exchange enhancement factor which, like PBEsol, tends to behave like the gradient expansion approximation for small reduced gradients. These results suggest the general-purpose nature of the class of vdW-DF functionals, with particular consequences for predicting material functionality across dense and sparse matter regimes. PMID:28256544
First-principles calculation of the reflectance of shock-compressed xenon

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

Norman, G. E.; Saitov, I. M., E-mail: saitovilnur@gmail.com; Stegailov, V. V.

2015-05-15

Within electron density functional theory (DFT), the reflectance of radiation from shock-compressed xenon plasma is calculated. The dependence of the reflectance on the frequency of the incident radiation and on the plasma density is considered. The Fresnel formula is used. The expression for the longitudinal dielectric tensor in the long-wavelength limit is used to calculate the imaginary part of the dielectric function (DF). The real part of the DF is determined by the Kramers-Kronig transformation. The results are compared with experimental data. An approach is proposed to estimate the plasma frequency in shock-compressed xenon.

Vibrational mode frequencies of H2S and H2O adsorbed on Ge(0 0 1)-(2 × 1) surfaces

NASA Astrophysics Data System (ADS)

Hartnett, M.; Fahy, S.

2015-02-01

The equilibrium geometry and vibrational modes of H2S and H2O-terminated Ge(0 0 1)-(2 × 1) surfaces are calculated in a supercell approach using first-principles density functional theory in the local density (LDA), generalized gradient (GGA) approximations and van der Waals (vdW) interactions. Mode frequencies are found using the frozen phonon method. For the H2S-passivated surface, the calculated frequencies in LDA (GGA) are 2429 cm-1 (2490) for the Hsbnd S stretch mode, 712 cm-1 (706) for the Hsbnd S bond bending mode, 377 cm-1 (36) for the Gesbnd S stretch mode and 328 cm-1 (337) for Hsbnd S wag mode. Frequencies for the H2O passivated surface are 3590 cm-1 (3600) for the Hsbnd O stretch mode, 921 cm-1 (947) for the bending mode, 609 cm-1 (559) for the Gesbnd O stretch, 1995 cm-1 (1991) for the Gesbnd H stretch mode, 498 cm-1 (478) for the Gesbnd H bending mode and 342 cm-1 (336) for the Hsbnd O wag mode. The differences between the functionals including vdW terms and the LDA or GGA are less than the differences between LDA and GGA for the vibrational mode frequencies.
Tuning the Schottky barrier in the arsenene/graphene van der Waals heterostructures by electric field

NASA Astrophysics Data System (ADS)

Li, Wei; Wang, Tian-Xing; Dai, Xian-Qi; Wang, Xiao-Long; Ma, Ya-Qiang; Chang, Shan-Shan; Tang, Ya-Nan

2017-04-01

Using density functional theory calculations, we investigate the electronic properties of arsenene/graphene van der Waals (vdW) heterostructures by applying external electric field perpendicular to the layers. It is demonstrated that weak vdW interactions dominate between arsenene and graphene with their intrinsic electronic properties preserved. We find that an n-type Schottky contact is formed at the arsenene/graphene interface with a Schottky barrier of 0.54 eV. Moreover, the vertical electric field can not only control the Schottky barrier height but also the Schottky contacts (n-type and p-type) and Ohmic contacts (n-type) at the interface. Tunable p-type doping in graphene is achieved under the negative electric field because electrons can transfer from the Dirac point of graphene to the conduction band of arsenene. The present study would open a new avenue for application of ultrathin arsenene/graphene heterostructures in future nano- and optoelectronics.
Long-Range Repulsion Between Spatially Confined van der Waals Dimers

NASA Astrophysics Data System (ADS)

Sadhukhan, Mainak; Tkatchenko, Alexandre

2017-05-01

It is an undisputed textbook fact that nonretarded van der Waals (vdW) interactions between isotropic dimers are attractive, regardless of the polarizability of the interacting systems or spatial dimensionality. The universality of vdW attraction is attributed to the dipolar coupling between fluctuating electron charge densities. Here, we demonstrate that the long-range interaction between spatially confined vdW dimers becomes repulsive when accounting for the full Coulomb interaction between charge fluctuations. Our analytic results are obtained by using the Coulomb potential as a perturbation over dipole-correlated states for two quantum harmonic oscillators embedded in spaces with reduced dimensionality; however, the long-range repulsion is expected to be a general phenomenon for spatially confined quantum systems. We suggest optical experiments to test our predictions, analyze their relevance in the context of intermolecular interactions in nanoscale environments, and rationalize the recent observation of anomalously strong screening of the lateral vdW interactions between aromatic hydrocarbons adsorbed on metal surfaces.
Characterizing water-metal interfaces and machine learning potential energy surfaces

NASA Astrophysics Data System (ADS)

Ryczko, Kevin

In this thesis, we first discuss the fundamentals of ab initio electronic structure theory and density functional theory (DFT). We also discuss statistics related to computing thermodynamic averages of molecular dynamics (MD). We then use this theory to analyze and compare the structural, dynamical, and electronic properties of liquid water next to prototypical metals including platinum, graphite, and graphene. Our results are built on Born-Oppenheimer molecular dynamics (BOMD) generated using density functional theory (DFT) which explicitly include van der Waals (vdW) interactions within a first principles approach. All calculations reported use large simulation cells, allowing for an accurate treatment of the water-electrode interfaces. We have included vdW interactions through the use of the optB86b-vdW exchange correlation functional. Comparisons with the Perdew-Burke-Ernzerhof (PBE) exchange correlation functional are also shown. We find an initial peak, due to chemisorption, in the density profile of the liquid water-Pt interface not seen in the liquid water-graphite interface, liquid watergraphene interface, nor interfaces studied previously. To further investigate this chemisorption peak, we also report differences in the electronic structure of single water molecules on both Pt and graphite surfaces. We find that a covalent bond forms between the single water molecule and the platinum surface, but not between the single water molecule and the graphite surface. We also discuss the effects that defects and dopants in the graphite and graphene surfaces have on the structure and dynamics of liquid water. Lastly, we introduce artificial neural networks (ANNs), and demonstrate how they can be used to machine learn electronic structure calculations. As a proof of principle, we show the success of an ANN potential energy surfaces for a dimer molecule with a Lennard-Jones potential.
Low-Dimensional Materials for Optoelectronic and Bioelectronic Applications

NASA Astrophysics Data System (ADS)

Hong, Tu

In this thesis, we first discuss the fundamentals of ab initio electronic structure theory and density functional theory (DFT). We also discuss statistics related to computing thermodynamic averages of molecular dynamics (MD). We then use this theory to analyze and compare the structural, dynamical, and electronic properties of liquid water next to prototypical metals including platinum, graphite, and graphene. Our results are built on Born-Oppenheimer molecular dynamics (BOMD) generated using density functional theory (DFT) which explicitly include van der Waals (vdW) interactions within a first principles approach. All calculations reported use large simulation cells, allowing for an accurate treatment of the water-electrode interfaces. We have included vdW interactions through the use of the optB86b-vdW exchange correlation functional. Comparisons with the Perdew-Burke-Ernzerhof (PBE) exchange correlation functional are also shown. We find an initial peak, due to chemisorption, in the density profile of the liquid water-Pt interface not seen in the liquid water-graphite interface, liquid watergraphene interface, nor interfaces studied previously. To further investigate this chemisorption peak, we also report differences in the electronic structure of single water molecules on both Pt and graphite surfaces. We find that a covalent bond forms between the single water molecule and the platinum surface, but not between the single water molecule and the graphite surface. We also discuss the effects that defects and dopants in the graphite and graphene surfaces have on the structure and dynamics of liquid water. Lastly, we introduce artificial neural networks (ANNs), and demonstrate how they can be used to machine learn electronic structure calculations. As a proof of principle, we show the success of an ANN potential energy surfaces for a dimer molecule with a Lennard-Jones potential.
Redshift-space distortions with the halo occupation distribution - II. Analytic model

NASA Astrophysics Data System (ADS)

Tinker, Jeremy L.

2007-01-01

We present an analytic model for the galaxy two-point correlation function in redshift space. The cosmological parameters of the model are the matter density Ωm, power spectrum normalization σ8, and velocity bias of galaxies αv, circumventing the linear theory distortion parameter β and eliminating nuisance parameters for non-linearities. The model is constructed within the framework of the halo occupation distribution (HOD), which quantifies galaxy bias on linear and non-linear scales. We model one-halo pairwise velocities by assuming that satellite galaxy velocities follow a Gaussian distribution with dispersion proportional to the virial dispersion of the host halo. Two-halo velocity statistics are a combination of virial motions and host halo motions. The velocity distribution function (DF) of halo pairs is a complex function with skewness and kurtosis that vary substantially with scale. Using a series of collisionless N-body simulations, we demonstrate that the shape of the velocity DF is determined primarily by the distribution of local densities around a halo pair, and at fixed density the velocity DF is close to Gaussian and nearly independent of halo mass. We calibrate a model for the conditional probability function of densities around halo pairs on these simulations. With this model, the full shape of the halo velocity DF can be accurately calculated as a function of halo mass, radial separation, angle and cosmology. The HOD approach to redshift-space distortions utilizes clustering data from linear to non-linear scales to break the standard degeneracies inherent in previous models of redshift-space clustering. The parameters of the occupation function are well constrained by real-space clustering alone, separating constraints on bias and cosmology. We demonstrate the ability of the model to separately constrain Ωm,σ8 and αv in models that are constructed to have the same value of β at large scales as well as the same finger-of-god distortions at small scales.
Modification of the electronic properties of hexagonal boron-nitride in BN/graphene vertical heterostructures

DOE PAGES

Pan, Minghu; Liang, Liangbo; Lin, Wenzhi; ...

2016-09-28

Van der Waals (vdW) heterostructures consist of isolated atomic planar structures, assembled layer- by-layer into desired structures in a well-defined sequence. Graphene deposited on hexagonal boron nitride (h-BN) has been first considered as a testbed system for vdW heterostructures, and many others have been demonstrated both theoretically and experimentally, revealing many attractive properties and phenomena. However, much less emphasis has been placed on how graphene actively affects h-BN properties. Here, we perform local probe measurements on single-layer h-BN grown over graphene and highlight the manifestation of a proximity effect that significantly affects the electronic properties of h-BN due to itsmore » coupling with the underlying graphene. We find electronic states originating from the graphene layer and the Cu substrate to be injected into the wide electronic gap of the h-BN top layer. Such proximity effect is further confirmed in a study of the variation of h-BN in-gap states with interlayer couplings, elucidated using a combination of topographical/ spectroscopic measurements and first-principles density functional theory calculations. In conclusion, the findings of this work indicate the potential of mutually engineering electronic properties of the components of vdW heterostructures.« less
One-step synthesis of van der Waals heterostructures of graphene and two-dimensional superconducting α -M o2C

NASA Astrophysics Data System (ADS)

Qiao, Jia-Bin; Gong, Yue; Zuo, Wei-Jie; Wei, Yi-Cong; Ma, Dong-Lin; Yang, Hong; Yang, Ning; Qiao, Kai-Yao; Shi, Jin-An; Gu, Lin; He, Lin

2017-05-01

Assembling different two-dimensional (2D) crystals, covering a very broad range of properties, into van der Waals (vdW) heterostructures enables unprecedented possibilities for combining the best of different ingredients in one objective material. So far, metallic, semiconducting, and insulating 2D crystals have been used successfully in making functional vdW heterostructures with properties by design. Here, we expand 2D superconducting crystals as a building block of vdW hererostructures. One-step growth of large-scale high-quality vdW heterostructures of graphene and 2D superconducting α -M o2C by using chemical vapor deposition is reported. The superconductivity and its 2D nature of the heterostructures are characterized by our scanning tunneling microscopy measurements. This adds 2D superconductivity, the most attractive property of condensed matter physics, to vdW heterostructures.
van der Waals torque and force between anisotropic topological insulator slabs

NASA Astrophysics Data System (ADS)

Lu, Bing-Sui

2018-01-01

We investigate the character of the van der Waals (vdW) torque and force between two coplanar and dielectrically anisotropic topological insulator (TI) slabs separated by a vacuum gap in the nonretardation regime, where the optic axes of the slabs are each perpendicular to the normal direction to the slab-gap interface and also generally differently oriented from each other. We find that in addition to the magnetoelectric coupling strength, the anisotropy can also influence the sign of the vdW force, viz., a repulsive vdW force can become attractive if the anisotropy is increased sufficiently. In addition, the vdW force oscillates as a function of the angular difference between the optic axes of the TI slabs, being most repulsive/least attractive (least repulsive/most attractive) for angular differences that are integer (half-integer) multiples of π . Our third finding is that the vdW torque for TI slabs is generally weaker than that for ordinary dielectric slabs. Our work provides an instance in which the vector potential appears in a calculation of the vdW interaction for which the limit is nonretarded or static.
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.
Luminosity and Stellar Mass Functions from the 6dF Galaxy Survey

NASA Astrophysics Data System (ADS)

Colless, M.; Jones, D. H.; Peterson, B. A.; Campbell, L.; Saunders, W.; Lah, P.

2007-12-01

The completed 6dF Galaxy Survey includes redshifts for over 124,000 galaxies. We present luminosity functions in optical and near-infrared passbands that span a range of 10^4 in luminosity. These luminosity functions show systematic deviations from the Schechter form. The corresponding luminosity densities in the optical and near-infrared are consistent with an old stellar population and a moderately declining star formation rate. Stellar mass functions, derived from the K band luminosities and simple stellar population models selected by b_J-r_F colour, lead to an estimate of the present-day stellar mass density of ρ_* = (5.00 ± 0.11) × 10^8 h M_⊙ Mpc^{-3}, corresponding to Ω_* h = (1.80 ± 0.04) × 10^{-3}.
Dispersion interactions with linear scaling DFT: a study of planar molecules on charged polar surfaces

NASA Astrophysics Data System (ADS)

Andrinopoulos, Lampros; Hine, Nicholas; Haynes, Peter; Mostofi, Arash

2010-03-01

The placement of organic molecules such as CuPc (copper phthalocyanine) on wurtzite ZnO (zinc oxide) charged surfaces has been proposed as a way of creating photovoltaic solar cellsfootnotetextG.D. Sharma et al., Solar Energy Materials & Solar Cells 90, 933 (2006) ; optimising their performance may be aided by computational simulation. Electronic structure calculations provide high accuracy at modest computational cost but two challenges are encountered for such layered systems. First, the system size is at or beyond the limit of traditional cubic-scaling Density Functional Theory (DFT). Second, traditional exchange-correlation functionals do not account for van der Waals (vdW) interactions, crucial for determining the structure of weakly bonded systems. We present an implementation of recently developed approachesfootnotetextP.L. Silvestrelli, P.R.L. 100, 102 (2008) to include vdW in DFT within ONETEPfootnotetextC.-K. Skylaris, P.D. Haynes, A.A. Mostofi and M.C. Payne, J.C.P. 122, 084119 (2005) , a linear-scaling package for performing DFT calculations using a basis of localised functions. We have applied this methodology to simple planar organic molecules, such as benzene and pentacene, on ZnO surfaces.
Van der Waals epitaxial growth of two-dimensional single-crystalline GaSe domains on graphene

DOE PAGES

Li, Xufan; Basile, Leonardo; Huang, Bing; ...

2015-07-22

Two-dimensional (2D) van der Waals (vdW) heterostructures are a family of artificially-structured materials that promise tunable optoelectronic properties for devices with enhanced functionalities. Compared to stamping, direct epitaxy of vdW heterostructures is ideal for clean interlayer interfaces and scalable device fabrication. Here, we explore the synthesis and preferred orientations of 2D GaSe atomic layers on graphene (Gr) by vdW epitaxy. Guided by the wrinkles on graphene, GaSe nuclei form that share a predominant lattice orientation. Due to vdW epitaxial growth many nuclei grow as perfectly aligned crystals and coalesce to form large (tens of microns), single-crystal flakes. Through theoretical investigationsmore » of interlayer energetics, and measurements of preferred orientations by atomic-resolution STEM and electron diffraction, a 10.9 interlayer rotation of the GaSe lattice with respect to the underlying graphene is found to be the most energetically preferred vdW heterostructure with the largest binding energy and the longest-range ordering. These GaSe/Gr vdW heterostructures exhibit an enhanced Raman E 2 1g band of monolayer GaSe along with highly-quenched photoluminescence due to strong charge transfer. Despite the very large lattice mismatch of GaSe/Gr through vdW epitaxy, the predominant orientation control and convergent formation of large single-crystal flakes demonstrated here is promising for the scalable synthesis of large-area vdW heterostructures for the development of new optical and optoelectronic devices.« less
Van der Waals epitaxial growth of two-dimensional single-crystalline GaSe domains on graphene

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

Li, Xufan; Basile, Leonardo; Huang, Bing

Two-dimensional (2D) van der Waals (vdW) heterostructures are a family of artificially-structured materials that promise tunable optoelectronic properties for devices with enhanced functionalities. Compared to stamping, direct epitaxy of vdW heterostructures is ideal for clean interlayer interfaces and scalable device fabrication. Here, we explore the synthesis and preferred orientations of 2D GaSe atomic layers on graphene (Gr) by vdW epitaxy. Guided by the wrinkles on graphene, GaSe nuclei form that share a predominant lattice orientation. Due to vdW epitaxial growth many nuclei grow as perfectly aligned crystals and coalesce to form large (tens of microns), single-crystal flakes. Through theoretical investigationsmore » of interlayer energetics, and measurements of preferred orientations by atomic-resolution STEM and electron diffraction, a 10.9 interlayer rotation of the GaSe lattice with respect to the underlying graphene is found to be the most energetically preferred vdW heterostructure with the largest binding energy and the longest-range ordering. These GaSe/Gr vdW heterostructures exhibit an enhanced Raman E 2 1g band of monolayer GaSe along with highly-quenched photoluminescence due to strong charge transfer. Despite the very large lattice mismatch of GaSe/Gr through vdW epitaxy, the predominant orientation control and convergent formation of large single-crystal flakes demonstrated here is promising for the scalable synthesis of large-area vdW heterostructures for the development of new optical and optoelectronic devices.« less
An Ab Initio Study of CuCO

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.

1994-01-01

Modified coupled-pair functional (MCPF) calculations and coupled cluster singles and doubles calculations, which include a perturbational estimate of the connected triples [CCSD(T)], yield a bent structure for CuCO, thus, supporting the prediction of a nonlinear structure based on density functional (DF) calculations. Our best estimate for the binding energy is 4.9 +/- 1.4 kcal/mol; this is in better agreement with experiment (6.0 +/- 1.2 kcal/mol) than the DF approach which yields a value (19.6 kcal/mol) significantly larger than experiment.
First-principles investigation of the interlayer coupling in chromium-trichloride-a layered magnetic insulator

NASA Astrophysics Data System (ADS)

Kc, Santosh; McGuire, Michael A.; Cooper, Valentino R.

The crystallographic, electronic and magnetic properties of layered CrCl3were investigated using density functional theory. We use the newly developed spin van der Waals density functional (svdW-DF) in order to explore the atomic, electronic and magnetic structure. Our results indicate that treatment of the long-range interlayer forces with the svdW-DF improves the accuracy of crystal structure predictions. The cleavage energy was estimated to be 0.29 J/m2 suggesting that CrCl3 should be cleavable using standard mechanical exfoliation techniques. The inclusion of spin in the non-local vdW-DF allows us to directly probe the coupling between the magnetic structure and lattice degrees of freedom. An understanding of the link between electronic, magnetic and structural properties can be useful for novel device applications such as magnetoelectric devices, spin transistors, and 2D magnet. Research was sponsored by the US DOE, Office of Science, BES, MSED and Early Career Research Programs and used resources at NERSC.
Communication: Effect of accidental mode degeneracy on Raman intensity in 2D materials: Hybrid functional study of bilayer phosphorene

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

Sun, Yi-Yang; Zhang, Shengbai

2016-07-14

Bulk black phosphorus has two optical phonon modes labeled as A{sub g}{sup 2} and B{sub 2u}, respectively, that are nearly degenerate in frequency. However, density functional theory calculations using local or semi-local functionals cannot reproduce this degeneracy. Here, we propose a hybrid functional approach aided by van der Waals (vdW) force fields, which can accurately describe the lattice dynamic and electronic properties of both bulk and few-layer black phosphorus (phosphorene). Using this approach we show that in bilayer phosphorene, the two Raman modes derived from the B{sub 2u} and A{sub g}{sup 2} modes could exhibit strong resonance as a resultmore » of the accidental degeneracy so that both modes could be observed in Raman experiment. Without the mode degeneracy, however, the Raman intensity of the B{sub 2u}-derived mode would be too weak to be observed. We further show that the accidental degeneracy is correlated to the applied strain, which enables Raman spectroscopy to be a powerful tool for characterizing built-in strains in 2D materials, e.g., due to the interaction with substrates, which has emerged as an important issue in vdW epitaxy.« less
Analytic energy gradients for orbital-optimized MP3 and MP2.5 with the density-fitting approximation: An efficient implementation.

PubMed

Bozkaya, Uğur

2018-03-15

Efficient implementations of analytic gradients for the orbital-optimized MP3 and MP2.5 and their standard versions with the density-fitting approximation, which are denoted as DF-MP3, DF-MP2.5, DF-OMP3, and DF-OMP2.5, are presented. The DF-MP3, DF-MP2.5, DF-OMP3, and DF-OMP2.5 methods are applied to a set of alkanes and noncovalent interaction complexes to compare the computational cost with the conventional MP3, MP2.5, OMP3, and OMP2.5. Our results demonstrate that density-fitted perturbation theory (DF-MP) methods considered substantially reduce the computational cost compared to conventional MP methods. The efficiency of our DF-MP methods arise from the reduced input/output (I/O) time and the acceleration of gradient related terms, such as computations of particle density and generalized Fock matrices (PDMs and GFM), solution of the Z-vector equation, back-transformations of PDMs and GFM, and evaluation of analytic gradients in the atomic orbital basis. Further, application results show that errors introduced by the DF approach are negligible. Mean absolute errors for bond lengths of a molecular set, with the cc-pCVQZ basis set, is 0.0001-0.0002 Å. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.
Modeling Adsorption and Reactions of Organic Molecules at Metal Surfaces

PubMed Central

2014-01-01

Conspectus The understanding of adsorption and reactions of (large) organic molecules at metal surfaces plays an increasingly important role in modern surface science and technology. Such hybrid inorganic/organic systems (HIOS) are relevant for many applications in catalysis, light-emitting diodes, single-molecule junctions, molecular sensors and switches, and photovoltaics. Obviously, the predictive modeling and understanding of the structure and stability of such hybrid systems is an essential prerequisite for tuning their electronic properties and functions. At present, density-functional theory (DFT) is the most promising approach to study the structure, stability, and electronic properties of complex systems, because it can be applied to both molecules and solids comprising thousands of atoms. However, state-of-the-art approximations to DFT do not provide a consistent and reliable description for HIOS, which is largely due to two issues: (i) the self-interaction of the electrons with themselves arising from the Hartree term of the total energy that is not fully compensated in approximate exchange-correlation functionals, and (ii) the lack of long-range part of the ubiquitous van der Waals (vdW) interactions. The self-interaction errors sometimes lead to incorrect description of charge transfer and electronic level alignment in HIOS, although for molecules adsorbed on metals these effects will often cancel out in total energy differences. Regarding vdW interactions, several promising vdW-inclusive DFT-based methods have been recently demonstrated to yield remarkable accuracy for intermolecular interactions in the gas phase. However, the majority of these approaches neglect the nonlocal collective electron response in the vdW energy tail, an effect that is particularly strong in condensed phases and at interfaces between different materials. Here we show that the recently developed DFT+vdWsurf method that accurately accounts for the collective electronic response effects enables reliable modeling of structure and stability for a broad class of organic molecules adsorbed on metal surfaces. This method was demonstrated to achieve quantitative accuracy for aromatic hydrocarbons (benzene, naphthalene, anthracene, and diindenoperylene), C60, and sulfur/oxygen-containing molecules (thiophene, NTCDA, and PTCDA) on close-packed and stepped metal surfaces, leading to an overall accuracy of 0.1 Å in adsorption heights and 0.1 eV in binding energies with respect to state-of-the-art experiments. An unexpected finding is that vdW interactions contribute more to the binding of strongly bound molecules on transition-metal surfaces than for molecules physisorbed on coinage metals. The accurate inclusion of vdW interactions also significantly improves tilting angles and adsorption heights for all the studied molecules, and can qualitatively change the potential-energy surface for adsorbed molecules with flexible functional groups. Activation barriers for molecular switches and reaction precursors are modified as well. PMID:24915492
Redox levels in aqueous solution: Effect of van der Waals interactions and hybrid functionals.

PubMed

Ambrosio, Francesco; Miceli, Giacomo; Pasquarello, Alfredo

2015-12-28

We investigate redox levels in aqueous solution using a combination of ab initio molecular dynamics (MD) simulations and thermodynamic integration methods. The molecular dynamics are performed with both the semilocal Perdew-Burke-Ernzerhof functional and a nonlocal functional (rVV10) accounting for van der Waals (vdW) interactions. The band edges are determined through three different schemes, namely, from the energy of the highest occupied and of the lowest unoccupied Kohn-Sham states, from total-energy differences, and from a linear extrapolation of the density of states. It is shown that the latter does not depend on the system size while the former two are subject to significant finite-size effects. For the redox levels, we provide a formulation in analogy to the definition of charge transition levels for defects in crystalline materials. We consider the H(+)/H2 level defining the standard hydrogen electrode, the OH(-)/OH(∗) level corresponding to the oxidation of the hydroxyl ion, and the H2O/OH(∗) level for the dehydrogenation of water. In spite of the large structural modifications induced in liquid water, vdW interactions do not lead to any significant structural effect on the calculated band gap and band edges. The effect on the redox levels is also small since the solvation properties of ionic species are little affected by vdW interactions. Since the electronic properties are not significantly affected by the underlying structural properties, it is justified to perform hybrid functional calculations on the configurations of our MD simulations. The redox levels calculated as a function of the fraction α of Fock exchange are found to remain constant, reproducing a general behavior previously observed for charge transition levels of defects. Comparison with experimental values shows very good agreement. At variance, the band edges and the band gap evolve linearly with α. For α ≃ 0.40, we achieve a band gap, band-edge positions, and redox levels in overall good agreement with experiment.

Redox levels in aqueous solution: Effect of van der Waals interactions and hybrid functionals

NASA Astrophysics Data System (ADS)

Ambrosio, Francesco; Miceli, Giacomo; Pasquarello, Alfredo

2015-12-01

We investigate redox levels in aqueous solution using a combination of ab initio molecular dynamics (MD) simulations and thermodynamic integration methods. The molecular dynamics are performed with both the semilocal Perdew-Burke-Ernzerhof functional and a nonlocal functional (rVV10) accounting for van der Waals (vdW) interactions. The band edges are determined through three different schemes, namely, from the energy of the highest occupied and of the lowest unoccupied Kohn-Sham states, from total-energy differences, and from a linear extrapolation of the density of states. It is shown that the latter does not depend on the system size while the former two are subject to significant finite-size effects. For the redox levels, we provide a formulation in analogy to the definition of charge transition levels for defects in crystalline materials. We consider the H+/H2 level defining the standard hydrogen electrode, the OH-/OH∗ level corresponding to the oxidation of the hydroxyl ion, and the H2O/OH∗ level for the dehydrogenation of water. In spite of the large structural modifications induced in liquid water, vdW interactions do not lead to any significant structural effect on the calculated band gap and band edges. The effect on the redox levels is also small since the solvation properties of ionic species are little affected by vdW interactions. Since the electronic properties are not significantly affected by the underlying structural properties, it is justified to perform hybrid functional calculations on the configurations of our MD simulations. The redox levels calculated as a function of the fraction α of Fock exchange are found to remain constant, reproducing a general behavior previously observed for charge transition levels of defects. Comparison with experimental values shows very good agreement. At variance, the band edges and the band gap evolve linearly with α. For α ≃ 0.40, we achieve a band gap, band-edge positions, and redox levels in overall good agreement with experiment.
Assembly of Nanowire Arrays: Exploring Interparticle Interactions, Particle Orientation, and Mixed Particle Arrays

NASA Astrophysics Data System (ADS)

Kirby, David J.

This dissertation explores the fundamental interparticle and particle-substrate forces that contribute to nanowire assembly. Nanowires have a large aspect ratio which has made them favorable materials for applications in energy and sensing technologies. However, this anisotropy means that nanowires must be positioned and oriented during an assembly process. Within this work, the roles of gravity, van der Waals (VDW) attractions, and electrostatic repulsions are explored when different nanowire assemblies are created. Particles were synthesized by the template electrodeposition process so that stripes of different materials and therefore different VDW interactions could be patterned along the particle length. Electrostatic repulsions were provided by a small molecule coating or a porous silica shell to prevent aggregation during the assembly process. Chapters 2, 3, 5, 6, and 8 all used particles whose asymmetry was further adjusted by removal of a sacrificial segment to leave a partially etched nanowire (PEN), a rigid silica shell partially filled with a metal core. For these particles, the role of gravity was amplified due to the drastic density differences between the two segments. Topographic and high VDW surface interactions were patterned onto assembly substrates using photolithographic processing. These forces served as a passive template to direct nanowire assembly. The segment anisotropy of PENs allowed gravity to drive their sedimentation with the long axis perpendicular to the surface. The density difference between the two ends allowed them to convert between the horizontal and vertical orientation as they diffused on the substrate. Vertical arrays formed as particle concentrations increased while VDW attractions from neighboring PENs or the physical barrier of a microwell wall supported this structure. While vertical arrays were typically PENs, microwell walls were also able to enforce a vertical orientation on solid Au nanowires. These particles typically formed horizontal arrays on planar surfaces, but careful design of the microwell and nanowire dimensions enabled these particles to take on the vertical orientation. Solid nanowires and PENs with greater segment symmetry aligned parallel to the surface as gravity did not allow a conversion to the vertical orientation. When concentrated, these particles formed smectic row arrangements which were previously shown to originate from a balance of VDW attractions and electrostatic repulsions. Within rows of segmented particles, a preference was observed for like orientation of nearest neighbor particles (Chapter 6). With the aid of Monte Carlo simulations, it was determined that this observation was the result of small differences in VDW attractions between the two nanowire ends. Differences in VDW attraction were also applied to patterned surfaces (Chapter 7). Stripes of high VDW material (Au) were placed on a silica surface (a low VDW material). When relatively low surface concentrations were used, the high VDW regions collected Au nanowires and organized them into rows that were reminiscent of those observed on un-patterned surfaces at high particle concentrations. VDW and the gravitational force were explored as they combined to influence array orientation in binary PEN mixtures. Depending on the geometries of the particles combined, the contributions of gravity and interparticle interactions exhibited different balance in creating the final array. VDW and gravitational forces could also act as a force for reconfigurable nanowire assembly. In chapter 8, fluid flow was used to concentrate PENs and force them into horizontal arrangements. When fluid flow was stopped, van der Waals forces and gravity were responsible for a reorientation of the assembled particles into a standing array. These studies represent early steps into the future of nanowire assembly methods. I conclude this dissertation by discussing the implications of my work and providing perspective on their importance to the scientific community. I also offer suggestions for future work in nanowire assembly. These areas focus on the development of assembled nanowire devices, mixed nanowire assembly techniques, and potential stimuli responsive reconfigurable assemblies.
Rotational superstructure in van der Waals heterostructure of self-assembled C 60 monolayer on the WSe 2 surface

DOE PAGES

Santos, Elton J. G.; Scullion, Declan; Chu, Ximo S.; ...

2017-08-23

Hybrid van der Waals (vdW) heterostructures composed of two-dimensional (2D) layered materials and self-assembled organic molecules are promising systems for electronic and optoelectronic applications with enhanced properties and performance. Control of molecular assembly is therefore paramount to fundamentally understand the nucleation, ordering, alignment, and electronic interaction of organic molecules with 2D materials. Here, we report the formation and detailed study of highly ordered, crystalline monolayers of C 60 molecules self-assembled on the surface of WSe 2 in well-ordered arrays with large grain sizes (~5 μm). Using high-resolution scanning tunneling microscopy (STM), we observe a periodic 2 × 2 superstructure inmore » the C 60 monolayer and identify four distinct molecular appearances. Using vdW-corrected ab initio density functional theory (DFT) simulations, we determine that the interplay between vdW and Coulomb interactions as well as adsorbate–adsorbate and adsorbate–substrate interactions results in specific rotational arrangements of the molecules forming the superstructure. The orbital ordering through the relative positions of bonds in adjacent molecules creates a charge redistribution that links the molecule units in a long-range network. Furthermore, this rotational superstructure extends throughout the self-assembled monolayer and opens a pathway towards engineering aligned hybrid organic/inorganic vdW heterostructures with 2D layered materials in a precise and controlled way.« less
Rotational superstructure in van der Waals heterostructure of self-assembled C 60 monolayer on the WSe 2 surface

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

Santos, Elton J. G.; Scullion, Declan; Chu, Ximo S.

Hybrid van der Waals (vdW) heterostructures composed of two-dimensional (2D) layered materials and self-assembled organic molecules are promising systems for electronic and optoelectronic applications with enhanced properties and performance. Control of molecular assembly is therefore paramount to fundamentally understand the nucleation, ordering, alignment, and electronic interaction of organic molecules with 2D materials. Here, we report the formation and detailed study of highly ordered, crystalline monolayers of C 60 molecules self-assembled on the surface of WSe 2 in well-ordered arrays with large grain sizes (~5 μm). Using high-resolution scanning tunneling microscopy (STM), we observe a periodic 2 × 2 superstructure inmore » the C 60 monolayer and identify four distinct molecular appearances. Using vdW-corrected ab initio density functional theory (DFT) simulations, we determine that the interplay between vdW and Coulomb interactions as well as adsorbate–adsorbate and adsorbate–substrate interactions results in specific rotational arrangements of the molecules forming the superstructure. The orbital ordering through the relative positions of bonds in adjacent molecules creates a charge redistribution that links the molecule units in a long-range network. Furthermore, this rotational superstructure extends throughout the self-assembled monolayer and opens a pathway towards engineering aligned hybrid organic/inorganic vdW heterostructures with 2D layered materials in a precise and controlled way.« less
Electronic properties of blue phosphorene/graphene and blue phosphorene/graphene-like gallium nitride heterostructures.

PubMed

Sun, Minglei; Chou, Jyh-Pin; Yu, Jin; Tang, Wencheng

2017-07-05

Blue phosphorene (BlueP) is a graphene-like phosphorus nanosheet which was synthesized very recently for the first time [Nano Lett., 2016, 16, 4903-4908]. The combination of electronic properties of two different two-dimensional materials in an ultrathin van der Waals (vdW) vertical heterostructure has been proved to be an effective approach to the design of novel electronic and optoelectronic devices. Therefore, we used density functional theory to investigate the structural and electronic properties of two BlueP-based heterostructures - BlueP/graphene (BlueP/G) and BlueP/graphene-like gallium nitride (BlueP/g-GaN). Our results showed that the semiconducting nature of BlueP and the Dirac cone of G are well preserved in the BlueP/G vdW heterostructure. Moreover, by applying a perpendicular electric field, it is possible to tune the position of the Dirac cone of G with respect to the band edge of BlueP, resulting in the ability to control the Schottky barrier height. For the BlueP/g-GaN vdW heterostructure, BlueP forms an interface with g-GaN with a type-II band alignment, which is a promising feature for unipolar electronic device applications. Furthermore, we discovered that both G and g-GaN can be used as an active layer for BlueP to facilitate charge injection and enhance the device performance.
Methylbenzenes on graphene

NASA Astrophysics Data System (ADS)

Borck, Øyvind; Schröder, Elsebeth

2017-10-01

We present a theory study of the physisorption of the series of methylbenzenes (toluene, xylene and mesitylene), as well as benzene, on graphene. The aim is two fold: we provide data that will be used as input to larger-scale methods like molecular-dynamics simulations, and at the same time we enhance the basic understanding of graphene used as a material for sensors and as an idealized model for the carbon in active carbon filters. The molecules are studied in a number of positions and orientations relative to graphene, using density functional theory with the van der Waals functional vdW-DF. The molecules are adsorbed fractional coverage. We focus on the vdW-DF1 and vdW-DF-cx functionals, and find that the binding energy of the molecules on graphene grows linearly with the number of methyl groups, at the rate of 0.09 eV (vdW-DF1) to 0.11 eV (vdW-DF-cx) per added methyl group. We further find that the orientation of the methyl groups of the molecules relative to graphene is at least as important as the lateral position of the whole molecule on graphene.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Reusch, L. M., E-mail: lmmcguire@wisc.edu; Den Hartog, D. J.; Goetz, J.

The two-color soft x-ray (SXR) tomography diagnostic on the Madison Symmetric Torus is capable of making electron temperature measurements via the double-filter technique; however, there has been a 15% systematic discrepancy between the SXR double-filter (SXR{sub DF}) temperature and Thomson scattering (TS) temperature. Here we discuss calibration of the Be filters used in the SXR{sub DF} measurement using empirical measurements of the transmission function versus energy at the BESSY II electron storage ring, electron microprobe analysis of filter contaminants, and measurement of the effective density. The calibration does not account for the TS and SXR{sub DF} discrepancy, and evidence frommore » experiments indicates that this discrepancy is due to physics missing from the SXR{sub DF} analysis rather than instrumentation effects.« less
Density-Dependent Formulation of Dispersion-Repulsion Interactions in Hybrid Multiscale Quantum/Molecular Mechanics (QM/MM) Models.

PubMed

Curutchet, Carles; Cupellini, Lorenzo; Kongsted, Jacob; Corni, Stefano; Frediani, Luca; Steindal, Arnfinn Hykkerud; Guido, Ciro A; Scalmani, Giovanni; Mennucci, Benedetta

2018-03-13

Mixed multiscale quantum/molecular mechanics (QM/MM) models are widely used to explore the structure, reactivity, and electronic properties of complex chemical systems. Whereas such models typically include electrostatics and potentially polarization in so-called electrostatic and polarizable embedding approaches, respectively, nonelectrostatic dispersion and repulsion interactions are instead commonly described through classical potentials despite their quantum mechanical origin. Here we present an extension of the Tkatchenko-Scheffler semiempirical van der Waals (vdW TS ) scheme aimed at describing dispersion and repulsion interactions between quantum and classical regions within a QM/MM polarizable embedding framework. Starting from the vdW TS expression, we define a dispersion and a repulsion term, both of them density-dependent and consistently based on a Lennard-Jones-like potential. We explore transferable atom type-based parametrization strategies for the MM parameters, based on either vdW TS calculations performed on isolated fragments or on a direct estimation of the parameters from atomic polarizabilities taken from a polarizable force field. We investigate the performance of the implementation by computing self-consistent interaction energies for the S22 benchmark set, designed to represent typical noncovalent interactions in biological systems, in both equilibrium and out-of-equilibrium geometries. Overall, our results suggest that the present implementation is a promising strategy to include dispersion and repulsion in multiscale QM/MM models incorporating their explicit dependence on the electronic density.
General theoretical description of angle-resolved photoemission spectroscopy of van der Waals structures

NASA Astrophysics Data System (ADS)

Amorim, B.

2018-04-01

We develop a general theory to model the angle-resolved photoemission spectroscopy (ARPES) of commensurate and incommensurate van der Waals (vdW) structures, formed by lattice mismatched and/or misaligned stacked layers of two-dimensional materials. The present theory is based on a tight-binding description of the structure and the concept of generalized umklapp processes, going beyond previous descriptions of ARPES in incommensurate vdW structures, which are based on continuous, low-energy models, being limited to structures with small lattice mismatch/misalignment. As applications of the general formalism, we study the ARPES bands and constant energy maps for two structures: twisted bilayer graphene and twisted bilayer MoS2. The present theory should be useful in correctly interpreting experimental results of ARPES of vdW structures and other systems displaying competition between different periodicities, such as two-dimensional materials weakly coupled to a substrate and materials with density wave phases.
Theoretical prediction of nuclear magnetic shieldings and indirect spin-spin coupling constants in 1,1-, cis-, and trans-1,2-difluoroethylenes

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

Nozirov, Farhod, E-mail: teobaldk@gmail.com, E-mail: farhod.nozirov@gmail.com; Stachów, Michał, E-mail: michal.stachow@gmail.com; Kupka, Teobald, E-mail: teobaldk@gmail.com, E-mail: farhod.nozirov@gmail.com

2014-04-14

A theoretical prediction of nuclear magnetic shieldings and indirect spin-spin coupling constants in 1,1-, cis- and trans-1,2-difluoroethylenes is reported. The results obtained using density functional theory (DFT) combined with large basis sets and gauge-independent atomic orbital calculations were critically compared with experiment and conventional, higher level correlated electronic structure methods. Accurate structural, vibrational, and NMR parameters of difluoroethylenes were obtained using several density functionals combined with dedicated basis sets. B3LYP/6-311++G(3df,2pd) optimized structures of difluoroethylenes closely reproduced experimental geometries and earlier reported benchmark coupled cluster results, while BLYP/6-311++G(3df,2pd) produced accurate harmonic vibrational frequencies. The most accurate vibrations were obtained using B3LYP/6-311++G(3df,2pd)more » with correction for anharmonicity. Becke half and half (BHandH) density functional predicted more accurate {sup 19}F isotropic shieldings and van Voorhis and Scuseria's τ-dependent gradient-corrected correlation functional yielded better carbon shieldings than B3LYP. A surprisingly good performance of Hartree-Fock (HF) method in predicting nuclear shieldings in these molecules was observed. Inclusion of zero-point vibrational correction markedly improved agreement with experiment for nuclear shieldings calculated by HF, MP2, CCSD, and CCSD(T) methods but worsened the DFT results. The threefold improvement in accuracy when predicting {sup 2}J(FF) in 1,1-difluoroethylene for BHandH density functional compared to B3LYP was observed (the deviations from experiment were −46 vs. −115 Hz)« less
The role of plasma chemistry on functional silicon nitride film properties deposited at low-temperature by mixing two frequency powers using PECVD.

PubMed

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

2016-05-14

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

PubMed Central

2016-01-01

Clay minerals are ubiquitous in nature, and the manner in which they interact with their surroundings has important industrial and environmental implications. Consequently, a molecular-level understanding of the adsorption of molecules on clay surfaces is crucial. In this regard computer simulations play an important role, yet the accuracy of widely used empirical force fields (FF) and density functional theory (DFT) exchange-correlation functionals is often unclear in adsorption systems dominated by weak interactions. Herein we present results from quantum Monte Carlo (QMC) for water and methanol adsorption on the prototypical clay kaolinite. To the best of our knowledge, this is the first time QMC has been used to investigate adsorption at a complex, natural surface such as a clay. As well as being valuable in their own right, the QMC benchmarks obtained provide reference data against which the performance of cheaper DFT methods can be tested. Indeed using various DFT exchange-correlation functionals yields a very broad range of adsorption energies, and it is unclear a priori which evaluation is better. QMC reveals that in the systems considered here it is essential to account for van der Waals (vdW) dispersion forces since this alters both the absolute and relative adsorption energies of water and methanol. We show, via FF simulations, that incorrect relative energies can lead to significant changes in the interfacial densities of water and methanol solutions at the kaolinite interface. Despite the clear improvements offered by the vdW-corrected and the vdW-inclusive functionals, absolute adsorption energies are often overestimated, suggesting that the treatment of vdW forces in DFT is not yet a solved problem. PMID:27917256
Smoothed particle hydrodynamics simulations of evaporation and explosive boiling of liquid drops in microgravity.

PubMed

Sigalotti, Leonardo Di G; Troconis, Jorge; Sira, Eloy; Peña-Polo, Franklin; Klapp, Jaime

2015-07-01

The rapid evaporation and explosive boiling of a van der Waals (vdW) liquid drop in microgravity is simulated numerically in two-space dimensions using the method of smoothed particle hydrodynamics. The numerical approach is fully adaptive and incorporates the effects of surface tension, latent heat, mass transfer across the interface, and liquid-vapor interface dynamics. Thermocapillary forces are modeled by coupling the hydrodynamics to a diffuse-interface description of the liquid-vapor interface. The models start from a nonequilibrium square-shaped liquid of varying density and temperature. For a fixed density, the drop temperature is increased gradually to predict the point separating normal boiling at subcritical heating from explosive boiling at the superheat limit for this vdW fluid. At subcritical heating, spontaneous evaporation produces stable drops floating in a vapor atmosphere, while at near-critical heating, a bubble is nucleated inside the drop, which then collapses upon itself, leaving a smaller equilibrated drop embedded in its own vapor. At the superheat limit, unstable bubble growth leads to either fragmentation or violent disruption of the liquid layer into small secondary drops, depending on the liquid density. At higher superheats, explosive boiling occurs for all densities. The experimentally observed wrinkling of the bubble surface driven by rapid evaporation followed by a Rayleigh-Taylor instability of the thin liquid layer and the linear growth of the bubble radius with time are reproduced by the simulations. The predicted superheat limit (T(s)≈0.96) is close to the theoretically derived value of T(s)=1 at zero ambient pressure for this vdW fluid.
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.
Vibrations of double-nanotube systems with mislocation via a newly developed van der Waals model

NASA Astrophysics Data System (ADS)

Kiani, Keivan

2015-06-01

This study deals with transverse vibrations of two adjacent-parallel-mislocated single-walled carbon nanotubes (SWCNTs) under various end conditions. These tubes interact with each other and their surrounding medium through the intertube van der Waals (vdW) forces, and existing bonds between their atoms and those of the elastic medium. The elastic energy of such forces due to the deflections of nanotubes is appropriately modeled by defining a vdW force density function. In the previous works, vdW forces between two identical tubes were idealized by a uniform form of this function. The newly introduced function enables us to investigate the influences of both intertube free distance and longitudinal mislocation on the natural transverse frequencies of the nanosystem which consists of two dissimilar tubes. Such crucial issues have not been addressed yet, even for simply supported tubes. Using nonlocal Timoshenko and higher-order beam theories as well as Hamilton's principle, the strong form of the equations of motion is established. Seeking for an explicit solution to these integro-partial differential equations is a very problematic task. Thereby, an energy-based method in conjunction with an efficient meshfree method is proposed and the nonlocal frequencies of the elastically embedded nanosystem are determined. For simply supported nanosystems, the predicted first five frequencies of the proposed model are checked with those of assumed mode method, and a reasonably good agreement is achieved. Through various studies, the roles of the tube's length ratio, intertube free space, mislocation, small-scale effect, slenderness ratio, radius of SWCNTs, and elastic constants of the elastic matrix on the natural frequencies of the nanosystem with various end conditions are explained. The limitations of the nonlocal Timoshenko beam theory are also addressed. This work can be considered as a vital step towards better realizing of a more complex system that consists of vertically aligned SWCNTs of various lengths.
Unconventional Behavior of Friction at the Nanoscale beyond Amontons' Law.

PubMed

Chen, Jingrun; Gao, Wang

2017-08-05

By means of a many-body van der Waals (vdW)-corrected density functional theory approach, the atomic-scale friction of a prototypical tip-substrate system consisting of an Si tip and a graphene substrate is studied. In a loading-sliding process, the tip-substrate distance is found to be essential for nanofrictional behavior, through determining the competition between vdW contributions and electronic contributions. As the tip approaches the substrate, this competition results in a smooth transition of normal forces from attraction to repulsion, and the friction coefficient in turn undergoes a sign change from negative to positive with possible giant magnitude and strong anisotropy. The loading-sliding process does not introduce any chemical modification of the underlying system. These findings reveal the boundary of validity of Amontons' law, unify negative and giant friction coefficients, rationalize the experimentally observed anisotropy of nanofriction, and are universal when vdW interactions are crucial, all of which are helpful to establish a comprehensive picture of nanofriction. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
First Principles Studies for Lithium Intercalation and Diffusion Behaviors in MoS2 treated with the Compressive Sensing Cluster Expansion

NASA Astrophysics Data System (ADS)

Liu, Chi-Ping; Zhou, Fei; Ozolins, Vidvuds

2014-03-01

Molybdenum disulfide (MoS2) is a good candidate electrode material for high capacity energy storage applications, such as lithium ion batteries and supercapacitors. In this work, we investigate lithium intercalation and diffusion kinetics in MoS2 by using first-principles density-functional theory (DFT) calculations. Two different lithium intercalation sites (1-H and 2-T) in MoS2 are found to be stable for lithium intercalation at different van der Waals' (vdW) gap distances. It is found that both thermodynamic and kinetic properties are highly related to the interlayer vdW gap distance, and that the optimal gap distance leads to effective solid-state diffusion in MoS2. Additionally, through the use of compressive sensing, we build accurate cluster expansion models to study the thermodynamic properties of MoS2 at high lithium content by truncating the higher order effective clusters with significant contributions. The results show that compressive sensing cluster expansion is a rigorous and powerful tool for model construction for advanced electrochemical applications in the future.
Pro-neurogenic, Memory-Enhancing and Anti-stress Effects of DF302, a Novel Fluorine Gamma-Carboline Derivative with Multi-target Mechanism of Action.

PubMed

Strekalova, Tatyana; Bahzenova, Nataliia; Trofimov, Alexander; Schmitt-Böhrer, Angelika G; Markova, Nataliia; Grigoriev, Vladimir; Zamoyski, Vladimir; Serkova, Tatiana; Redkozubova, Olga; Vinogradova, Daria; Umriukhin, Alexei; Fisenko, Vladimir; Lillesaar, Christina; Shevtsova, Elena; Sokolov, Vladimir; Aksinenko, Alexey; Lesch, Klaus-Peter; Bachurin, Sergey

2018-01-01

A comparative study performed in mice investigating the action of DF302, a novel fluoride-containing gamma-carboline derivative, in comparison to the structurally similar neuroprotective drug dimebon. Drug effects on learning and memory, emotionality, hippocampal neurogenesis and mitochondrial functions, as well as AMPA-mediated currents and the 5-HT6 receptor are reported. In the step-down avoidance and fear-conditioning paradigms, bolus administration of drugs at doses of 10 or 40 mg/kg showed that only the higher dose of DF302 improved long-term memory while dimebon was ineffective at either dosage. Short-term memory and fear extinction remained unaltered across treatment groups. During the 5-day predation stress paradigm, oral drug treatment over a period of 2 weeks at the higher dosage regimen decreased anxiety-like behaviour. Both compounds supressed inter-male aggression in CD1 mice, the most eminent being the effects of DF302 in its highest dose. DF302 at the higher dose decreased floating behaviour in a 2-day swim test and after 21-day ultrasound stress. The density of Ki67-positive cells, a marker of adult neurogenesis, was reduced in the dentate gyrus of stressed dimebon-treated and non-treated mice, but not in DF302-treated mice. Non-stressed mice that received DF302 had a higher density of Ki67-positive cells than controls unlike dimebon-treated mice. Similar to dimebon, DF302 effectively potentiated AMPA receptor-mediated currents, bound to the 5-HT6 receptor, inhibited mitochondrial permeability transition and displayed cytoprotective properties in cellular models of neurodegeneration. Thus, DF302 exerts multi-target effects on the key mechanisms of neurodegenerative pathologies and can be considered as an optimized novel analogue of the neuroprotective agent dimebon.
Accurate van der Waals force field for gas adsorption in porous materials.

PubMed

Sun, Lei; Yang, Li; Zhang, Ya-Dong; Shi, Qi; Lu, Rui-Feng; Deng, Wei-Qiao

2017-09-05

An accurate van der Waals force field (VDW FF) was derived from highly precise quantum mechanical (QM) calculations. Small molecular clusters were used to explore van der Waals interactions between gas molecules and porous materials. The parameters of the accurate van der Waals force field were determined by QM calculations. To validate the force field, the prediction results from the VDW FF were compared with standard FFs, such as UFF, Dreiding, Pcff, and Compass. The results from the VDW FF were in excellent agreement with the experimental measurements. This force field can be applied to the prediction of the gas density (H 2 , CO 2 , C 2 H 4 , CH 4 , N 2 , O 2 ) and adsorption performance inside porous materials, such as covalent organic frameworks (COFs), zeolites and metal organic frameworks (MOFs), consisting of H, B, N, C, O, S, Si, Al, Zn, Mg, Ni, and Co. This work provides a solid basis for studying gas adsorption in porous materials. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.
Bonding between graphene and MoS 2 monolayers without and with Li intercalation

DOE PAGES

Ahmed, Towfiq; Modine, N. A.; Zhu, Jian-Xin

2015-07-27

We performed density functional theory (DFT) calculations for a bi-layered heterostructure combining a graphene layer with a MoS 2 layer with and without intercalated Li atoms. Our calculations demonstrate the importance of the van der Waals (vdW) interaction, which is crucial for forming stable bonding between the layers. Our DFT calculation correctly reproduces the linear dispersion, or Dirac cone, feature at the Fermi energy for the isolated graphene monolayer and the band gap for the MoS 2 monolayer. For the combined graphene/MoS 2 bi-layer, we observe interesting electronic structure and density of states (DOS) characteristics near the Fermi energy, showingmore » both the gap like features of the MoS 2 layer and in-gap states with linear dispersion contributed mostly by the graphene layer. Our calculated total DOS in this vdW heterostructure reveals that the graphene layer significantly contributes to pinning the Fermi energy at the center of the band gap of MoS 2. We also find that intercalating Li ions in between the layers of the graphene/MoS2 heterostructure enhances the binding energy through orbital hybridizations between cations (Li adatoms) and anions (graphene and MoS 2 monolayers). Moreover, we calculate the dielectric function of the Li intercalated graphene/MoS 2 heterostructure, the imaginary component of which can be directly compared with experimental measurements of optical conductivity in order to validate our theoretical prediction. We observe sharp features in the imaginary component of the dielectric function, which shows the presence of a Drude peak in the optical conductivity, and therefore metallicity in the lithiated graphene/MoS 2 heterostructure.« less

Redox levels in aqueous solution: Effect of van der Waals interactions and hybrid functionals

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

Ambrosio, Francesco, E-mail: Francesco.Ambrosio@epfl.ch; Miceli, Giacomo; Pasquarello, Alfredo

2015-12-28

We investigate redox levels in aqueous solution using a combination of ab initio molecular dynamics (MD) simulations and thermodynamic integration methods. The molecular dynamics are performed with both the semilocal Perdew-Burke-Ernzerhof functional and a nonlocal functional (rVV10) accounting for van der Waals (vdW) interactions. The band edges are determined through three different schemes, namely, from the energy of the highest occupied and of the lowest unoccupied Kohn-Sham states, from total-energy differences, and from a linear extrapolation of the density of states. It is shown that the latter does not depend on the system size while the former two are subjectmore » to significant finite-size effects. For the redox levels, we provide a formulation in analogy to the definition of charge transition levels for defects in crystalline materials. We consider the H{sup +}/H{sub 2} level defining the standard hydrogen electrode, the OH{sup −}/OH{sup ∗} level corresponding to the oxidation of the hydroxyl ion, and the H{sub 2}O/OH{sup ∗} level for the dehydrogenation of water. In spite of the large structural modifications induced in liquid water, vdW interactions do not lead to any significant structural effect on the calculated band gap and band edges. The effect on the redox levels is also small since the solvation properties of ionic species are little affected by vdW interactions. Since the electronic properties are not significantly affected by the underlying structural properties, it is justified to perform hybrid functional calculations on the configurations of our MD simulations. The redox levels calculated as a function of the fraction α of Fock exchange are found to remain constant, reproducing a general behavior previously observed for charge transition levels of defects. Comparison with experimental values shows very good agreement. At variance, the band edges and the band gap evolve linearly with α. For α ≃ 0.40, we achieve a band gap, band-edge positions, and redox levels in overall good agreement with experiment.« less
Quantum dynamics of the vibrations of helium bound to the nanosurface of a large planar organic molecule: phthalocyanine . He van der Waals complex.

PubMed

Gibbons, Brittney R; Xu, Minzhong; Bacić, Zlatko

2009-04-23

We report rigorous quantum three-dimensional calculations of highly excited intermolecular vibrational states of the van der Waals (vdW) complex phthalocyanine.He (Pc.He). The Pc molecule was treated as rigid and the intermolecular potential energy surface (IPES) was represented as a sum of atom-atom Lennard-Jones pair potentials. The IPES has four equivalent global minima on the diagonals of the square-shaped Pc, inside its five-membered rings, and four slightly shallower local minima between them, creating a distinctive corrugation pattern of the molecular nanosurface. The vdW vibrational states analyzed in this work extend to about two-thirds of the well depth of the IPES. For the assignment of the in-plane (xy) vdW vibrational excitations it was necessary to resort to two sets of quantum numbers, the Cartesian quantum numbers [nu(x), nu(y)] and the quantum numbers (v, l) of the 2D isotropic oscillator, depending on the nodal structure and the symmetry of the wave functions. The delocalization of the He atom parallel to the molecular surface is large already in the ground vdW state. It increases rapidly with the number of quanta in the in-plane vdW vibrations, with the maximum root-mean-square amplitudes Deltax and Deltay of about 7 au at the excitation energies around 40 cm(-1). The wave functions of the highly excited states tend to be delocalized over the entire nanosurface and often have a square shape, reflecting that of the substrate.
Coupled-cluster, Möller Plesset (MP2), Density Fitted Local MP2, and Density Functional Theory Examination of the Energetic and Structural Features of Hydrophobic Solvation: Water and Pentane

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

Ghadar, Yasaman; Clark, Aurora E.

2012-02-02

The interaction potentials between immiscible polar and non-polar solvents are a major driving force behind the formation of liquid:liquid interfaces. In this work, the interaction energy of water–pentane dimer has been determined using coupled-cluster theory with single double (triple) excitations [CCSD(T)], 2nd order Möller Plesset perturbation theory (MP2), density fitted local MP2 (DF-LMP2), as well as density functional theory using a wide variety of density functionals and several different basis sets. The M05-2X exchange correlation functionals exhibit excellent agreement with CCSD(T) and DF-LMP2 after taking into account basis set superposition error. The gas phase water–pentane interaction energy is found tomore » be quite sensitive to the specific pentane isomer (2,2- dimethylpropane vs. n-pentane) and relative orientation of the monomeric constituents. Subsequent solution phase cluster calculations of 2,2-dimethylpropane and n-pentane solvated by water indicate a positive free energy of solvation that is in good agreement with available experimental data. Structural parameters are quite sensitive to the density functional employed and reflect differences in the two-body interaction energy calculated by each method. In contrast, cluster calculations of pentane solvation of H2O solute are found to be inadequate for describing the organic solvent, likely due to limitations associated with the functionals employed (B3LYP, BHandH, and M05-2X).« less
Room Temperature Intrinsic Ferromagnetism in Epitaxial Manganese Selenide Films in the Monolayer Limit

NASA Astrophysics Data System (ADS)

O'Hara, Dante J.; Zhu, Tiancong; Trout, Amanda H.; Ahmed, Adam S.; Luo, Yunqiu Kelly; Lee, Choong Hee; Brenner, Mark R.; Rajan, Siddharth; Gupta, Jay A.; McComb, David W.; Kawakami, Roland K.

2018-05-01

Monolayer van der Waals (vdW) magnets provide an exciting opportunity for exploring two-dimensional (2D) magnetism for scientific and technological advances, but the intrinsic ferromagnetism has only been observed at low temperatures. Here, we report the observation of room temperature ferromagnetism in manganese selenide (MnSe$_x$) films grown by molecular beam epitaxy (MBE). Magnetic and structural characterization provides strong evidence that in the monolayer limit, the ferromagnetism originates from a vdW manganese diselenide (MnSe$_2$) monolayer, while for thicker films it could originate from a combination of vdW MnSe$_2$ and/or interfacial magnetism of $\\alpha$-MnSe(111). Magnetization measurements of monolayer MnSe$_x$ films on GaSe and SnSe$_2$ epilayers show ferromagnetic ordering with large saturation magnetization of ~ 4 Bohr magnetons per Mn, which is consistent with density functional theory calculations predicting ferromagnetism in monolayer 1T-MnSe$_2$. Growing MnSe$_x$ films on GaSe up to high thickness (~ 40 nm) produces $\\alpha$-MnSe(111), and an enhanced magnetic moment (~ 2x) compared to the monolayer MnSe$_x$ samples. Detailed structural characterization by scanning transmission electron microscopy (STEM), scanning tunneling microscopy (STM), and reflection high energy electron diffraction (RHEED) reveal an abrupt and clean interface between GaSe(0001) and $\\alpha$-MnSe(111). In particular, the structure measured by STEM is consistent with the presence of a MnSe$_2$ monolayer at the interface. These results hold promise for potential applications in energy efficient information storage and processing.
Polarization functions for the modified m6-31G basis sets for atoms Ga through Kr.

PubMed

Mitin, Alexander V

2013-09-05

The 2df polarization functions for the modified m6-31G basis sets of the third-row atoms Ga through Kr (Int J Quantum Chem, 2007, 107, 3028; Int J. Quantum Chem, 2009, 109, 1158) are proposed. The performances of the m6-31G, m6-31G(d,p), and m6-31G(2df,p) basis sets were examined in molecular calculations carried out by the density functional theory (DFT) method with B3LYP hybrid functional, Møller-Plesset perturbation theory of the second order (MP2), quadratic configuration interaction method with single and double substitutions and were compared with those for the known 6-31G basis sets as well as with the other similar 641 and 6-311G basis sets with and without polarization functions. Obtained results have shown that the performances of the m6-31G, m6-31G(d,p), and m6-31G(2df,p) basis sets are better in comparison with the performances of the known 6-31G, 6-31G(d,p) and 6-31G(2df,p) basis sets. These improvements are mainly reached due to better approximations of different electrons belonging to the different atomic shells in the modified basis sets. Applicability of the modified basis sets in thermochemical calculations is also discussed. © 2013 Wiley Periodicals, Inc.
Rationale for switching to nonlocal functionals in density functional theory

NASA Astrophysics Data System (ADS)

Lazić, P.; Atodiresei, N.; Caciuc, V.; Brako, R.; Gumhalter, B.; Blügel, S.

2012-10-01

Density functional theory (DFT) has been steadily improving over the past few decades, becoming the standard tool for electronic structure calculations. The early local functionals (LDA) were eventually replaced by more accurate semilocal functionals (GGA) which are in use today. A major persisting drawback is the lack of the nonlocal correlation which is at the core of dispersive (van der Waals) forces, so that a large and important class of systems remains outside the scope of DFT. The vdW-DF correlation functional of Langreth and Lundqvist, published in 2004, was the first nonlocal functional which could be easily implemented. Beyond expectations, the nonlocal functional has brought significant improvement to systems that were believed not to be sensitive to nonlocal correlations. In this paper, we use the example of graphene nanodomes growing on the Ir(111) surface, where with an increase of the size of the graphene islands the character of the bonding changes from strong chemisorption towards almost pure physisorption. We demonstrate how the seamless character of the vdW-DF functionals makes it possible to treat all regimes self-consistently, proving to be a systematic and consistent improvement of DFT regardless of the nature of bonding. We also discuss the typical surface science example of CO adsorption on (111) surfaces of metals, which shows that the nonlocal correlation may also be crucial for strongly chemisorbed systems. We briefly discuss open questions, in particular the choice of the most appropriate exchange part of the functional. As the vdW-DF begins to appear implemented self-consistently in a number of popular DFT codes, with numerical costs close to the GGA calculations, we draw the attention of the DFT community to the advantages and benefits of the adoption of this new class of functionals.
Rationale for switching to nonlocal functionals in density functional theory.

PubMed

Lazić, P; Atodiresei, N; Caciuc, V; Brako, R; Gumhalter, B; Blügel, S

2012-10-24

Density functional theory (DFT) has been steadily improving over the past few decades, becoming the standard tool for electronic structure calculations. The early local functionals (LDA) were eventually replaced by more accurate semilocal functionals (GGA) which are in use today. A major persisting drawback is the lack of the nonlocal correlation which is at the core of dispersive (van der Waals) forces, so that a large and important class of systems remains outside the scope of DFT. The vdW-DF correlation functional of Langreth and Lundqvist, published in 2004, was the first nonlocal functional which could be easily implemented. Beyond expectations, the nonlocal functional has brought significant improvement to systems that were believed not to be sensitive to nonlocal correlations. In this paper, we use the example of graphene nanodomes growing on the Ir(111) surface, where with an increase of the size of the graphene islands the character of the bonding changes from strong chemisorption towards almost pure physisorption. We demonstrate how the seamless character of the vdW-DF functionals makes it possible to treat all regimes self-consistently, proving to be a systematic and consistent improvement of DFT regardless of the nature of bonding. We also discuss the typical surface science example of CO adsorption on (111) surfaces of metals, which shows that the nonlocal correlation may also be crucial for strongly chemisorbed systems. We briefly discuss open questions, in particular the choice of the most appropriate exchange part of the functional. As the vdW-DF begins to appear implemented self-consistently in a number of popular DFT codes, with numerical costs close to the GGA calculations, we draw the attention of the DFT community to the advantages and benefits of the adoption of this new class of functionals.
Unusual reaction paths of SN2 nucleophile substitution reactions CH4 + H- → CH4 + H- and CH4 + F- → CH3F + H-: Quantum chemical calculations

NASA Astrophysics Data System (ADS)

Minyaev, Ruslan M.; Quapp, Wolfgang; Schmidt, Benjamin; Getmanskii, Ilya V.; Koval, Vitaliy V.

2013-11-01

Quantum chemical (CCSD(full)/6-311++G(3df,3pd), CCSD(T)(full)/6-311++G(3df,3pd)) and density function theory (B3LYP/6-311++G(3df,3pd)) calculations were performed for the SN2 nucleophile substitution reactions CH4 + H- → CH4 + H- and CH4 + F- → CH3F + H-. The calculated gradient reaction pathways for both reactions have an unusual behavior. An unusual stationary point of index 2 lies on the gradient reaction path. Using Newton trajectories for the reaction path, we can detect VRI point at which the reaction path branches.
Protein-protein interfaces are vdW dominant with selective H-bonds and (or) electrostatics towards broad functional specificity.

PubMed

Nilofer, Christina; Sukhwal, Anshul; Mohanapriya, Arumugam; Kangueane, Pandjassarame

2017-01-01

Several catalysis, cellular regulation, immune function, cell wall assembly, transport, signaling and inhibition occur through Protein- Protein Interactions (PPI). This is possible with the formation of specific yet stable protein-protein interfaces. Therefore, it is of interest to understand its molecular principles using structural data in relation to known function. Several interface features have been documented using known X-ray structures of protein complexes since 1975. This has improved our understanding of the interface using structural features such as interface area, binding energy, hydrophobicity, relative hydrophobicity, salt bridges and hydrogen bonds. The strength of binding between two proteins is dependent on interface size (number of residues at the interface) and thus its corresponding interface area. It is known that large interfaces have high binding energy (sum of (van der Waals) vdW, H-bonds, electrostatics). However, the selective role played by each of these energy components and more especially that of vdW is not explicitly known. Therefore, it is important to document their individual role in known protein-protein structural complexes. It is of interest to relate interface size with vdW, H-bonds and electrostatic interactions at the interfaces of protein structural complexes with known function using statistical and multiple linear regression analysis methods to identify the prominent force. We used the manually curated non-redundant dataset of 278 hetero-dimeric protein structural complexes grouped using known functions by Sowmya et al. (2015) to gain additional insight to this phenomenon using a robust inter-atomic non-covalent interaction analyzing tool PPCheck (Anshul and Sowdhamini, 2015). This dataset consists of obligatory (enzymes, regulator, biological assembly), immune and nonobligatory (enzyme and regulator inhibitors) complexes. Results show that the total binding energy is more for large interfaces. However, this is not true for its individual energy factors. Analysis shows that vdW energies contribute to about 75% ± 11% on average among all complexes and it also increases with interface size (r2 ranging from 0.67 to 0.89 with p<0.01) at 95% confidence limit irrespective of molecular function. Thus, vdW is both dominant and proportional at the interface independent of molecular function. Nevertheless, H bond energy contributes to 15% ± 6.5% on average in these complexes. It also moderately increases with interface size (r2 ranging from 0.43 to 0.61 with p<0.01) only among obligatory and immune complexes. Moreover, there is about 11.3% ± 8.7% contribution by electrostatic energy. It increases with interface size specifically among non-obligatory regulator-inhibitors (r2 = 0.44). It is implied that both H-bonds and electrostatics are neither dominant nor proportional at the interface. Nonetheless, their presence cannot be ignored in binding. Therefore, H-bonds and (or) electrostatic energy having specific role for improved stability in complexes is implied. Thus, vdW is common at the interface stabilized further with selective H-bonds and (or) electrostatic interactions at an atomic level in almost all complexes. Comparison of this observation with residue level analysis of the interface is compelling. The role by H-bonds (14.83% ± 6.5% and r2 = 0.61 with p<0.01) among obligatory and electrostatic energy (8.8% ± 4.77% and r2 = 0.63 with p <0.01) among non-obligatory complexes within interfaces (class A) having more non-polar residues than surface is influencing our inference. However, interfaces (class B) having less non-polar residues than surface show 1.5 fold more electrostatic energy on average. The interpretation of the interface using inter-atomic (vdW, H-bonds, electrostatic) interactions combined with inter-residue predominance (class A and class B) in relation to known function is the key to reveal its molecular principles with new challenges.
First-Principles Thermodynamics of Energetic Materials

DTIC Science & Technology

2012-01-01

thermal and zero-point energy ( ZPE ) effects on the crystalline environment [8]. By including vdW, thermal, and ZPE effects into DFT (DFT+vdW+T...by their relation to experiment (triangles) pure DFT over-predicts, while DFT+vdW under-predicts the EOSs. Only when temperature and ZPE effects...crystals with ZPE effects still included. To get a sense of how the vdW damping function might affect the calculation of the dynamical matrix, the
Benchmarking density functional theory predictions of framework structures and properties in a chemically diverse test set of metal-organic frameworks

DOE PAGES

Nazarian, Dalar; Ganesh, P.; Sholl, David S.

2015-09-30

We compiled a test set of chemically and topologically diverse Metal–Organic Frameworks (MOFs) with high accuracy experimentally derived crystallographic structure data. The test set was used to benchmark the performance of Density Functional Theory (DFT) functionals (M06L, PBE, PW91, PBE-D2, PBE-D3, and vdW-DF2) for predicting lattice parameters, unit cell volume, bonded parameters and pore descriptors. On average PBE-D2, PBE-D3, and vdW-DF2 predict more accurate structures, but all functionals predicted pore diameters within 0.5 Å of the experimental diameter for every MOF in the test set. The test set was also used to assess the variance in performance of DFT functionalsmore » for elastic properties and atomic partial charges. The DFT predicted elastic properties such as minimum shear modulus and Young's modulus can differ by an average of 3 and 9 GPa for rigid MOFs such as those in the test set. Moreover, we calculated the partial charges by vdW-DF2 deviate the most from other functionals while there is no significant difference between the partial charges calculated by M06L, PBE, PW91, PBE-D2 and PBE-D3 for the MOFs in the test set. We find that while there are differences in the magnitude of the properties predicted by the various functionals, these discrepancies are small compared to the accuracy necessary for most practical applications.« less
Multibody correlations in the hydrophobic solvation of glycine peptides

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

Harris, Robert C.; Drake, Justin A.; Pettitt, B. Montgomery, E-mail: mpettitt@utmb.edu

2014-12-14

Protein collapse during folding is often assumed to be driven by a hydrophobic solvation energy (ΔG{sub vdw}) that scales linearly with solvent-accessible surface area (A). In a previous study, we argued that ΔG{sub vdw}, as well as its attractive (ΔG{sub att}) and repulsive (ΔG{sub rep}) components, was not simply a linear function of A. We found that the surface tensions, γ{sub rep}, γ{sub att}, and γ{sub vdw}, gotten from ΔG{sub rep}, ΔG{sub att}, and ΔG{sub vdw} against A for four configurations of deca-alanine differed from those obtained for a set of alkanes. In the present study, we extend our analysismore » to fifty decaglycine structures and atomic decompositions. We find that different configurations of decaglycine generate different estimates of γ{sub rep}. Additionally, we considered the reconstruction of the solvation free energy from scaling the free energy of solvation of each atom type, free in solution. The free energy of the isolated atoms, scaled by the inverse surface area the atom would expose in the molecule does not reproduce the γ{sub rep} for the intact decaglycines. Finally, γ{sub att} for the decaglycine conformations is much larger in magnitude than those for deca-alanine or the alkanes, leading to large negative values of γ{sub vdw} (−74 and −56 cal/mol/Å{sup 2} for CHARMM27 and AMBER ff12sb force fields, respectively). These findings imply that ΔG{sub vdw} favors extended rather than compact structures for decaglycine. We find that ΔG{sub rep} and ΔG{sub vdw} have complicated dependencies on multibody correlations between solute atoms, on the geometry of the molecular surface, and on the chemical identities of the atoms.« less
Structure and vibrational spectra of low-energy silicon clusters

NASA Astrophysics Data System (ADS)

Sieck, A.; Porezag, D.; Frauenheim, Th.; Pederson, M. R.; Jackson, K.

1997-12-01

We have identified low-energy structures of silicon clusters with 9 to 14 atoms using a nonorthogonal tight-binding method (TB) based on density-functional theory (DF). We have further investigated the resulting structures with an accurate all-electron first-principles technique. The results for cohesive energies, cluster geometries, and highest occupied to lowest unoccupied molecular orbital (HOMO-LUMO) gaps show an overall good agreement between DF-TB and self-consistent-field (SCF) DF theory. For Si9 and Si14, we have found equilibrium structures, whereas for Si11, Si12, and Si13, we present clusters with energies close to that of the corresponding ground-state structure recently proposed in the literature. The bonding scheme of clusters in this size range is different from the bulk tetrahedral symmetry. The most stable structures, characterized by low energies and large HOMO-LUMO gaps, have similar common subunits. To aid in their experimental identification, we have computed the full vibrational spectra of the structures, along with the Raman activities, IR intensities, and static polarizabilities, using SCF-DF theory within the local-density approximation (LDA). This method has already been successfully applied to the determination of Raman and IR spectra of silicon clusters with 3-8, 10, 13, 20, and 21 atoms.
Orbital-Optimized MP3 and MP2.5 with Density-Fitting and Cholesky Decomposition Approximations.

PubMed

Bozkaya, Uğur

2016-03-08

Efficient implementations of the orbital-optimized MP3 and MP2.5 methods with the density-fitting (DF-OMP3 and DF-OMP2.5) and Cholesky decomposition (CD-OMP3 and CD-OMP2.5) approaches are presented. The DF/CD-OMP3 and DF/CD-OMP2.5 methods are applied to a set of alkanes to compare the computational cost with the conventional orbital-optimized MP3 (OMP3) [Bozkaya J. Chem. Phys. 2011, 135, 224103] and the orbital-optimized MP2.5 (OMP2.5) [Bozkaya and Sherrill J. Chem. Phys. 2014, 141, 204105]. Our results demonstrate that the DF-OMP3 and DF-OMP2.5 methods provide considerably lower computational costs than OMP3 and OMP2.5. Further application results show that the orbital-optimized methods are very helpful for the study of open-shell noncovalent interactions, aromatic bond dissociation energies, and hydrogen transfer reactions. We conclude that the DF-OMP3 and DF-OMP2.5 methods are very promising for molecular systems with challenging electronic structures.
Persistent photoconductivity in two-dimensional Mo 1-xW xSe 2–MoSe 2 van der Waals heterojunctions

DOE PAGES

Puretzky, Alexander A.; Basile, Leonardo; Idrobo, Juan Carlos; ...

2016-02-16

Van der Waals (vdW) heterojunctions consisting of vertically-stacked individual or multiple layers of two-dimensional (2D) layered semiconductors, especially the transition metal dichalcogenides (TMDs), are fascinating new artificial solids just nanometers-thin that promise novel optoelectronic functionalities due to the sensitivity of their electronic and optical properties to strong quantum confinement and interfacial interactions. Here, monolayers of n-type MoSe 2 and p-type Mo 1-xW xSe 2–MoSe 2 are grown by vapor transport methods, then transferred and stamped to form artificial vdW heterostructures with different interlayer orientations. Atomic-resolution Z-contrast electron microscopy and electron diffraction are used to characterize both the individual monolayers andmore » the atomic registry between layers in the bilayer vdW heterostructures. These measurements are compared with photoluminescence and low-frequency Raman spectroscopy, which indicates strong interlayer coupling in heterostructures. Remarkably, the heterojunctions exhibit an unprecedented photoconductivity effect that persists at room temperature for several days. This persistent photoconductivity is shown to be tunable by applying a gate bias that equilibrates the charge distribution. Furthermore, these measurements indicate that such ultrathin vdW heterojunctions can function as rewritable optoelectronic switches or memory elements under time-dependent photo-illumination, an effect which appears promising for new monolayer TMDs-based optoelectronic devices applications.« less
Probing Carrier Transport and Structure-Property Relationship of Highly Ordered Organic Semiconductors at the Two-Dimensional Limit.

PubMed

Zhang, Yuhan; Qiao, Jingsi; Gao, Si; Hu, Fengrui; He, Daowei; Wu, Bing; Yang, Ziyi; Xu, Bingchen; Li, Yun; Shi, Yi; Ji, Wei; Wang, Peng; Wang, Xiaoyong; Xiao, Min; Xu, Hangxun; Xu, Jian-Bin; Wang, Xinran

2016-01-08

One of the basic assumptions in organic field-effect transistors, the most fundamental device unit in organic electronics, is that charge transport occurs two dimensionally in the first few molecular layers near the dielectric interface. Although the mobility of bulk organic semiconductors has increased dramatically, direct probing of intrinsic charge transport in the two-dimensional limit has not been possible due to excessive disorders and traps in ultrathin organic thin films. Here, highly ordered single-crystalline mono- to tetralayer pentacene crystals are realized by van der Waals (vdW) epitaxy on hexagonal BN. We find that the charge transport is dominated by hopping in the first conductive layer, but transforms to bandlike in subsequent layers. Such an abrupt phase transition is attributed to strong modulation of the molecular packing by interfacial vdW interactions, as corroborated by quantitative structural characterization and density functional theory calculations. The structural modulation becomes negligible beyond the second conductive layer, leading to a mobility saturation thickness of only ∼3 nm. Highly ordered organic ultrathin films provide a platform for new physics and device structures (such as heterostructures and quantum wells) that are not possible in conventional bulk crystals.
The Nature of Bonding in Bulk Tellurium Composed of One-Dimensional Helical Chains.

PubMed

Yi, Seho; Zhu, Zhili; Cai, Xiaolin; Jia, Yu; Cho, Jun-Hyung

2018-05-07

Bulk tellurium (Te) is composed of one-dimensional (1D) helical chains which have been considered to be coupled by van der Waals (vdW) interactions. However, on the basis of first-principles density functional theory calculations, we here propose a different bonding nature between neighboring chains: i.e., helical chains made of normal covalent bonds are connected together by coordinate covalent bonds. It is revealed that the lone pairs of electrons of Te atoms participate in forming coordinate covalent bonds between neighboring chains, where each Te atom behaves as both an electron donor to neighboring chains and an electron acceptor from neighboring chains. This ligand-metal-like bonding nature in bulk Te results in the same order of bulk moduli along the directions parallel and perpendicular to the chains, contrasting with the large anisotropy of bulk moduli in vdW crystals. We further find that the electron effective masses parallel and perpendicular to the chains are almost the same as each other, consistent with the observed nearly isotropic electrical resistivity. It is thus demonstrated that the normal/coordinate covalent bonds parallel/perpendicular to the chains in bulk Te lead to a minor anisotropy in structural and transport properties.
Probing Carrier Transport and Structure-Property Relationship of Highly Ordered Organic Semiconductors at the Two-Dimensional Limit

NASA Astrophysics Data System (ADS)

Zhang, Yuhan; Qiao, Jingsi; Gao, Si; Hu, Fengrui; He, Daowei; Wu, Bing; Yang, Ziyi; Xu, Bingchen; Li, Yun; Shi, Yi; Ji, Wei; Wang, Peng; Wang, Xiaoyong; Xiao, Min; Xu, Hangxun; Xu, Jian-Bin; Wang, Xinran

2016-01-01

One of the basic assumptions in organic field-effect transistors, the most fundamental device unit in organic electronics, is that charge transport occurs two dimensionally in the first few molecular layers near the dielectric interface. Although the mobility of bulk organic semiconductors has increased dramatically, direct probing of intrinsic charge transport in the two-dimensional limit has not been possible due to excessive disorders and traps in ultrathin organic thin films. Here, highly ordered single-crystalline mono- to tetralayer pentacene crystals are realized by van der Waals (vdW) epitaxy on hexagonal BN. We find that the charge transport is dominated by hopping in the first conductive layer, but transforms to bandlike in subsequent layers. Such an abrupt phase transition is attributed to strong modulation of the molecular packing by interfacial vdW interactions, as corroborated by quantitative structural characterization and density functional theory calculations. The structural modulation becomes negligible beyond the second conductive layer, leading to a mobility saturation thickness of only ˜3 nm . Highly ordered organic ultrathin films provide a platform for new physics and device structures (such as heterostructures and quantum wells) that are not possible in conventional bulk crystals.
PS1-20: VDW Operational Committee: Current Activities and Future Directions

PubMed Central

Brown, Jeffrey; McDonald, Sarah; Moore, Kristen; Saylor, Gwyn; Hart, Gene; Hornbrook, Mark; Magid, David; Go, Alan

2010-01-01

Background/Aims: The Virtual Data Warehouse (VDW) is the HMO Research Network (HMORN) approach for facilitating multisite research while protecting the privacy of members and proprietary corporate information. A valid and sustainable VDW is critical to the success of the HMORN, and is needed for HMORN’s inclusion in many of the most important public health initiatives planned for the next few years. Methods: In November 2007 the HMORN Governing Board approved the VDW 5-Year Strategic Plan, including creation of a VDW Operational Committee (VOC), reporting to the Assets Stewardship Committee (ASC) and providing coordinated oversight of the development, maintenance, and enhancement of the VDW. The seven members of the VOC are investigators and analysts representing HMORN’s major consortia projects: CERT, CVRN and CRN. Results: In 2008, the VOC accomplished two major short term goals: Creation of a comprehensive data quality checking system, implemented by seven content area expert Working Groups (WGs) consisting of 23 investigators and 23 programmer\\analysts. The content areas of the WGs are enrollment and demographics, pharmacy, utilization, tumor, vital signs, laboratory, and census. The WGs assessed data availability and completeness for their content area and reported findings to the VOC and ASC, including recommendations for changes and enhancements. WG reports will form the basis for ongoing VDW documentation that will be used to standardize HMORN VDW descriptions for grants and proposals; Development of a budget, staffing plan and priorities for 2009. The 2009 priorities include development of VOC standard operating procedures for creating new data content areas and changing current data areas/definitions, documenting policies for use of the VDW, promoting use of the VDW, and creation of additional WGs for death (new VDW content area), informatics, implementation, and data documentation. The documentation WG will oversee issues such as data dictionaries, data checking documentation, programming resources, a clinical concepts library, user guides, and incorporating updated VDW information in the HMORN Collaboration Toolkit. Looking forward, the VDW 5-year Strategic Plan includes streamlining IRB approval for multisite research and enhancing HMORN informatics capabilities. Conclusions: The newly created VOC has made substantial progress in helping make the HMORN VDW an even more valuable and useful resource for the network.
PS3-21: Extracting Utilization Data from Clarity into VDW Using Oracle and SAS

PubMed Central

Chimmula, Srivardhan

2013-01-01

Background/Aims The purpose of the presentation is to demonstrate how we use SAS and Oracle to load VDW_Utilization, VDW_DX, and VDW_PX tables from Clarity at the Kaiser Permanente Northern California (KPNC) Division of Research (DOR) site. Methods DOR uses the best of Oracle PL/ SQL and SAS capabilities in building Extract Transform and Load (ETL) processes. These processes extract patient encounter, diagnosis, and procedure data from Teradata-based Clarity. The data is then transformed to fit HMORN’s VDW definitions of the table. This data is then loaded into the Oracle-based VDW table on DOR’s research database and then finally a copy of the table is also created as a SAS dataset. Results DOR builds robust and efficient ETL processes that refresh VDW Utilization table on a monthly basis processing millions of records/observations. The ETL processes have the capability to identify daily changes in Clarity and update the VDW tables on a daily basis. Conclusions KPNC DOR combines the best of both Oracle and SAS worlds to build ETL processes that load the data into VDW Utilization tables efficiently.

Derivation of general analytic gradient expressions for density-fitted post-Hartree-Fock methods: An efficient implementation for the density-fitted second-order Møller–Plesset perturbation theory

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

Bozkaya, Uğur, E-mail: ugur.bozkaya@atauni.edu.tr

General analytic gradient expressions (with the frozen-core approximation) are presented for density-fitted post-HF methods. An efficient implementation of frozen-core analytic gradients for the second-order Møller–Plesset perturbation theory (MP2) with the density-fitting (DF) approximation (applying to both reference and correlation energies), which is denoted as DF-MP2, is reported. The DF-MP2 method is applied to a set of alkanes, conjugated dienes, and noncovalent interaction complexes to compare the computational cost of single point analytic gradients with MP2 with the resolution of the identity approach (RI-MP2) [F. Weigend and M. Häser, Theor. Chem. Acc. 97, 331 (1997); R. A. Distasio, R. P. Steele,more » Y. M. Rhee, Y. Shao, and M. Head-Gordon, J. Comput. Chem. 28, 839 (2007)]. In the RI-MP2 method, the DF approach is used only for the correlation energy. Our results demonstrate that the DF-MP2 method substantially accelerate the RI-MP2 method for analytic gradient computations due to the reduced input/output (I/O) time. Because in the DF-MP2 method the DF approach is used for both reference and correlation energies, the storage of 4-index electron repulsion integrals (ERIs) are avoided, 3-index ERI tensors are employed instead. Further, as in case of integrals, our gradient equation is completely avoid construction or storage of the 4-index two-particle density matrix (TPDM), instead we use 2- and 3-index TPDMs. Hence, the I/O bottleneck of a gradient computation is significantly overcome. Therefore, the cost of the generalized-Fock matrix (GFM), TPDM, solution of Z-vector equations, the back transformation of TPDM, and integral derivatives are substantially reduced when the DF approach is used for the entire energy expression. Further application results show that the DF approach introduce negligible errors for closed-shell reaction energies and equilibrium bond lengths.« less
Two-dimensional GaSe/MoSe 2 misfit bilayer heterojunctions by van der Waals epitaxy

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

Li, Xufan; Lin, Ming-Wei; Lin, Junhao

Two-dimensional (2D) heterostructures hold the promise for future atomically-thin electronics and optoelectronics due to their diverse functionalities. While heterostructures consisting of different transition metal dichacolgenide monolayers with well-matched lattices and novel physical properties have been successfully fabricated via van der Waals (vdW) or edge epitaxy, constructing heterostructures from monolayers of layered semiconductors with large lattice misfits still remains challenging. Here, we report the growth of monolayer GaSe/MoSe 2 heterostructures with large lattice misfit by two-step chemical vapor deposition (CVD). Both vertically stacked and lateral heterostructures are demonstrated. The vertically stacked GaSe/MoSe 2 heterostructures exhibit vdW epitaxy with well-aligned lattice orientationmore » between the two layers, forming an incommensurate vdW heterostructure. However, the lateral heterostructures exhibit no lateral epitaxial alignment at the interface between GaSe and MoSe 2 crystalline domains. Instead of a direct lateral connection at the boundary region where the same lattice orientation is observed between GaSe and MoSe 2 monolayer domains in lateral GaSe/MoSe 2 heterostructures, GaSe monolayers are found to overgrow MoSe 2 during CVD, forming a stripe of vertically stacked vdW heterostructure at the crystal interface. Such vertically-stacked vdW GaSe/MoSe 2 heterostructures are shown to form p-n junctions with effective transport and separation of photo-generated charge carriers between layers, resulting in a gate-tunable photovoltaic response. In conclusion, these GaSe/MoSe 2 vdW heterostructures should have applications as gate-tunable field-effect transistors, photodetectors, and solar cells.« less
Two-dimensional GaSe/MoSe 2 misfit bilayer heterojunctions by van der Waals epitaxy

DOE PAGES

Li, Xufan; Lin, Ming-Wei; Lin, Junhao; ...

2016-04-01

Two-dimensional (2D) heterostructures hold the promise for future atomically-thin electronics and optoelectronics due to their diverse functionalities. While heterostructures consisting of different transition metal dichacolgenide monolayers with well-matched lattices and novel physical properties have been successfully fabricated via van der Waals (vdW) or edge epitaxy, constructing heterostructures from monolayers of layered semiconductors with large lattice misfits still remains challenging. Here, we report the growth of monolayer GaSe/MoSe 2 heterostructures with large lattice misfit by two-step chemical vapor deposition (CVD). Both vertically stacked and lateral heterostructures are demonstrated. The vertically stacked GaSe/MoSe 2 heterostructures exhibit vdW epitaxy with well-aligned lattice orientationmore » between the two layers, forming an incommensurate vdW heterostructure. However, the lateral heterostructures exhibit no lateral epitaxial alignment at the interface between GaSe and MoSe 2 crystalline domains. Instead of a direct lateral connection at the boundary region where the same lattice orientation is observed between GaSe and MoSe 2 monolayer domains in lateral GaSe/MoSe 2 heterostructures, GaSe monolayers are found to overgrow MoSe 2 during CVD, forming a stripe of vertically stacked vdW heterostructure at the crystal interface. Such vertically-stacked vdW GaSe/MoSe 2 heterostructures are shown to form p-n junctions with effective transport and separation of photo-generated charge carriers between layers, resulting in a gate-tunable photovoltaic response. In conclusion, these GaSe/MoSe 2 vdW heterostructures should have applications as gate-tunable field-effect transistors, photodetectors, and solar cells.« less
Tensor hypercontraction density fitting. I. Quartic scaling second- and third-order Møller-Plesset perturbation theory

NASA Astrophysics Data System (ADS)

Hohenstein, Edward G.; Parrish, Robert M.; Martínez, Todd J.

2012-07-01

Many approximations have been developed to help deal with the O(N4) growth of the electron repulsion integral (ERI) tensor, where N is the number of one-electron basis functions used to represent the electronic wavefunction. Of these, the density fitting (DF) approximation is currently the most widely used despite the fact that it is often incapable of altering the underlying scaling of computational effort with respect to molecular size. We present a method for exploiting sparsity in three-center overlap integrals through tensor decomposition to obtain a low-rank approximation to density fitting (tensor hypercontraction density fitting or THC-DF). This new approximation reduces the 4th-order ERI tensor to a product of five matrices, simultaneously reducing the storage requirement as well as increasing the flexibility to regroup terms and reduce scaling behavior. As an example, we demonstrate such a scaling reduction for second- and third-order perturbation theory (MP2 and MP3), showing that both can be carried out in O(N4) operations. This should be compared to the usual scaling behavior of O(N5) and O(N6) for MP2 and MP3, respectively. The THC-DF technique can also be applied to other methods in electronic structure theory, such as coupled-cluster and configuration interaction, promising significant gains in computational efficiency and storage reduction.
CROSS-DISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY: The Fractal Dimensions of Complex Networks

NASA Astrophysics Data System (ADS)

Guo, Long; Cai, XU

2009-08-01

It is shown that many real complex networks share distinctive features, such as the small-world effect and the heterogeneous property of connectivity of vertices, which are different from random networks and regular lattices. Although these features capture the important characteristics of complex networks, their applicability depends on the style of networks. To unravel the universal characteristics many complex networks have in common, we study the fractal dimensions of complex networks using the method introduced by Shanker. We find that the average 'density' (ρ(r)) of complex networks follows a better power-law function as a function of distance r with the exponent df, which is defined as the fractal dimension, in some real complex networks. Furthermore, we study the relation between df and the shortcuts Nadd in small-world networks and the size N in regular lattices. Our present work provides a new perspective to understand the dependence of the fractal dimension df on the complex network structure.
Polytypism and unexpected strong interlayer coupling in two-dimensional layered ReS2

NASA Astrophysics Data System (ADS)

Qiao, Xiao-Fen; Wu, Jiang-Bin; Zhou, Linwei; Qiao, Jingsi; Shi, Wei; Chen, Tao; Zhang, Xin; Zhang, Jun; Ji, Wei; Tan, Ping-Heng

2016-04-01

Anisotropic two-dimensional (2D) van der Waals (vdW) layered materials, with both scientific interest and application potential, offer one more dimension than isotropic 2D materials to tune their physical properties. Various physical properties of 2D multi-layer materials are modulated by varying their stacking orders owing to significant interlayer vdW coupling. Multilayer rhenium disulfide (ReS2), a representative anisotropic 2D material, was expected to be randomly stacked and lack interlayer coupling. Here, we demonstrate two stable stacking orders, namely isotropic-like (IS) and anisotropic-like (AI) N layer (NL, N > 1) ReS2 are revealed by ultralow- and high-frequency Raman spectroscopy, photoluminescence and first-principles density functional theory calculation. Two interlayer shear modes are observed in AI-NL-ReS2 while only one shear mode appears in IS-NL-ReS2, suggesting anisotropic- and isotropic-like stacking orders in IS- and AI-NL-ReS2, respectively. This explicit difference in the observed frequencies identifies an unexpected strong interlayer coupling in IS- and AI-NL-ReS2. Quantitatively, the force constants of them are found to be around 55-90% of those of multilayer MoS2. The revealed strong interlayer coupling and polytypism in multi-layer ReS2 may stimulate future studies on engineering physical properties of other anisotropic 2D materials by stacking orders.Anisotropic two-dimensional (2D) van der Waals (vdW) layered materials, with both scientific interest and application potential, offer one more dimension than isotropic 2D materials to tune their physical properties. Various physical properties of 2D multi-layer materials are modulated by varying their stacking orders owing to significant interlayer vdW coupling. Multilayer rhenium disulfide (ReS2), a representative anisotropic 2D material, was expected to be randomly stacked and lack interlayer coupling. Here, we demonstrate two stable stacking orders, namely isotropic-like (IS) and anisotropic-like (AI) N layer (NL, N > 1) ReS2 are revealed by ultralow- and high-frequency Raman spectroscopy, photoluminescence and first-principles density functional theory calculation. Two interlayer shear modes are observed in AI-NL-ReS2 while only one shear mode appears in IS-NL-ReS2, suggesting anisotropic- and isotropic-like stacking orders in IS- and AI-NL-ReS2, respectively. This explicit difference in the observed frequencies identifies an unexpected strong interlayer coupling in IS- and AI-NL-ReS2. Quantitatively, the force constants of them are found to be around 55-90% of those of multilayer MoS2. The revealed strong interlayer coupling and polytypism in multi-layer ReS2 may stimulate future studies on engineering physical properties of other anisotropic 2D materials by stacking orders. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr01569g
Effect of population density on reproduction in Microtus fortis under laboratory conditions.

PubMed

Han, Qunhua; Zhang, Meiwen; Guo, Cong; Shen, Guo; Wang, Yong; Li, Bo; Xu, Zhenggang

2014-06-01

Between December 2011 and March 2012, the reproductive characteristics of Microtus fortis reared in the laboratory at different population densities were assessed. In all, 258 male and female voles were randomly divided into 4 groups and reared at densities of 2, 4, 6, and 8 animals per cage (sex ratio: 1:1). The results showed that the pregnancy rate (χ2 = 21.671, df = 3, P < 0.001) and first farrowing interval (F = 12.355, df = 3, P < 0.001) were significantly different among the different population density groups, but the mean litter size (mean ± SD) was not (F = 2.669, df = 3, P > 0.05). In particular, the reproductive index and sex hormone levels showed a significant difference among the different density groups studied.
C-A1-03: Considerations in the Design and Use of an Oracle-based Virtual Data Warehouse

PubMed Central

Bredfeldt, Christine; McFarland, Lela

2011-01-01

Background/Aims The amount of clinical data available for research is growing exponentially. As it grows, increasing the efficiency of both data storage and data access becomes critical. Relational database management systems (rDBMS) such as Oracle are ideal solutions for managing longitudinal clinical data because they support large-scale data storage and highly efficient data retrieval. In addition, they can greatly simplify the management of large data warehouses, including security management and regular data refreshes. However, the HMORN Virtual Data Warehouse (VDW) was originally designed based on SAS datasets, and this design choice has a number of implications for both the design and use of an Oracle-based VDW. From a design standpoint, VDW tables are designed as flat SAS datasets, which do not take full advantage of Oracle indexing capabilities. From a data retrieval standpoint, standard VDW SAS scripts do not take advantage of SAS pass-through SQL capabilities to enable Oracle to perform the processing required to narrow datasets to the population of interest. Methods Beginning in 2009, the research department at Kaiser Permanente in the Mid-Atlantic States (KPMA) has developed an Oracle-based VDW according to the HMORN v3 specifications. In order to take advantage of the strengths of relational databases, KPMA introduced an interface layer to the VDW data, using views to provide access to standardized VDW variables. In addition, KPMA has developed SAS programs that provide access to SQL pass-through processing for first-pass data extraction into SAS VDW datasets for processing by standard VDW scripts. Results We discuss both the design and performance considerations specific to the KPMA Oracle-based VDW. We benchmarked performance of the Oracle-based VDW using both standard VDW scripts and an initial pre-processing layer to evaluate speed and accuracy of data return. Conclusions Adapting the VDW for deployment in an Oracle environment required minor changes to the underlying structure of the data. Further modifications of the underlying data structure would lead to performance enhancements. Maximally efficient data access for standard VDW scripts requires an extra step that involves restricting the data to the population of interest at the data server level prior to standard processing.
Effects of partial La filling and Sb vacancy defects on CoS b 3 skutterudites

DOE PAGES

Hu, Chongze; Zeng, Xiaoyu; Liu, Yufei; ...

2017-04-25

Over the past decade, the open frame ("cagey") structure of CoSb 3 skutterudite has invited intensive filling studies with various rare-earth elements for delivering state-of-the-art mid-temperature thermoelectric performance. In order to rationalize previously reported experimental results and provide new insight into the underexplored roles of La fillers and Sb vacancies, ab initio density functional theory studies, along with semi-classical Boltzmann transport theory calculations, are performed for pristine CoSb 3 of different lattice settings and La-filled CoSb 3 with and without Sb s mono- and di-vacancy defects. We examine the effects of van der Waals (vdW) interactions, spin-orbit coupling (SOC), spinmore » polarization, partial La-filling, and Sb vacancy defects on the structural, electronic, and thermoelectric properties. The vdW interactions profoundly affect the lattice constant, which in turn affects the band gap. The SOC shows minor effects on the electronic and thermoelectric properties. The peculiar quasi-Dirac band in the pristine CoSb 3 largely survives La filling but not Sb vacancies, which instead introduce dispersive bands in the band gap region. Importantly, the band structure, density of states, and Fermi surface of La-filled CoSb 3 are significantly spin polarized, giving rise to spin-dependent thermoelectric properties. Seebeck coefficients directly calculated as a function of chemical potential are interpreted in connection with the electronic structures. Temperature-dependent Seebeck coefficients derived for the experimentally studied materials agree well with available experimental data. Seebeck coefficients obtained as a function of charge carrier concentration corroborate a thermoelectrically favorable role at high filling fractions played by the electron/hole pockets on the Fermi surface associated with the degenerate valleys/hills in the conduction/valence bands, respectively. Our results serve to advance the understanding of CoSb 3 skutterudite, a class of materials with important fundamental and application implications for thermoelectrics and spintronics.« less
Effects of partial La filling and Sb vacancy defects on CoS b 3 skutterudites

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

Hu, Chongze; Zeng, Xiaoyu; Liu, Yufei

Over the past decade, the open frame ("cagey") structure of CoSb 3 skutterudite has invited intensive filling studies with various rare-earth elements for delivering state-of-the-art mid-temperature thermoelectric performance. In order to rationalize previously reported experimental results and provide new insight into the underexplored roles of La fillers and Sb vacancies, ab initio density functional theory studies, along with semi-classical Boltzmann transport theory calculations, are performed for pristine CoSb 3 of different lattice settings and La-filled CoSb 3 with and without Sb s mono- and di-vacancy defects. We examine the effects of van der Waals (vdW) interactions, spin-orbit coupling (SOC), spinmore » polarization, partial La-filling, and Sb vacancy defects on the structural, electronic, and thermoelectric properties. The vdW interactions profoundly affect the lattice constant, which in turn affects the band gap. The SOC shows minor effects on the electronic and thermoelectric properties. The peculiar quasi-Dirac band in the pristine CoSb 3 largely survives La filling but not Sb vacancies, which instead introduce dispersive bands in the band gap region. Importantly, the band structure, density of states, and Fermi surface of La-filled CoSb 3 are significantly spin polarized, giving rise to spin-dependent thermoelectric properties. Seebeck coefficients directly calculated as a function of chemical potential are interpreted in connection with the electronic structures. Temperature-dependent Seebeck coefficients derived for the experimentally studied materials agree well with available experimental data. Seebeck coefficients obtained as a function of charge carrier concentration corroborate a thermoelectrically favorable role at high filling fractions played by the electron/hole pockets on the Fermi surface associated with the degenerate valleys/hills in the conduction/valence bands, respectively. Our results serve to advance the understanding of CoSb 3 skutterudite, a class of materials with important fundamental and application implications for thermoelectrics and spintronics.« less
Coarse-Grained Model for Water Involving a Virtual Site.

PubMed

Deng, Mingsen; Shen, Hujun

2016-02-04

In this work, we propose a new coarse-grained (CG) model for water by combining the features of two popular CG water models (BMW and MARTINI models) as well as by adopting a topology similar to that of the TIP4P water model. In this CG model, a CG unit, representing four real water molecules, consists of a virtual site, two positively charged particles, and a van der Waals (vdW) interaction center. Distance constraint is applied to the bonds formed between the vdW interaction center and the positively charged particles. The virtual site, which carries a negative charge, is determined by the locations of the two positively charged particles and the vdW interaction center. For the new CG model of water, we coined the name "CAVS" (charge is attached to a virtual site) due to the involvment of the virtual site. After being tested in molecular dynamic (MD) simulations of bulk water at various time steps, under different temperatures and in different salt (NaCl) concentrations, the CAVS model offers encouraging predictions for some bulk properties of water (such as density, dielectric constant, etc.) when compared to experimental ones.
Analytic energy gradients for the coupled-cluster singles and doubles method with the density-fitting approximation

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

Bozkaya, Uğur, E-mail: ugur.bozkaya@hacettepe.edu.tr; Department of Chemistry, Atatürk University, Erzurum 25240; Sherrill, C. David

2016-05-07

An efficient implementation is presented for analytic gradients of the coupled-cluster singles and doubles (CCSD) method with the density-fitting approximation, denoted DF-CCSD. Frozen core terms are also included. When applied to a set of alkanes, the DF-CCSD analytic gradients are significantly accelerated compared to conventional CCSD for larger molecules. The efficiency of our DF-CCSD algorithm arises from the acceleration of several different terms, which are designated as the “gradient terms”: computation of particle density matrices (PDMs), generalized Fock-matrix (GFM), solution of the Z-vector equation, formation of the relaxed PDMs and GFM, back-transformation of PDMs and GFM to the atomic orbitalmore » (AO) basis, and evaluation of gradients in the AO basis. For the largest member of the alkane set (C{sub 10}H{sub 22}), the computational times for the gradient terms (with the cc-pVTZ basis set) are 2582.6 (CCSD) and 310.7 (DF-CCSD) min, respectively, a speed up of more than 8-folds. For gradient related terms, the DF approach avoids the usage of four-index electron repulsion integrals. Based on our previous study [U. Bozkaya, J. Chem. Phys. 141, 124108 (2014)], our formalism completely avoids construction or storage of the 4-index two-particle density matrix (TPDM), using instead 2- and 3-index TPDMs. The DF approach introduces negligible errors for equilibrium bond lengths and harmonic vibrational frequencies.« less
Wave function delocalization and large-amplitude vibrations of helium on corrugated aromatic microsurfaces: tetracene.He and pentacene.He van der Waals complexes.

PubMed

Xu, Minzhong; Bacić, Zlatko

2007-08-09

We report accurate quantum three-dimensional calculations of highly excited intermolecular vibrational states of the van der Waals (vdW) complexes tetracene.He and pentacene.He in the S1 excited electronic state. The aromatic molecules were taken to be rigid and the intermolecular potential energy surfaces (IPESs) were modeled as a sum of atom-atom Lennard-Jones pair potentials. The IPESs are corrugated in the direction of the long (x) axis of the aromatic molecules, due to the presence of the symmetrically equivalent global double minimum for tetracene.He, and a triple minimum (central global minimum and two equivalent local minima) for pentacene.He, on each side of the aromatic plane. Both IPESs have two additional minor equivalent local minima further away from the center of the molecule. The vdW vibrational states analyzed in this work cover about 80% of the well depths of the IPESs. The mode coupling is generally weak for those states whose out-of-plane (z) mode is unexcited. However, the z-mode fundamental is strongly coupled to the short-axis (y) in-plane mode, so that the pure z-mode excitation could not be identified. The He atom exhibits large in-plane spatial delocalizaton already in the ground vdW vibrational state, which increases rapidly upon the excitation of the in-plane x and y modes, with little hindrance by the corrugation of the aromatic microsurfaces. For the vdW vibrational energies considered, the He atom spatial delocalization reaches Deltax and Deltay values of approximately 5 and 4 A, respectively, and is limited only by the finite size of the aromatic substrates. Side-crossing delocalization of the wave functions on both sides of the molecular plane is found at excitation energies >30 cm(-1), giving rise to the energy splittings of the pairs of states symmetric/antisymmetric with respect to the aromatic plane; the splittings show strong vdW vibrational mode specificity.
Assessing the Accuracy of Density Functional and Semiempirical Wave Function Methods for Water Nanoparticles: Comparing Binding and Relative Energies of (H2O)16 and (H2O)17 to CCSD(T) Results.

PubMed

Leverentz, Hannah R; Qi, Helena W; Truhlar, Donald G

2013-02-12

The binding energies and relative conformational energies of five configurations of the water 16-mer are computed using 61 levels of density functional (DF) theory, 12 methods combining DF theory with molecular mechanics damped dispersion (DF-MM), seven semiempirical-wave function (SWF) methods, and five methods combining SWF theory with molecular mechanics damped dispersion (SWF-MM). The accuracies of the computed energies are assessed by comparing them to recent high-level ab initio results; this assessment is more relevant to bulk water than previous tests on small clusters because a 16-mer is large enough to have water molecules that participate in more than three hydrogen bonds. We find that for water 16-mer binding energies the best DF, DF-MM, SWF, and SWF-MM methods (and their mean unsigned errors in kcal/mol) are respectively M06-2X (1.6), ωB97X-D (2.3), SCC-DFTB-γ(h) (35.2), and PM3-D (3.2). We also mention the good performance of CAM-B3LYP (1.8), M05-2X (1.9), and TPSSLYP (3.0). In contrast, for relative energies of various water nanoparticle 16-mer structures, the best methods (and mean unsigned errors in kcal/mol), in the same order of classes of methods, are SOGGA11-X (0.3), ωB97X-D (0.2), PM6 (0.4), and PMOv1 (0.6). We also mention the good performance of LC-ωPBE-D3 (0.3) and ωB97X (0.4). When both relative and binding energies are taken into consideration, the best methods overall (out of the 85 tested) are M05-2X without molecular mechanics and ωB97X-D when molecular mechanics corrections are included; with considerably higher average errors and considerably lower cost, the best SWF or SWF-MM method is PMOv1. We use six of the best methods for binding energies of the water 16-mers to calculate the binding energies of water hexamers and water 17-mers to test whether these methods are also reliable for binding energy calculations on other types of water clusters.
Equations of state for real gases on the nuclear scale

NASA Astrophysics Data System (ADS)

Vovchenko, Volodymyr

2017-07-01

The formalism to augment the classical models of the equation of state for real gases with quantum statistical effects is presented. It allows an arbitrary excluded volume procedure to model repulsive interactions, and an arbitrary density-dependent mean field to model attractive interactions. Variations on the excluded volume mechanism include van der Waals (VDW) and Carnahan-Starling models, while the mean fields are based on VDW, Redlich-Kwong-Soave, Peng-Robinson, and Clausius equations of state. The VDW parameters of the nucleon-nucleon interaction are fitted in each model to the properties of the ground state of nuclear matter, and the following range of values is obtained: a =330 -430 MeV fm3 and b =2.5 -4.4 fm3 . In the context of the excluded volume approach, the fits to the nuclear ground state disfavor the values of the effective hard-core radius of a nucleon significantly smaller than 0.5 fm , at least for the nuclear matter region of the phase diagram. Modifications to the standard VDW repulsion and attraction terms allow one to improve significantly the value of the nuclear incompressibility factor K0, bringing it closer to empirical estimates. The generalization to include the baryon-baryon interactions into the hadron resonance gas model is performed. The behavior of the baryon-related lattice QCD observables at zero chemical potential is shown to be strongly correlated to the nuclear matter properties: an improved description of the nuclear incompressibility also yields an improved description of the lattice data at μ =0 .
Van der Waals Epitaxy of GaSe/Graphene Heterostructure: Electronic and Interfacial Properties.

PubMed

Ben Aziza, Zeineb; Henck, Hugo; Pierucci, Debora; Silly, Mathieu G; Lhuillier, Emmanuel; Patriarche, Gilles; Sirotti, Fausto; Eddrief, Mahmoud; Ouerghi, Abdelkarim

2016-10-07

Stacking two-dimensional materials in so-called van der Waals (vdW) heterostructures, like the combination of GaSe and graphene, provides the ability to obtain hybrid systems which are suitable to design optoelectronic devices. Here, we report the structural and electronic properties of the direct growth of multilayered GaSe by Molecular beam Epitaxy (MBE) on graphene. Reflection high-energy electron diffraction (RHEED) images exhibited sharp streaky features indicative of high quality GaSe layer produced via a vdW epitaxy. Micro-Raman spectroscopy showed that, after the vdW hetero-interface formation, the Raman signature of pristine graphene is preserved. However, the GaSe film tuned the charge density of graphene layer by shifting the Dirac point by about 80 meV toward lower binding energies, attesting an electron transfer from graphene to GaSe. Angle-resolved photoemission spectroscopy (ARPES) measurements showed that the maximum of the valence band of few layers of GaSe are located at the Γ point at a binding energy of about -0.73 eV relatively to the Fermi level (p-type doping). From the ARPES measurements, a hole effective mass defined along the ΓM direction and equal to about m*/m0 = -1.1 was determined. By coupling the ARPES data with high resolution X-ray photoemission spectroscopy (HR-XPS) measurements, the Schottky interface barrier height was estimated to be 1.2 eV. These findings allow deeper understanding of the interlayer interactions and the electronic structure of GaSe/graphene vdW heterostructure.
Capillary waves and the decay of density correlations at liquid surfaces

NASA Astrophysics Data System (ADS)

Hernández-Muñoz, Jose; Chacón, Enrique; Tarazona, Pedro

2016-12-01

Wertheim predicted strong density-density correlations at free liquid surfaces, produced by capillary wave fluctuations of the interface [M. S. Wertheim, J. Chem. Phys. 65, 2377 (1976), 10.1063/1.433352]. That prediction has been used to search for a link between capillary wave (CW) theory and density functional (DF) formalism for classical fluids. In particular, Parry et al. have recently analyzed the decaying tails of these CW effects moving away from the interface as a clue for the extended CW theory [A. O. Parry et al., J. Phys.: Condens. Matter 28, 244013 (2016), 10.1088/0953-8984/28/24/244013], beyond the strict long-wavelength limit studied by Wertheim. Some apparently fundamental inconsistencies between the CW and the DF theoretical views of the fluid interfaces arose from the asymptotic analysis of the CW signal. In this paper we revisit the problem of the CW asymptotic decay with a separation of local non-CW surface correlation effects from those that are a truly nonlocal propagation of the CW fluctuations from the surface towards the liquid bulk.
Adsorption of benzene on low index surfaces of platinum in the presence of van der Waals interactions

NASA Astrophysics Data System (ADS)

K, Ayishabi P.; Chatanathodi, Raghu

2017-10-01

We have studied the adsorption of benzene on three low index surfaces of platinum using plane-wave Density Functional Theory (DFT) calculations, taking into consideration van der Waals (vdW) interaction. Experimentally, it is known that benzene adsorbs at the bridge site on the (111) surface, but in case of (110) and (100), this is not known yet. Our calculations show that benzene preferably adsorbs on bridge position on Pt(111) surface, whereas on Pt(110) and Pt(100) surfaces, the hollow position is energetically more favoured. The structural and electronic modifications of molecule and the surfaces are also examined. In all cases, adsorption-induced distortions of adsorbate-substrate complex are found to be modest in character, but relatively maximum in case of the (110) facet. The molecule is bound most strongly to the (110) surface. Importantly, we find that adsorption at bridge and atop positions are energetically feasible on the (110) surface, with the canting of benzene ring at a small angle from the metal plane. We study changes in electronic structure and the net charge transfer upon adsorption of benzene on all three low index planes. Inclusion of vdW interactions is important for obtaining realistic adsorption strengths for benzene on various Pt facets.
Two-dimensional GaSe/MoSe2 misfit bilayer heterojunctions by van der Waals epitaxy.

PubMed

Li, Xufan; Lin, Ming-Wei; Lin, Junhao; Huang, Bing; Puretzky, Alexander A; Ma, Cheng; Wang, Kai; Zhou, Wu; Pantelides, Sokrates T; Chi, Miaofang; Kravchenko, Ivan; Fowlkes, Jason; Rouleau, Christopher M; Geohegan, David B; Xiao, Kai

2016-04-01

Two-dimensional (2D) heterostructures hold the promise for future atomically thin electronics and optoelectronics because of their diverse functionalities. Although heterostructures consisting of different 2D materials with well-matched lattices and novel physical properties have been successfully fabricated via van der Waals (vdW) epitaxy, constructing heterostructures from layered semiconductors with large lattice misfits remains challenging. We report the growth of 2D GaSe/MoSe2 heterostructures with a large lattice misfit using two-step chemical vapor deposition (CVD). Both vertically stacked and lateral heterostructures are demonstrated. The vertically stacked GaSe/MoSe2 heterostructures exhibit vdW epitaxy with well-aligned lattice orientation between the two layers, forming a periodic superlattice. However, the lateral heterostructures exhibit no lateral epitaxial alignment at the interface between GaSe and MoSe2 crystalline domains. Instead of a direct lateral connection at the boundary region where the same lattice orientation is observed between GaSe and MoSe2 monolayer domains in lateral GaSe/MoSe2 heterostructures, GaSe monolayers are found to overgrow MoSe2 during CVD, forming a stripe of vertically stacked vdW heterostructures at the crystal interface. Such vertically stacked vdW GaSe/MoSe2 heterostructures are shown to form p-n junctions with effective transport and separation of photogenerated charge carriers between layers, resulting in a gate-tunable photovoltaic response. These GaSe/MoSe2 vdW heterostructures should have applications as gate-tunable field-effect transistors, photodetectors, and solar cells.
Two-dimensional GaSe/MoSe2 misfit bilayer heterojunctions by van der Waals epitaxy

PubMed Central

Li, Xufan; Lin, Ming-Wei; Lin, Junhao; Huang, Bing; Puretzky, Alexander A.; Ma, Cheng; Wang, Kai; Zhou, Wu; Pantelides, Sokrates T.; Chi, Miaofang; Kravchenko, Ivan; Fowlkes, Jason; Rouleau, Christopher M.; Geohegan, David B.; Xiao, Kai

2016-01-01

Two-dimensional (2D) heterostructures hold the promise for future atomically thin electronics and optoelectronics because of their diverse functionalities. Although heterostructures consisting of different 2D materials with well-matched lattices and novel physical properties have been successfully fabricated via van der Waals (vdW) epitaxy, constructing heterostructures from layered semiconductors with large lattice misfits remains challenging. We report the growth of 2D GaSe/MoSe2 heterostructures with a large lattice misfit using two-step chemical vapor deposition (CVD). Both vertically stacked and lateral heterostructures are demonstrated. The vertically stacked GaSe/MoSe2 heterostructures exhibit vdW epitaxy with well-aligned lattice orientation between the two layers, forming a periodic superlattice. However, the lateral heterostructures exhibit no lateral epitaxial alignment at the interface between GaSe and MoSe2 crystalline domains. Instead of a direct lateral connection at the boundary region where the same lattice orientation is observed between GaSe and MoSe2 monolayer domains in lateral GaSe/MoSe2 heterostructures, GaSe monolayers are found to overgrow MoSe2 during CVD, forming a stripe of vertically stacked vdW heterostructures at the crystal interface. Such vertically stacked vdW GaSe/MoSe2 heterostructures are shown to form p-n junctions with effective transport and separation of photogenerated charge carriers between layers, resulting in a gate-tunable photovoltaic response. These GaSe/MoSe2 vdW heterostructures should have applications as gate-tunable field-effect transistors, photodetectors, and solar cells. PMID:27152356

Physical adsorption at the nanoscale: Towards controllable scaling of the substrate-adsorbate van der Waals interaction

NASA Astrophysics Data System (ADS)

Ambrosetti, Alberto; Silvestrelli, Pier Luigi; Tkatchenko, Alexandre

2017-06-01

The Lifshitz-Zaremba-Kohn (LZK) theory is commonly considered as the correct large-distance limit for the van der Waals (vdW) interaction of adsorbates (atoms, molecules, or nanoparticles) with solid substrates. In the standard approximate form, implicitly based on local dielectric functions, the LZK approach predicts universal power laws for vdW interactions depending only on the dimensionality of the interacting objects. However, recent experimental findings are challenging the universality of this theoretical approach at finite distances of relevance for nanoscale assembly. Here, we present a combined analytical and numerical many-body study demonstrating that physical adsorption can be significantly enhanced at the nanoscale. Regardless of the band gap or the nature of the adsorbate specie, we find deviations from conventional LZK power laws that extend to separation distances of up to 10-20 nm. Comparison with recent experimental observations of ultra-long-ranged vdW interactions in the delamination of graphene from a silicon substrate reveals qualitative agreement with the present theory. The sensitivity of vdW interactions to the substrate response and to the adsorbate characteristic excitation frequency also suggests that adsorption strength can be effectively tuned in experiments, paving the way to an improved control of physical adsorption at the nanoscale.
Assessing the performance of dispersionless and dispersion-accounting methods: helium interaction with cluster models of the TiO2(110) surface.

PubMed

de Lara-Castells, María Pilar; Stoll, Hermann; Mitrushchenkov, Alexander O

2014-08-21

As a prototypical dispersion-dominated physisorption problem, we analyze here the performance of dispersionless and dispersion-accounting methodologies on the helium interaction with cluster models of the TiO2(110) surface. A special focus has been given to the dispersionless density functional dlDF and the dlDF+Das construction for the total interaction energy (K. Pernal, R. Podeswa, K. Patkowski, and K. Szalewicz, Phys. Rev. Lett. 2009, 109, 263201), where Das is an effective interatomic pairwise functional form for the dispersion. Likewise, the performance of symmetry-adapted perturbation theory (SAPT) method is evaluated, where the interacting monomers are described by density functional theory (DFT) with the dlDF, PBE, and PBE0 functionals. Our benchmarks include CCSD(T)-F12b calculations and comparative analysis on the nuclear bound states supported by the He-cluster potentials. Moreover, intra- and intermonomer correlation contributions to the physisorption interaction are analyzed through the method of increments (H. Stoll, J. Chem. Phys. 1992, 97, 8449) at the CCSD(T) level of theory. This method is further applied in conjunction with a partitioning of the Hartree-Fock interaction energy to estimate individual interaction energy components, comparing them with those obtained using the different SAPT(DFT) approaches. The cluster size evolution of dispersionless and dispersion-accounting energy components is then discussed, revealing the reduced role of the dispersionless interaction and intramonomer correlation when the extended nature of the surface is better accounted for. On the contrary, both post-Hartree-Fock and SAPT(DFT) results clearly demonstrate the high-transferability character of the effective pairwise dispersion interaction whatever the cluster model is. Our contribution also illustrates how the method of increments can be used as a valuable tool not only to achieve the accuracy of CCSD(T) calculations using large cluster models but also to evaluate the performance of SAPT(DFT) methods for the physically well-defined contributions to the total interaction energy. Overall, our work indicates the excellent performance of a dlDF+Das approach in which the parameters are optimized using the smallest cluster model of the target surface to treat van der Waals adsorbate-surface interactions.
Optimization of an exchange-correlation density functional for water

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

Fritz, Michelle; Fernández-Serra, Marivi; Institute for Advanced Computational Science, Stony Brook University, Stony Brook, New York 11794-3800

2016-06-14

We describe a method, that we call data projection onto parameter space (DPPS), to optimize an energy functional of the electron density, so that it reproduces a dataset of experimental magnitudes. Our scheme, based on Bayes theorem, constrains the optimized functional not to depart unphysically from existing ab initio functionals. The resulting functional maximizes the probability of being the “correct” parameterization of a given functional form, in the sense of Bayes theory. The application of DPPS to water sheds new light on why density functional theory has performed rather poorly for liquid water, on what improvements are needed, and onmore » the intrinsic limitations of the generalized gradient approximation to electron exchange and correlation. Finally, we present tests of our water-optimized functional, that we call vdW-DF-w, showing that it performs very well for a variety of condensed water systems.« less
Use of femur bone density to segregate wild from farmed Dybowski's frog (Rana dybowskii).

PubMed

Yang, Shu Hui; Huang, Xiao Ming; Xia, Rui; Xu, Yan Chun; Dahmer, Thomas D

2011-04-15

Wildlife has been utilized by humans throughout history and demand continues to grow today. Farming of wildlife can supplement the supply of wild-harvested wildlife products and, in theory, can reduce pressure on free-ranging populations. However, poached wildlife products frequently enter legal markets where they are fraudulently sold as farmed wildlife products. To effectively close this illegal trade in wild-captured wildlife, there is a need to discriminate wild products from farmed products. Because of the strong market demand for wild-captured frog meat and the resulting strong downward pressure on wild populations, we undertook research to develop a method to discriminate wild from farmed Dybowski's frog (Rana dybowskii) based on femur bone density. We measured femur bone density (D(f)) as the ratio of bone mass to bone volume. D(f) of wild frogs revealed a slightly increasing linear trend with increasing age (R(2)=0.214 in males and R(2)=0.111 in females, p=0.000). Wild males and wild females of age classes from 2 to ≥ 5 years had similar D(f) values. In contrast, 2-year-old farmed frogs showed significantly higher D(f) values (p=0.000) among males (mean D(f)=0.623 ± 0.011 g/ml, n=32) than females (mean D(f)=0.558 ± 0.011 g/ml, n=27). For both sexes, D(f) of wild frogs was significantly higher than that of farmed frogs (p=0.000). Among males, 87.5% (28 of 32 individuals) of farmed frogs were correctly identified as farmed frogs and 86.3% (69 of 80 individuals) of wild frogs were correctly identified as wild frogs. These results suggest that femur bone density is one reliable tool for discriminating between wild and farmed Dybowski's frog. This study also highlights a novel strategy with explicit forensic potential to discriminate wild from captive bred wildlife species. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.
Predicting Local Dengue Transmission in Guangzhou, China, through the Influence of Imported Cases, Mosquito Density and Climate Variability

PubMed Central

Sang, Shaowei; Yin, Wenwu; Bi, Peng; Zhang, Honglong; Wang, Chenggang; Liu, Xiaobo; Chen, Bin; Yang, Weizhong; Liu, Qiyong

2014-01-01

Introduction Each year there are approximately 390 million dengue infections worldwide. Weather variables have a significant impact on the transmission of Dengue Fever (DF), a mosquito borne viral disease. DF in mainland China is characterized as an imported disease. Hence it is necessary to explore the roles of imported cases, mosquito density and climate variability in dengue transmission in China. The study was to identify the relationship between dengue occurrence and possible risk factors and to develop a predicting model for dengue’s control and prevention purpose. Methodology and Principal Findings Three traditional suburbs and one district with an international airport in Guangzhou city were selected as the study areas. Autocorrelation and cross-correlation analysis were used to perform univariate analysis to identify possible risk factors, with relevant lagged effects, associated with local dengue cases. Principal component analysis (PCA) was applied to extract principal components and PCA score was used to represent the original variables to reduce multi-collinearity. Combining the univariate analysis and prior knowledge, time-series Poisson regression analysis was conducted to quantify the relationship between weather variables, Breteau Index, imported DF cases and the local dengue transmission in Guangzhou, China. The goodness-of-fit of the constructed model was determined by pseudo-R2, Akaike information criterion (AIC) and residual test. There were a total of 707 notified local DF cases from March 2006 to December 2012, with a seasonal distribution from August to November. There were a total of 65 notified imported DF cases from 20 countries, with forty-six cases (70.8%) imported from Southeast Asia. The model showed that local DF cases were positively associated with mosquito density, imported cases, temperature, precipitation, vapour pressure and minimum relative humidity, whilst being negatively associated with air pressure, with different time lags. Conclusions Imported DF cases and mosquito density play a critical role in local DF transmission, together with weather variables. The establishment of an early warning system, using existing surveillance datasets will help to control and prevent dengue in Guangzhou, China. PMID:25019967
Predicting local dengue transmission in Guangzhou, China, through the influence of imported cases, mosquito density and climate variability.

PubMed

Sang, Shaowei; Yin, Wenwu; Bi, Peng; Zhang, Honglong; Wang, Chenggang; Liu, Xiaobo; Chen, Bin; Yang, Weizhong; Liu, Qiyong

2014-01-01

Each year there are approximately 390 million dengue infections worldwide. Weather variables have a significant impact on the transmission of Dengue Fever (DF), a mosquito borne viral disease. DF in mainland China is characterized as an imported disease. Hence it is necessary to explore the roles of imported cases, mosquito density and climate variability in dengue transmission in China. The study was to identify the relationship between dengue occurrence and possible risk factors and to develop a predicting model for dengue's control and prevention purpose. Three traditional suburbs and one district with an international airport in Guangzhou city were selected as the study areas. Autocorrelation and cross-correlation analysis were used to perform univariate analysis to identify possible risk factors, with relevant lagged effects, associated with local dengue cases. Principal component analysis (PCA) was applied to extract principal components and PCA score was used to represent the original variables to reduce multi-collinearity. Combining the univariate analysis and prior knowledge, time-series Poisson regression analysis was conducted to quantify the relationship between weather variables, Breteau Index, imported DF cases and the local dengue transmission in Guangzhou, China. The goodness-of-fit of the constructed model was determined by pseudo-R2, Akaike information criterion (AIC) and residual test. There were a total of 707 notified local DF cases from March 2006 to December 2012, with a seasonal distribution from August to November. There were a total of 65 notified imported DF cases from 20 countries, with forty-six cases (70.8%) imported from Southeast Asia. The model showed that local DF cases were positively associated with mosquito density, imported cases, temperature, precipitation, vapour pressure and minimum relative humidity, whilst being negatively associated with air pressure, with different time lags. Imported DF cases and mosquito density play a critical role in local DF transmission, together with weather variables. The establishment of an early warning system, using existing surveillance datasets will help to control and prevent dengue in Guangzhou, China.
Non-additivity of molecule-surface van der Waals potentials from force measurements.

PubMed

Wagner, Christian; Fournier, Norman; Ruiz, Victor G; Li, Chen; Müllen, Klaus; Rohlfing, Michael; Tkatchenko, Alexandre; Temirov, Ruslan; Tautz, F Stefan

2014-11-26

Van der Waals (vdW) forces act ubiquitously in condensed matter. Despite being weak on an atomic level, they substantially influence molecular and biological systems due to their long range and system-size scaling. The difficulty to isolate and measure vdW forces on a single-molecule level causes our present understanding to be strongly theory based. Here we show measurements of the attractive potential between differently sized organic molecules and a metal surface using an atomic force microscope. Our choice of molecules and the large molecule-surface separation cause this attraction to be purely of vdW type. The experiment allows testing the asymptotic vdW force law and its validity range. We find a superlinear growth of the vdW attraction with molecular size, originating from the increased deconfinement of electrons in the molecules. Because such non-additive vdW contributions are not accounted for in most first-principles or empirical calculations, we suggest further development in that direction.
Density functional Gaussian-type-orbital approach to theoretical study of nitric oxide dimers

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

Jursic, B.S.; Zdravkovski, Z.

Structure and total energies of the cis NO dimer, the trans NO dimer, and the NO monomer were calculated by ab initio methods (UHF, UMP2, and MP3) and density functional theory methods (LSDA and BLYP) with different basis sets [from 3-21G* to 6-311++(3df,3pd)]. The system is especially hard to model because two NO molecules are weakly associated in a dimer that has very long N-N bond. The results obtained by different methods are compared and the necessity of correlational methods for studying these systems is discussed.
Biotic and abiotic correlates with black bullhead population characteristics in Nebraska sandhill lakes

USGS Publications Warehouse

Phelps, Q.E.; Ward, M.J.; Paukert, C.P.; Chipps, S.R.; Willis, D.W.

2005-01-01

We explored relationships among black bullhead (Ameiurus melas) population characteristics and physicochemical attributes in shallow lakes and quantified relationships between population characteristics of black bullhead and sport fishes. Lake characteristics and fisheries survey data were collected from the Sandhills region of northcentral Nebraska from May through June, 1998 and 1999. Relative abundance of black bullheads was inversely related to proportional stock density (r=-0.672, df=15, P=0.004); however, neither relative weight nor growth was significantly (P ??? 0.20) related to black bullhead relative abundance. Population characteristics of common panfish species such as bluegill (Lepomis macrochirus), green sunfish (L. cyanellus), pumpkinseed (L. gibbosus), and yellow perch (Perca flavescens) were not correlated with black bullhead relative abundance or size structure. Rather, proportional stock density (r=0.655, df=10, P=0.029) and growth (r=0.59, df=11, P=0.04) of black bullhead were positively related to relative abundance of largemouth bass (Micropterus salmoides). Similarly, black bullhead relative abundance was inversely related to largemouth bass size structure (r=-0.51, df=14, P= 0.05). Black bullhead mean length at age 3 was positively related to total phosphorous concentration (r=0.65, df=16, P=0.004), and bullhead relative abundance was positively related to shoreline development index (r=0.46, df=22, P=0.03). Population characteristics of black bullhead appeared to have little influence on panfish communities. Rather, black bullhead abundance, predator density, and lake productivity exhibited stronger relationships with black bullhead population characteristics.
Effect of cation size and charge on the interaction between silica surfaces in 1:1, 2:1, and 3:1 aqueous electrolytes.

PubMed

Dishon, Matan; Zohar, Ohad; Sivan, Uri

2011-11-01

Application of two complementary AFM measurements, force vs separation and adhesion force, reveals the combined effects of cation size and charge (valency) on the interaction between silica surfaces in three 1:1, three 2:1, and three 3:1 metal chloride aqueous solutions of different concentrations. The interaction between the silica surfaces in 1:1 and 2:1 salt solutions is fully accounted for by ion-independent van der Waals (vdW) attraction and electric double-layer repulsion modified by cation specific adsorption to the silica surfaces. The deduced ranking of mono- and divalent cation adsorption capacity (adsorbability) to silica, Mg(2+) < Ca(2+) < Na(+) < Sr(2+) < K(+) < Cs(+), follows cation bare size as well as cation solvation energy but does not correlate with hydrated ionic radius or with volume or surface ionic charge density. In the presence of 3:1 salts, the coarse phenomenology of the force between the silica surfaces as a function of salt concentration resembles that in 1:1 and 2:1 electrolytes. Nevertheless, two fundamental differences should be noticed. First, the attraction between the silica surfaces is too large to be attributed solely to vdW force, hence implying an additional attraction mechanism or gross modification of the conventional vdW attraction. Second, neutralization of the silica surfaces occurs at trivalent cation concentrations that are 3 orders of magnitude smaller than those characterizing surface neutralization by mono- and divalent cations. Consequently, when trivalent cations are added to our cation adsorbability series the correlation with bare ion size breaks down abruptly. The strong adsorbability of trivalent cations to silica contrasts straightforward expectations based on ranking of the cationic solvation energies, thus suggesting a different adsorption mechanism which is inoperative or weak for mono- and divalent cations.
Tuning electronic transport in epitaxial graphene-based van der Waals heterostructures

NASA Astrophysics Data System (ADS)

Lin, Yu-Chuan; Li, Jun; de La Barrera, Sergio C.; Eichfeld, Sarah M.; Nie, Yifan; Addou, Rafik; Mende, Patrick C.; Wallace, Robert M.; Cho, Kyeongjae; Feenstra, Randall M.; Robinson, Joshua A.

2016-04-01

Two-dimensional tungsten diselenide (WSe2) has been used as a component in atomically thin photovoltaic devices, field effect transistors, and tunneling diodes in tandem with graphene. In some applications it is necessary to achieve efficient charge transport across the interface of layered WSe2-graphene, a semiconductor to semimetal junction with a van der Waals (vdW) gap. In such cases, band alignment engineering is required to ensure a low-resistance, ohmic contact. In this work, we investigate the impact of graphene electronic properties on the transport at the WSe2-graphene interface. Electrical transport measurements reveal a lower resistance between WSe2 and fully hydrogenated epitaxial graphene (EGFH) compared to WSe2 grown on partially hydrogenated epitaxial graphene (EGPH). Using low-energy electron microscopy and reflectivity on these samples, we extract the work function difference between the WSe2 and graphene and employ a charge transfer model to determine the WSe2 carrier density in both cases. The results indicate that WSe2-EGFH displays ohmic behavior at small biases due to a large hole density in the WSe2, whereas WSe2-EGPH forms a Schottky barrier junction.Two-dimensional tungsten diselenide (WSe2) has been used as a component in atomically thin photovoltaic devices, field effect transistors, and tunneling diodes in tandem with graphene. In some applications it is necessary to achieve efficient charge transport across the interface of layered WSe2-graphene, a semiconductor to semimetal junction with a van der Waals (vdW) gap. In such cases, band alignment engineering is required to ensure a low-resistance, ohmic contact. In this work, we investigate the impact of graphene electronic properties on the transport at the WSe2-graphene interface. Electrical transport measurements reveal a lower resistance between WSe2 and fully hydrogenated epitaxial graphene (EGFH) compared to WSe2 grown on partially hydrogenated epitaxial graphene (EGPH). Using low-energy electron microscopy and reflectivity on these samples, we extract the work function difference between the WSe2 and graphene and employ a charge transfer model to determine the WSe2 carrier density in both cases. The results indicate that WSe2-EGFH displays ohmic behavior at small biases due to a large hole density in the WSe2, whereas WSe2-EGPH forms a Schottky barrier junction. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr01902a
Late-time Near-infrared Observations of SN 2005df

NASA Astrophysics Data System (ADS)

Diamond, Tiara R.; Hoeflich, Peter; Gerardy, Christopher L.

2015-06-01

We present late-time near-infrared (NIR) spectral evolution, at 200-400 days, for the Type Ia supernova SN 2005df. The spectra show numerous strong emission features of [Co ii], [Co iii], and [Fe ii] throughout the 0.8-1.8 μm region. As the spectrum ages, the cobalt features fade as would be expected from the decay of 56Co to 56Fe. We show that the strong and isolated [Fe ii] emission line at 1.644 μ {m} provides a unique tool to analyze NIR spectra of SNe Ia. Normalization of spectra to this line allows the separation of features produced by stable versus unstable isotopes of iron group elements. We develop a new method of determining the initial central density, {ρ }c, and the magnetic field, B, of the white dwarf (WD) using the width of the 1.644 μ {m} line. The line width (LW) is sensitive because of electron capture in the early stages of burning, which increases as a function of density. The sensitivity of the LW to B increases with time, and the effects of the magnetic field shift toward later times with decreasing {ρ }c. Through comparison with spherical models, the initial central density for SN 2005df is measured as {ρ }c=0.9(+/- 0.2)× {10}9 {g} {{cm}}-3, which corresponds to a WD close to the Chandrasekhar mass, with {M}{WD}=1.31(+/- 0.03) {M}⊙ and systematic error less than 0.04 {M}⊙. This error estimate is based on spherical models. We discuss the potential uncertainties due to multi-dimensional effects, mixing, and rotation. The latter two effects would increase the estimate of the WD mass. Within {M}{Ch} explosions, however, the central density found for SN 2005df is very low for a H-accretor, possibly suggesting a helium star companion or a tidally disrupted WD companion. As an alternative, we suggest mixing of the central region. We find some support for high initial magnetic fields of strength {10}6 {G} for SN 2005df, however, 0 {G} cannot be ruled out because of noise in the spectra combined with low {ρ }c. We discuss our findings in the context of mixing by Rayleigh-Taylor instabilities during deflagration burning and a wide variety of explosion scenarios. Observations strongly support a very limited amount of mixing during a deflagration phase and high central densities characteristic of a {M}{Ch} WD.
The dietary fiber profile of fruit peels and functionality modifications induced by high hydrostatic pressure treatments.

PubMed

Tejada-Ortigoza, Viridiana; García-Amezquita, Luis Eduardo; Serna-Saldívar, Sergio O; Welti-Chanes, Jorge

2017-07-01

The effect of high hydrostatic pressure (HHP) and temperature on composition of non-conventional dietary fiber (DF) sources and functional properties were evaluated. Mango, orange, or prickly pear peels were processed at 600 MPa during 10 min at 22 ℃ and 55 ℃. Total (TDF), soluble (SDF), and insoluble (IDF) dietary fiber, water/oil holding, and retention capacity, solubility, swelling capacity, and bulk density were assayed. An increment in the SDF content was observed due to the effect of pressure with the greatest changes noticed in mango peel, increasing from 37.4% (control) to 45.7% (SDF/TDF) in the HHP-treated (55 ℃) sample. Constant values of TDF after the treatments suggest a conversion of IDF to SDF in mango (38.9%-40.5% dw) and orange (49.0%-50.8% dw) peels. The highest fiber solubility values were observed for mango peel ranging between 80.3% and 83.9%, but the highest increase, from 55.1% to 62.3%, due to treatment was displayed in orange peel processed at 22 ℃. A relationship between DF modifications induced by HHP treatment and changes in the functional properties of the materials was established. Application of HHP opens up the opportunity to modify non-conventional sources of DF and to obtain novel functional properties for different food applications.
The RPA Atomization Energy Puzzle.

PubMed

Ruzsinszky, Adrienn; Perdew, John P; Csonka, Gábor I

2010-01-12

There is current interest in the random phase approximation (RPA), a "fifth-rung" density functional for the exchange-correlation energy. RPA has full exact exchange and constructs the correlation with the help of the unoccupied Kohn-Sham orbitals. In many cases (uniform electron gas, jellium surface, and free atom), the correction to RPA is a short-ranged effect that is captured by a local spin density approximation (LSDA) or a generalized gradient approximation (GGA). Nonempirical density functionals for the correction to RPA were constructed earlier at the LSDA and GGA levels (RPA+), but they are constructed here at the fully nonlocal level (RPA++), using the van der Waals density functional (vdW-DF) of Langreth, Lundqvist, and collaborators. While they make important and helpful corrections to RPA total and ionization energies of free atoms, they correct the RPA atomization energies of molecules by only about 1 kcal/mol. Thus, it is puzzling that RPA atomization energies are, on average, about 10 kcal/mol lower than those of accurate values from experiment. We find here that a hybrid of 50% Perdew-Burke-Ernzerhof GGA with 50% RPA+ yields atomization energies much more accurate than either one does alone. This suggests a solution to the puzzle: While the proper correction to RPA is short-ranged in some systems, its contribution to the correlation hole can spread out in a molecule with multiple atomic centers, canceling part of the spread of the exact exchange hole (more so than in RPA or RPA+), making the true exchange-correlation hole more localized than in RPA or RPA+. This effect is not captured even by the vdW-DF nonlocality, but it requires the different kind of full nonlocality present in a hybrid functional.
Interface characteristics at an organic/metal junction: pentacene on Cu stepped surfaces.

PubMed

Matos, Jeronimo; Kara, Abdelkader

2016-11-09

The adsorption of pentacene on Cu (2 2 1), Cu (5 1 1) and Cu (9 1 1) is investigated using density functional theory (DFT) with the self-consistent inclusion of van der Waals (vdW) interactions. Cu (2 1 1) is a vicinal of Cu (1 1 1) while Cu (5 1 1) and (9 1 1) are vicinals of Cu (1 0 0). For all the three surfaces, we found pentacene to prefer to adsorb parallel to the surface and near the steps. The addition of vdW interactions resulted in an enhancement in adsorption energies, with reference to the PBE functional, of around 2 eV. With vdWs inclusion, the adsorption energies were found to be 2.98 eV, 3.20 eV and 3.49 eV for Cu (2 2 1), Cu (5 1 1) and Cu (9 1 1) respectively. These values reflect that pentacene adsorbs stronger on (1 0 0) terraces with a preference for larger terraces. The molecule tilts upon adsorption with a small tilt angle on the (1 0 0) vicinals (about a few degrees) as compared to a large one on Cu (2 2 1) where the tilt angle is found to be about 20°. We find that the adsorption results in a net charge transfer to the molecule of ~1 electron, for all surfaces.
mBEEF-vdW: Robust fitting of error estimation density functionals

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

Lundgaard, Keld T.; Wellendorff, Jess; Voss, Johannes

Here, we propose a general-purpose semilocal/nonlocal exchange-correlation functional approximation, named mBEEF-vdW. The exchange is a meta generalized gradient approximation, and the correlation is a semilocal and nonlocal mixture, with the Rutgers-Chalmers approximation for van der Waals (vdW) forces. The functional is fitted within the Bayesian error estimation functional (BEEF) framework. We improve the previously used fitting procedures by introducing a robust MM-estimator based loss function, reducing the sensitivity to outliers in the datasets. To more reliably determine the optimal model complexity, we furthermore introduce a generalization of the bootstrap 0.632 estimator with hierarchical bootstrap sampling and geometric mean estimator overmore » the training datasets. Using this estimator, we show that the robust loss function leads to a 10% improvement in the estimated prediction error over the previously used least-squares loss function. The mBEEF-vdW functional is benchmarked against popular density functional approximations over a wide range of datasets relevant for heterogeneous catalysis, including datasets that were not used for its training. Overall, we find that mBEEF-vdW has a higher general accuracy than competing popular functionals, and it is one of the best performing functionals on chemisorption systems, surface energies, lattice constants, and dispersion. We also show the potential-energy curve of graphene on the nickel(111) surface, where mBEEF-vdW matches the experimental binding length. mBEEF-vdW is currently available in gpaw and other density functional theory codes through Libxc, version 3.0.0.« less
mBEEF-vdW: Robust fitting of error estimation density functionals

DOE PAGES

Lundgaard, Keld T.; Wellendorff, Jess; Voss, Johannes; ...

2016-06-15

Here, we propose a general-purpose semilocal/nonlocal exchange-correlation functional approximation, named mBEEF-vdW. The exchange is a meta generalized gradient approximation, and the correlation is a semilocal and nonlocal mixture, with the Rutgers-Chalmers approximation for van der Waals (vdW) forces. The functional is fitted within the Bayesian error estimation functional (BEEF) framework. We improve the previously used fitting procedures by introducing a robust MM-estimator based loss function, reducing the sensitivity to outliers in the datasets. To more reliably determine the optimal model complexity, we furthermore introduce a generalization of the bootstrap 0.632 estimator with hierarchical bootstrap sampling and geometric mean estimator overmore » the training datasets. Using this estimator, we show that the robust loss function leads to a 10% improvement in the estimated prediction error over the previously used least-squares loss function. The mBEEF-vdW functional is benchmarked against popular density functional approximations over a wide range of datasets relevant for heterogeneous catalysis, including datasets that were not used for its training. Overall, we find that mBEEF-vdW has a higher general accuracy than competing popular functionals, and it is one of the best performing functionals on chemisorption systems, surface energies, lattice constants, and dispersion. We also show the potential-energy curve of graphene on the nickel(111) surface, where mBEEF-vdW matches the experimental binding length. mBEEF-vdW is currently available in gpaw and other density functional theory codes through Libxc, version 3.0.0.« less
Understanding the adsorption of CuPc and ZnPc on noble metal surfaces by combining quantum-mechanical modelling and photoelectron spectroscopy.

PubMed

Huang, Yu Li; Wruss, Elisabeth; Egger, David A; Kera, Satoshi; Ueno, Nobuo; Saidi, Wissam A; Bucko, Tomas; Wee, Andrew T S; Zojer, Egbert

2014-03-07

Phthalocyanines are an important class of organic semiconductors and, thus, their interfaces with metals are both of fundamental and practical relevance. In the present contribution we provide a combined theoretical and experimental study, in which we show that state-of-the-art quantum-mechanical simulations are nowadays capable of treating most properties of such interfaces in a quantitatively reliable manner. This is shown for Cu-phthalocyanine (CuPc) and Zn-phthalocyanine (ZnPc) on Au(111) and Ag(111) surfaces. Using a recently developed approach for efficiently treating van der Waals (vdW) interactions at metal/organic interfaces, we calculate adsorption geometries in excellent agreement with experiments. With these geometries available, we are then able to accurately describe the interfacial electronic structure arising from molecular adsorption. We find that bonding is dominated by vdW forces for all studied interfaces. Concomitantly, charge rearrangements on Au(111) are exclusively due to Pauli pushback. On Ag(111), we additionally observe charge transfer from the metal to one of the spin-channels associated with the lowest unoccupied π-states of the molecules. Comparing the interfacial density of states with our ultraviolet photoelectron spectroscopy (UPS) experiments, we find that the use of a hybrid functionals is necessary to obtain the correct order of the electronic states.
Magnetic engineering in InSe/black-phosphorus heterostructure by transition-metal-atom Sc-Zn doping in the van der Waals gap

NASA Astrophysics Data System (ADS)

Ding, Yi-min; Shi, Jun-jie; Zhang, Min; Zhu, Yao-hui; Wu, Meng; Wang, Hui; Cen, Yu-lang; Guo, Wen-hui; Pan, Shu-hang

2018-07-01

Within the framework of the spin-polarized density-functional theory, we have studied the electronic and magnetic properties of InSe/black-phosphorus (BP) heterostructure doped with 3d transition-metal (TM) atoms from Sc to Zn. The calculated binding energies show that TM-atom doping in the van der Waals (vdW) gap of InSe/BP heterostructure is energetically favorable. Our results indicate that magnetic moments are induced in the Sc-, Ti-, V-, Cr-, Mn- and Co-doped InSe/BP heterostructures due to the existence of non-bonding 3d electrons. The Ni-, Cu- and Zn-doped InSe/BP heterostructures still show nonmagnetic semiconductor characteristics. Furthermore, in the Fe-doped InSe/BP heterostructure, the half-metal property is found and a high spin polarization of 100% at the Fermi level is achieved. The Cr-doped InSe/BP has the largest magnetic moment of 4.9 μB. The Sc-, Ti-, V-, Cr- and Mn-doped InSe/BP heterostructures exhibit antiferromagnetic ground state. Moreover, the Fe- and Co-doped systems display a weak ferromagnetic and paramagnetic coupling, respectively. Our studies demonstrate that the TM doping in the vdW gap of InSe/BP heterostructure is an effective way to modify its electronic and magnetic properties.
Carbon Nanotube Oscillator Surface Profiling Device and Method of Use

DTIC Science & Technology

2011-11-15

distance p. The constants A and B are the Hamaker constants, which depend on the materials of the two interacting bodies. The total vdW inter...wall CNT 45 with 2L1 =2L2 =150 A and a sample of specific material char- acterized with atomic density a, Hamaker constants A and B, and a friction

Dominant frequency increase rate predicts transition from paroxysmal to long-term persistent atrial fibrillation.

PubMed

Martins, Raphael P; Kaur, Kuljeet; Hwang, Elliot; Ramirez, Rafael J; Willis, B Cicero; Filgueiras-Rama, David; Ennis, Steven R; Takemoto, Yoshio; Ponce-Balbuena, Daniela; Zarzoso, Manuel; O'Connell, Ryan P; Musa, Hassan; Guerrero-Serna, Guadalupe; Avula, Uma Mahesh R; Swartz, Michael F; Bhushal, Sandesh; Deo, Makarand; Pandit, Sandeep V; Berenfeld, Omer; Jalife, José

2014-04-08

Little is known about the mechanisms underlying the transition from paroxysmal to persistent atrial fibrillation (AF). In an ovine model of long-standing persistent AF we tested the hypothesis that the rate of electric and structural remodeling, assessed by dominant frequency (DF) changes, determines the time at which AF becomes persistent. Self-sustained AF was induced by atrial tachypacing. Seven sheep were euthanized 11.5±2.3 days after the transition to persistent AF and without reversal to sinus rhythm; 7 sheep were euthanized after 341.3±16.7 days of long-standing persistent AF. Seven sham-operated animals were in sinus rhythm for 1 year. DF was monitored continuously in each group. Real-time polymerase chain reaction, Western blotting, patch clamping, and histological analyses were used to determine the changes in functional ion channel expression and structural remodeling. Atrial dilatation, mitral valve regurgitation, myocyte hypertrophy, and atrial fibrosis occurred progressively and became statistically significant after the transition to persistent AF, with no evidence for left ventricular dysfunction. DF increased progressively during the paroxysmal-to-persistent AF transition and stabilized when AF became persistent. Importantly, the rate of DF increase correlated strongly with the time to persistent AF. Significant action potential duration abbreviation, secondary to functional ion channel protein expression changes (CaV1.2, NaV1.5, and KV4.2 decrease; Kir2.3 increase), was already present at the transition and persisted for 1 year of follow up. In the sheep model of long-standing persistent AF, the rate of DF increase predicts the time at which AF stabilizes and becomes persistent, reflecting changes in action potential duration and densities of sodium, L-type calcium, and inward rectifier currents.
A noniterative asymmetric triple excitation correction for the density-fitted coupled-cluster singles and doubles method: Preliminary applications

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

Bozkaya, Uğur, E-mail: ugrbzky@gmail.com

2016-04-14

An efficient implementation of the asymmetric triples correction for the coupled-cluster singles and doubles [ΛCCSD(T)] method [S. A. Kucharski and R. J. Bartlett, J. Chem. Phys. 108, 5243 (1998); T. D. Crawford and J. F. Stanton, Int. J. Quantum Chem. 70, 601 (1998)] with the density-fitting [DF-ΛCCSD(T)] approach is presented. The computational time for the DF-ΛCCSD(T) method is compared with that of ΛCCSD(T). Our results demonstrate that the DF-ΛCCSD(T) method provide substantially lower computational costs than ΛCCSD(T). Further application results show that the ΛCCSD(T) and DF-ΛCCSD(T) methods are very beneficial for the study of single bond breaking problems as wellmore » as noncovalent interactions and transition states. We conclude that ΛCCSD(T) and DF-ΛCCSD(T) are very promising for the study of challenging chemical systems, where the coupled-cluster singles and doubles with perturbative triples method fails.« less
Functional Independent Scaling Relation for ORR/OER Catalysts

DOE PAGES

Christensen, Rune; Hansen, Heine A.; Dickens, Colin F.; ...

2016-10-11

A widely used adsorption energy scaling relation between OH* and OOH* intermediates in the oxygen reduction reaction (ORR) and oxygen evolution reaction (OER), has previously been determined using density functional theory and shown to dictate a minimum thermodynamic overpotential for both reactions. Here, we show that the oxygen–oxygen bond in the OOH* intermediate is, however, not well described with the previously used class of exchange-correlation functionals. By quantifying and correcting the systematic error, an improved description of gaseous peroxide species versus experimental data and a reduction in calculational uncertainty is obtained. For adsorbates, we find that the systematic error largelymore » cancels the vdW interaction missing in the original determination of the scaling relation. An improved scaling relation, which is fully independent of the applied exchange–correlation functional, is obtained and found to differ by 0.1 eV from the original. Lastly, this largely confirms that, although obtained with a method suffering from systematic errors, the previously obtained scaling relation is applicable for predictions of catalytic activity.« less
Ab Initio Study of Polarizabilities of Oligothiophene, Oligocyclopentadiene and Oligofulvene and their Cyano Substituted Oligomers

NASA Astrophysics Data System (ADS)

Lagowski, Jolanta; Ferdous, Sultana

2005-03-01

Ab Initio polarizabilities of thiophene, fulvene and cyclopentadiene based conducting oligomers and polymers and their cyano derivatives have been calculated using the Hartree-Fock (HF), configuration interaction (singles) (CIS ) and density functional (DF) theories with 3-21G* basis using Gaussian software. The main motivation of this investigation is to determine the correlation between the excitation energies and polarizabilities for the conjugated systems studied. It has been found that HF and DF approaches give similar magnitudes for polarizabilities whereas CIS theory provides results that are considerably different. All three methods predict similar trends in polarizabilities as a function of oligomer length and bond alternation along the backbone of the oligomers. It has also been observed that the end groups and the number of `double' bonds have a significant effect on the magnitude of polarizability per C-C bond. Comparison with experimental results will be made where possible.
Structure and properties of fullerene molecular crystals with linear-scaling van der Waals density functional theory

NASA Astrophysics Data System (ADS)

Mostofi, Arash; Andrinopoulos, Lampros; Hine, Nicholas

2014-03-01

Fullerene molecular crystals are of technological promise for their use in heterojunction photovoltaic cells. An improved theoretical understanding of their structure and properties would be a step towards the rational design of new devices. Simulations based on density-functional theory (DFT) are invaluable for developing such insight, but standard semi-local functionals do not capture the important inter-molecular van der Waals (vdW) interactions in fullerene crystals. Furthermore the computational cost associated with the large unit cells needed are at the limit or beyond the capabilities of traditional DFT methods. In this work we overcome these limitations by using our implementation of a number of vdW-DFs in the ONETEP linear-scaling DFT code to study the structural properties of C60 molecular crystals. Powder neutron diffraction shows that the low-temperature Pa-3 phase is orientationally ordered with individual C60 units rotated around the [111] direction. We fully explore the energy landscape associated with the rotation angle and find two stable structures that are energetically very close, one of which corresponds to the experimentally observed structure. We further consider the effect of orientational disorder in very large supercells of thousands of atoms.
Development of a macrophyte-based index of biotic integrity for Minnesota lakes

USGS Publications Warehouse

Beck, M.W.; Hatch, L.K.; Vondracek, B.; Valley, R.D.

2010-01-01

Traditional approaches for managing aquatic resources have often failed to account for effects of anthropogenic disturbances on biota that are not directly reflected by chemical and physical proxies of environmental condition. The index of biotic integrity (IBI) is a potentially effective assessment method to integrate ecological, functional, and structural aspects of aquatic systems. A macrophyte-based IBI was developed for Minnesota lakes to assess the ability of aquatic plant communities to indicate environmental condition. The index was developed using quantitative point intercept vegetation surveys for 97 lakes that represent a range of limnological and watershed characteristics. We followed an approach similar to that used in Wisconsin to develop the aquatic macrophyte community index (AMCI). Regional adaptation of the AMCI required the identification of species representative of macrophyte communities in Minnesota. Metrics and scaling methods were also substantially modified to produce a more empirically robust index. Regression analyses indicated that IBI scores reflected statewide differences in lake trophic state (R2 = 0.57, F = 130.3, df = 1, 95, p < 0.005), agricultural (R2 = 0.51, F = 83.0, df = 1, 79, p < 0.005), urban (R2 = 0.22, F = 23.0, df = 1, 79, p < 0.005), and forested land uses (R2 = 0.51, F = 84.7, df = 1, 79, p < 0.005), and county population density (R2 = 0.14, F = 16.6, df = 1, 95, p < 0.005). Variance partitioning analyses using multiple regression models indicated a unique response of the IBI to human-induced stress separate from a response to natural lake characteristics. The IBI was minimally affected by differences in sample point density as indicated by Monte Carlo analyses of reduced sampling effort. Our analysis indicates that a macrophyte IBI calibrated for Minnesota lakes could be useful for identifying differences in environmental condition attributed to human-induced stress gradients. ?? 2010 Elsevier Ltd.
Effects of an electric field on interaction of aromatic systems.

PubMed

Youn, Il Seung; Cho, Woo Jong; Kim, Kwang S

2016-04-30

The effect of uniform external electric field on the interactions between small aromatic compounds and an argon atom is investigated using post-HF (MP2, SCS-MP2, and CCSD(T)) and density functional (PBE0-D3, PBE0-TS, and vdW-DF2) methods. The electric field effect is quantified by the difference of interaction energy calculated in the presence and absence of the electric field. All the post-HF methods describe electric field effects accurately although the interaction energy itself is overestimated by MP2. The electric field effect is explained by classical electrostatic models, where the permanent dipole moment from mutual polarization mainly determines its sign. The size of π-conjugated system does not have significant effect on the electric field dependence. We found out that PBE0-based methods give reasonable interaction energies and electric field response in every case, while vdW-DF2 sometimes shows spurious artifact owing to its sensitivity toward the real space electron density. © 2015 Wiley Periodicals, Inc.
Optimization of extraction efficiency by shear emulsifying assisted enzymatic hydrolysis and functional properties of dietary fiber from deoiled cumin (Cuminum cyminum L.).

PubMed

Ma, Mengmei; Mu, Taihua; Sun, Hongnan; Zhang, Miao; Chen, Jingwang; Yan, Zhibin

2015-07-15

This study evaluated the optimal conditions for extracting dietary fiber (DF) from deoiled cumin by shear emulsifying assisted enzymatic hydrolysis (SEAEH) using the response surface methodology. Fat adsorption capacity (FAC), glucose adsorption capacity (GAC), and bile acid retardation index (BRI) were measured to evaluate the functional properties of the extracted DF. The results revealed that the optimal extraction conditions included an enzyme to substrate ratio of 4.5%, a reaction temperature of 57 °C, a pH value of 7.7, and a reaction time of 155 min. Under these conditions, DF extraction efficiency and total dietary fiber content were 95.12% and 84.18%, respectively. The major components of deoiled cumin DF were hemicellulose (37.25%) and cellulose (33.40%). FAC and GAC increased with decreasing DF particle size (51-100 μm), but decreased with DF particle sizes <26 μm; BRI increased with decreasing DF particle size. The results revealed that SEAEH is an effective method for extracting DF. DF with particle size 26-51 μm had improved functional properties. Copyright © 2015. Published by Elsevier Ltd.
Reprint of "Theoretical description of metal/oxide interfacial properties: The case of MgO/Ag(001)"

NASA Astrophysics Data System (ADS)

Prada, Stefano; Giordano, Livia; Pacchioni, Gianfranco; Goniakowski, Jacek

2017-02-01

We compare the performances of different DFT functionals applied to ultra-thin MgO(100) films supported on the Ag(100) surface, a prototypical system of a weakly interacting oxide/metal interface, extensively studied in the past. Beyond semi-local DFT-GGA approximation, we also use the hybrid DFT-HSE approach to improve the description of the oxide electronic structure. Moreover, to better account for the interfacial adhesion, we include the van de Waals interactions by means of either the semi-empirical force fields by Grimme (DFT-D2 and DFT-D2*) or the self-consistent density functional optB88-vdW. We compare and discuss the results on the structural, electronic, and adhesion characteristics of the interface as obtained for pristine and oxygen-deficient Ag-supported MgO films in the 1-4 ML thickness range.
Theoretical description of metal/oxide interfacial properties: The case of MgO/Ag(001)

NASA Astrophysics Data System (ADS)

Prada, Stefano; Giordano, Livia; Pacchioni, Gianfranco; Goniakowski, Jacek

2016-12-01

We compare the performances of different DFT functionals applied to ultra-thin MgO(100) films supported on the Ag(100) surface, a prototypical system of a weakly interacting oxide/metal interface, extensively studied in the past. Beyond semi-local DFT-GGA approximation, we also use the hybrid DFT-HSE approach to improve the description of the oxide electronic structure. Moreover, to better account for the interfacial adhesion, we include the van de Waals interactions by means of either the semi-empirical force fields by Grimme (DFT-D2 and DFT-D2*) or the self-consistent density functional optB88-vdW. We compare and discuss the results on the structural, electronic, and adhesion characteristics of the interface as obtained for pristine and oxygen-deficient Ag-supported MgO films in the 1-4 ML thickness range.
Combination Rules for Morse-Based van der Waals Force Fields.

PubMed

Yang, Li; Sun, Lei; Deng, Wei-Qiao

2018-02-15

In traditional force fields (FFs), van der Waals interactions have been usually described by the Lennard-Jones potentials. Conventional combination rules for the parameters of van der Waals (VDW) cross-termed interactions were developed for the Lennard-Jones based FFs. Here, we report that the Morse potentials were a better function to describe VDW interactions calculated by highly precise quantum mechanics methods. A new set of combination rules was developed for Morse-based FFs, in which VDW interactions were described by Morse potentials. The new set of combination rules has been verified by comparing the second virial coefficients of 11 noble gas mixtures. For all of the mixed binaries considered in this work, the combination rules work very well and are superior to all three other existing sets of combination rules reported in the literature. We further used the Morse-based FF by using the combination rules to simulate the adsorption isotherms of CH 4 at 298 K in four covalent-organic frameworks (COFs). The overall agreement is great, which supports the further applications of this new set of combination rules in more realistic simulation systems.
Constructing high-accuracy intermolecular potential energy surface with multi-dimension Morse/Long-Range model

NASA Astrophysics Data System (ADS)

Zhai, Yu; Li, Hui; Le Roy, Robert J.

2018-04-01

Spectroscopically accurate Potential Energy Surfaces (PESs) are fundamental for explaining and making predictions of the infrared and microwave spectra of van der Waals (vdW) complexes, and the model used for the potential energy function is critically important for providing accurate, robust and portable analytical PESs. The Morse/Long-Range (MLR) model has proved to be one of the most general, flexible and accurate one-dimensional (1D) model potentials, as it has physically meaningful parameters, is flexible, smooth and differentiable everywhere, to all orders and extrapolates sensibly at both long and short ranges. The Multi-Dimensional Morse/Long-Range (mdMLR) potential energy model described herein is based on that 1D MLR model, and has proved to be effective and accurate in the potentiology of various types of vdW complexes. In this paper, we review the current status of development of the mdMLR model and its application to vdW complexes. The future of the mdMLR model is also discussed. This review can serve as a tutorial for the construction of an mdMLR PES.
Density functional theory for molecular and periodic systems using density fitting and continuous fast multipole method: Analytical gradients.

PubMed

Łazarski, Roman; Burow, Asbjörn Manfred; Grajciar, Lukáš; Sierka, Marek

2016-10-30

A full implementation of analytical energy gradients for molecular and periodic systems is reported in the TURBOMOLE program package within the framework of Kohn-Sham density functional theory using Gaussian-type orbitals as basis functions. Its key component is a combination of density fitting (DF) approximation and continuous fast multipole method (CFMM) that allows for an efficient calculation of the Coulomb energy gradient. For exchange-correlation part the hierarchical numerical integration scheme (Burow and Sierka, Journal of Chemical Theory and Computation 2011, 7, 3097) is extended to energy gradients. Computational efficiency and asymptotic O(N) scaling behavior of the implementation is demonstrated for various molecular and periodic model systems, with the largest unit cell of hematite containing 640 atoms and 19,072 basis functions. The overall computational effort of energy gradient is comparable to that of the Kohn-Sham matrix formation. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.
The mechanism of protein export enhancement by the SecDF membrane component

PubMed Central

Tsukazaki, Tomoya; Nureki, Osamu

2011-01-01

Protein transport across membranes is a fundamental and essential cellular activity in all organisms. In bacteria, protein export across the cytoplasmic membrane, driven by dynamic interplays between the protein-conducting SecYEG channel (Sec translocon) and the SecA ATPase, is enhanced by the proton motive force (PMF) and a membrane-integrated Sec component, SecDF. However, the structure and function of SecDF have remained unclear. We solved the first crystal structure of SecDF, consisting of a pseudo-symmetrical 12-helix transmembrane domain and two protruding periplasmic domains. Based on the structural features, we proposed that SecDF functions as a membrane-integrated chaperone, which drives protein movement without using the major energetic currency, ATP, but with remarkable cycles of conformational changes, powered by the proton gradient across the membrane. By a series of biochemical and biophysical approaches, several functionally important residues in the transmembrane region have been identified and our model of the SecDF function has been verified. PMID:27857601
Dynamical Friction in Multi-component Evolving Globular Clusters

NASA Astrophysics Data System (ADS)

Alessandrini, Emiliano; Lanzoni, Barbara; Miocchi, Paolo; Ciotti, Luca; Ferraro, Francesco R.

2014-11-01

We use the Chandrasekhar formalism and direct N-body simulations to study the effect of dynamical friction on a test object only slightly more massive than the field stars, orbiting a spherically symmetric background of particles with a mass spectrum. The main goal is to verify whether the dynamical friction time (t DF) develops a non-monotonic radial dependence that could explain the bimodality of the blue straggler radial distributions observed in globular clusters. In these systems, in fact, relaxation effects lead to a mass and velocity radial segregation of the different mass components, so that mass-spectrum effects on t DF are expected to be dependent on radius. We find that in spite of the presence of different masses, t DF is always a monotonic function of radius, at all evolutionary times and independently of the initial concentration of the simulated cluster. This is because the radial dependence of t DF is largely dominated by the total mass density profile of the background stars (which is monotonically decreasing with radius). Hence, a progressive temporal erosion of the blue straggler star (BSS) population at larger and larger distances from the cluster center remains the simplest and the most likely explanation of the shape of the observed BSS radial distributions, as suggested in previous works. We also confirm the theoretical expectation that approximating a multi-mass globular cluster as made of (averaged) equal-mass stars can lead to significant overestimations of t DF within the half-mass radius.
Enhanced van der Waals epitaxy via electron transfer enabled interfacial dative bond formation

DOE PAGES

Xie, Weiyu; Lu, Toh -Ming; Wang, Gwo -Ching; ...

2017-11-14

Enhanced van der Waals (vdW) epitaxy of semiconductors on a layered vdW substrate is identified as the formation of dative bonds. For example, despite that NbSe 2 is a vdW layeredmaterial, first-principles calculations reveal that the bond strength at a CdTe-NbSe 2 interface is five times as large as that of vdW interactions at a CdTe-graphene interface. Finally, the unconventional chemistry here is enabled by an effective net electron transfer from Cd dangling-bond states at a CdTe surface to metallic nonbonding NbSe 2 states, which is a necessary condition to activate the Cd for enhanced binding with Se.
Enhanced van der Waals epitaxy via electron transfer enabled interfacial dative bond formation

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

Xie, Weiyu; Lu, Toh -Ming; Wang, Gwo -Ching

Enhanced van der Waals (vdW) epitaxy of semiconductors on a layered vdW substrate is identified as the formation of dative bonds. For example, despite that NbSe 2 is a vdW layeredmaterial, first-principles calculations reveal that the bond strength at a CdTe-NbSe 2 interface is five times as large as that of vdW interactions at a CdTe-graphene interface. Finally, the unconventional chemistry here is enabled by an effective net electron transfer from Cd dangling-bond states at a CdTe surface to metallic nonbonding NbSe 2 states, which is a necessary condition to activate the Cd for enhanced binding with Se.
Shock-Compressed Hydrogen

NASA Astrophysics Data System (ADS)

Bickham, S. R.; Collins, L. A.; Kress, J. D.; Lenosky, T. J.

1999-06-01

To investigate recent gas-gun and laser experiments on hydrogen at elevated temperatures and high densities, we have performed quantum molecular dynamics simulations using a variety of sophisticated models, ranging from tight-binding(TB) to density functional(DF)(T.J. Lenosky, J.D. Kress, L.A. Collins, and I. Kwon Phys. Rev. B 55), R11907(1997) and references therein.. The TB models have been especially tailored to reproduce experimental findings, such as Diamond-Anvil Cell data, and ab initio calculations, such as H_2, H_3, and H4 potential energy surfaces. The DF calculations have employed the local-density approximation(LDA) as well as generalized gradient corrections(GGA) with large numbers of plane-waves ( ~10^5) that represent a very broad range of excited and continuum electronic states. Good agreement obtains among all these models. The simulations exhibit a rapidly rising electrical conductivity at low temperatures and high pressures in good agreement with the gas-gun results. This conduction property stems from a mobility of the electrons provided principally by the dissociated monomers. The Hugoniot for the conditions of the laser experiment, generated from the TB Equation-of-State, shows a maximum compression of around four instead of the observed six. We also report optical properties of the hydrogen media.
Ankle Dorsiflexion in Childhood Cancer Patients: A Review of the Literature.

PubMed

Beulertz, Julia; Wurz, Amanda; Culos-Reed, Nicole; Chamorro Viña, Carolina; Bloch, Wilhelm; Baumann, Freerk T

2015-01-01

Improved treatment protocols necessary for survival in pediatric oncology are associated with the development of serious late effects. Of particular importance, especially with regard to physical activity, may be ankle dorsiflexion (DF). This review summarizes the results of observational and exercise intervention studies exploring ankle DF-range of motion (DF-ROM) and/or ankle DF strength in pediatric oncology. PUBMED, Medline, Cochrane library, and SportDiscus were searched by 2 researchers using predefined search terms. The reference lists of included papers and Google scholar were then searched to that ensure all appropriate articles were included. Twelve studies were identified and were observational (n = 8), providing information regarding the status of DF-ROM and/or DF strength, or intervention studies (n = 4) using exercise as a strategy to improve DF function. All observational studies reported some degree of impairment in ankle DF. Two intervention studies found a positive effect of exercise on ankle DF-ROM. The preliminary results suggest that pediatric cancer patients and survivors suffer from limitations in ankle DF with interventions varying in efficacy. It is hoped that this review will enhance the recognition of the limited ankle DF function in pediatric oncology and initiate further research programs focused on targeting and evaluating ankle DF.
mBEEF-vdW: Robust fitting of error estimation density functionals

NASA Astrophysics Data System (ADS)

Lundgaard, Keld T.; Wellendorff, Jess; Voss, Johannes; Jacobsen, Karsten W.; Bligaard, Thomas

2016-06-01

We propose a general-purpose semilocal/nonlocal exchange-correlation functional approximation, named mBEEF-vdW. The exchange is a meta generalized gradient approximation, and the correlation is a semilocal and nonlocal mixture, with the Rutgers-Chalmers approximation for van der Waals (vdW) forces. The functional is fitted within the Bayesian error estimation functional (BEEF) framework [J. Wellendorff et al., Phys. Rev. B 85, 235149 (2012), 10.1103/PhysRevB.85.235149; J. Wellendorff et al., J. Chem. Phys. 140, 144107 (2014), 10.1063/1.4870397]. We improve the previously used fitting procedures by introducing a robust MM-estimator based loss function, reducing the sensitivity to outliers in the datasets. To more reliably determine the optimal model complexity, we furthermore introduce a generalization of the bootstrap 0.632 estimator with hierarchical bootstrap sampling and geometric mean estimator over the training datasets. Using this estimator, we show that the robust loss function leads to a 10 % improvement in the estimated prediction error over the previously used least-squares loss function. The mBEEF-vdW functional is benchmarked against popular density functional approximations over a wide range of datasets relevant for heterogeneous catalysis, including datasets that were not used for its training. Overall, we find that mBEEF-vdW has a higher general accuracy than competing popular functionals, and it is one of the best performing functionals on chemisorption systems, surface energies, lattice constants, and dispersion. We also show the potential-energy curve of graphene on the nickel(111) surface, where mBEEF-vdW matches the experimental binding length. mBEEF-vdW is currently available in gpaw and other density functional theory codes through Libxc, version 3.0.0.

Dynamics of vortex domain walls in ferromagnetic nanowires - A possible method for chirality manipulation

NASA Astrophysics Data System (ADS)

Li, Y.; Lu, Z.; Chen, C.; Cheng, M.; Yin, H.; Wang, W.; Li, C.; Liu, Y.; Xiong, R.; Shi, J.

2018-06-01

The dynamic behaviors of vortex domain walls (VDWs) in ferromagnetic nanowires driven by a magnetic field above Walker breakdown field (Hw) were investigated using micromagnetic simulation. It was found when nanowire has proper geometrical dimensions, the VDW may oscillate in a chirality invariant mode or a chirality switching mode depending on applied field and damping constant. At fixed damping constant, the oscillation mode can be controlled by applied field - with the increase of applied field, the oscillation of VDW change from a chirality invariant mode to a variant one. As the oscillation of VDW changes from chirality invariant regime to chirality switching regime, the oscillation frequency and amplification will undergo an abnormal change, which may offer a fingerprint for the switch of oscillation mode. Our finding proposes a simple way to control the chirality of a VDW by properly manipulating nanowire geometry and applied field, which may have important applications in VDW-based devices.
Hybrid density functional study on the mechanism for the enhanced photocatalytic properties of the ultrathin hybrid layered nanocomposite g-C3N4/BiOCl

NASA Astrophysics Data System (ADS)

Yao, Wenzhi; Zhang, Jihua; Wang, Yuanxu; Ren, Fengzhu

2018-03-01

To investigate the origin of the high photocatalytic performance of experimentally synthesized g-C3N4/ BiOCl, we studied its geometry structure, electronic structure, and photocatalytic properties by means of hybrid density-functional theory (DFT). The calculated band alignment of g-C3N4 and few-layer BiOCl sheets clearly shows that g-C3N4/ BiOCl is a standard type-II nanocomposite. The density of states, Bader charge, partial charge density, charge density difference, and the effective masses show that electron-hole pair can be effectively separated in the g-C3N4/BiOCl interface. The calculated absorption coefficients indicate an obvious redshift of the absorption edge. The band gap of g-C3N4/BiOCl can be modulated by external electric field, and a semiconductor-semimetal transition is observed. The type-II vdW heterostructure is still maintained during the changes of external electric field. Especially, when the electric field reaches to +0.7 V/Å, the impurity states have been eliminated with the band gap of 2.3 eV. An analysis of optical properties shows that the absorption coefficient in the visible-light region is enhanced considerably as the electric-field strength increases. Our calculation results suggest that the ultrathin hybrid layered g-C3N4/BiOCl nanocomposite may have significant advantages for visible-light photocatalysis.
Comparison of block and event-related experimental designs in diffusion-weighted functional MRI.

PubMed

Williams, Rebecca J; McMahon, Katie L; Hocking, Julia; Reutens, David C

2014-08-01

To compare diffusion-weighted functional magnetic resonance imaging (DfMRI), a novel alternative to the blood oxygenation level-dependent (BOLD) contrast, in a functional MRI experiment. Nine participants viewed contrast reversing (7.5 Hz) black-and-white checkerboard stimuli using block and event-related paradigms. DfMRI (b = 1800 mm/s(2)) and BOLD sequences were acquired. Four parameters describing the observed signal were assessed: percent signal change, spatial extent of the activation, the Euclidean distance between peak voxel locations, and the time-to-peak of the best fitting impulse response for different paradigms and sequences. The BOLD conditions showed a higher percent signal change relative to DfMRI; however, event-related DfMRI showed the strongest group activation (t = 21.23, P < 0.0005). Activation was more diffuse and spatially closer to the BOLD response for DfMRI when the block design was used. DfMRIevent showed the shortest TTP (4.4 ± 0.88 sec). The hemodynamic contribution to DfMRI may increase with the use of block designs. © 2013 Wiley Periodicals, Inc.
Near-zero hysteresis and near-ideal subthreshold swing in h-BN encapsulated single-layer MoS2 field-effect transistors

NASA Astrophysics Data System (ADS)

Vu, Quoc An; Fan, Sidi; Hyup Lee, Sang; Joo, Min-Kyu; Jong Yu, Woo; Lee, Young Hee

2018-07-01

While two-dimensional (2D) van der Waals (vdW) layered materials are promising channel materials for wearable electronics and energy-efficient field-effect transistors (FETs), large hysteresis and large subthreshold swing induced by either dangling bonds at gate oxide dielectrics and/or trap molecules in bubbles at vdW interface are a serious drawback, hampering implementation of the 2D-material based FETs in real electronics. Here, we report a monolayer MoS2 FET with near-zero hysteresis reaching 0.15% of the sweeping range of the gate bias, a record-value observed so far in 2D FETs. This was realized by squeezing the MoS2 channel between top h-BN layer and bottom h-BN gate dielectrics and further removing the trap molecules in bubbles at the vdW interfaces via post-annealing. By segregating the bubbles out to the edge of the channel, we also obtain excellent switching characteristics with a minimum subthreshold swing of 63 mV/dec, an average subthreshold slope of 69 mV/dec for a current range of four orders of magnitude at room temperature, and a high on/off current ratio of 108 at a small operating voltage (<1 V). Such a near-zero hysteresis and a near-ideal subthreshold limit originate from the reduced trap density of ~5.2 × 109 cm‑2 eV‑1, a thousand times smaller than previously reported values.
Physicochemical and functional properties of dietary fiber from maca (Lepidium meyenii Walp.) liquor residue.

PubMed

Chen, Jinjin; Zhao, Qingsheng; Wang, Liwei; Zha, Shenghua; Zhang, Lijun; Zhao, Bing

2015-11-05

Using maca (Lepidium meyenii) liquor residue as the raw material, dietary fiber (DF) was prepared by chemical (MCDF) and enzymatic (MEDF) methods, respectively, of which the physicochemical and functional properties were comparatively studied. High contents of DF were found in MCDF (55.63%) and MEDF (81.10%). Both fibers showed good functional properties, including swelling capacity, water holding capacity, oil holding capacity, glucose adsorption capacity and glucose retardation index. MEDF showed better functional properties, which could be attributed to its higher content of DF, more irregular surface and more abundant monosaccharide composition. The results herein suggest that maca DF prepared by enzymatic method from liquor residue is a good functional ingredient in food products. Copyright © 2015 Elsevier Ltd. All rights reserved.
Dual frequency diffuse dielectric barrier discharge in atmospheric-pressure air-like gas mixture for thin film deposition

NASA Astrophysics Data System (ADS)

Liu, Yaoge; Starostin, Serguei; Welzel, Stefan; van de Sanden, M. C. M.; de Vries, Hindrik; Fom Institute-Differ Team; Eindhoven University Of Technology Team; Fujifilm Manufacturing Europe B. v. Team

2016-09-01

A dual frequency (DF) diffuse discharge was obtained in an atmospheric-pressure dielectric barrier discharge reactor in air-like gas mixtures. By adding a radio frequency (RF) voltage to a low frequency (LF) voltage, we aim to increase the plasma power density. In this study, the discussion is mainly focused on the discharge characteristics and the thin film deposition. According to the spatio-temporal emission, the discharge shows a glow-like structure with both LF and DF voltages. By fitting the spectral lines of the second positive system of N2, the gas temperature was estimated which does not obviously increase with the extra RF signal. Moreover, SiO2-like film was deposited from TEOS using the DF power supply. Thin film properties such as surface morphology, microstructure and stoichiometry were analyzed by AFM, FTIR and XPS, respectively. Because of the higher plasma power density, the DF power supply can be an efficient approach to improve the properties and to increase the throughput of the thin film deposition.
Assessing Ion-Water Interactions in the AMOEBA Force Field Using Energy Decomposition Analysis of Electronic Structure Calculations.

PubMed

Mao, Yuezhi; Demerdash, Omar; Head-Gordon, Martin; Head-Gordon, Teresa

2016-11-08

AMOEBA is a molecular mechanics force field that addresses some of the shortcomings of a fixed partial charge model, by including permanent atomic point multipoles through quadrupoles, as well as many-body polarization through the use of point inducible dipoles. In this work, we investigate how well AMOEBA formulates its non-bonded interactions, and how it implicitly incorporates quantum mechanical effects such as charge penetration (CP) and charge transfer (CT), for water-water and water-ion interactions. We find that AMOEBA's total interaction energies, as a function of distance and over angular scans for the water dimer and for a range of water-monovalent cations, agree well with an advanced density functional theory (DFT) model, whereas the water-halides and water-divalent cations show significant disagreement with the DFT result, especially in the compressed region when the two fragments overlap. We use a second-generation energy decomposition analysis (EDA) scheme based on absolutely localized molecular orbitals (ALMOs) to show that in the best cases AMOEBA relies on cancellation of errors by softening of the van der Waals (vdW) wall to balance permanent electrostatics that are too unfavorable, thereby compensating for the missing CP effect. CT, as another important stabilizing effect not explicitly taken into account in AMOEBA, is also found to be incorporated by the softened vdW interaction. For the water-halides and water-divalent cations, this compensatory approach is not as well executed by AMOEBA over all distances and angles, wherein permanent electrostatics remains too unfavorable and polarization is overdamped in the former while overestimated in the latter. We conclude that the DFT-based EDA approach can help refine a next-generation AMOEBA model that either realizes a better cancellation of errors for problematic cases like those illustrated here, or serves to guide the parametrization of explicit functional forms for short-range contributions from CP and/or CT.
Reversible Tailoring of Mechanical Properties of Carbon Nanotube Forests by Immersing in Solvents

DTIC Science & Technology

2014-12-07

quantify the strength of vdW interactions between CNTs, Hamaker constant of CNTs in vacuum, Av ¼ V 12pD 2 G , was evaluated where ‘V’ is the vdW...effectively do not interact with each other. Therefore, we assumed curved surface–surface vdW interaction between two CNTs to evaluate the Hamaker ...of the vdW forces are directly proportional to Hamaker constant, which depends on the macroscopic properties of the interacting objects and the
Dietary Fiber Supplements: Effects in Obesity and Metabolic Syndrome and Relationship to Gastrointestinal Functions

PubMed Central

Papathanasopoulos, Athanasios; Camilleri, Michael

2010-01-01

Dietary fiber (DF) is a term that reflects to a heterogenous group of natural food sources, processed grains and commercial supplements. Several forms of DF have been used as complementary or alternative agents in the management of manifestations of the metabolic syndrome, including obesity. Not surprisingly, there is a great variation in the biological efficacy of DF in metabolic syndrome and body weight control. Diverse factors and mechanisms have been reported as mediators of the effects of DF on the metabolic syndrome and obesity. Among this array of mechanisms, the modulation of gastric sensorimotor influences appears to be crucial for the effects of DF, but also quite variable. This article focuses on the role, mechanism of action and benefits of different forms of fiber and supplements on obesity and metabolic syndrome, glycemia, dyslipidemia, cardiovascular risk, and explores the effects of DF on gastric sensorimotor function and satiety in mediating these actions of DF. PMID:19931537
Functional localization of the human color center by decreased water displacement using diffusion-weighted fMRI.

PubMed

Williams, Rebecca J; Reutens, David C; Hocking, Julia

2015-11-01

Decreased water displacement following increased neural activity has been observed using diffusion-weighted functional MRI (DfMRI) at high b-values. The physiological mechanisms underlying the diffusion signal change may be unique from the standard blood oxygenation level-dependent (BOLD) contrast and closer to the source of neural activity. Whether DfMRI reflects neural activity more directly than BOLD outside the primary cerebral regions remains unclear. Colored and achromatic Mondrian visual stimuli were statistically contrasted to functionally localize the human color center Area V4 in neurologically intact adults. Spatial and temporal properties of DfMRI and BOLD activation were examined across regions of the visual cortex. At the individual level, DfMRI activation patterns showed greater spatial specificity to V4 than BOLD. The BOLD activation patterns were more prominent in the primary visual cortex than DfMRI, where activation was localized to the ventral temporal lobe. Temporally, the diffusion signal change in V4 and V1 both preceded the corresponding hemodynamic response, however the early diffusion signal change was more evident in V1. DfMRI may be of use in imaging applications implementing cognitive subtraction paradigms, and where highly precise individual functional localization is required.
Absorption and resonance Raman study of the pyromellitic diahydride anion via density functional theory

NASA Astrophysics Data System (ADS)

Andruniow, T.; Pawlikowski, M.

2000-05-01

The electronic structure of the low-energy states of the pyromellitic diahydride (PMDA) anion is investigated in terms of the VWN (Vosco-Wilk-Nusair) the BP (Becke-Perdew) and the B3LYP density functional (DF) methods employed with 6-31G * basis sets. All the methods are shown to reproduce correctly the absorption and resonance Raman spectra in the region corresponding to the low-energy 1 2Au→1 2B3g transition. The discrepancies between the theory and experiment are attributed to a (weak) Dushinsky effect predominately due to a mixing of the ν3=1593 cm -1 and ν4=1342 cm -1 vibrations in the 1 2B3 g state of the PMDA radical.
Measuring and predicting Delta(vap)H298 values of ionic liquids.

PubMed

Deyko, Alexey; Lovelock, Kevin R J; Corfield, Jo-Anne; Taylor, Alasdair W; Gooden, Peter N; Villar-Garcia, Ignacio J; Licence, Peter; Jones, Robert G; Krasovskiy, Vladimir G; Chernikova, Elena A; Kustov, Leonid M

2009-10-14

We report the enthalpies of vaporisation (measured using temperature programmed desorption by mass spectrometry) of twelve ionic liquids (ILs), covering four imidazolium, [C(m)C(n)Im]+, five pyrrolidinium, [C(n)C(m)Pyrr]+, two pyridinium, [C(n)Py]+, and a dication, [C3(C1Im)2]2+ based IL. These cations were paired with a range of anions: [BF4]-, [FeCl4]-, [N(CN)2]-, [PF3(C2F5)3]- ([FAP]-), [(CF3SO2)2N]- ([Tf2N]-) and [SCN]-. Using these results, plus those for a further eight imidazolium based ILs published earlier (which include the anions [CF3SO3]- ([TfO]-), [PF6]- and [EtSO4]-), we show that the enthalpies of vaporisation can be decomposed into three components. The first component is the Coulombic interaction between the ions, DeltaU(Cou,R), which is a function of the IL molar volume, V(m), and a parameter R(r) which quantifies the relative change in anion-cation distance on evaporation from the liquid phase to the ion pair in the gas phase. The second and third components are the van der Waals contributions from the anion, DeltaH(vdw,A), and the cation, DeltaH(vdw,C). We derive a universal value for R(r), and individual values of DeltaH(vdw,A) and DeltaH(vdw,C) for each of the anions and cations considered in this study. Given the molar volume, it is possible to estimate the enthalpies of vaporisation of ILs composed of any combination of the ions considered here; values for fourteen ILs which have not yet been studied experimentally are given.
Evaluation of Two New Electronic Apex-Locator-Controlled Handpieces Using a NiTi Rotary File: An In Vitro Study.

PubMed

Nazarimoghadam, Kiumarz; Labaf, Hossein

2013-11-01

The aim of this in-vitro study was to compare the accuracy of two new electronic apex-locator controlled handpieces (EALHs) using the first rotary Mtwo file while rotating in the canal. A total of 36 extracted mandibular molar teeth were selected. The lengths of the mesio-buccal canals to the major foramina were measured directly using a size 10 K-file introduced in the canal until the tip was visible under a loupe and then 0.5 mm was subtracted from the recorded lengths as the actual working lengths (AWLs). Subsequently, the teeth were randomly assigned to two groups and embedded in an alginate model. Auto-stop function of the EALHs was preset at "0.5" mark and then electrical working lengths (EWLs) in groups 1 and 2 were recorded by VDW GOLD and Dentaport ZX, respectively. Analysis of variance (ANOVA, 1-way) and Tukey pairwise multiple comparison intervals (0.05) were used to compare the accuracy of the two electronic devices. For VDW GOLD, 61.1% of the measurements were within ±0.5 mm and 88.9% were within ±1 mm of the AWL. For Dentaport ZX, 88.9% of the measurements were within ±0.5 mm and 94.4% were within ±1mm of the AWL. There was no significant difference between AWLs and EWLs (p=0.466 for Dentaport ZX and p=0.283 for VDW Gold) and between the accuracy of the two devices in determining the EWL (p=0.8). Both Dentaport ZX and VDW Gold were suitable for determining working length using a rotary file. To avoid over instrumenting the canal, we recommend setting the devices to automatically stop or reverse the rotary file at 1 mm level.
Defibrotide: an endothelium protecting and stabilizing drug, has an anti-angiogenic potential in vitro and in vivo.

PubMed

Koehl, Gudrun E; Geissler, Edward K; Iacobelli, Massimo; Frei, Caroline; Burger, Verena; Haffner, Silvia; Holler, Ernst; Andreesen, Reinhard; Schlitt, Hans J; Eissner, Günther

2007-05-01

Defibrotide (DF) is a polydisperse mixture of 90% single-stranded oligonucleotides with anti-thrombotic and anti-apoptotic functions. DF is used in the treatment of endothelial complications in the course of allogeneic stem cell transplantation. Recent preclinical evidence suggests that DF might also have anti-neoplastic properties. In the present study we hypothesized that DF might inhibit tumors via an anti-angiogenic effect. The anti-angiogenic potential of DF was tested in vitro using human microvascular endothelial cells forming vessel structures across a layer of dermal fibroblasts. Our results show that pharmacologic DF concentrations (100 mug/ml) significantly reduced vessel formation in this assay. Similarly, DF blocked sprouting from cultured rat aortic rings. In vivo, angiogenesis in a human gastric tumor (TMK1) implanted in dorsal skin-fold chambers (in nude mice) was inhibited by i.v. application of 450 mg/kg DF. Notably, due to its short half-life, DF was most effective when given on a daily basis. Although the precise mechanism of DF remains to be elucidated, initial Western blots show that DF reduces phosphorylation-activation of p70S6 kinase, which is a key target in the PI3K/Akt/mTOR signaling pathway linked to endothelial cell and pericyte proliferation and activation. However, in vitro data suggest that DF acts independently of vascular endothelial growth factor. Taken together, our data suggest that while DF is known for its endothelium-protecting function in SCT, it also inhibits formation of new blood vessels, and thus should be considered for further testing as an adjuvant anti-cancer agent, either alone, or in combination with other drugs.
Review: Dietary fiber utilization and its effects on physiological functions and gut health of swine.

PubMed

Jha, R; Berrocoso, J D

2015-09-01

Although dietary fiber (DF) negatively affects energy and nutrient digestibility, there is growing interest for the inclusion of its fermentable fraction in pig diets due to their functional properties and potential health benefits beyond supplying energy to the animals. This paper reviews some of the relevant information available on the role of different types of DF on digestion of nutrients in different sections of the gut, the fermentation process and its influence on gut environment, especially production and utilization of metabolites, microbial community and gut health of swine. Focus has been given on DF from feed ingredients (grains and coproducts) commonly used in pig diets. Some information on the role DF in purified form in comparison with DF in whole matrix of feed ingredients is also presented. First, composition and fractions of DF in different feed ingredients are briefly reviewed. Then, roles of different fractions of DF on digestion characteristics and physiological functions in the gastrointestinal tract (GIT) are presented. Specific roles of different fractions of DF on fermentation characteristics and their effects on production and utilization of metabolites in the GIT have been discussed. In addition, roles of DF fermentation on metabolic activity and microbial community in the intestine and their effects on intestinal health are reviewed and discussed. Evidence presented in this review indicates that there is wide variation in the composition and content of DF among feed ingredients, thereby their physico-chemical properties in the GIT of swine. These variations, in turn, affect the digestion and fermentation characteristics in the GIT of swine. Digestibility of DF from different feed ingredients is more variable and lower than that of other nutrients like starch, sugars, fat and CP. Soluble fractions of DF are fermented faster, produce higher amounts of volatile fatty acid than insoluble fractions, and favors growth of beneficial microbiota. Thus, selective inclusion of DF in diets can be used as a nutritional strategy to optimize the intestinal health of pigs, despite its lower digestibility and consequential negative effect on digestibility of other nutrients.
Strong magnetization and Chern insulators in compressed graphene/CrI 3 van der Waals heterostructures

NASA Astrophysics Data System (ADS)

Zhang, Jiayong; Zhao, Bao; Zhou, Tong; Xue, Yang; Ma, Chunlan; Yang, Zhongqin

2018-02-01

Graphene-based heterostructures are a promising material system for designing the topologically nontrivial Chern insulating devices. Recently, a two-dimensional monolayer ferromagnetic insulator CrI3 was successfully synthesized in experiments [B. Huang et al., Nature (London) 546, 270 (2017), 10.1038/nature22391]. Here, these two interesting materials are proposed to build a heterostructure (Gr /CrI3). Our first-principles calculations show that the system forms a van der Waals (vdW) heterostructure, which is relatively facilely fabricated in experiments. A Chern insulating state is acquired in the Gr /CrI3 heterostructure if the vdW gap is compressed to a distance between about 3.3 and 2.4 Å, corresponding to a required external pressure between about 1.4 and 18.3 GPa. Amazingly, very strong magnetization (about 150 meV) is found in graphene, induced by the substrate CrI3, despite the vdW interactions between them. A low-energy effective model is employed to understand the mechanism. The work functions, contact types, and band alignments of the Gr /CrI3 heterostructure system are also studied. Our work demonstrates that the Gr /CrI3 heterostructure is a promising system to observe the quantum anomalous Hall effect at high temperatures (up to 45 K) in experiments.
Impact of Ocean Wave Climate on Double-Frequency Microseisms and Evaluation of Seismic Site Effect in Northern Mississippi, USA

NASA Astrophysics Data System (ADS)

Guo, Z.; Aydin, A.; Xue, M.

2017-12-01

This research presents the power spectral density (PSD) of double-frequency (DF) microseisms in both vertical (V) and resultant horizontal (H) directions and horizontal-to-vertical spectral ratios (HVSR) of 13 continuous single point long-term ambient noise recordings (LTR) at 5 inland and 2 coastal locations selected in Mississippi Embayment, and frequency value and PSD at DF peak (PSD@DF), predominant frequency (f0) and HVSR value at f0 (HVSR@f0) at 234 single point short-term ambient noise recordings (STR) over a large range of unconsolidated sediment thickness (UST) in Northern Mississippi. By correlating PSD of LTRs with the simultaneous ocean wave climate data of Atlantic Ocean and Gulf of Mexico, DF microseisms observed in Northern Mississippi were shown to be shaped by a combined impact of wave climates of both Atlantic Ocean and Gulf of Mexico. Polarization analysis conducted separately for LTRs and STRs strengthen this conclusion. The LTRs show stable estimates of f0, on the other hand, time-dependent variations on HVSR@f0 value. The plots of DFH-UST, rather than DFV-UST, coincide well with plots of f0-UST within area where UST is larger than 300 m, which indicates that the shear wave resonance in thick sediments modifies the DF microseisms more obviously in horizontal direction than in vertical direction. Transfer functions between HVSR@f0 and ocean data indicates that the variation of HVSR@f0 is caused by variations of source location and energy level of DF microseisms, i.e. ocean wave activities in Atlantic Ocean and Gulf of Mexico. Additionally, 3D microseism spectra of each LTR and those of all STRs within each 100 m-UST group are converted into spatial spectral vectors and projected on stereographic nets. Patterns of the clusters formed by these projections show that the HVSR@f0 values are related to both UST and vibration source location and energy level.
Genome-wide differential gene expression in immortalized DF-1 chicken embryo fibroblast cell line

PubMed Central

2011-01-01

Background When compared to primary chicken embryo fibroblast (CEF) cells, the immortal DF-1 CEF line exhibits enhanced growth rates and susceptibility to oxidative stress. Although genes responsible for cell cycle regulation and antioxidant functions have been identified, the genome-wide transcription profile of immortal DF-1 CEF cells has not been previously reported. Global gene expression in primary CEF and DF-1 cells was performed using a 4X44K chicken oligo microarray. Results A total of 3876 differentially expressed genes were identified with a 2 fold level cutoff that included 1706 up-regulated and 2170 down-regulated genes in DF-1 cells. Network and functional analyses using Ingenuity Pathways Analysis (IPA, Ingenuity® Systems, http://www.ingenuity.com) revealed that 902 of 3876 differentially expressed genes were classified into a number of functional groups including cellular growth and proliferation, cell cycle, cellular movement, cancer, genetic disorders, and cell death. Also, the top 5 gene networks with intermolecular connections were identified. Bioinformatic analyses suggested that DF-1 cells were characterized by enhanced molecular mechanisms for cell cycle progression and proliferation, suppressing cell death pathways, altered cellular morphogenesis, and accelerated capacity for molecule transport. Key molecules for these functions include E2F1, BRCA1, SRC, CASP3, and the peroxidases. Conclusions The global gene expression profiles provide insight into the cellular mechanisms that regulate the unique characteristics observed in immortal DF-1 CEF cells. PMID:22111699
Solvation Free Energies of Alanine Peptides: The Effect of Flexibility

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

Kokubo, Hironori; Harris, Robert C.; Asthagiri, Dilip

The electrostatic (?Gel), cavity-formation (?Gvdw), and total (?G) solvation free energies for 10 alanine peptides ranging in length (n) from 1 to 10 monomers were calculated. The free energies were computed both with xed, extended conformations of the peptides and again for some of the peptides without constraints. The solvation free energies, ?Gel, ?Gvdw, and ?G, were found to be linear in n, with the slopes of the best-fit lines being gamma_el, gamma_vdw, and gamma, respectively. Both gamma_el and gamma were negative for fixed and flexible peptides, and gamma_vdw was negative for fixed peptides. That gamma_vdw was negative was surprising,more » as experimental data on alkanes, theoretical models, and MD computations on small molecules and model systems generally suggest that gamma_vdw should be positive. A negative gamma_vdw seemingly contradicts the notion that ?Gvdw drives the initial collapse of the protein when it folds by favoring conformations with small surface areas, but when we computed ?Gvdw for the flexible peptides, thereby allowing the peptides to assume natural ensembles of more compact conformations, gamma-vdw was positive. Because most proteins do not assume extended conformations, a ?Gvdw that increases with increasing surface area may be typical for globular proteins. An alternative hypothesis is that the collapse is driven by intramolecular interactions. We show that the intramolecular van der Waal's interaction energy is more favorable for the flexible than for the extended peptides, seemingly favoring this hypothesis, but the large fluctuations in this energy may make attributing the collapse of the peptide to this intramolecular energy difficult.« less
Chemical Gating of a Weak Topological Insulator: Bi14Rh3I9.

PubMed

Ghimire, Madhav Prasad; Richter, Manuel

2017-10-11

The compound Bi 14 Rh 3 I 9 has recently been suggested as a weak three-dimensional topological insulator on the basis of angle-resolved photoemission and scanning-tunneling experiments in combination with density functional (DF) electronic structure calculations. These methods unanimously support the topological character of the headline compound, but a compelling confirmation could only be obtained by dedicated transport experiments. The latter, however, are biased by an intrinsic n-doping of the material's surface due to its polarity. Electronic reconstruction of the polar surface shifts the topological gap below the Fermi energy, which would also prevent any future device application. Here, we report the results of DF slab calculations for chemically gated and counter-doped surfaces of Bi 14 Rh 3 I 9 . We demonstrate that both methods can be used to compensate the surface polarity without closing the electronic gap.

Distribution functions for orbits trapped at the resonances in the Galactic disc

NASA Astrophysics Data System (ADS)

Monari, G.

2017-12-01

The present-day response of a Galactic disc stellar population to a non-axisymmetric perturbation of the potential has previously been computed through perturbation theory within the phase-space coordinates of the unperturbed axisymmetric system. Such an Eulerian linearized treatment however leads to singularities at resonances, which prevent quantitative comparisons with data. Monari et al. manage to capture the behaviour of the distribution function (DF) at a resonance in a Lagrangian approach, by averaging the Hamiltonian over fast angle variables and re-expressing the DF in terms of a new set of canonical actions and angles variables valid in the resonant region. They then follow the prescription of Binney (2016), assigning to the resonant DF the time average along the orbits of the axisymmetric DF expressed in the new set of actions and angles. This boils down to phase-mixing the DF in terms of the new angles, such that the DF for trapped orbits only depends on the new set of actions. This opens the way to quantitatively fitting the effects of the bar and spirals to Gaia data in terms of distribution functions in action space.
Evolution of Moiré Profiles from van der Waals Superstructures of Boron Nitride Nanosheets

PubMed Central

Liao, Yunlong; Cao, Wei; Connell, John W.; Chen, Zhongfang; Lin, Yi

2016-01-01

Two-dimensional (2D) van der Waals (vdW) superstructures, or vdW solids, are formed by the precise restacking of 2D nanosheet lattices, which can lead to unique physical and electronic properties that are not available in the parent nanosheets. Moiré patterns formed by the crystalline mismatch between adjacent nanosheets are the most direct features for vdW superstructures under microscopic imaging. In this article, transmission electron microscopy (TEM) observation of hexagonal Moiré patterns with unusually large micrometer-sized lateral areas (up to ~1 μm2) and periodicities (up to ~50 nm) from restacking of liquid exfoliated hexagonal boron nitride nanosheets (BNNSs) is reported. This observation was attributed to the long range crystallinity and the contaminant-free surfaces of these chemically inert nanosheets. Parallel-line-like Moiré fringes with similarly large periodicities were also observed. The simulations and experiments unambiguously revealed that the hexagonal patterns and the parallel fringes originated from the same rotationally mismatched vdW stacking of BNNSs and can be inter-converted by simply tilting the TEM specimen following designated directions. This finding may pave the way for further structural decoding of other 2D vdW superstructure systems with more complex Moiré images. PMID:27188697
Evolution of single-particle structure and beta-decay near 78Ni

NASA Astrophysics Data System (ADS)

Borzov, I. N.

2012-12-01

The extended self-consistent beta-decay model has been applied for bet-decay rates and delayed neutron emission probabilities of spherical neutron-rich isotopes near the r-process paths. Unlike a popular global FRDM+RPA model, in our fully microscopic approach, the Gamow-Teller and first-forbidden decays are treated on the same footing. The model has been augmented by blocking of the odd particle in order to account for important ground-state spin-parity inversion effect which has been shown to exist in the region of the most neutron-rich doubly-magic nucleus 78Ni. Finally, a newly developed form of density functional DF3a has been employed which gives a better spin-orbit splitting due to the modified tensor components of the density functional.
Gas Adsorption and Selectivity in Zeolitic Imidazolate Frameworks from First Principles Calculations

NASA Astrophysics Data System (ADS)

Ray, Keith; Olmsted, David; He, Ning; Houndonougbo, Yao; Laird, Brian; Asta, Mark

2012-02-01

Zeolitic Imidazolate Framework (ZIFs) are excellent candidate materials for carbon capture and gas separation. Here we employ the van der Waals density functional (vdW-DF) [1] in an analysis of the binding energetics for CO2, CH4 and N2 molecules in a set of ZIFs featuring different chemical functionalizations. We investigate multiple low-energy binding sites, which differ in their positions relative to functional groups on the imidazole linkers. In all cases an accurate treatment of van der Waals forces appears essential to provide reasonable binding energy magnitudes. We report results obtained from different parameterizations of the vdW-DF, providing comparisons between calculations and experimental values of the heat of adsorption [2]. This research is supported by the Energy Frontier Research Center ``Molecularly Engineered Energy Materials,'' funded by the US Department of Energy, Office of Science, Office of Basic Energy Sciences under Award Number DE-SC0001342. [1] M. Dion, H. Rydberg, E. Schroder, D. C. Langreth, B. I. Lundqvist, Phys. Rev. Let. 92, 246401 (2004) [2] W. Morris, B. Leung, H. Furukawa, O. K. Yaghi, N. He, H. Hayashi, Y. Houndonougbo, M. Asta, B. B. Laird, O. M. Yaghi, J. AM. CHEM. SOC. 2010, 132, 11006-11008
Ab initio study of structural and mechanical property of solid molecular hydrogens

NASA Astrophysics Data System (ADS)

Ye, Yingting; Yang, Li; Yang, Tianle; Nie, Jinlan; Peng, Shuming; Long, Xinggui; Zu, Xiaotao; Du, Jincheng

2015-06-01

Ab initio calculations based on density functional theory (DFT) were performed to investigate the structural and the elastic properties of solid molecular hydrogens (H2). The influence of molecular axes of H2 on structural relative stabilities of hexagonal close-packed (hcp) and face-centered cubic (fcc) structured hydrogen molecular crystals were systematically investigated. Our results indicate that for hcp structures, disordered hydrogen molecule structure is more stable, while for fcc structures, Pa3 hydrogen molecular crystal is most stable. The cohesive energy of fcc H2 crystal was found to be lower than hcp. The mechanical properties of fcc and hcp hydrogen molecular crystals were obtained, with results consistent with previous theoretical calculations. In addition, the effects of zero point energy (ZPE) and van der Waals (vdW) correction on the cohesive energy and the stability of hydrogen molecular crystals were systematically studied and discussed.
Gut Fermentation of Dietary Fibres: Physico-Chemistry of Plant Cell Walls and Implications for Health

PubMed Central

Williams, Barbara A.; Grant, Lucas J.; Gidley, Michael J.; Mikkelsen, Deirdre

2017-01-01

The majority of dietary fibre (DF) originates from plant cell walls. Chemically, DF mostly comprise carbohydrate polymers, which resist hydrolysis by digestive enzymes in the mammalian small intestine, but can be fermented by large intestinal bacteria. One of the main benefits of DF relate to its fermentability, which affects microbial diversity and function within the gastro-intestinal tract (GIT), as well as the by-products of the fermentation process. Much work examining DF tends to focus on various purified ingredients, which have been extracted from plants. Increasingly, the validity of this is being questioned in terms of human nutrition, as there is evidence to suggest that it is the actual complexity of DF which affects the complexity of the GIT microbiota. Here, we review the literature comparing results of fermentation of purified DF substrates, with whole plant foods. There are strong indications that the more complex and varied the diet (and its ingredients), the more complex and varied the GIT microbiota is likely to be. Therefore, it is proposed that as the DF fermentability resulting from this complex microbial population has such profound effects on human health in relation to diet, it would be appropriate to include DF fermentability in its characterization—a functional approach of immediate relevance to nutrition. PMID:29053599
Gut Fermentation of Dietary Fibres: Physico-Chemistry of Plant Cell Walls and Implications for Health.

PubMed

Williams, Barbara A; Grant, Lucas J; Gidley, Michael J; Mikkelsen, Deirdre

2017-10-20

The majority of dietary fibre (DF) originates from plant cell walls. Chemically, DF mostly comprise carbohydrate polymers, which resist hydrolysis by digestive enzymes in the mammalian small intestine, but can be fermented by large intestinal bacteria. One of the main benefits of DF relate to its fermentability, which affects microbial diversity and function within the gastro-intestinal tract (GIT), as well as the by-products of the fermentation process. Much work examining DF tends to focus on various purified ingredients, which have been extracted from plants. Increasingly, the validity of this is being questioned in terms of human nutrition, as there is evidence to suggest that it is the actual complexity of DF which affects the complexity of the GIT microbiota. Here, we review the literature comparing results of fermentation of purified DF substrates, with whole plant foods. There are strong indications that the more complex and varied the diet (and its ingredients), the more complex and varied the GIT microbiota is likely to be. Therefore, it is proposed that as the DF fermentability resulting from this complex microbial population has such profound effects on human health in relation to diet, it would be appropriate to include DF fermentability in its characterization-a functional approach of immediate relevance to nutrition.
Analytical nuclear gradients for the range-separated many-body dispersion model of noncovalent interactions.

PubMed

Blood-Forsythe, Martin A; Markovich, Thomas; DiStasio, Robert A; Car, Roberto; Aspuru-Guzik, Alán

2016-03-01

An accurate treatment of the long-range electron correlation energy, including van der Waals (vdW) or dispersion interactions, is essential for describing the structure, dynamics, and function of a wide variety of systems. Among the most accurate models for including dispersion into density functional theory (DFT) is the range-separated many-body dispersion (MBD) method [A. Ambrosetti et al. , J. Chem. Phys. , 2014, 140 , 18A508], in which the correlation energy is modeled at short-range by a semi-local density functional and at long-range by a model system of coupled quantum harmonic oscillators. In this work, we develop analytical gradients of the MBD energy with respect to nuclear coordinates, including all implicit coordinate dependencies arising from the partitioning of the charge density into Hirshfeld effective volumes. To demonstrate the efficiency and accuracy of these MBD gradients for geometry optimizations of systems with intermolecular and intramolecular interactions, we optimized conformers of the benzene dimer and isolated small peptides with aromatic side-chains. We find excellent agreement with the wavefunction theory reference geometries of these systems (at a fraction of the computational cost) and find that MBD consistently outperforms the popular TS and D3(BJ) dispersion corrections. To demonstrate the performance of the MBD model on a larger system with supramolecular interactions, we optimized the C 60 @C 60 H 28 buckyball catcher host-guest complex. In our analysis, we also find that neglecting the implicit nuclear coordinate dependence arising from the charge density partitioning, as has been done in prior numerical treatments, leads to an unacceptable error in the MBD forces, with relative errors of ∼20% (on average) that can extend well beyond 100%.
The potential for fast van der Waals computations for layered materials using a Lifshitz model

NASA Astrophysics Data System (ADS)

Zhou, Yao; Pellouchoud, Lenson A.; Reed, Evan J.

2017-06-01

Computation of the van der Waals (vdW) interactions plays a crucial role in the study of layered materials. The adiabatic-connection fluctuation-dissipation theorem within random phase approximation (ACFDT-RPA) has been empirically reported to be the most accurate of commonly used methods, but it is limited to small systems due to its computational complexity. Without a computationally tractable vdW correction, fictitious strains are often introduced in the study of multilayer heterostructures, which, we find, can change the vdW binding energy by as much as 15%. In this work, we employed for the first time a defined Lifshitz model to provide the vdW potentials for a spectrum of layered materials orders of magnitude faster than the ACFDT-RPA for representative layered material structures. We find that a suitably defined Lifshitz model gives the correlation component of the binding energy to within 8-20% of the ACFDT-RPA calculations for a variety of layered heterostructures. Using this fast Lifshitz model, we studied the vdW binding properties of 210 three-layered heterostructures. Our results demonstrate that the three-body vdW effects are generally small (10% of the binding energy) in layered materials for most cases, and that non-negligible second-nearest neighbor layer interaction and three-body effects are observed for only those cases in which the middle layer is atomically thin (e.g. BN or graphene). We find that there is potential for particular combinations of stacked layers to exhibit repulsive three-body van der Waals effects, although these effects are likely to be much smaller than two-body effects.
Ab initio studies of hydrogen adatoms on bilayer graphene

NASA Astrophysics Data System (ADS)

Mapasha, R. E.; Ukpong, A. M.; Chetty, N.

2012-05-01

We present a comparative density functional study of the adsorption of hydrogen on bilayer graphene. Six different exchange-correlation functionals are employed to explore the possible configurations of hydrogen adsorption at 50% coverage. Using the four variants of the nonlocal van der Waals density functional, we identify three distinct competing configurations that retain the coupled bilayer structure at 0 K. One of the configurations undergoes a spontaneous transformation from hexagonal to tetrahedral structure, under hydrogenation, with heat of formation ranging between -0.03 eV (vdW-DF) and -0.37 eV (vdW-DFC09x). This configuration has a finite band gap of around 3 eV, whereas all other competing configurations are either semimetallic or metallic. We also find two unique low-energy competing configurations of decoupled bilayer graphene, and therefore suggest the possibility of graphene exfoliation by hydrogen intercalation.
By-product from decoction process of Hibiscus sabdariffa L. calyces as a source of polyphenols and dietary fiber.

PubMed

Sáyago-Ayerdi, Sonia G; Velázquez-López, Carolina; Montalvo-González, Efigenia; Goñi, Isabel

2014-03-30

Dietary fiber (DF) and antioxidant compounds are widely used as functional ingredients. The market in this field is competitive and the search for new types of quality ingredients for the food industry is intensifying. The aim of this study was to evaluate the composition and antioxidant activity of by-products generated during the decoction of calyces of four Mexican Hibiscus sabdariffa L. cultivars ('Criolla', 'China', 'Rosalis' and 'Tecoanapa') in order to assess them as a source of functional ingredients. Some calyx components were partially transferred to the beverage during the decoction process, while most were retained in the decoction residues. These by-products proved to be a good source of DF (407.4-457.0 g kg⁻¹ dry matter) and natural antioxidants (50.7-121.8 µmol Trolox equivalent g⁻¹ dry matter). The decoction process extracted some soluble carbohydrates, ash and some extractable polyphenols. The DF content changed in the dried residues, which could be considered as high-DF materials with a high proportion of soluble DF (∼20% of total DF) and considerable antioxidant capacity. These by-products could be used as an antioxidant DF source. © 2013 Society of Chemical Industry.
Gate-tunable diode-like current rectification and ambipolar transport in multilayer van der Waals ReSe2/WS2 p-n heterojunctions.

PubMed

Wang, Cong; Yang, Shengxue; Xiong, Wenqi; Xia, Congxin; Cai, Hui; Chen, Bin; Wang, Xiaoting; Zhang, Xinzheng; Wei, Zhongming; Tongay, Sefaattin; Li, Jingbo; Liu, Qian

2016-10-12

Vertically stacked van der Waals (vdW) heterojunctions of two-dimensional (2D) transition metal dichalcogenides (TMDs) have attracted a great deal of attention due to their fascinating properties. In this work, we report two important gate-tunable phenomena in new artificial vdW p-n heterojunctions created by vertically stacking p-type multilayer ReSe 2 and n-type multilayer WS 2 : (1) well-defined strong gate-tunable diode-like current rectification across the p-n interface is observed, and the tunability of the electronic processes is attributed to the tunneling-assisted interlayer recombination induced by majority carriers across the vdW interface; (2) the distinct ambipolar behavior under gate voltage modulation both at forward and reverse bias voltages is found in the vdW ReSe 2 /WS 2 heterojunction transistors and a corresponding transport model is proposed for the tunable polarity behaviors. The findings may provide some new opportunities for building nanoscale electronic and optoelectronic devices.
Tunable Schottky barrier and electronic properties in borophene/g-C2N van der Waals heterostructures

NASA Astrophysics Data System (ADS)

Jiang, J. W.; Wang, X. C.; Song, Y.; Mi, W. B.

2018-05-01

By stacking different layers of two dimensional (2D) monolayer materials, the electronic properties of the 2D van der Waals (vdW) heterostructures can be tailored. However, the Schottky barrier formed between 2D semiconductor and metallic electrode has greatly limited the application of 2D semiconductor in nanoelectronic and optoelectronic devices. Herewith, we investigate the electronic properties of borophene/g-C2N vdW heterostructures by first-principles calculations. The results indicate that electronic structures of borophene and g-C2N are preserved in borophene/g-C2N vdW heterostructures. Meanwhile, upon the external electric field, a transition from the n-type Schottky contact to Ohmic contact is induced, and the carrier concentration between the borophene and g-C2N interfaces can be tuned. These results are expected to provide useful insight in the nanoelectronic and optoelectronic devices based on the borophene/g-C2N vdW heterostructures.
Predicting the influence of long-range molecular interactions on macroscopic-scale diffusion by homogenization of the Smoluchowski equation

NASA Astrophysics Data System (ADS)

Kekenes-Huskey, P. M.; Gillette, A. K.; McCammon, J. A.

2014-05-01

The macroscopic diffusion constant for a charged diffuser is in part dependent on (1) the volume excluded by solute "obstacles" and (2) long-range interactions between those obstacles and the diffuser. Increasing excluded volume reduces transport of the diffuser, while long-range interactions can either increase or decrease diffusivity, depending on the nature of the potential. We previously demonstrated [P. M. Kekenes-Huskey et al., Biophys. J. 105, 2130 (2013)] using homogenization theory that the configuration of molecular-scale obstacles can both hinder diffusion and induce diffusional anisotropy for small ions. As the density of molecular obstacles increases, van der Waals (vdW) and electrostatic interactions between obstacle and a diffuser become significant and can strongly influence the latter's diffusivity, which was neglected in our original model. Here, we extend this methodology to include a fixed (time-independent) potential of mean force, through homogenization of the Smoluchowski equation. We consider the diffusion of ions in crowded, hydrophilic environments at physiological ionic strengths and find that electrostatic and vdW interactions can enhance or depress effective diffusion rates for attractive or repulsive forces, respectively. Additionally, we show that the observed diffusion rate may be reduced independent of non-specific electrostatic and vdW interactions by treating obstacles that exhibit specific binding interactions as "buffers" that absorb free diffusers. Finally, we demonstrate that effective diffusion rates are sensitive to distribution of surface charge on a globular protein, Troponin C, suggesting that the use of molecular structures with atomistic-scale resolution can account for electrostatic influences on substrate transport. This approach offers new insight into the influence of molecular-scale, long-range interactions on transport of charged species, particularly for diffusion-influenced signaling events occurring in crowded cellular environments.
Anterior pituitary cells defective in the cell-autonomous factor, df, undergo cell lineage specification but not expansion.

PubMed

Gage, P J; Roller, M L; Saunders, T L; Scarlett, L M; Camper, S A

1996-01-01

The Ames dwarf mouse transmits a recessive mutation (df) resulting in a profound anterior pituitary hypocellularity due to a general lack of thyrotropes, somatotropes and lactotropes. These cell types are also dependent on the pituitary-specific transcription factor, Pit-1. We present evidence that expression of Pit-1 and limited commitment to these cells lineages occurs in df/df pituitaries. Thus, the crucial role of df may be in lineage-specific proliferation, rather than cytodifferentiation. The presence of all three Pit-1-dependent cell types in clonally derived clusters provides compelling evidence that these three lineages share a common, pluripotent precursor cell. Clusters containing different combinations of Pit-1-dependent cell types suggests that the Pit-1+ precursor cells choose from multiple developmental options during ontogeny. Characterization of df/df<-->+/+ chimeric mice demonstrated that df functions by a cell-autonomous mechanism. Therefore, df and Pit-1 are both cell-autonomous factors required for thyrotrope, somatotrope and lactotrope ontogeny, but their relative roles are different.
III-Nitride, SiC and Diamond Materials for Electronic Devices. Symposium Held April 8-12 1996, San Francisco, California, U.S.A. Volume 423.

DTIC Science & Technology

1996-12-01

gallium, nitrogen and gallium nitride structures. Thus it can be shown to be transferable and efficient for predictive molecular -dynamic simulations on...potentials and forces for the molecular dynamics simulations are derived by means of a density-functional based nonorthogonal tight-binding (DF-TB) scheme...LDA). Molecular -dynamics simulations for determining the different reconstructions of the SiC surface use the slab method (two-dimensional periodic
A correction for Dupuit-Forchheimer interface flow models of seawater intrusion in unconfined coastal aquifers

NASA Astrophysics Data System (ADS)

Koussis, Antonis D.; Mazi, Katerina; Riou, Fabien; Destouni, Georgia

2015-06-01

Interface flow models that use the Dupuit-Forchheimer (DF) approximation for assessing the freshwater lens and the seawater intrusion in coastal aquifers lack representation of the gap through which fresh groundwater discharges to the sea. In these models, the interface outcrops unrealistically at the same point as the free surface, is too shallow and intersects the aquifer base too far inland, thus overestimating an intruding seawater front. To correct this shortcoming of DF-type interface solutions for unconfined aquifers, we here adapt the outflow gap estimate of an analytical 2-D interface solution for infinitely thick aquifers to fit the 50%-salinity contour of variable-density solutions for finite-depth aquifers. We further improve the accuracy of the interface toe location predicted with depth-integrated DF interface solutions by ∼20% (relative to the 50%-salinity contour of variable-density solutions) by combining the outflow-gap adjusted aquifer depth at the sea with a transverse-dispersion adjusted density ratio (Pool and Carrera, 2011), appropriately modified for unconfined flow. The effectiveness of the combined correction is exemplified for two regional Mediterranean aquifers, the Israel Coastal and Nile Delta aquifers.
Size of graphene sheets determines the structural and mechanical properties of 3D graphene foams

NASA Astrophysics Data System (ADS)

Shen, Zhiqiang; Ye, Huilin; Zhou, Chi; Kröger, Martin; Li, Ying

2018-03-01

Graphene is recognized as an emerging 2D nanomaterial for many applications. Assembly of graphene sheets into 3D structures is an attractive way to enable their macroscopic applications and to preserve the exceptional mechanical and physical properties of their constituents. In this study, we develop a coarse-grained (CG) model for 3D graphene foams (GFs) based on the CG model for a 2D graphene sheet by Ruiz et al (2015 Carbon 82 103-15). We find that the size of graphene sheets plays an important role in both the structural and mechanical properties of 3D GFs. When their size is smaller than 10 nm, the graphene sheets can easily stack together under the influence of van der Waals interactions (vdW). These stacks behave like building blocks and are tightly packed together within 3D GFs, leading to high density, small pore radii, and a large Young’s modulus. However, if the sheet sizes exceed 10 nm, they are staggered together with a significant amount of deformation (bending). Therefore, the density of 3D GFs has been dramatically reduced due to the loosely packed graphene sheets, accompanied by large pore radii and a small Young’s modulus. Under uniaxial compression, rubber-like stress-strain curves are observed for all 3D GFs. This material characteristic is dominated by the vdW interactions between different graphene layers and slightly affected by the out-of-plane deformation of the graphene sheets. We find a simple scaling law E˜ {ρ }4.2 between the density ρ and Young’s modulus E for a model of 3D GFs. The simulation results reveal structure-property relations of 3D GFs, which can be applied to guide the design of 3D graphene assemblies with exceptional properties.
Interlayer coupling effects on Schottky barrier in the arsenene-graphene van der Waals heterostructures

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

Xia, Congxin, E-mail: xiacongxin@htu.edu.cn; Xue, Bin; Wang, Tianxing

The electronic characteristics of arsenene-graphene van der Waals (vdW) heterostructures are studied by using first-principles methods. The results show that a linear Dirac-like dispersion relation around the Fermi level can be quite well preserved in the vdW heterostructures. Moreover, the p-type Schottky barrier (0.18 eV) to n-type Schottky barrier (0.31 eV) transition occurs when the interlayer distance increases from 2.8 to 4.5 Å, which indicates that the Schottky barrier can be tuned effectively by the interlayer distance in the vdW heterostructures.
Centimeter Scale Patterned Growth of Vertically Stacked Few Layer Only 2D MoS2/WS2 van der Waals Heterostructure.

PubMed

Choudhary, Nitin; Park, Juhong; Hwang, Jun Yeon; Chung, Hee-Suk; Dumas, Kenneth H; Khondaker, Saiful I; Choi, Wonbong; Jung, Yeonwoong

2016-05-05

Two-dimensional (2D) van der Waal (vdW) heterostructures composed of vertically-stacked multiple transition metal dichalcogenides (TMDs) such as molybdenum disulfide (MoS2) and tungsten disulfide (WS2) are envisioned to present unprecedented materials properties unobtainable from any other material systems. Conventional fabrications of these hybrid materials have relied on the low-yield manual exfoliation and stacking of individual 2D TMD layers, which remain impractical for scaled-up applications. Attempts to chemically synthesize these materials have been recently pursued, which are presently limited to randomly and scarcely grown 2D layers with uncontrolled layer numbers on very small areas. Here, we report the chemical vapor deposition (CVD) growth of large-area (>2 cm(2)) patterned 2D vdW heterostructures composed of few layer, vertically-stacked MoS2 and WS2. Detailed structural characterizations by Raman spectroscopy and high-resolution/scanning transmission electron microscopy (HRTEM/STEM) directly evidence the structural integrity of two distinct 2D TMD layers with atomically sharp vdW heterointerfaces. Electrical transport measurements of these materials reveal diode-like behavior with clear current rectification, further confirming the formation of high-quality heterointerfaces. The intrinsic scalability and controllability of the CVD method presented in this study opens up a wide range of opportunities for emerging applications based on the unconventional functionalities of these uniquely structured materials.

A partition function-based weighting scheme in force field parameter development using ab initio calculation results in global configurational space.

PubMed

Wu, Yao; Dai, Xiaodong; Huang, Niu; Zhao, Lifeng

2013-06-05

In force field parameter development using ab initio potential energy surfaces (PES) as target data, an important but often neglected matter is the lack of a weighting scheme with optimal discrimination power to fit the target data. Here, we developed a novel partition function-based weighting scheme, which not only fits the target potential energies exponentially like the general Boltzmann weighting method, but also reduces the effect of fitting errors leading to overfitting. The van der Waals (vdW) parameters of benzene and propane were reparameterized by using the new weighting scheme to fit the high-level ab initio PESs probed by a water molecule in global configurational space. The molecular simulation results indicate that the newly derived parameters are capable of reproducing experimental properties in a broader range of temperatures, which supports the partition function-based weighting scheme. Our simulation results also suggest that structural properties are more sensitive to vdW parameters than partial atomic charge parameters in these systems although the electrostatic interactions are still important in energetic properties. As no prerequisite conditions are required, the partition function-based weighting method may be applied in developing any types of force field parameters. Copyright © 2013 Wiley Periodicals, Inc.
Intermolecular orbital interaction in π systems

NASA Astrophysics Data System (ADS)

Zhao, Rundong; Zhang, Rui-Qin

2018-04-01

Intermolecular interactions, in regard to which people tend to emphasise the noncovalent van der Waals (vdW) forces when conducting investigations throughout chemistry, can influence the structure, stability and function of molecules and materials. Despite the ubiquitous nature of vdW interactions, a simplified electrostatic model has been popularly adopted to explain common intermolecular interactions, especially those existing in π-involved systems. However, this classical model has come under fire in revealing specific issues such as substituent effects, due to its roughness; and it has been followed in past decades by sundry explanations which sometimes bring in nebulous descriptions. In this account, we try to summarise and present a unified model for describing and analysing the binding mechanism of such systems from the viewpoint of energy decomposition. We also emphasise a commonly ignored factor - orbital interaction, pointing out that the noncovalent intermolecular orbital interactions actually exhibit similar bonding and antibonding phenomena as those in covalent bonds.
Distribution functions for resonantly trapped orbits in the Galactic disc

NASA Astrophysics Data System (ADS)

Monari, Giacomo; Famaey, Benoit; Fouvry, Jean-Baptiste; Binney, James

2017-11-01

The present-day response of a Galactic disc stellar population to a non-axisymmetric perturbation of the potential has previously been computed through perturbation theory within the phase-space coordinates of the unperturbed axisymmetric system. Such an Eulerian linearized treatment, however, leads to singularities at resonances, which prevent quantitative comparisons with data. Here, we manage to capture the behaviour of the distribution function (DF) at a resonance in a Lagrangian approach, by averaging the Hamiltonian over fast angle variables and re-expressing the DF in terms of a new set of canonical actions and angles variables valid in the resonant region. We then follow the prescription of Binney, assigning to the resonant DF the time average along the orbits of the axisymmetric DF expressed in the new set of actions and angles. This boils down to phase-mixing the DF in terms of the new angles, such that the DF for trapped orbits depends only on the new set of actions. This opens the way to quantitatively fitting the effects of the bar and spirals to Gaia data in terms of DFs in action space.
The quadrupole moments of Cd and Zn isotopes - an apology

NASA Astrophysics Data System (ADS)

Haas, H.; Barbosa, M. B.; Correia, J. G.

2016-12-01

In 2010 we presented an update of the nuclear quadrupole moments (Q) for the Cd and Zn isotopes, based essentially on straightforward density functional (DF) calculations (H. Haas and J.G. Correia, Hyperfine Interact 198, 133-137 (2010)). It has been apparent for some years that the standard DF procedure obviously fails, however, to reproduce the known electric-field gradient (EFG) for various systems, typical cases being Cu2O, As and Sb, and the solid halogens. Recently a cure for this deficiency has been found in the hybrid DF technique. This method is now applied to solid Cd and Zn, and the resultant quadrupole moments are about 15 % smaller than in our earlier report. Also nuclear systematics, using the recently revised values of Q for the long-lived 11/2 isomers in111Cd to129Cd, together with earlier PAD data for107,109Cd, leads to the same conclusion. In addition, EFG calculations for the cadmium dimethyl molecule further support the new values: Q(111Cd, 5/2+) = .683(20) b, Q(67Zn, gs) = .132(5) b. This implies, that the value for the atomic EFG in the 3it {P}1 state of Zn must be revised, as it has been for Cd.
A spatiotemporal characterization method for the dynamic cytoskeleton.

PubMed

Alhussein, Ghada; Shanti, Aya; Farhat, Ilyas A H; Timraz, Sara B H; Alwahab, Noaf S A; Pearson, Yanthe E; Martin, Matthew N; Christoforou, Nicolas; Teo, Jeremy C M

2016-05-01

The significant gap between quantitative and qualitative understanding of cytoskeletal function is a pressing problem; microscopy and labeling techniques have improved qualitative investigations of localized cytoskeleton behavior, whereas quantitative analyses of whole cell cytoskeleton networks remain challenging. Here we present a method that accurately quantifies cytoskeleton dynamics. Our approach digitally subdivides cytoskeleton images using interrogation windows, within which box-counting is used to infer a fractal dimension (Df ) to characterize spatial arrangement, and gray value intensity (GVI) to determine actin density. A partitioning algorithm further obtains cytoskeleton characteristics from the perinuclear, cytosolic, and periphery cellular regions. We validated our measurement approach on Cytochalasin-treated cells using transgenically modified dermal fibroblast cells expressing fluorescent actin cytoskeletons. This method differentiates between normal and chemically disrupted actin networks, and quantifies rates of cytoskeletal degradation. Furthermore, GVI distributions were found to be inversely proportional to Df , having several biophysical implications for cytoskeleton formation/degradation. We additionally demonstrated detection sensitivity of differences in Df and GVI for cells seeded on substrates with varying degrees of stiffness, and coated with different attachment proteins. This general approach can be further implemented to gain insights on dynamic growth, disruption, and structure of the cytoskeleton (and other complex biological morphology) due to biological, chemical, or physical stimuli. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.
Reduced-cost linear-response CC2 method based on natural orbitals and natural auxiliary functions

PubMed Central

Mester, Dávid

2017-01-01

A reduced-cost density fitting (DF) linear-response second-order coupled-cluster (CC2) method has been developed for the evaluation of excitation energies. The method is based on the simultaneous truncation of the molecular orbital (MO) basis and the auxiliary basis set used for the DF approximation. For the reduction of the size of the MO basis, state-specific natural orbitals (NOs) are constructed for each excited state using the average of the second-order Møller–Plesset (MP2) and the corresponding configuration interaction singles with perturbative doubles [CIS(D)] density matrices. After removing the NOs of low occupation number, natural auxiliary functions (NAFs) are constructed [M. Kállay, J. Chem. Phys. 141, 244113 (2014)], and the NAF basis is also truncated. Our results show that, for a triple-zeta basis set, about 60% of the virtual MOs can be dropped, while the size of the fitting basis can be reduced by a factor of five. This results in a dramatic reduction of the computational costs of the solution of the CC2 equations, which are in our approach about as expensive as the evaluation of the MP2 and CIS(D) density matrices. All in all, an average speedup of more than an order of magnitude can be achieved at the expense of a mean absolute error of 0.02 eV in the calculated excitation energies compared to the canonical CC2 results. Our benchmark calculations demonstrate that the new approach enables the efficient computation of CC2 excitation energies for excited states of all types of medium-sized molecules composed of up to 100 atoms with triple-zeta quality basis sets. PMID:28527453
Assessing the risk for dengue fever based on socioeconomic and environmental variables in a geographical information system environment.

PubMed

Khormi, Hassan M; Kumar, Lalit

2012-05-01

An important option in preventing the spread of dengue fever (DF) is to control and monitor its vector (Aedes aegypti) as well as to locate and destroy suitable mosquito breeding environments. The aim of the present study was to use a combination of environmental and socioeconomic variables to model areas at risk of DF. These variables include clinically confirmed DF cases, mosquito counts, population density in inhabited areas, total populations per district, water access, neighbourhood quality and the spatio-temporal risk of DF based on the average, weekly frequency of DF incidence. Out of 111 districts investigated, 17 (15%), covering a total area of 121 km2, were identified as of high risk, 25 (22%), covering 133 km2, were identified as of medium risk, 18 (16%), covering 180 km2, were identified as of low risk and 51 (46%), covering 726 km2, were identified as of very low risk. The resultant model shows that most areas at risk of DF were concentrated in the central part of Jeddah county, Saudi Arabia. The methods used can be implemented as routine procedures for control and prevention. A concerted intervention in the medium- and high-risk level districts identified in this study could be highly effective in reducing transmission of DF in the area as a whole.
Evaluation of MELD score and Maddrey discriminant function for mortality prediction in patients with alcoholic hepatitis.

PubMed

Monsanto, Pedro; Almeida, Nuno; Lrias, Clotilde; Pina, Jos Eduardo; Sofia, Carlos

2013-01-01

Maddrey discriminant function (DF) is the traditional model for evaluating the severity and prognosis in alcoholic hepatitis (AH). However, MELD has also been used for this purpose. We aimed to determine the predictive parameters and compare the ability of Maddrey DF and MELD to predict short-term mortality in patients with AH. Retrospective study of 45 patients admitted in our department with AH between 2000 and 2010. Demographic, clinical and laboratory parameters were collected. MELD and Maddrey DF were calculated on admission. Short-term mortality was assessed at 30 and 90 days. Student t-test, χ2 test, univariate analysis, logistic regression and receiver operating characteristic curves were performed. Thirty-day and 90-day mortality was 27% and 42%, respectively. In multivariate analysis, Maddrey DF was the only independent predictor of mortality for these two periods. Receiver operating characteristic curves for Maddrey DF revealed an excellent discriminatory ability to predict 30-day and 90-day mortality for a Maddrey DF greater than 65 and 60, respectively. Discriminatory ability to predict 30-day and 90-day mortality for MELD was low. AH remains associated with a high short-term mortality. Maddrey DF is a more valuable model than MELD to predict short-term mortality in patients with AH.
CH4 dissociation on Ru(0001): A view from both sides of the barrier

NASA Astrophysics Data System (ADS)

Mortensen, H.; Diekhöner, L.; Baurichter, A.; Luntz, A. C.

2002-04-01

This paper reports measurements of both dissociative adsorption on and associative desorption from CH4 on Ru(0001). We consider the former a view of dissociation from the front side of the barrier, while the latter is considered as a view of dissociation from the back side of the barrier. A combination of both previous and new molecular beam measurements of dissociative adsorption shows that S0 depends on all experimental variables (E, Tn, Ts and isotope) in a manner similar to other close-packed transition metals. The interpretation of this behavior in terms of a theoretical description of the dissociation is discussed critically, with special emphasis on insights from new theoretical studies. The energy-resolved desorption flux Df(E,Ts) is obtained in associative desorption experiments using the technique of laser assisted associative desorption (LAAD). Measurements at several Ts allow both a direct determination of the adiabatic barrier V*(0) and considerable insight into the dynamics of dissociation. The V*(0) obtained from Df(E,Ts) is in excellent agreement with density functional theory (DFT) calculations and with the value indirectly inferred from molecular beam experiments. The chief dynamic conclusion from an analysis of Df(E,Ts) is that both bending and stretching coordinates must be produced in associative desorption, although they are not populated statistically. The absence of an isotope effect in the shape of Df(E,Ts) argues against the importance of tunneling in the desorption/adsorption. When reactive fluxes are compared via detailed balance, both the molecular beam experiment and the LAAD experiment are in good agreement.
Adhesion of Particulate Materials to Mesostructured Polypyrrole

NASA Astrophysics Data System (ADS)

Hoss, Darby; Knepper, Robert; Hotchkiss, Peter; Tappan, Alexander; Boudouris, Bryan; Beaudoin, Stephen

Interactions based on van der Waals (vdW) forces will influence the performance and reliability of mesostructured polypyrrole swabs used for the collection and detection of trace particles. The vdW adhesion force between materials is described by the Hamaker constant, and these constants are measured via optical and dielectric properties (i.e., according to Lifshitz theory), inverse gas chromatography (IGC), and contact angle measurements. Here, contact angle measurements were performed on films of several common materials and used to estimate Hamaker constants. This, in turn, will allow for the tuning of the design properties associated with the polypyrrole swabs. A comparison of these results to Hamaker constants estimated using Lifshitz Theory and IGC reveals the fundamental behavior of the materials. The Hamaker constants were then used in a new computational vdW adhesion model. The idealized model describes particle adhesion to an array of mesostrucures. This model elucidates the importance of where the particle makes contact with the mesostructure and the independence of vdW forces generated by each mesostructure. These results will facilitate the rational design of polypyrrole swabs optimized for harvesting microscale particles of trace materials.
A climate-based spatiotemporal prediction for dengue fever epidemics: a case study in southern Taiwan

NASA Astrophysics Data System (ADS)

Yu, H.-L.; Yang, S.-J.; Lin, Y.-C.

2012-04-01

Dengue Fever (DF) has been identified by the World Health organization (WHO) as one of the most serious vector-borne infectious diseases in tropical and sub-tropical areas. DF has been one of the most important epidemics in Taiwan which occur annually especially in southern Taiwan during summer and autumn. Most DF studies have focused mainly on temporal DF patterns and its close association with climatic covariates, whereas few studies have investigated the spatial DF patterns (spatial dependence and clustering) and composite space-time effects of the DF epidemics. The present study proposes a spatio-temporal DF prediction approach based on stochastic Bayesian Maximum Entropy (BME) analysis. Core and site-specific knowledge bases are considered, including climate and health datasets under conditions of uncertainty, space-time dependence functions, and a Poisson regression model of climatic variables contributing to DF occurrences in southern Taiwan during 2007, when the highest number of DF cases was recorded in the history of Taiwan epidemics (over 2000). The obtained results show that the DF outbreaks in the study area are highly influenced by climatic conditions. Furthermore, the analysis can provide the required "one-week-ahead" outbreak warnings based on spatio-temporal predictions of DF distributions. Therefore, the proposed analysis can provide the Taiwan Disease Control Agency with a valuable tool to timely identify, control, and even efficiently prevent DF spreading across space-time.
Variation of DNA Fragmentation Levels During Density Gradient Sperm Selection for Assisted Reproduction Techniques

PubMed Central

Muratori, Monica; Tarozzi, Nicoletta; Cambi, Marta; Boni, Luca; Iorio, Anna Lisa; Passaro, Claudia; Luppino, Benedetta; Nadalini, Marco; Marchiani, Sara; Tamburrino, Lara; Forti, Gianni; Maggi, Mario; Baldi, Elisabetta; Borini, Andrea

2016-01-01

Abstract Predicting the outcome of in vitro fertilization (IVF)/intracytoplasmic sperm injection (ICSI) is one main goal of the present research on assisted reproduction. To understand whether density gradient centrifugation (DGC), used to select sperm, can affect sperm DNA integrity and impact pregnancy rate (PR), we prospectively evaluated sperm DNA fragmentation (sDF) by TUNEL/PI, before and after DGC. sDF was studied in a cohort of 90 infertile couples the same day of IVF/ICSI treatment. After DGC, sDF increased in 41 samples (Group A, median sDF value: 29.25% [interquartile range, IQR: 16.01–41.63] in pre- and 60.40% [IQR: 32.92–93.53] in post-DGC) and decreased in 49 (Group B, median sDF value: 18.84% [IQR: 13.70–35.47] in pre- and 8.98% [IQR: 6.24–15.58] in post-DGC). PR was 17.1% and 34.4% in Group A and B, respectively (odds ratio [OR]: 2.58, 95% confidence interval [CI]: 0.95–7.04, P = 0.056). After adjustment for female factor, female and male age and female BMI, the estimated OR increased to 3.12 (95% CI: 1.05–9.27, P = 0.041). According to the subgroup analysis for presence/absence of female factor, heterogeneity in the association between the Group A and B and PR emerged (OR: 4.22, 95% CI: 1.16–15.30 and OR: 1.53, 95% CI: 0.23–10.40, respectively, for couples without, n = 59, and with, n = 31, female factor). This study provides the first evidence that the DGC procedure produces an increase in sDF in about half of the subjects undergoing IVF/ICSI, who then show a much lower probability of pregnancy, raising concerns about the safety of this selection procedure. Evaluation of sDF before and after DGC configures as a possible new prognostic parameter of pregnancy outcome in IVF/ICSI. Alternative sperm selection strategies are recommended for those subjects who undergo the damage after DGC. PMID:27196465
Variation of DNA Fragmentation Levels During Density Gradient Sperm Selection for Assisted Reproduction Techniques: A Possible New Male Predictive Parameter of Pregnancy?

PubMed

Muratori, Monica; Tarozzi, Nicoletta; Cambi, Marta; Boni, Luca; Iorio, Anna Lisa; Passaro, Claudia; Luppino, Benedetta; Nadalini, Marco; Marchiani, Sara; Tamburrino, Lara; Forti, Gianni; Maggi, Mario; Baldi, Elisabetta; Borini, Andrea

2016-05-01

Predicting the outcome of in vitro fertilization (IVF)/intracytoplasmic sperm injection (ICSI) is one main goal of the present research on assisted reproduction. To understand whether density gradient centrifugation (DGC), used to select sperm, can affect sperm DNA integrity and impact pregnancy rate (PR), we prospectively evaluated sperm DNA fragmentation (sDF) by TUNEL/PI, before and after DGC. sDF was studied in a cohort of 90 infertile couples the same day of IVF/ICSI treatment. After DGC, sDF increased in 41 samples (Group A, median sDF value: 29.25% [interquartile range, IQR: 16.01-41.63] in pre- and 60.40% [IQR: 32.92-93.53] in post-DGC) and decreased in 49 (Group B, median sDF value: 18.84% [IQR: 13.70-35.47] in pre- and 8.98% [IQR: 6.24-15.58] in post-DGC). PR was 17.1% and 34.4% in Group A and B, respectively (odds ratio [OR]: 2.58, 95% confidence interval [CI]: 0.95-7.04, P = 0.056). After adjustment for female factor, female and male age and female BMI, the estimated OR increased to 3.12 (95% CI: 1.05-9.27, P = 0.041). According to the subgroup analysis for presence/absence of female factor, heterogeneity in the association between the Group A and B and PR emerged (OR: 4.22, 95% CI: 1.16-15.30 and OR: 1.53, 95% CI: 0.23-10.40, respectively, for couples without, n = 59, and with, n = 31, female factor).This study provides the first evidence that the DGC procedure produces an increase in sDF in about half of the subjects undergoing IVF/ICSI, who then show a much lower probability of pregnancy, raising concerns about the safety of this selection procedure. Evaluation of sDF before and after DGC configures as a possible new prognostic parameter of pregnancy outcome in IVF/ICSI. Alternative sperm selection strategies are recommended for those subjects who undergo the damage after DGC.
Object recognition and localization from 3D point clouds by maximum-likelihood estimation

NASA Astrophysics Data System (ADS)

Dantanarayana, Harshana G.; Huntley, Jonathan M.

2017-08-01

We present an algorithm based on maximum-likelihood analysis for the automated recognition of objects, and estimation of their pose, from 3D point clouds. Surfaces segmented from depth images are used as the features, unlike `interest point'-based algorithms which normally discard such data. Compared to the 6D Hough transform, it has negligible memory requirements, and is computationally efficient compared to iterative closest point algorithms. The same method is applicable to both the initial recognition/pose estimation problem as well as subsequent pose refinement through appropriate choice of the dispersion of the probability density functions. This single unified approach therefore avoids the usual requirement for different algorithms for these two tasks. In addition to the theoretical description, a simple 2 degrees of freedom (d.f.) example is given, followed by a full 6 d.f. analysis of 3D point cloud data from a cluttered scene acquired by a projected fringe-based scanner, which demonstrated an RMS alignment error as low as 0.3 mm.
Nonpolar Solvation Free Energy from Proximal Distribution Functions

PubMed Central

Ou, Shu-Ching; Drake, Justin A.; Pettitt, B. Montgomery

2017-01-01

Using precomputed near neighbor or proximal distribution functions (pDFs) that approximate solvent density about atoms in a chemically bonded context one can estimate the solvation structures around complex solutes and the corresponding solute–solvent energetics. In this contribution, we extend this technique to calculate the solvation free energies (ΔG) of a variety of solutes. In particular we use pDFs computed for small peptide molecules to estimate ΔG for larger peptide systems. We separately compute the non polar (ΔGvdW) and electrostatic (ΔGelec) components of the underlying potential model. Here we show how the former can be estimated by thermodynamic integration using pDF-reconstructed solute–solvent interaction energy. The electrostatic component can be approximated with Linear Response theory as half of the electrostatic solute–solvent interaction energy. We test the method by calculating the solvation free energies of butane, propanol, polyalanine, and polyglycine and by comparing with traditional free energy simulations. Results indicate that the pDF-reconstruction algorithm approximately reproduces ΔGvdW calculated by benchmark free energy simulations to within ~ kcal/mol accuracy. The use of transferable pDFs for each solute atom allows for a rapid estimation of ΔG for arbitrary molecular systems. PMID:27992228
The effects of wetland habitat structure on Florida apple snail density

USGS Publications Warehouse

Karunaratne, L.B.; Darby, P.C.; Bennetts, R.E.

2006-01-01

Wetlands often support a variety of juxtaposed habitat patches (e.g., grass-, shrub- or tree-dominated) differentially suited to support the inhabiting fauna. The proportion of available habitat types has been affected by human activity and consequently has contributed to degrading habitat quality for some species. The Florida apple snail (Pomacea paludosa) has drawn attention as a critical prey item for wetlands wildlife and as an indicator of wetlands restoration success in peninsular Florida, USA. An apparent contradiction has evolved wherein this species appears intolerant of drying events, but these disturbances may be necessary to maintain suitable habitat structure for apple snails. We recently reported that assertions regarding intolerance to dry downs in this species were inaccurate. Here, we compared snail density in habitats with (wet prairie) and without (slough) emergent macrophytes, as well as evaluating the effects of structural attributes within the broad wet prairie habitat type. Snail densities were greater in prairies relative to sloughs (??2= 12.90, df=1, P=0.0003), often by a factor of two to three. Within wet prairie habitats, we found greater snail densities in Panicum hemitomon as compared to Eleocharis cellulosa (??2=31.45, df=1, P=0.0001). Significantly fewer snails were found in dense E. cellulosa as compared to habitats with lower stem density (??2= 10.73, df=1, P=0.011). Our results indicate that wet prairie habitat supports greater snail densities than nymphaea-dominatd slough. Our results have implications for wetlands water management in that continuous inundation has been shown to convert wet prairie to slough habitat, and we suggest this should be avoided in support of apple snails and their predators. ?? 2006, The Society of Wetland Scientists.
Error estimates for (semi-)empirical dispersion terms and large biomacromolecules.

PubMed

Korth, Martin

2013-10-14

The first-principles modeling of biomaterials has made tremendous advances over the last few years with the ongoing growth of computing power and impressive developments in the application of density functional theory (DFT) codes to large systems. One important step forward was the development of dispersion corrections for DFT methods, which account for the otherwise neglected dispersive van der Waals (vdW) interactions. Approaches at different levels of theory exist, with the most often used (semi-)empirical ones based on pair-wise interatomic C6R(-6) terms. Similar terms are now also used in connection with semiempirical QM (SQM) methods and density functional tight binding methods (SCC-DFTB). Their basic structure equals the attractive term in Lennard-Jones potentials, common to most force field approaches, but they usually use some type of cutoff function to make the mixing of the (long-range) dispersion term with the already existing (short-range) dispersion and exchange-repulsion effects from the electronic structure theory methods possible. All these dispersion approximations were found to perform accurately for smaller systems, but error estimates for larger systems are very rare and completely missing for really large biomolecules. We derive such estimates for the dispersion terms of DFT, SQM and MM methods using error statistics for smaller systems and dispersion contribution estimates for the PDBbind database of protein-ligand interactions. We find that dispersion terms will usually not be a limiting factor for reaching chemical accuracy, though some force fields and large ligand sizes are problematic.
Increased mitochondrial-encoded gene transcription in immortal DF-1 cells.

PubMed

Kim, H; You, S; Kim, I J; Farris, J; Foster, L K; Foster, D N

2001-05-01

We have established, in continuous cell culture, a spontaneously immortalized chicken embryo fibroblast (CEF) cell line (DF-1) as well as several other immortal CEF cell lines. The immortal DF-1 cells divided more rapidly than primary and other immortal CEF cells. To identify the genes involved in rapidly dividing DF-1 cells, we have used differential display RT-PCR. Of the numerous genes analyzed, three mitochondrial-encoded genes (ATPase 8/6, 16S rRNA, and cytochrome b) were shown to express at higher levels in DF-1 cells compared to primary and other immortal CEF cells. The inhibition of mitochondrial translation by treatment with chloramphenicol markedly decreased ATP production and cell proliferation in DF-1 cells, while not affecting growth in either primary or other immortal CEF cells. This result suggests a correlation between rapid cell proliferation and the increased mitochondrial respiratory functions. We also determined that the increased transcription of mitochondrial-encoded genes in DF-1 cells is due to increased de novo transcript synthesis as shown by mitochondrial run-on assays, and not the result of either increased mitochondrial biogenesis or mitochondrial transcript half-lives. Together, the present studies suggest that the transcriptional activation of mitochondrial-encoded genes and the elevated respiratory function should be one of the characteristics of rapidly dividing immortal cells. Copyright 2001 Academic Press.
A novel method for rapid and non-invasive detection of plants senescence using delayed fluorescence technique

NASA Astrophysics Data System (ADS)

Zhang, Lingrui; Xing, Da; Wang, Junsheng; Zeng, Lizhang; Li, Qiang

2007-05-01

Plants senescence is a phase of plants ontogeny marked by declining photosynthetic activity that is paralleled by a decline in chloroplast function. The photosystem II ( PSII ) in a plant is considered the primary site where light-induced delayed fluorescence (DF) is produced. With the leaves of Catharanthus roseus (Catharanthus roseus (L.) G.Don) as testing models, we have studied the effects of plants senescence induced by dark and/or exogenous hormones treatments on characteristics of DF by using a home-made portable DF detection system, which can enable various DF parameters, such as DF decay kinetic curve and DF intensity, to be rapidly produced for the plants in a short time. The results show that the changes in DF intensity of green plants can truly reflect the changes in photosynthetic capacity and chlorophyll content. Therefore, DF may be used an important means of evaluating in vivo plants senescence physiology. The changes in DF intensity may provide a new approach for the rapid and early detection of plants senescence caused by age or other senescence-related factors. DF technique could be potential useful for high throughput screening and less time-consuming and automated identifying the interesting mutants with genetic modifications that change plants senescence progress.
The Twinkling Fractal Theory of the Glass Transition: Applications to Soft Matter

NASA Astrophysics Data System (ADS)

Wool, Richard

2012-02-01

The Twinkling Fractal Theory (TFT) of the glass transition has recently been demonstrated experimentally [J.F. Stanzione et al., J. Non Cryst. Sol., (2011, 357,311]. The hard to-soft matter transition is characterized by the presence of solid fractal clusters with liquid-like pools that are dynamically interchanging via their anharmonic intermolecular potentials with Boltzmann energy populations with a characteristic temperature dependent vibrational density of states g(φ) ˜ φ^df . The twinkling fractal frequencies φ cover a range of 10^12 Hz to 10-10Hz and the fractal solid clusters of size R have a lifetime τ ˜ R^Df/df, where the fractal dimension Df 2.4 and the fracton dimension df = 4/3. Here we explore its application to a number of soft matter issues. These include (a) Confinement effects on Tg reduction in thin films of thickness h, where by virtue of large cluster exclusion, δTg ˜ 1/h^Df/df; (b) Tg gradients near bulk surfaces, where the smaller clusters on the surface have a faster relaxation time; (c) Effect of twinkling surfaces on cell growth, where at T Tg + 20 C, there exists a twinkling fractal range that leads to bell-shaped enhancement of cell growth and chemical up-regulation via the twinkling surfaces ``communicating `` with the cells through their vibrations; and (d) adhesion above and below Tg where topological fluctuations associated with g(φ) promotes the development of nano-nails at the interface.

Improved modification for the density-functional theory calculation of thermodynamic properties for C-H-O composite compounds.

PubMed

Liu, Min Hsien; Chen, Cheng; Hong, Yaw Shun

2005-02-08

A three-parametric modification equation and the least-squares approach are adopted to calibrating hybrid density-functional theory energies of C(1)-C(10) straight-chain aldehydes, alcohols, and alkoxides to accurate enthalpies of formation DeltaH(f) and Gibbs free energies of formation DeltaG(f), respectively. All calculated energies of the C-H-O composite compounds were obtained based on B3LYP6-311++G(3df,2pd) single-point energies and the related thermal corrections of B3LYP6-31G(d,p) optimized geometries. This investigation revealed that all compounds had 0.05% average absolute relative error (ARE) for the atomization energies, with mean value of absolute error (MAE) of just 2.1 kJ/mol (0.5 kcal/mol) for the DeltaH(f) and 2.4 kJ/mol (0.6 kcal/mol) for the DeltaG(f) of formation.
Nascent chain-monitored remodeling of the Sec machinery for salinity adaptation of marine bacteria

PubMed Central

Ishii, Eiji; Chiba, Shinobu; Hashimoto, Narimasa; Kojima, Seiji; Homma, Michio; Ito, Koreaki; Akiyama, Yoshinori; Mori, Hiroyuki

2015-01-01

SecDF interacts with the SecYEG translocon in bacteria and enhances protein export in a proton-motive-force-dependent manner. Vibrio alginolyticus, a marine-estuarine bacterium, contains two SecDF paralogs, V.SecDF1 and V.SecDF2. Here, we show that the export-enhancing function of V.SecDF1 requires Na+ instead of H+, whereas V.SecDF2 is Na+-independent, presumably requiring H+. In accord with the cation-preference difference, V.SecDF2 was only expressed under limited Na+ concentrations whereas V.SecDF1 was constitutive. However, it is not the decreased concentration of Na+ per se that the bacterium senses to up-regulate the V.SecDF2 expression, because marked up-regulation of the V.SecDF2 synthesis was observed irrespective of Na+ concentrations under certain genetic/physiological conditions: (i) when the secDF1VA gene was deleted and (ii) whenever the Sec export machinery was inhibited. VemP (Vibrio export monitoring polypeptide), a secretory polypeptide encoded by the upstream ORF of secDF2VA, plays the primary role in this regulation by undergoing regulated translational elongation arrest, which leads to unfolding of the Shine–Dalgarno sequence for translation of secDF2VA. Genetic analysis of V. alginolyticus established that the VemP-mediated regulation of SecDF2 is essential for the survival of this marine bacterium in low-salinity environments. These results reveal that a class of marine bacteria exploits nascent-chain ribosome interactions to optimize their protein export pathways to propagate efficiently under different ionic environments that they face in their life cycles. PMID:26392525
A Study of Vertical Transport through Graphene toward Control of Quantum Tunneling.

PubMed

Zhu, Xiaodan; Lei, Sidong; Tsai, Shin-Hung; Zhang, Xiang; Liu, Jun; Yin, Gen; Tang, Min; Torres, Carlos M; Navabi, Aryan; Jin, Zehua; Tsai, Shiao-Po; Qasem, Hussam; Wang, Yong; Vajtai, Robert; Lake, Roger K; Ajayan, Pulickel M; Wang, Kang L

2018-02-14

Vertical integration of van der Waals (vdW) materials with atomic precision is an intriguing possibility brought forward by these two-dimensional (2D) materials. Essential to the design and analysis of these structures is a fundamental understanding of the vertical transport of charge carriers into and across vdW materials, yet little has been done in this area. In this report, we explore the important roles of single layer graphene in the vertical tunneling process as a tunneling barrier. Although a semimetal in the lateral lattice plane, graphene together with the vdW gap act as a tunneling barrier that is nearly transparent to the vertically tunneling electrons due to its atomic thickness and the transverse momenta mismatch between the injected electrons and the graphene band structure. This is accentuated using electron tunneling spectroscopy (ETS) showing a lack of features corresponding to the Dirac cone band structure. Meanwhile, the graphene acts as a lateral conductor through which the potential and charge distribution across the tunneling barrier can be tuned. These unique properties make graphene an excellent 2D atomic grid, transparent to charge carriers, and yet can control the carrier flux via the electrical potential. A new model on the quantum capacitance's effect on vertical tunneling is developed to further elucidate the role of graphene in modulating the tunneling process. This work may serve as a general guideline for the design and analysis of vdW vertical tunneling devices and heterostructures, as well as the study of electron/spin injection through and into vdW materials.
Mechanistic Origin of the Ultrastrong Adhesion between Graphene and a-SiO2: Beyond van der Waals.

PubMed

Kumar, Sandeep; Parks, David; Kamrin, Ken

2016-07-26

The origin of the ultrastrong adhesion between graphene and a-SiO2 has remained a mystery. This adhesion is believed to be predominantly van der Waals (vdW) in nature. By rigorously analyzing recently reported blistering and nanoindentation experiments, we show that the ultrastrong adhesion between graphene and a-SiO2 cannot be attributed to vdW forces alone. Our analyses show that the fracture toughness of the graphene/a-SiO2 interface, when the interfacial adhesion is modeled with vdW forces alone, is anomalously weak compared to the measured values. The anomaly is related to an ultrasmall fracture process zone (FPZ): owing to the lack of a third dimension in graphene, the FPZ for the graphene/a-SiO2 interface is extremely small, and the combination of predominantly tensile vdW forces, distributed over such a small area, is bound to result in a correspondingly small interfacial fracture toughness. Through multiscale modeling, combining the results of finite element analysis and molecular dynamics simulations, we show that the adhesion between graphene and a-SiO2 involves two different kinds of interactions: one, a weak, long-range interaction arising from vdW adhesion and, second, discrete, short-range interactions originating from graphene clinging to the undercoordinated Si (≡Si·) and the nonbridging O (≡Si-O·) defects on a-SiO2. A strong resistance to relative opening and sliding provided by the latter mechanism is identified as the operative mechanism responsible for the ultrastrong adhesion between graphene and a-SiO2.
Binding and Diffusion of Lithium in Graphite: Quantum Monte Carlo Benchmarks and Validation of van der Waals Density Functional Methods

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

Ganesh, P.; Kim, Jeongnim; Park, Changwon

2014-11-03

In highly accurate diffusion quantum Monte Carlo (QMC) studies of the adsorption and diffusion of atomic lithium in AA-stacked graphite are compared with van der Waals-including density functional theory (DFT) calculations. Predicted QMC lattice constants for pure AA graphite agree with experiment. Pure AA-stacked graphite is shown to challenge many van der Waals methods even when they are accurate for conventional AB graphite. Moreover, the highest overall DFT accuracy, considering pure AA-stacked graphite as well as lithium binding and diffusion, is obtained by the self-consistent van der Waals functional vdW-DF2, although errors in binding energies remain. Empirical approaches based onmore » point charges such as DFT-D are inaccurate unless the local charge transfer is assessed. Our results demonstrate that the lithium carbon system requires a simultaneous highly accurate description of both charge transfer and van der Waals interactions, favoring self-consistent approaches.« less
Dietary Fibers and Cardiometabolic Diseases

PubMed Central

Riccioni, Graziano; Sblendorio, Valeriana; Gemello, Eugenio; Di Bello, Barbara; Scotti, Luca; Cusenza, Salvatore; D’Orazio, Nicolantonio

2012-01-01

The high prevalence of cardiovascular disease (CVD) is largely attributable to the contemporary lifestyle that is often sedentary and includes a diet high in saturated fats and sugars and low ingestion of polyunsaturated fatty acids (PUFAs), fruit, vegetables, and fiber. Experimental data from both animals and humans suggest an association between increased dietary fiber (DF) intakes and improved plasma lipid profiles, including reduced low density lipoprotein cholesterol (LDL-C) concentrations. These observations underline that the intake of DF may protect against heart disease and stroke. PMID:22408406
The OH-initiated atmospheric chemical reactions of polyfluorinated dibenzofurans and polychlorinated dibenzofurans: A comparative theoretical study.

PubMed

Zeng, Xiaolan; Chen, Jing; Qu, Ruijuan; Pan, Xiaoxue; Wang, Zunyao

2017-02-01

The atmospheric chemical reactions of some polyfluorinated dibenzofurans (PFDFs) and polychlorinated dibenzofurans (PCDFs), initiated by OH radical, were investigated by performing theoretical calculations using density functional theory (DFT) and B3LYP/6-311++G(2df,p) method. The obtained results indicate that OH addition reactions of PFDFs and PCDFs occurring at C 1∼4 and C A sites are thermodynamic spontaneous changes and the branching ratio of the PF(C)DF-OH adducts is decided primarily by kinetic factor. The OH addition reactions of PFDFs taking place at fluorinated C 1∼4 positions are kinetically comparable with those occurring at nonfluorinated C 1∼4 positions, while OH addition reactions of PCDFs occurring at chlorinated C 1∼4 sites are negligible. The total rate constants of the addition reactions of PFDFs or PCDFs become smaller with consecutive fluorination or chlorination, and substituting at C 1 position has more adverse effects than substitution at other sites. The succedent O 2 addition reactions of PF(C)DF-OH adducts are thermodynamic nonspontaneous processes under the atmospheric conditions, and have high Gibbs free energies of activation (Δ r G ≠ ). The substituted dibenzofuranols are the primary oxidation products for PCDFs under the atmospheric conditions. However, other oxidative products may also be available for PFDFs besides substituted dibenzofuranols. Copyright © 2016 Elsevier Ltd. All rights reserved.
Modeling the interaction of seven bisphosphonates with the hydroxyapatite(100) face.

PubMed

Chen, Chunyu; Xia, Mingzhu; Wu, Lei; Zhou, Chao; Wang, Fengyun

2012-09-01

The interaction of seven pamidronate bisphosphonate (Pami-BPs) and its analogs with the hydroxyapatite (HAP) (100) surface was studied using density functional theory (DFT) and molecular dynamic (MD) methods. Partial Mulliken oxygen atomic charges in protonated structures were calculated at the level of B3LYP/6-31G*. The MD simulation was performed using the Discover module of Material Studio by compass force field. The results indicate the abilities of donating electrons of the oxygen atoms of the phosphate groups that are closely associated with the antiresorptive potency. The binding energies, including vdw and electrostatic, are used to discuss the mechanism of antiresorption. The results of calculations show that the strength of interaction of the HAP (100) face with the bisphosphonates is N(4) > N(6) > N(7) > N(5) > N(3) > N(2) > N(1) according to their experimental pIC(50) values.
Modification of deoiled cumin dietary fiber with laccase and cellulase under high hydrostatic pressure.

PubMed

Ma, Mengmei; Mu, Taihua

2016-01-20

In this study, we evaluated the effects of high hydrostatic pressure (HHP) and enzyme (laccase and cellulase) treatment on the structural, physicochemical, and functional properties and antioxidant activity of deoiled cumin dietary fiber (DF). HHP-enzyme treatment increased the contents of soluble dietary fiber (SDF) (30.37 g/100g), monosaccharides (except for glucose), uronic acids, and total polyphenol. HHP-enzyme treatment altered the honey-comb structure of DF and generated new polysaccharides. DF modified by HHP-enzyme treatment exhibited improved water retention capacity (10.02 g/g), water swelling capacity (11.19 mL/g), fat and glucose absorption capacities (10.44 g/g, 22.18-63.54 mmol/g), α-amylase activity inhibition ration (37.95%), and bile acid retardation index (48.85-52.58%). The antioxidant activity of DF was mainly correlated to total polyphenol content (R=0.8742). Therefore, DF modified by HHP-enzyme treatment from deoiled cumin could be used as a fiber-rich ingredient in functional foods. Copyright © 2015. Published by Elsevier Ltd.
Damping Factor as a Diagnostic Parameter for Assessment of Osseointegration during the Dental Implant Healing Process: An Experimental Study in Rabbits.

PubMed

Feng, Sheng-Wei; Ho, Kuo-Ning; Chan, Ya-Hui; Chang, Kai-Jung; Lai, Wei-Yi; Huang, Haw-Ming

2016-12-01

The purpose of this study was to evaluate the possibility of using damping factor (DF) analysis to provide additional information on osseointegration of dental implants during the healing period. A total of 30 dental implants were installed in the bilateral femoral condyles of 15 rabbits. A DF analyzer detected with an impulse-forced vibration method and a commercialized dental implant stability analyzer based on resonance frequency (RF) analysis were used to measure the implant stability immediately after implant placement and 1, 2, 4, and 8 weeks post-surgically. Results of DF and RF analyses at different time points were compared with the corresponding osseointegration performance of dental implants via micro-computed tomography (micro-CT), histological and histomorphometrical analysis. The DF values revealed a decrease with time and reached 0.062 ± 0.007 at 8 weeks after implantation, which is almost 50% lower than the initial value. Moreover, highly significant correlations between DF values and bone volume densities (R 2 = 0.9797) and percentages of bone-to-implant contact measured at trabecular bone area (R 2 = 0.9773) were also observed. These results suggested that DF analysis combined with RF analysis results in a more sensitive assessment of changes in the dental implant/bone complex during the healing period than RF analysis alone.
Madm (Mlf1 adapter molecule) cooperates with Bunched A to promote growth in Drosophila.

PubMed

Gluderer, Silvia; Brunner, Erich; Germann, Markus; Jovaisaite, Virginija; Li, Changqing; Rentsch, Cyrill A; Hafen, Ernst; Stocker, Hugo

2010-01-01

The TSC-22 domain family (TSC22DF) consists of putative transcription factors harboring a DNA-binding TSC-box and an adjacent leucine zipper at their carboxyl termini. Both short and long TSC22DF isoforms are conserved from flies to humans. Whereas the short isoforms include the tumor suppressor TSC-22 (Transforming growth factor-beta1 stimulated clone-22), the long isoforms are largely uncharacterized. In Drosophila, the long isoform Bunched A (BunA) acts as a growth promoter, but how BunA controls growth has remained obscure. In order to test for functional conservation among TSC22DF members, we expressed the human TSC22DF proteins in the fly and found that all long isoforms can replace BunA function. Furthermore, we combined a proteomics-based approach with a genetic screen to identify proteins that interact with BunA. Madm (Mlf1 adapter molecule) physically associates with BunA via a conserved motif that is only contained in long TSC22DF proteins. Moreover, Drosophila Madm acts as a growth-promoting gene that displays growth phenotypes strikingly similar to bunA phenotypes. When overexpressed, Madm and BunA synergize to increase organ growth. The growth-promoting potential of long TSC22DF proteins is evolutionarily conserved. Furthermore, we provide biochemical and genetic evidence for a growth-regulating complex involving the long TSC22DF protein BunA and the adapter molecule Madm.
Sub-Doppler Electronic Spectrum of the BENZENE-D2 Complex

NASA Astrophysics Data System (ADS)

Hayashi, Masato; Ohshima, Yasuhiro

2014-06-01

Excitation spectrum of the benzene-D2 van der Waals (vdW) complex in the vicinity of the S1 ← S0 601 vibronic transition of the monomer was recorded by utilizing mass-selective two-color resonance-enhanced two-photon ionization. Extensive adiabatic cooling with the rotational temperature of ěrb|<| 0.5 K was conducted by the high-pressure pulsed expansion, and sub-Doppler resolution yielding the line width of 250 MHz was realized in a collimated molecular beam by employing Fourier-transform-limited ultraviolet pulses for the excitation. In contrast to our previous study on the benzene-H2 complex, weaker binding ortho nuclear-spin isomer, correlating to the j = 0 state of a freely rotating D2, was observed in addition to the stronger binding para isomer (with j = 1), by using a gas sample of normal D2. Three and two vibronic bands involving vdW-mode excitation were observed for the para and ortho isomers, respectively. By comparing the present results with those of the benzene-H2 complex, we made unambiguous assignments on the vdW modes involved in each observed band, and obtained complete sets of vibrational frequencies of all the three vdW modes for the both H2 and D2 isotopomers in the S1 61 manifold. One of the vdW frequency correlates to the splitting between the m = 0 and ± 1 sublevels in the j = 1 state of a freely rotating H2/D2 molecule, and the potential barrier for the hindered internal rotation has been evaluated to be ca. 60 cm-1 from the values. Ratio of the vdW frequencies between the H2 and D2 species deviate significantly from the value for the harmonic vibration (i.e., √{2} ≈ 1.4), indicating substantial anharmonic character of the vdW modes in the complex. M. Hayashi and Y. Ohshima, Chem. Phys. 419, 131-137 (2013). M. Hayashi and Y. Ohshima, J. Phys. Chem. A 117, 9819-9830 (2013).
DfM requirements and ROI analysis for system-on-chip

NASA Astrophysics Data System (ADS)

Balasinski, Artur

2005-11-01

DfM (Design-for-Manufacturability) has become staple requirement beyond 100 nm technology node for efficient generation of mask data, cost reduction, and optimal circuit performance. Layout pattern has to comply to many requirements pertaining to database structure and complexity, suitability for image enhancement by the optical proximity correction, and mask data pattern density and distribution over the image field. These requirements are of particular complexity for Systems-on-Chip (SoC). A number of macro-, meso-, and microscopic effects such as reticle macroloading, planarization dishing, and pattern bridging or breaking would compromise fab yield, device performance, or both. In order to determine the optimal set of DfM rules applicable to the particular designs, Return-on-Investment and Failure Mode and Effect Analysis (FMEA) are proposed.
Psychometric properties of the PROMIS Physical Function item bank in patients receiving physical therapy.

PubMed

Crins, Martine H P; van der Wees, Philip J; Klausch, Thomas; van Dulmen, Simone A; Roorda, Leo D; Terwee, Caroline B

2018-01-01

The Patient-Reported Outcomes Measurement Information System (PROMIS) is a universally applicable set of instruments, including item banks, short forms and computer adaptive tests (CATs), measuring patient-reported health across different patient populations. PROMIS CATs are highly efficient and the use in practice is considered feasible with little administration time, offering standardized and routine patient monitoring. Before an item bank can be used as CAT, the psychometric properties of the item bank have to be examined. Therefore, the objective was to assess the psychometric properties of the Dutch-Flemish PROMIS Physical Function item bank (DF-PROMIS-PF) in Dutch patients receiving physical therapy. Cross-sectional study. 805 patients >18 years, who received any kind of physical therapy in primary care in the past year, completed the full DF-PROMIS-PF (121 items). Unidimensionality was examined by Confirmatory Factor Analysis and local dependence and monotonicity were evaluated. A Graded Response Model was fitted. Construct validity was examined with correlations between DF-PROMIS-PF T-scores and scores on two legacy instruments (SF-36 Health Survey Physical Functioning scale [SF36-PF10] and the Health Assessment Questionnaire Disability-Index [HAQ-DI]). Reliability (standard errors of theta) was assessed. The results for unidimensionality were mixed (scaled CFI = 0.924, TLI = 0.923, RMSEA = 0.045, 1th factor explained 61.5% of variance). Some local dependence was found (8.2% of item pairs). The item bank showed a broad coverage of the physical function construct (threshold-parameters range: -4.28-2.33) and good construct validity (correlation with SF36-PF10 = 0.84 and HAQ-DI = -0.85). Furthermore, the DF-PROMIS-PF showed greater reliability over a broader score-range than the SF36-PF10 and HAQ-DI. The psychometric properties of the DF-PROMIS-PF item bank are sufficient. The DF-PROMIS-PF can now be used as short forms or CAT to measure the level of physical function of physiotherapy patients.
A direct examination of the dynamics of dipolarization fronts using MMS

NASA Astrophysics Data System (ADS)

Yao, Z. H.; Rae, I. J.; Guo, R. L.; Fazakerley, A. N.; Owen, C. J.; Nakamura, R.; Baumjohann, W.; Watt, C. E. J.; Hwang, K. J.; Giles, B. L.; Russell, C. T.; Torbert, R. B.; Varsani, A.; Fu, H. S.; Shi, Q. Q.; Zhang, X.-J.

2017-04-01

Energy conversion on the dipolarization fronts (DFs) has attracted much research attention through the suggestion that intense current densities associated with DFs can modify the more global magnetotail current system. The current structures associated with a DF are at the scale of one to a few ion gyroradii, and their duration is comparable to a spacecraft's spin period. Hence, it is crucial to understand the physical mechanisms of DFs with measurements at a timescale shorter than a spin period. We present a case study whereby we use measurements from the Magnetospheric Multiscale (MMS) Mission, which provides full 3-D particle distributions with a cadence much shorter than a spin period. We provide a cross validation amongst the current density calculations and examine the assumptions that have been adopted in previous literature using the advantages of MMS mission (i.e., small-scale tetrahedron and high temporal resolution). We also provide a cross validation on the terms in the generalized Ohm's law using these advantageous measurements. Our results clearly show that the majority of the currents on the DF are contributed by both ion and electron diamagnetic drifts. Our analysis also implies that the ion frozen-in condition does not hold on the DF, while electron frozen-in condition likely holds. The new experimental capabilities allow us to accurately calculate Joule heating within the DF, which shows that plasma energy is being converted to magnetic energy in our event.
Mobility propagation and dynamic facilitation in superionic conductors

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

Annamareddy, Ajay, E-mail: vkannama@ncsu.edu; Eapen, Jacob, E-mail: jacob.eapen@ncsu.edu

2015-11-21

In an earlier work [V. A. Annamareddy et al., Phys. Rev. E 89, 010301(R) (2014)], we showed the manifestation of dynamical heterogeneity (DH)—the presence of clustered mobile and immobile regions—in UO{sub 2}, a model type II superionic conductor. In the current work, we demonstrate the mechanism of dynamic facilitation (DF) in two superionic conductors (CaF{sub 2} and UO{sub 2}) using atomistic simulations. Using the mobility transfer function, DF is shown to vary non-monotonically with temperature with the intensity of DF peaking at temperatures close to the superionic transition temperature (T{sub λ}). Both the metrics quantifying DH and DF show remarkablemore » correspondence implying that DF, in the framework of kinematically constrained models, underpins the heterogeneous dynamics in type II superionic conductors.« less
Structural and functional changes across the visual cortex of a patient with visual form agnosia.

PubMed

Bridge, Holly; Thomas, Owen M; Minini, Loredana; Cavina-Pratesi, Cristiana; Milner, A David; Parker, Andrew J

2013-07-31

Loss of shape recognition in visual-form agnosia occurs without equivalent losses in the use of vision to guide actions, providing support for the hypothesis of two visual systems (for "perception" and "action"). The human individual DF received a toxic exposure to carbon monoxide some years ago, which resulted in a persisting visual-form agnosia that has been extensively characterized at the behavioral level. We conducted a detailed high-resolution MRI study of DF's cortex, combining structural and functional measurements. We present the first accurate quantification of the changes in thickness across DF's occipital cortex, finding the most substantial loss in the lateral occipital cortex (LOC). There are reduced white matter connections between LOC and other areas. Functional measures show pockets of activity that survive within structurally damaged areas. The topographic mapping of visual areas showed that ordered retinotopic maps were evident for DF in the ventral portions of visual cortical areas V1, V2, V3, and hV4. Although V1 shows evidence of topographic order in its dorsal portion, such maps could not be found in the dorsal parts of V2 and V3. We conclude that it is not possible to understand fully the deficits in object perception in visual-form agnosia without the exploitation of both structural and functional measurements. Our results also highlight for DF the cortical routes through which visual information is able to pass to support her well-documented abilities to use visual information to guide actions.
Benchmarking density functionals for hydrogen-helium mixtures with quantum Monte Carlo: Energetics, pressures, and forces

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

Clay, Raymond C.; Holzmann, Markus; Ceperley, David M.

An accurate understanding of the phase diagram of dense hydrogen and helium mixtures is a crucial component in the construction of accurate models of Jupiter, Saturn, and Jovian extrasolar planets. Though DFT based rst principles methods have the potential to provide the accuracy and computational e ciency required for this task, recent benchmarking in hydrogen has shown that achieving this accuracy requires a judicious choice of functional, and a quanti cation of the errors introduced. In this work, we present a quantum Monte Carlo based benchmarking study of a wide range of density functionals for use in hydrogen-helium mixtures atmore » thermodynamic conditions relevant for Jovian planets. Not only do we continue our program of benchmarking energetics and pressures, but we deploy QMC based force estimators and use them to gain insights into how well the local liquid structure is captured by di erent density functionals. We nd that TPSS, BLYP and vdW-DF are the most accurate functionals by most metrics, and that the enthalpy, energy, and pressure errors are very well behaved as a function of helium concentration. Beyond this, we highlight and analyze the major error trends and relative di erences exhibited by the major classes of functionals, and estimate the magnitudes of these e ects when possible.« less
Benchmarking density functionals for hydrogen-helium mixtures with quantum Monte Carlo: Energetics, pressures, and forces

DOE PAGES

Clay, Raymond C.; Holzmann, Markus; Ceperley, David M.; ...

2016-01-19

An accurate understanding of the phase diagram of dense hydrogen and helium mixtures is a crucial component in the construction of accurate models of Jupiter, Saturn, and Jovian extrasolar planets. Though DFT based rst principles methods have the potential to provide the accuracy and computational e ciency required for this task, recent benchmarking in hydrogen has shown that achieving this accuracy requires a judicious choice of functional, and a quanti cation of the errors introduced. In this work, we present a quantum Monte Carlo based benchmarking study of a wide range of density functionals for use in hydrogen-helium mixtures atmore » thermodynamic conditions relevant for Jovian planets. Not only do we continue our program of benchmarking energetics and pressures, but we deploy QMC based force estimators and use them to gain insights into how well the local liquid structure is captured by di erent density functionals. We nd that TPSS, BLYP and vdW-DF are the most accurate functionals by most metrics, and that the enthalpy, energy, and pressure errors are very well behaved as a function of helium concentration. Beyond this, we highlight and analyze the major error trends and relative di erences exhibited by the major classes of functionals, and estimate the magnitudes of these e ects when possible.« less
Band engineering in twisted molybdenum disulfide bilayers

NASA Astrophysics Data System (ADS)

Zhao, Yipeng; Liao, Chengwei; Ouyang, Gang

2018-05-01

In order to explore the theoretical relationship between interlayer spacing, interaction and band offset at the atomic level in vertically stacked two-dimensional (2D) van der Waals (vdW) structures, we propose an analytical model to address the evolution of interlayer vdW coupling with random stacking configurations in MoS2 bilayers based on the atomic-bond-relaxation correlation mechanism. We found that interlayer spacing changes substantially with respect to the orientations, and the bandgap increases from 1.53 eV (AB stacking) to 1.68 eV (AA stacking). Our results reveal that the evolution of interlayer vdW coupling originates from the interlayer interaction, leading to interlayer separations and electronic properties changing with stacking configurations. Our predictions constitute a demonstration of twist engineering the band shift in the emergent class of 2D crystals, transition-metal dichalcogenides.

A wavelet-based estimator of the degrees of freedom in denoised fMRI time series for probabilistic testing of functional connectivity and brain graphs.

PubMed

Patel, Ameera X; Bullmore, Edward T

2016-11-15

Connectome mapping using techniques such as functional magnetic resonance imaging (fMRI) has become a focus of systems neuroscience. There remain many statistical challenges in analysis of functional connectivity and network architecture from BOLD fMRI multivariate time series. One key statistic for any time series is its (effective) degrees of freedom, df, which will generally be less than the number of time points (or nominal degrees of freedom, N). If we know the df, then probabilistic inference on other fMRI statistics, such as the correlation between two voxel or regional time series, is feasible. However, we currently lack good estimators of df in fMRI time series, especially after the degrees of freedom of the "raw" data have been modified substantially by denoising algorithms for head movement. Here, we used a wavelet-based method both to denoise fMRI data and to estimate the (effective) df of the denoised process. We show that seed voxel correlations corrected for locally variable df could be tested for false positive connectivity with better control over Type I error and greater specificity of anatomical mapping than probabilistic connectivity maps using the nominal degrees of freedom. We also show that wavelet despiked statistics can be used to estimate all pairwise correlations between a set of regional nodes, assign a P value to each edge, and then iteratively add edges to the graph in order of increasing P. These probabilistically thresholded graphs are likely more robust to regional variation in head movement effects than comparable graphs constructed by thresholding correlations. Finally, we show that time-windowed estimates of df can be used for probabilistic connectivity testing or dynamic network analysis so that apparent changes in the functional connectome are appropriately corrected for the effects of transient noise bursts. Wavelet despiking is both an algorithm for fMRI time series denoising and an estimator of the (effective) df of denoised fMRI time series. Accurate estimation of df offers many potential advantages for probabilistically thresholding functional connectivity and network statistics tested in the context of spatially variant and non-stationary noise. Code for wavelet despiking, seed correlational testing and probabilistic graph construction is freely available to download as part of the BrainWavelet Toolbox at www.brainwavelet.org. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.
Localized orbital corrections applied to thermochemical errors in density functional theory: The role of basis set and application to molecular reactions

NASA Astrophysics Data System (ADS)

Goldfeld, Dahlia A.; Bochevarov, Arteum D.; Friesner, Richard A.

2008-12-01

This paper is a logical continuation of the 22 parameter, localized orbital correction (LOC) methodology that we developed in previous papers [R. A. Friesner et al., J. Chem. Phys. 125, 124107 (2006); E. H. Knoll and R. A. Friesner, J. Phys. Chem. B 110, 18787 (2006).] This methodology allows one to redress systematic density functional theory (DFT) errors, rooted in DFT's inherent inability to accurately describe nondynamical correlation. Variants of the LOC scheme, in conjunction with B3LYP (denoted as B3LYP-LOC), were previously applied to enthalpies of formation, ionization potentials, and electron affinities and showed impressive reduction in the errors. In this paper, we demonstrate for the first time that the B3LYP-LOC scheme is robust across different basis sets [6-31G∗, 6-311++G(3df,3pd), cc-pVTZ, and aug-cc-pVTZ] and reaction types (atomization reactions and molecular reactions). For example, for a test set of 70 molecular reactions, the LOC scheme reduces their mean unsigned error from 4.7 kcal/mol [obtained with B3LYP/6-311++G(3df,3pd)] to 0.8 kcal/mol. We also verified whether the LOC methodology would be equally successful if applied to the promising M05-2X functional. We conclude that although M05-2X produces better reaction enthalpies than B3LYP, the LOC scheme does not combine nearly as successfully with M05-2X than with B3LYP. A brief analysis of another functional, M06-2X, reveals that it is more accurate than M05-2X but its combination with LOC still cannot compete in accuracy with B3LYP-LOC. Indeed, B3LYP-LOC remains the best method of computing reaction enthalpies.
A kinetic Monte Carlo simulation method of van der Waals epitaxy for atomistic nucleation-growth processes of transition metal dichalcogenides.

PubMed

Nie, Yifan; Liang, Chaoping; Cha, Pil-Ryung; Colombo, Luigi; Wallace, Robert M; Cho, Kyeongjae

2017-06-07

Controlled growth of crystalline solids is critical for device applications, and atomistic modeling methods have been developed for bulk crystalline solids. Kinetic Monte Carlo (KMC) simulation method provides detailed atomic scale processes during a solid growth over realistic time scales, but its application to the growth modeling of van der Waals (vdW) heterostructures has not yet been developed. Specifically, the growth of single-layered transition metal dichalcogenides (TMDs) is currently facing tremendous challenges, and a detailed understanding based on KMC simulations would provide critical guidance to enable controlled growth of vdW heterostructures. In this work, a KMC simulation method is developed for the growth modeling on the vdW epitaxy of TMDs. The KMC method has introduced full material parameters for TMDs in bottom-up synthesis: metal and chalcogen adsorption/desorption/diffusion on substrate and grown TMD surface, TMD stacking sequence, chalcogen/metal ratio, flake edge diffusion and vacancy diffusion. The KMC processes result in multiple kinetic behaviors associated with various growth behaviors observed in experiments. Different phenomena observed during vdW epitaxy process are analysed in terms of complex competitions among multiple kinetic processes. The KMC method is used in the investigation and prediction of growth mechanisms, which provide qualitative suggestions to guide experimental study.
Topological mosaics in moiré superlattices of van der Waals heterobilayers

NASA Astrophysics Data System (ADS)

Tong, Qingjun; Yu, Hongyi; Zhu, Qizhong; Wang, Yong; Xu, Xiaodong; Yao, Wang

2017-04-01

Van der Waals (vdW) heterostructures formed by two-dimensional atomic crystals provide a powerful approach towards designer condensed matter systems. Incommensurate heterobilayers with small twisting and/or lattice mismatch lead to the interesting concept of moiré superlattices, where the atomic registry is locally indistinguishable from commensurate bilayers but has local-to-local variation over long range. Here we show that such moiré superlattices can lead to periodic modulation of local topological order in vdW heterobilayers formed by two massive Dirac materials. By tuning the vdW heterojunction from normal to the inverted type-II regime via an interlayer bias, the commensurate heterobilayer can become a topological insulator (TI), depending on the interlayer hybridization controlled by the atomic registry between the vdW layers. This results in a mosaic pattern of TI regions and normal insulator (NI) regions in moiré superlattices, where topologically protected helical modes exist at the TI/NI phase boundaries. By using symmetry-based k .p and tight-binding models, we predict that this topological phenomenon can be present in inverted transition metal dichalcogenides heterobilayers. Our work points to a new means of realizing programmable and electrically switchable topological superstructures from two-dimensional arrays of TI nano-dots to one-dimensional arrays of TI nano-stripes.
Towards understanding the effects of van der Waals strengths on the electric double-layer structures and capacitive behaviors

NASA Astrophysics Data System (ADS)

Yang, Huachao; Bo, Zheng; Yang, Jinyuan; Yan, Jianhua; Cen, Kefa

2017-10-01

Solid-liquid interactions are considered to play a crucial role in charge storage capability of electric double-layer capacitors (EDLCs). In this work, effects of van der Waals (VDW) strengths on the EDL structures and capacitive performances within two representative electrolytes of solvated aqueous solutions and solvent-free ionic liquids are illuminated by molecular dynamics simulations. Single crystalline metals with similar lattice constant but diverse VDW potentials are employed as electrodes. Upon enhancing VDW strengths, capacitance of aqueous electrolytes first increases conspicuously by ∼34.0% and then descends, manifesting a non-monotonic trend, which goes beyond traditional perspectives. Such unusual observation is interpreted by the excluded-volume effects stemmed from ion-solvent competitions. Stimulated by predominant coulombic interactions, more ions are aggregated at the interface despite of the increasing VDW potentials, facilitating superior screening efficiency and capacitance. However, further enhancing strengths preferentially attracts more solvents instead of ions to the electrified surface, which in turn strikingly repels ions from Helmholtz layers, deteriorating electrode capacitance. An essentially similar feather is also recognized for ionic liquids, while the corresponding mechanisms are prominently ascribed to the suppressed ionic separations issued from cation-anion competitions. We highlight that constructing electrode materials with a moderate-hydrophilicity could further advance the performances of EDLCs.
The formation of organic (propolis films)/inorganic (layered crystals) interfaces for optoelectronic applications

NASA Astrophysics Data System (ADS)

Drapak, S. I.; Bakhtinov, A. P.; Gavrylyuk, S. V.; Kovalyuk, Z. D.; Lytvyn, O. S.

2008-10-01

Propolis (honeybee glue) organic films were prepared from an alcoholic solution on the surfaces of inorganic layered semiconductors (indium, gallium and bismuth selenides). Atomic force microscopy (AFM) and X-ray diffraction (XRD) are used to characterize structural properties of an organic/inorganic interfaces. It is shown that nanodimensional linear defects and nanodimensional cavities of various shapes are formed on the van der Waals (VDW) surfaces of layered crystals as a result of chemical interaction between the components of propolis (flavonoids, aminoacids and phenolic acids) and the VDW surfaces as well as deformation interaction between the VDW surfaces and propolis films during their polymerization. The nanocavities are formed as a result of the rupture of strong covalent bonds in the upper layers of layered crystals and have the shape of hexagons or triangles in the (0001) plane. The shape, lateral size and distribution of nanodimensional defects on the VDW surfaces depends on the type of crystals, the magnitude and distribution of surface stresses. We have obtained self-organized nanofold structures of propolis/InSe interface. It is established that such heterostructures have photosensitivity in the infrared range hν<1.2 eV (the values of energy gap are 1.2 eV for InSe and 3.07 eV for propolis films at room temperature).
Mechanical properties of hydrogenated bilayer graphene

NASA Astrophysics Data System (ADS)

Andrew, R. C.; Mapasha, R. E.; Chetty, N.

2013-06-01

Using first principle methods, we study the mechanical properties of monolayer and bilayer graphene with 50% and 100% coverage of hydrogen. We employ the vdW-DF, vdW-DF-C09x, and vdW-DF2-C09x van der Waals functionals for the exchange correlation interactions that give significantly improved interlayer spacings and energies. We also use the PBE form for the generalized gradient corrected exchange correlation functional for comparison. We present a consistent theoretical framework for the in-plane layer modulus and the out-of-plane interlayer modulus and we calculate, for the first time, these properties for these systems. This gives a measure of the change of the strength properties when monolayer and bilayer graphene are hydrogenated. Moreover, comparing the relative performance of these functionals in describing hydrogenated bilayered graphenes, we also benchmark these functionals in how they calculate the properties of graphite.
Does Talocrural Joint-Thrust Manipulation Improve Outcomes After Inversion Ankle Sprain?

PubMed

Krueger, Brett; Becker, Laura; Leemkuil, Greta; Durall, Christopher

2015-08-01

Clinical Scenario: Ankle sprains account for roughly 10% of sport-related injuries in the active population. The majority of these injuries occur from excessive ankle inversion, leading to lateral ligamentous injury. In addition to pain and swelling, limitations in ankle range of motion (ROM) and self-reported function are common findings. These limitations are thought to be due in part to loss of mobility in the talocrural joint. Accordingly, some investigators have reported using high-velocity, low-amplitude thrust-manipulation techniques directed at the talocrural joint to address deficits in dorsiflexion (DF) ROM and function. This review was conducted to ascertain the impact of talocrural joint-thrust manipulation (TJM) on DF ROM, self-reported function, and pain in patients with a history of ankle sprain. Focused Clinical Question: In patients with a history of inversion ankle sprain, does TJM improve outcomes in DF ROM, self-reported function, and/or pain?
Madm (Mlf1 adapter molecule) cooperates with Bunched A to promote growth in Drosophila

PubMed Central

2010-01-01

Background The TSC-22 domain family (TSC22DF) consists of putative transcription factors harboring a DNA-binding TSC-box and an adjacent leucine zipper at their carboxyl termini. Both short and long TSC22DF isoforms are conserved from flies to humans. Whereas the short isoforms include the tumor suppressor TSC-22 (Transforming growth factor-β1 stimulated clone-22), the long isoforms are largely uncharacterized. In Drosophila, the long isoform Bunched A (BunA) acts as a growth promoter, but how BunA controls growth has remained obscure. Results In order to test for functional conservation among TSC22DF members, we expressed the human TSC22DF proteins in the fly and found that all long isoforms can replace BunA function. Furthermore, we combined a proteomics-based approach with a genetic screen to identify proteins that interact with BunA. Madm (Mlf1 adapter molecule) physically associates with BunA via a conserved motif that is only contained in long TSC22DF proteins. Moreover, Drosophila Madm acts as a growth-promoting gene that displays growth phenotypes strikingly similar to bunA phenotypes. When overexpressed, Madm and BunA synergize to increase organ growth. Conclusions The growth-promoting potential of long TSC22DF proteins is evolutionarily conserved. Furthermore, we provide biochemical and genetic evidence for a growth-regulating complex involving the long TSC22DF protein BunA and the adapter molecule Madm. See minireview at http://jbiol.com/content/9/1/8. PMID:20149264
The Ames dwarf gene, df, is required early in pituitary ontogeny for the extinction of Rpx transcription and initiation of lineage-specific cell proliferation.

PubMed

Gage, P J; Brinkmeier, M L; Scarlett, L M; Knapp, L T; Camper, S A; Mahon, K A

1996-12-01

Two nonallelic dwarfing mutations in mice define genes important for pituitary development and function. Mice homozygous for either the Ames (df) or Snell (Pit 1dw) dwarf mutations exhibit severe proportional dwarfism, hypothyroidism, and infertility due to the cytodifferentiation failure of three anterior pituitary cell types: thyrotropes, somatotropes, and lactotropes. Analysis of double heterozygotes and double mutants has provided evidence that the df and dw genes act sequentially in the same genetic pathway. Double heterozygotes had no reduction in growth rate or final adult size. Double homozygotes had essentially the same phenotype as the single mutants and were recovered at the predicted frequency, indicating that there are no previously unrecognized, redundant functions of the two genes. Several lines of evidence demonstrate that df acts earlier in the differentiation pathway than Pit1. The df mutants fail to extinguish expression of the homeobox gene Rpx on embryonic day 13.5 (e13.5), and the size of their nascent pituitary glands is reduced by e14.5. In contrast, Pit1dw mutants down-regulate Rpx appropriately and exhibit normal cell proliferation up to e14.5. The failure to extinguish Rpx and the concomitant hypocellularity of df pituitaries suggest the importance of Rpx repression in lineage-specific cell proliferation before the appearance of lineage-specific markers. Later, Pit-1 and hypothalamic neuropeptides act sequentially to regulate marker gene transcription and cell proliferation. These results establish the time of df action in a cascade of genes that regulate pituitary ontogeny.
Characterization of fructans and dietary fibre profiles in raw and steamed vegetables.

PubMed

Kalala, Gaétan; Kambashi, Bienvenu; Everaert, Nadia; Beckers, Yves; Richel, Aurore; Pachikian, Barbara; Neyrinck, Audrey M; Delzenne, Nathalie M; Bindelle, Jérôme

2017-12-18

Dietary fibre (DF) has many positive effects on human health associated with its functionality in the gastrointestinal tract. These benefits vary according to the type of DF. Vegetables can be a natural source of DF in the diet. However, to provide adequate nutritional advice, the content and profile of their various DF types must be characterised. This study aimed to determine the DF profile of 29 vegetables cultivated in Wallonia (Belgium) and the impact of steaming on these profiles. Using a combination of enzymatic, gravimetric and chromatographic methods, fructans, total dietary fibre (TDF), low- and high-molecular-weight soluble dietary fibre (SDF), and insoluble dietary fibre (IDF) were analysed. Results show that the DF content varies considerably among the 29 investigated vegetable varieties and species, but the influence of steaming is limited to a shift from IDF to high-molecular-weight SDF for 18 of the 29 tested vegetables, while fructans are preserved with not actual reduction in the DP.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Anderson, Brian B.; Kirkegaard, Marie C.; Miskowiec, Andrew J.

Uranyl fluoride (UO 2F 2) is a hygroscopic powder with two main structural phases: an anhydrous crystal and a partially hydrated crystal of the same R¯3m symmetry. The formally closed-shell electron structure of anhydrous UO 2F 2 is amenable to density functional theory calculations. We use density functional perturbation theory (DFPT) to calculate the vibrational frequencies of the anhydrous crystal structure and employ complementary inelastic neutron scattering and temperature-dependent Raman scattering to validate those frequencies. As a model closed-shell actinide, we investigated the effect of LDA, GGA, and non-local vdW functionals as well as the spherically-averaged Hubbard +U correction onmore » vibrational frequencies, electronic structure, and geometry of anhydrous UO 2F 2. A particular choice of U eff = 5.5 eV yields the correct U Oyl bond distance and vibrational frequencies for the characteristic Eg and A1g modes that are within the resolution of experiment. Inelastic neutron scattering and Raman scattering suggest a degree of water coupling to the lattice vibrations in the more experimentally accessible partially hydrated UO 2F 2 system, with the symmetric O-U-O stretching vibration shifted approximately 47 cm -1 lower in energy compared to the anhydrous structure. Evidence of water interaction with the uranyl ion is present from a two-peak decomposition of the uranyl stretching vibration in the Raman spectra and anion hydrogen stretching vibrations in the inelastic neutron scattering spectra. A first-order dehydration phase transition temperature is definitively identified to be 125 °C using temperature-dependent Raman scattering.« less
Vibrational Properties of Anhydrous and Partially Hydrated Uranyl Fluoride

DOE PAGES

Anderson, Brian B.; Kirkegaard, Marie C.; Miskowiec, Andrew J.; ...

2017-01-01

Uranyl fluoride (UO 2F 2) is a hygroscopic powder with two main structural phases: an anhydrous crystal and a partially hydrated crystal of the same R¯3m symmetry. The formally closed-shell electron structure of anhydrous UO 2F 2 is amenable to density functional theory calculations. We use density functional perturbation theory (DFPT) to calculate the vibrational frequencies of the anhydrous crystal structure and employ complementary inelastic neutron scattering and temperature-dependent Raman scattering to validate those frequencies. As a model closed-shell actinide, we investigated the effect of LDA, GGA, and non-local vdW functionals as well as the spherically-averaged Hubbard +U correction onmore » vibrational frequencies, electronic structure, and geometry of anhydrous UO 2F 2. A particular choice of U eff = 5.5 eV yields the correct U Oyl bond distance and vibrational frequencies for the characteristic Eg and A1g modes that are within the resolution of experiment. Inelastic neutron scattering and Raman scattering suggest a degree of water coupling to the lattice vibrations in the more experimentally accessible partially hydrated UO 2F 2 system, with the symmetric O-U-O stretching vibration shifted approximately 47 cm -1 lower in energy compared to the anhydrous structure. Evidence of water interaction with the uranyl ion is present from a two-peak decomposition of the uranyl stretching vibration in the Raman spectra and anion hydrogen stretching vibrations in the inelastic neutron scattering spectra. A first-order dehydration phase transition temperature is definitively identified to be 125 °C using temperature-dependent Raman scattering.« less
libvdwxc: a library for exchange-correlation functionals in the vdW-DF family

NASA Astrophysics Data System (ADS)

Hjorth Larsen, Ask; Kuisma, Mikael; Löfgren, Joakim; Pouillon, Yann; Erhart, Paul; Hyldgaard, Per

2017-09-01

We present libvdwxc, a general library for evaluating the energy and potential for the family of vdW-DF exchange-correlation functionals. libvdwxc is written in C and provides an efficient implementation of the vdW-DF method and can be interfaced with various general-purpose DFT codes. Currently, the Gpaw and Octopus codes implement interfaces to libvdwxc. The present implementation emphasizes scalability and parallel performance, and thereby enables ab initio calculations of nanometer-scale complexes. The numerical accuracy is benchmarked on the S22 test set whereas parallel performance is benchmarked on ligand-protected gold nanoparticles ({{Au}}144{({{SC}}11{{NH}}25)}60) up to 9696 atoms.
Few-layer and symmetry-breaking effects on the electrical properties of ordered CF3Cl phases on graphene

NASA Astrophysics Data System (ADS)

Morales-Cifuentes, Josue; Wang, Yilin; Reutt-Robey, Janice; Einstein, T. L.

2014-03-01

An effective pseudopotential mechanism for breaking the inherent sub-lattice symmetry of graphene has been studied using DFT calculations on hexagonal boron nitride. Electrical detection of CF3Cl phase transitions on graphene shows the existence of a commensurate ordered phase in which this can be tested. We study the electronic properties of this phase using VASP ver 5.3.3, with ab initio van der Waals density functionals (vdW-DF1 and vdW-DF2). Consistent with a physisorbed phase, binding energies and charge transfer per CF3Cl molecule are calculated to be on the order of 280meV and 0.01e, respectively. By exploring different coverages and orientations of this ordered phase we are able to open a band gap in some configurations; said gap is in the range of 8 to 80meV depending on the strength of the effective pseudopotential. Furthermore, we calculate the screening of these effects in bi-layer and tri-layer graphene. Work supported by NSF-MRSEC at UMD, grant DMR 05-20471 and NSF-CHE 13-05892.
Relative electronic and free energies of octane's unique conformations

NASA Astrophysics Data System (ADS)

Kirschner, Karl N.; Heiden, Wolfgang; Reith, Dirk

2017-06-01

This study reports the geometries and electronic energies of n-octane's unique conformations using perturbation methods that best mimic CCSD(T) results. In total, the fully optimised minima of n-butane (2 conformations), n-pentane (4 conformations), n-hexane (12 conformations) and n-octane (96 conformations) were investigated at several different theory levels and basis sets. We find that DF-MP2.5/aug-cc-pVTZ is in very good agreement with the more expensive CCSD(T) results. At this level, we can clearly confirm the 96 stable minima which were previously found using a reparameterised density functional theory (DFT). Excellent agreement was found between their DFT results and our DF-MP2.5 perturbation results. Subsequent Gibbs free energy calculations, using scaled MP2/aug-cc-pVTZ zero-point vibrational energy and frequencies, indicate a significant temperature dependency of the relative energies, with a change in the predicted global minimum. The results of this work will be important for future computational investigations of fuel-related octane reactions and for optimisation of molecular force fields (e.g. lipids).
Two-Dimensional Semiconductor Optoelectronics Based on van der Waals Heterostructures.

PubMed

Lee, Jae Yoon; Shin, Jun-Hwan; Lee, Gwan-Hyoung; Lee, Chul-Ho

2016-10-27

Two-dimensional (2D) semiconductors such as transition metal dichalcogenides (TMDCs) and black phosphorous have drawn tremendous attention as an emerging optical material due to their unique and remarkable optical properties. In addition, the ability to create the atomically-controlled van der Waals (vdW) heterostructures enables realizing novel optoelectronic devices that are distinct from conventional bulk counterparts. In this short review, we first present the atomic and electronic structures of 2D semiconducting TMDCs and their exceptional optical properties, and further discuss the fabrication and distinctive features of vdW heterostructures assembled from different kinds of 2D materials with various physical properties. We then focus on reviewing the recent progress on the fabrication of 2D semiconductor optoelectronic devices based on vdW heterostructures including photodetectors, solar cells, and light-emitting devices. Finally, we highlight the perspectives and challenges of optoelectronics based on 2D semiconductor heterostructures.
Mechanics of rolling of nanoribbon on tube and sphere.

PubMed

Yin, Qifang; Shi, Xinghua

2013-06-21

The configuration of graphene nano-ribbon (GNR) assembly on carbon nanotube (CNT) and sphere is studied through theoretical modeling and molecular simulation. The GNR can spontaneously wind onto the CNT due to van der Waals (vdW) interaction and form two basic configurations: helix and scroll. The final configuration arises from the competition among three energy terms: the bending energy of the GNR, the vdW interaction between GNR and CNT, the vdW between the GNR itself. We derive analytical solutions by accounting for the three energy parts, with which we draw phase diagrams and predict the final configuration (helix or scroll) based on the selected parameters. The molecular simulations are conducted to verify the model with the results agree well with the model predicted. Our work can be used to actively control and transfer the tube-like nanoparticles and viruses as well as to assemble ribbon-like nanomaterials.
Two-Dimensional Semiconductor Optoelectronics Based on van der Waals Heterostructures

PubMed Central

Lee, Jae Yoon; Shin, Jun-Hwan; Lee, Gwan-Hyoung; Lee, Chul-Ho

2016-01-01

Two-dimensional (2D) semiconductors such as transition metal dichalcogenides (TMDCs) and black phosphorous have drawn tremendous attention as an emerging optical material due to their unique and remarkable optical properties. In addition, the ability to create the atomically-controlled van der Waals (vdW) heterostructures enables realizing novel optoelectronic devices that are distinct from conventional bulk counterparts. In this short review, we first present the atomic and electronic structures of 2D semiconducting TMDCs and their exceptional optical properties, and further discuss the fabrication and distinctive features of vdW heterostructures assembled from different kinds of 2D materials with various physical properties. We then focus on reviewing the recent progress on the fabrication of 2D semiconductor optoelectronic devices based on vdW heterostructures including photodetectors, solar cells, and light-emitting devices. Finally, we highlight the perspectives and challenges of optoelectronics based on 2D semiconductor heterostructures. PMID:28335321
Self-Assembly of Nanoclusters into Mono-, Few-, and Multilayered Sheets via Dipole-Induced Asymmetric van der Waals Attraction.

PubMed

Wu, Zhennan; Liu, Jiale; Li, Yanchun; Cheng, Ziyi; Li, Tingting; Zhang, Hao; Lu, Zhongyuan; Yang, Bai

2015-06-23

Two-dimensional (2D) nanomaterials possessing regular layered structures and versatile chemical composition are highly expected in many applications. Despite the importance of van der Waals (vdW) attraction in constructing and maintaining layered structures, the origin of 2D anisotropy is not fully understood, yet. Here, we report the 2D self-assembly of ligand-capped Au15 nanoclusters into mono-, few-, and multilayered sheets in colloidal solution. Both the experimental results and computer simulation reveal that the 2D self-assembly is initiated by 1D dipolar attraction common in nanometer-sized objects. The dense 1D attachment of Au15 leads to a redistribution of the surface ligands, thus generating asymmetric vdW attraction. The deliberate control of the coordination of dipolar and vdW attraction further allows to manipulate the thickness and morphologies of 2D self-assembly architectures.

Theoretical investigations of the gas phase reaction of limonene (C10H16) with OH radical

NASA Astrophysics Data System (ADS)

Ranjan Dash, Manas; Rajakumar, B.

2015-11-01

The rate coefficients of hydroxyl radical (OH) reaction with limonene were computed using canonical variational transition state theory with small-curvature tunnelling between 275 and 400 K. The geometries and frequencies of all the stationary points are calculated using hybrid density functional theory methods M06-2X and MPWB1K with 6-31+G(d,p), 6-311++G(d,p), and 6-311+G(2df,2p) basis sets. Both addition and abstraction channels of the title reaction were explored. The rate coefficients obtained over the temperature range of 275-400 K were used to derive the Arrhenius expressions: k(T) = 4.06×10-34 T7.07 exp[4515/T] and k(T) = 7.37×10-25 T3.9 exp[3169/T] cm3 molecule-1 s-1 at M06-2X/6-311+G(2df,2p) and MPWB1K/6-311+G(2df,2p) levels of theory, respectively. Kinetic study indicated that addition reactions are major contributors to the total reaction in the studied temperature range. The atmospheric lifetime (τ) of limonene due to its reactions with various tropospheric oxidants was calculated and concluded that limonene is lost in the atmosphere within a few hours after it is released. The ozone production potential of limonene was computed to be (14-18) ppm, which indicated that degradation of limonene would lead to a significant amount of ozone production in the troposphere.
Three-dimensional dominant frequency mapping using autoregressive spectral analysis of atrial electrograms of patients in persistent atrial fibrillation.

PubMed

Salinet, João L; Masca, Nicholas; Stafford, Peter J; Ng, G André; Schlindwein, Fernando S

2016-03-08

Areas with high frequency activity within the atrium are thought to be 'drivers' of the rhythm in patients with atrial fibrillation (AF) and ablation of these areas seems to be an effective therapy in eliminating DF gradient and restoring sinus rhythm. Clinical groups have applied the traditional FFT-based approach to generate the three-dimensional dominant frequency (3D DF) maps during electrophysiology (EP) procedures but literature is restricted on using alternative spectral estimation techniques that can have a better frequency resolution that FFT-based spectral estimation. Autoregressive (AR) model-based spectral estimation techniques, with emphasis on selection of appropriate sampling rate and AR model order, were implemented to generate high-density 3D DF maps of atrial electrograms (AEGs) in persistent atrial fibrillation (persAF). For each patient, 2048 simultaneous AEGs were recorded for 20.478 s-long segments in the left atrium (LA) and exported for analysis, together with their anatomical locations. After the DFs were identified using AR-based spectral estimation, they were colour coded to produce sequential 3D DF maps. These maps were systematically compared with maps found using the Fourier-based approach. 3D DF maps can be obtained using AR-based spectral estimation after AEGs downsampling (DS) and the resulting maps are very similar to those obtained using FFT-based spectral estimation (mean 90.23 %). There were no significant differences between AR techniques (p = 0.62). The processing time for AR-based approach was considerably shorter (from 5.44 to 5.05 s) when lower sampling frequencies and model order values were used. Higher levels of DS presented higher rates of DF agreement (sampling frequency of 37.5 Hz). We have demonstrated the feasibility of using AR spectral estimation methods for producing 3D DF maps and characterised their differences to the maps produced using the FFT technique, offering an alternative approach for 3D DF computation in human persAF studies.
Kinetic Assembly of Near-IR Active Gold Nanoclusters using Weakly Adsorbing Polymers to Control Size

PubMed Central

Tam, Jasmine M.; Murthy, Avinash K.; Ingram, Davis R.; Nguyen, Robin; Sokolov, Konstantin V.; Johnston, Keith P.

2013-01-01

Clusters of metal nanoparticles with an overall size less than 100 nm and high metal loadings for strong optical functionality, are of interest in various fields including microelectronics, sensors, optoelectronics and biomedical imaging and therapeutics. Herein we assemble ~5 nm gold particles into clusters with controlled size, as small as 30 nm and up to 100 nm, which contain only small amounts of polymeric stabilizers. The assembly is kinetically controlled with weakly adsorbing polymers, PLA(2K)-b-PEG(10K)-b-PLA(2K) or PEG (MW = 3350), by manipulating electrostatic, van der Waals (VDW), steric, and depletion forces. The cluster size and optical properties are tuned as a function of particle volume fractions and polymer/gold ratios to modulate the interparticle interactions. The close spacing between the constituent gold nanoparticles and high gold loadings (80–85% w/w gold) produce a strong absorbance cross section of ~9×10−15 m2 in the NIR at 700 nm. This morphology results from VDW and depletion attractive interactions that exclude the weakly adsorbed polymeric stabilizer from the cluster interior. The generality of this kinetic assembly platform is demonstrated for gold nanoparticles with a range of surface charges from highly negative to neutral, with the two different polymers. PMID:20361735
Physicochemical and functional properties of micronized jincheng orange by-products (Citrus sinensis Osbeck) dietary fiber and its application as a fat replacer in yogurt.

PubMed

Yi, Tian; Huang, Xingjian; Pan, Siyi; Wang, Lufeng

2014-08-01

Orange by-products from juice extraction are generally discarded or used in animal feed due to their low market value. However, orange by-products show potential as dietary fiber (DF) and fat replacers in products such as yogurt. This study assessed the benefits of using orange by-products in DF-enriched materials such as DF powders (OP) and micronized DF with ball-milling (MDF). The study also investigated the effects of adding different levels of OP and MDF on the quality of low-fat yogurt. Results show that MDF showed better physicochemical and functional properties than OP, and that 2% MDF as a fat replacer in yogurt retained most of the textural and sensory properties of full-fat yogurt. Therefore, this study showed that MDF is a promising alternative as a fat replacer in low-fat yogurt, without sacrificing good taste and other qualities of full-fat yogurt.
A review of the characteristics of dietary fibers relevant to appetite and energy intake outcomes in human intervention trials.

PubMed

Poutanen, Kaisa S; Dussort, Pierre; Erkner, Alfrun; Fiszman, Susana; Karnik, Kavita; Kristensen, Mette; Marsaux, Cyril Fm; Miquel-Kergoat, Sophie; Pentikäinen, Saara P; Putz, Peter; Slavin, Joanne L; Steinert, Robert E; Mela, David J

2017-09-01

Background: Many intervention studies have tested the effect of dietary fibers (DFs) on appetite-related outcomes, with inconsistent results. However, DFs comprise a wide range of compounds with diverse properties, and the specific contribution of these to appetite control is not well characterized. Objective: The influence of specific DF characteristics [i.e., viscosity, gel-forming capacity, fermentability, or molecular weight (MW)] on appetite-related outcomes was assessed in healthy humans. Design: Controlled human intervention trials that tested the effects of well-characterized DFs on appetite ratings or energy intake were identified from a systematic search of literature. Studies were included only if they reported 1 ) DF name and origin and 2 ) data on viscosity, gelling properties, fermentability, or MW of the DF materials or DF-containing matrixes. Results: A high proportion of the potentially relevant literature was excluded because of lack of adequate DF characterization. In total, 49 articles that met these criteria were identified, which reported 90 comparisons of various DFs in foods, beverages, or supplements in acute or sustained-exposure trials. In 51 of the 90 comparisons, the DF-containing material of interest was efficacious for ≥1 appetite-related outcome. Reported differences in material viscosity, MW, or fermentability did not clearly correspond to differences in efficacy, whereas gel-forming DF sources were consistently efficacious (but with very few comparisons). Conclusions: The overall inconsistent relations of DF properties with respect to efficacy may reflect variation in measurement methodology, nature of the DF preparation and matrix, and study designs. Methods of DF characterization, incorporation, and study design are too inconsistent to allow generalized conclusions about the effects of DF properties on appetite and preclude the development of reliable, predictive, structure-function relations. Improved standards for characterization and reporting of DF sources and DF-containing materials are strongly recommended for future studies on the effects of DF on human physiology. This trial was registered at http://www.crd.york.ac.uk/PROSPERO as CRD42015015336. © 2017 American Society for Nutrition.
Influence of container design on predation rate of potential biocontrol agent, Toxorhynchites splendens (Diptera: Culicidae) against dengue vector.

PubMed

Mohamad, N; Zuharah, W F

2014-03-01

Toxorhynchites splendens larvae are a natural predator of dengue vector mosquito larvae, Aedes albopictus. This study was carried out to evaluate the predation rate of Tx. splendens third instar larvae on Ae. albopictus larvae in 24 h. Each predator was offered prey at a density between 10 to 50 individuals. Predation rate of Tx. splendens were also tested with two manipulated factors; various types of container and different water volumes. The experiment was evaluated in man-made containers (tin cans, plastic drinking glasses and rubber tires) and natural container (bamboo stumps) which were filled with different water volumes (full, half full, 1/4 full, and 1/8 full). The prey density and the characteristics of the container were found as significant factors which influence the predation rate of Tx. splendens. The predator consumed significantly more prey at higher prey densities (40 and 50 preys) compared to the lowest density (10 preys) (F=3.935, df=4, p=0.008). The results showed significantly higher consumption in horizontal shaped container of rubber tire than in vertical shape of bamboo stumps (F=3.100, df=3, p=0.029). However, the water volume had no significant effect on predation rate of Tx. splendens (F=1.736, df=3, p=0.162). We generally suggest that Tx. splendens is best to be released in discarded tires or any other containers with horizontal shape design with wide opening since Tx. splendens can become more effective in searching prey in this type of container design. This predator is also a suitable biocontrol candidates to be introduced either in wet and dry seasons in Malaysia.
Molecular Beam Epitaxial Growth and Characterization of Graphene and Hexagonal Boron Nitride Two-Dimensional Layers

NASA Astrophysics Data System (ADS)

Zheng, Renjing

Van der Waals (vdW) materials (also called as two-dimensional (2D) material in some literature) systems have received extensive attention recently due to their potential applications in next-generation electronics platform. Exciting properties have been discovered in this field, however, the performance and properties of the systems rely on the materials' quality and interface significantly, leading to the urgent need for scalable synthesis of high-quality vdW crystals and heterostructures. Toward this direction, this dissertation is devoted on the study of Molecular Beam Epitaxy (MBE) growth and various characterization of vdW materials and heterostructures, especially graphene and hexagonal boron nitride (h-BN). The goal is to achieve high-quality vdW materials and related heterostructures. There are mainly four projects discussed in this dissertation. The first project (Chapter 2) is about MBE growth of large-area h-BN on copper foil. After the growth, the film was transferred onto SiO2 substrate for characterization. It is observed that as-grown film gives evident h-BN Raman spectrum; what's more, h-BN peak intensity and position is dependent on film thickness. N-1s and B-1s XPS peaks further suggest the formation of h-BN. AFM and SEM images show the film is flat and continuous over large area. Our synthesis method shows it's possible to use MBE to achieve h-BN growth and could also pave a way for some unique structure, such as h-BN/graphene heterostructures and doped h-BN films by MBE. The second project (Chapter 3) is focused on establishment of grapehene/h-BN heterostructure on cobalt (Co) film. In-situ epitaxial growth of graphene/h-BN heterostructures on Co film substrate was achieved by using plasma-assisted MBE. The direct graphene/h-BN vertical stacking structures were demonstrated and further confirmed by various characterizations, such as Raman spectroscopy, SEM, XPS and TEM. Large area heterostructures consisting of single- /bilayer graphene and multilayer h-BN were achieved. The mismatch angle between graphene and h-BN is below 1º. The third project (Chapter 4) is about graphene growth on Fe by MBE at low temperature. Temperature-dependent growth of graphene on Fe using MBE is studied. Two-dimensional (2D), large-area graphene samples were grown on Fe thin films, and characterized by Raman, X-ray photoelectron spectroscopy, X-ray diffraction, optical microscopy, transmission electron microscopy and atomic force microscopy. Graphene is achieved on Fe at a wide growth temperature range and as low as 400 °C. The growth mechanism is studied and shows graphene growth is associated with formation and decomposition of iron carbide. The forth part is about a convenient way to produce vdW heterostructures: graphene growth of exfoliated h-BN on Co. We demonstrated graphene/h-BN heterostructures by growing graphene onto the substrates which consist of exfoliated h-BN on Co thin film using MBE. The heterostructure samples grown at different temperatures and growth durations were characterized by Raman, optical microscopy, atomic force microscopy, microwave impedance microscopy and scanning tunneling microscopy. It is found that the graphene/h-BN heterostructures were formed by the formation of graphene underneath rather than on top of the h-BN flakes. The growth mechanism is discussed. In summary, we develop and optimize growth of vdW materials (h-BN and graphene), and vdW heterostructures by MBE. Various characterization has been carried out to evaluate properties of the films in structural, optical and electrical aspects. Our results reveal that MBE can provide an excellent alternative way for reliable growth of high-quality and large-size vdW materials and related heterostructures, which will attract more attention for the utilization of MBE in vdW materials research.
Increased treatment durations lead to greater improvements in non-weight bearing dorsiflexion range of motion for asymptomatic individuals immediately following an anteroposterior grade IV mobilisation of the talus.

PubMed

Holland, Christopher James; Campbell, Kevin; Hutt, Kim

2015-08-01

Manual therapy aims to minimise pain and restore joint mobility and function. Joint mobilisations are integral to these techniques, with anteroposterior (AP) talocrural joint mobilisations purported to increase dorsiflexion range of motion (DF-ROM). This study aimed to determine whether different treatment durations of single grade IV anteroposterior talocrural joint mobilisations elicit statistically significant differences in DF-ROM. Sixteen asymptomatic male football players (age = 27.1 ± 5.3 years) participated in the study. Non-weight bearing (NWB) and weight bearing (WB) DF-ROM was measured before and after 4 randomised treatment conditions: control treatment, 30 s, 1 min, 2 min. NWB DF-ROM was measured using a universal goniometer, and WB DF-ROM using the weight-bearing lunge test. A within-subjects design was employed so that all participants received each of the treatment conditions. A 4 × 4 balanced Latin square design and 1 week interval between sessions reduced any residual effects. Two-way repeated measures ANOVA revealed a significant improvement in DF-ROM following all AP mobilisation treatments (p < 0.001). The within subjects contrasts showed that increases in treatment duration was associated with statistically significant improvements in DF-ROM (NWB DF-ROM control = 0.01%, 30 s = 14.2%, 1 min = 21.6%, 2 min = 32.8%; WB DF-ROM control = 0.01%, 30 s = 5.0%, 1 min = 7.6%, 2 min = 10.9%; p < 0.05). However, WB DF-ROM improvements were below the minimal detectable change scores needed to conclude that improvements were not a consequence of measurement error. This research shows that single session mobilisations can elicit NWB DF-ROM improvements in asymptomatic individuals in the absence of pain, whilst increases in treatment duration confer greater improvements in NWB DF-ROM within this population. Copyright © 2015 Elsevier Ltd. All rights reserved.
Esaki Diodes in van der Waals Heterojunctions with Broken-Gap Energy Band Alignment.

PubMed

Yan, Rusen; Fathipour, Sara; Han, Yimo; Song, Bo; Xiao, Shudong; Li, Mingda; Ma, Nan; Protasenko, Vladimir; Muller, David A; Jena, Debdeep; Xing, Huili Grace

2015-09-09

van der Waals (vdW) heterojunctions composed of two-dimensional (2D) layered materials are emerging as a solid-state materials family that exhibits novel physics phenomena that can power a range of electronic and photonic applications. Here, we present the first demonstration of an important building block in vdW solids: room temperature Esaki tunnel diodes. The Esaki diodes were realized in vdW heterostructures made of black phosphorus (BP) and tin diselenide (SnSe2), two layered semiconductors that possess a broken-gap energy band offset. The presence of a thin insulating barrier between BP and SnSe2 enabled the observation of a prominent negative differential resistance (NDR) region in the forward-bias current-voltage characteristics, with a peak to valley ratio of 1.8 at 300 K and 2.8 at 80 K. A weak temperature dependence of the NDR indicates electron tunneling being the dominant transport mechanism, and a theoretical model shows excellent agreement with the experimental results. Furthermore, the broken-gap band alignment is confirmed by the junction photoresponse, and the phosphorus double planes in a single layer of BP are resolved in transmission electron microscopy (TEM) for the first time. Our results represent a significant advance in the fundamental understanding of vdW heterojunctions and broaden the potential applications of 2D layered materials.
Thermionic Energy Conversion Based on Graphene van der Waals Heterostructures

PubMed Central

Liang, Shi-Jun; Liu, Bo; Hu, Wei; Zhou, Kun; Ang, L. K.

2017-01-01

Seeking for thermoelectric (TE) materials with high figure of merit (or ZT), which can directly converts low-grade wasted heat (400 to 500 K) into electricity, has been a big challenge. Inspired by the concept of multilayer thermionic devices, we propose and design a solid-state thermionic devices (as a power generator or a refrigerator) in using van der Waals (vdW) heterostructure sandwiched between two graphene electrodes, to achieve high energy conversion efficiency in the temperature range of 400 to 500 K. The vdW heterostructure is composed of suitable multiple layers of transition metal dichalcogenides (TMDs), such as MoS2, MoSe2, WS2 and WSe2. From our calculations, WSe2 and MoSe2 are identified as two ideal TMDs (using the reported experimental material’s properties), which can harvest waste heat at 400 K with efficiencies about 7% to 8%. To our best knowledge, this design is the first in combining the advantages of graphene electrodes and TMDs to function as a thermionic-based device. PMID:28387363
DOE Office of Scientific and Technical Information (OSTI.GOV)

Shirkov, Leonid; Makarewicz, Jan, E-mail: jama@amu.edu.pl

An ab initio intermolecular potential energy surface (PES) has been constructed for the benzene-krypton (BKr) van der Waals (vdW) complex. The interaction energy has been calculated at the coupled cluster level of theory with single, double, and perturbatively included triple excitations using different basis sets. As a result, a few analytical PESs of the complex have been determined. They allowed a prediction of the complex structure and its vibrational vdW states. The vibrational energy level pattern exhibits a distinct polyad structure. Comparison of the equilibrium structure, the dipole moment, and vibrational levels of BKr with their experimental counterparts has allowedmore » us to design an optimal basis set composed of a small Dunning’s basis set for the benzene monomer, a larger effective core potential adapted basis set for Kr and additional midbond functions. Such a basis set yields vibrational energy levels that agree very well with the experimental ones as well as with those calculated from the available empirical PES derived from the microwave spectra of the BKr complex. The basis proposed can be applied to larger complexes including Kr because of a reasonable computational cost and accurate results.« less
Charge Separation at Mixed-Dimensional Single and Multilayer MoS2/Silicon Nanowire Heterojunctions.

PubMed

Henning, Alex; Sangwan, Vinod K; Bergeron, Hadallia; Balla, Itamar; Sun, Zhiyuan; Hersam, Mark C; Lauhon, Lincoln J

2018-05-16

Layered two-dimensional (2-D) semiconductors can be combined with other low-dimensional semiconductors to form nonplanar mixed-dimensional van der Waals (vdW) heterojunctions whose charge transport behavior is influenced by the heterojunction geometry, providing a new degree of freedom to engineer device functions. Toward that end, we investigated the photoresponse of Si nanowire/MoS 2 heterojunction diodes with scanning photocurrent microscopy and time-resolved photocurrent measurements. Comparison of n-Si/MoS 2 isotype heterojunctions with p-Si/MoS 2 heterojunction diodes under varying biases shows that the depletion region in the p-n heterojunction promotes exciton dissociation and carrier collection. We measure an instrument-limited response time of 1 μs, which is 10 times faster than the previously reported response times for planar Si/MoS 2 devices, highlighting the advantages of the 1-D/2-D heterojunction. Finite element simulations of device models provide a detailed understanding of how the electrostatics affect charge transport in nanowire/vdW heterojunctions and inform the design of future vdW heterojunction photodetectors and transistors.
What formulas are good for representing dipole and generalized oscillator-strength spectra

NASA Astrophysics Data System (ADS)

Inokuti, M.; Dillon, M. A.

The dipole oscillator-strength distribution df/depsilon for a single continuum excitation of an atom or molecule is a function of the kinetic energy epsilon of an outgoing electron. The distribution describes many optical phenomena such as absorption, refraction, and reflection; in particular, df/depsilon is equal to the cross section for ionization by a photon with energy epsilon + I, apart from an universal constant, where I is the ionization threshold for the relevant shell. Furthermore, df/depsilon governs the ionization by glancing collisions of fast charged particles. Recent years have seen considerable accumulation of experimental data on df/depsilon. Those data are indeed valuable for many aplications in radiation physics, plasma physics, atmospheric physics, and astrophysics. In most of these applications, one needs a comprehensive set of data, i.e., numerical values of df/depsilon over a wide range of epsilon, say, from several eV to many keV; most often, one needs data at all epsilon at which df/depsilon is appreciable. A method for systematizing the data so that one can extrapolate or interpolate them dependably was sought.
Trends on band alignments: Validity of Anderson's rule in SnS2- and SnSe2-based van der Waals heterostructures

NASA Astrophysics Data System (ADS)

Koda, Daniel S.; Bechstedt, Friedhelm; Marques, Marcelo; Teles, Lara K.

2018-04-01

Van der Waals (vdW) heterostructures are promising candidates for building blocks in novel electronic and optoelectronic devices with tailored properties, since their electronic action is dominated by the band alignments upon their contact. In this work, we analyze 10 vdW heterobilayers based on tin dichalcogenides by first-principles calculations. Structural studies show that all systems are stable, and that commensurability leads to smaller interlayer distances. Using hybrid functional calculations, we derive electronic properties and band alignments for all the heterosystems and isolated two-dimensional (2D) crystals. Natural band offsets are derived from calculated electron affinities and ionization energies of 11 freestanding 2D crystals. They are compared with band alignments in true heterojunctions, using a quantum mechanical criterion, and available experimental data. For the hBN/SnSe 2 system, we show that hBN suffers an increase in band gap, while leaving almost unchanged the electronic properties of SnSe2. Similarly, MX2 (M = Mo, W; X = S, Se) over SnX2 preserve the natural discontinuities from each side of the heterobilayer. Significant charge transfer occurs in junctions with graphene, which becomes p-doped and forms an Ohmic contact with SnX2. Zirconium and hafnium dichalcogenides display stronger interlayer interactions, leading to larger shifts in band alignments with tin dichalcogenides. Significant orbital overlap is found, which creates zero conduction band offset systems. The validity of the Anderson electron affinity rule is discussed. Failures of this model are traced back to interlayer interaction, band hybridization, and quantum dipoles. The systematic work sheds light on interfacial engineering for future vdW electronic and optoelectronic devices.
Irreversible evolution of angular-dependent coercivity in Fe80Ni20 nanowire arrays: Detection of a single vortex state

NASA Astrophysics Data System (ADS)

Alikhani, M.; Ramazani, A.; Almasi Kashi, M.; Samanifar, S.; Montazer, A. H.

2016-09-01

The irreversible evolution of magnetic coercivity in arrays of 75 nm diameter Fe80Ni20 nanowires (NWs) has been explored by means of first-order reversal curve (FORC) analysis as a function of the angle between the magnetic field and the NW axis (0°≤θ≤90°). The Fe80Ni20 NWs with lengths up to 60 μm were fabricated using a pulsed electrodeposition method into hard-anodic aluminum oxide templates with an interpore distance of 275 nm. Investigating the interwire and intrawire magnetostatic interactions, the angular FORC (AFORC) diagrams indicated enhanced intrawire interactions with increasing length and θ (<90°), induced by a magnetization reversal through vortex domain wall (VDW) propagation. Intriguingly, in addition to the VDW mode, a single vortex state with broad irreversible switching of nucleation and annihilation fields was detected at θ=83° for 60 μm long NWs. At θ=90°, the NWs reversed magnetization through transverse domain wall, involving a reversible component by a fraction of 95%. Furthermore, the transition angle between the reversal modes was found to decrease with increasing aspect ratio from 200 to 800. The irreversible angular-dependent coercivity (HcIrrev(θ)) of Fe80Ni20 NWs was extracted from the AFORC measurements and compared with the major angular dependence of coercivity (HcMajor(θ)) obtained from the conventional hysteresis loop measurements. While HcMajor(θ) showed a non-monotonic behavior, HcIrrev(θ) constantly increased with increasing θ (<90°). On the other hand, using analytical models, a 93% agreement was obtained between the theoretical angular-dependent nucleation field and experimental HcIrrev(θ) for irreversible switching of VDW when 0°≤θ≤86°.
Development of a Windbreak Dust Predictive Model and Mitigation Planning Tool

DTIC Science & Technology

2013-12-01

laminar and turbulent flow (Uo = 5 m/s and Ls = 1 cm). Figure 28 Deposition fraction, DF, as a function of Stk * showing the collapse of the artificial...Figure 30 Deposition fraction, DF, as a function of the modified Stokes number ( Stk *). Figure 31 The measured decrease in horizontal PM10 flux, F...concentration. Sb Particle travel distance vi SERDP Strategic Environmental Research and Development Program Stk Stokes number Stk * Modified Stokes
Lack of small-scale clustering in 21-cm intensity maps crossed with 2dF galaxy densities at z ~ 0.08

NASA Astrophysics Data System (ADS)

Anderson, Christopher; Luciw, Nicholas; Li, Yi-Chao; Kuo, Cheng-Yu; Yadav, Jaswant; Masui, Kiyoshi; Chang, Tzu-Ching; Chen, Xuelei; Oppermann, Niels; Pen, Ue-Li; Timbie, Peter T.

2017-06-01

I report results from 21-cm intensity maps acquired from the Parkes radio telescope and cross-correlated with galaxy maps from the 2dF galaxy survey. The data span the redshift range 0.057
Gel point and fractal microstructure of incipient blood clots are significant new markers of hemostasis for healthy and anticoagulated blood.

PubMed

Evans, Phillip A; Hawkins, Karl; Morris, Roger H K; Thirumalai, Naresh; Munro, Roger; Wakeman, Lisa; Lawrence, Matthew J; Williams, P Rhodri

2010-10-28

Here we report the first application of a fractal analysis of the viscoelastic properties of incipient blood clots. We sought to ascertain whether the incipient clot's fractal dimension, D(f,) could be used as a functional biomarker of hemostasis. The incipient clot is formed at the gel point (GP) of coagulating blood, the GP demarcating a functional change from viscoelastic liquid to a viscoelastic solid. Incipient clots formed in whole healthy blood show a clearly defined value of D(f) within a narrow range that represents an index of clotting in health, where D(f) = 1.74 (± 0.07). A significant relationship is found between the incipient clot formation time, T(GP), and the activated partial thromboplastin time, whereas the association of D(f) with the microstructural characteristics of the incipient clot is supported by its significant correlation with fibrinogen. Our study reveals that unfractionated heparin not only prolongs the onset of clot formation but has a significant effect on its fractal microstructure. A progressive increase in unfractionated heparin concentration results in a linear decrease in D(f) and a corresponding prolongation in T(GP). The results represent a new, quantitative measure of clot quality derived from measurements on whole blood samples.
Comparison of capnovolumetry-derived dead space parameters with pulmonary function test in normal adults using histamine provocation.

PubMed

Sun, Xiaoli; Zhang, Yan; Yang, Wenlan; Liu, Jinming

2015-04-01

This study in healthy adults was conducted to explore the clinical application of capnovolumetric indices as compared to lung function parameters using histamine provocation. Forty healthy subjects received aerosol histamine or salbutamol in an automatic stimulation system with escalating doses of histamine. Dead space volumes of capnovolumetry and lung function parameters were examined with increased concentrations of histamine at a fixed time interval. The doses of histamine were selected from 0.0562 mg-2.2 mg and 0.1 mg salbutamol was inhaled when a maximal dose of histamine was reached. Baseline values in each group were calculated prior to histamine inhalation. Fowler dead space (VDF), Wolff dead space (VDW), threshold dead space (VDT), Bohr dead space (VDB), forced expiratory volume in 1 s (FEV1 ) and peak expiratory flow (PEF) showed a dose-dependent reduction following histamine provocation, but there were no statistical differences in the measurements at baseline and post S6 provocation. The value of dC3/DV at the maximal dose was significantly increased over its baseline value (P < 0.05). VDF, VDT and VDW were significantly increased after bronchodilator use (P < 0.05 or <0.01). The changes in capnovolumetry did not correspond with the results of lung function test. The dC3/DV and airway dead spaces of capnovolumetry in healthy adults are significantly increased compared to lung function parameters before or after bronchodilator use, suggesting that capnovolumetry is feasible in diagnostic evaluation of airway reactivity, especially for persons who are unable to undertake lung function test. © 2014 John Wiley & Sons Ltd.
Spectroscopic and metal-binding properties of DF3: an artificial protein able to accommodate different metal ions

PubMed Central

Torres Martin de Rosales, Rafael; Faiella, Marina; Farquhar, Erik; Que, Lawrence; Andreozzi, Concetta; Pavone, Vincenzo; Maglio, Ornella; Nastri, Flavia

2010-01-01

The design, synthesis, and metal-binding properties of DF3, a new de novo designed di-iron protein model are described (“DF” represents due ferri, Italian for “two iron,” “di-iron”). DF3 is the latest member of the DF family of synthetic proteins. They consist of helix–loop–helix hairpins, designed to dimerize and form an antiparallel four-helix bundle that encompasses a metal-binding site similar to those of non-heme carboxylate-bridged di-iron proteins. Unlike previous DF proteins, DF3 is highly soluble in water (up to 3 mM) and forms stable complexes with several metal ions (Zn, Co, and Mn), with the desired secondary structure and the expected stoichiometry of two ions per protein. UV–vis studies of Co(II) and Fe(III) complexes confirm a metal-binding environment similar to previous di-Co(II)- and di-Fe(III)-DF proteins, including the presence of a µ-oxo-di-Fe(III) unit. Interestingly, UV–vis, EPR, and resonance Raman studies suggest the interaction of a tyro-sine adjacent to the di-Fe(III) center. The design of DF3 was aimed at increasing the accessibility of small molecules to the active site of the four-helix bundle. Indeed, binding of azide to the di-Fe(III) site demonstrates a more accessible metal site compared with previous DFs. In fact, fitting of the binding curve to the Hill equation allows us to quantify a 150% accessibility enhancement, with respect to DF2. All these results represent a significant step towards the development of a functional synthetic DF metalloprotein. PMID:20225070

CODEX-aligned dietary fiber definitions help to bridge the ‘fiber gap’

PubMed Central

2014-01-01

A comprehensive dietary fiber (DF) definition was adopted by the CODEX Alimentarius Commission (CAC) (1) to reflect the current state of knowledge about DF, (2) to recognize that all substances that behave like fiber regardless of how they are produced can be named as DF if they show physiological benefits, and (3) to promote international harmonization for food labeling and food composition tables. This review gives the history and evolution of the state of DF knowledge as looked at by refinements in DF methods and definitions subsequent to the launch of the DF hypothesis. The refinements parallel both interventional and epidemiological research leading to better understanding of the role of DF in contributing to the numerous physiological benefits imparted by all the various digestion resistant carbohydrates. A comparison of the CODEX definition (including its footnote that authorizes the inclusion of polymers with DP 3–9) and approved CODEX Type 1 methods with other existing definitions and methods will point out differences and emphasize the importance of adoption of CODEX-aligned definitions by all jurisdictions. Such harmonization enables comparison of nutrition research, recommendations, food composition tables and nutrition labels the world over. A case will be made that fibers are analogous to vitamins, in that they vary in structure, function and amount needed, but each when present in the right amount contributes to optimal health. Since the intake of DF is significantly below recommended levels throughout the world, the recognition that ‘all fibers fit’ is an important strategy in bridging the ‘fiber gap’ by enfranchising and encouraging greater intake of foods with inherent and added DF. Fortifying foods with added DF makes it easier to increase intakes while maintaining calories at recommended levels. PMID:24725724
SCAPs Regulate Differentiation of DFSCs During Tooth Root Development in Swine

PubMed Central

Wu, Xiaoshan; Hu, Lei; Li, Yan; Li, Yang; Wang, Fu; Ma, Ping; Wang, Jinsong; Zhang, Chunmei; Jiang, Canhua; Wang, Songlin

2018-01-01

The tooth root transmits and balances occlusal forces through the periodontium to the alveolar bone. The periodontium, including the gingiva, the periodontal ligament, the cementum and the partial alveolar bone, derives from the dental follicle (DF), except for the gingiva. In the early developmental stages, the DF surrounds the tooth germ as a sphere and functions to promote tooth eruption. However, the morphological dynamics and factors regulating the differentiation of the DF during root elongation remain largely unknown. Miniature pigs are regarded as a useful experimental animal for modeling in craniofacial research because they are similar to humans with respect to dentition and mandible anatomy. In the present study, we used the third deciduous incisor of miniature pig as the model to investigate the factors influencing DF differentiation during root development. We found that the DF was shaped like a crescent and was located between the root apical and the alveolar bone. The expression levels of WNT5a, β-Catenin, and COL-I gradually increased from the center of the DF (beneath the apical foramen) to the lateral coronal corner, where the DF differentiates into the periodontium. To determine the potential regulatory role of the apical papilla on DF cell differentiation, we co-cultured dental follicle stem cells (DFSCs) with stem cells of the apical papilla (SCAPs). The osteogenesis and fibrogenesis abilities of DFSCs were inhibited when being co-cultured with SCAPs, suggesting that the fate of the DF can be regulated by signals from the apical papilla. The apical papilla may sustain the undifferentiated status of DFSCs before root development finishes. These data yield insight into the interaction between the root apex and surrounding DF tissues in root and periodontium development and shed light on the future study of root regeneration in large mammals. PMID:29511365
CODEX-aligned dietary fiber definitions help to bridge the 'fiber gap'.

PubMed

Jones, Julie Miller

2014-04-12

A comprehensive dietary fiber (DF) definition was adopted by the CODEX Alimentarius Commission (CAC) (1) to reflect the current state of knowledge about DF, (2) to recognize that all substances that behave like fiber regardless of how they are produced can be named as DF if they show physiological benefits, and (3) to promote international harmonization for food labeling and food composition tables. This review gives the history and evolution of the state of DF knowledge as looked at by refinements in DF methods and definitions subsequent to the launch of the DF hypothesis. The refinements parallel both interventional and epidemiological research leading to better understanding of the role of DF in contributing to the numerous physiological benefits imparted by all the various digestion resistant carbohydrates. A comparison of the CODEX definition (including its footnote that authorizes the inclusion of polymers with DP 3-9) and approved CODEX Type 1 methods with other existing definitions and methods will point out differences and emphasize the importance of adoption of CODEX-aligned definitions by all jurisdictions. Such harmonization enables comparison of nutrition research, recommendations, food composition tables and nutrition labels the world over. A case will be made that fibers are analogous to vitamins, in that they vary in structure, function and amount needed, but each when present in the right amount contributes to optimal health. Since the intake of DF is significantly below recommended levels throughout the world, the recognition that 'all fibers fit' is an important strategy in bridging the 'fiber gap' by enfranchising and encouraging greater intake of foods with inherent and added DF. Fortifying foods with added DF makes it easier to increase intakes while maintaining calories at recommended levels.
Temperature Dependence of Densities and Excess Molar Volumes of the Ternary Mixture (1-Butanol + Chloroform + Benzene) and its Binary Constituents (1-Butanol + Chloroform and 1-Butanol + Benzene)

NASA Astrophysics Data System (ADS)

Smiljanić, Jelena D.; Kijevčanin, Mirjana Lj.; Djordjević, Bojan D.; Grozdanić, Dušan K.; Šerbanović, Slobodan P.

2008-04-01

Densities ρ of the 1-butanol + chloroform + benzene ternary mixture and the 1-butanol + chloroform and 1-butanol + benzene binaries have been measured at six temperatures (288.15, 293.15, 298.15, 303.15, 308.15, and 313.15) K and atmospheric pressure, using an oscillating U-tube densimeter. From these densities, excess molar volumes ( V E) were calculated and fitted to the Redlich Kister equation for all binary mixtures and to the Nagata and Tamura equation for the ternary system. The Radojković et al. equation has been used to predict excess molar volumes of the ternary mixtures. Also, V E data of the binary systems were correlated by the van der Waals (vdW1) and Twu Coon Bluck Tilton (TCBT) mixing rules coupled with the Peng Robinson Stryjek Vera (PRSV) equation of state. The prediction and correlation of V E data for the ternary system were performed by the same models.
The 1-ethyl-3-methylimidazolium bis(trifluoro-methylsulfonyl)-imide ionic liquid nanodroplets on solid surfaces and in electric field: A molecular dynamics simulation study

NASA Astrophysics Data System (ADS)

Dong, Dengpan; Vatamanu, Jenel P.; Wei, Xiaoyu; Bedrov, Dmitry

2018-05-01

Atomistic molecular dynamics simulations were conducted to study the wetting states of 1-ethyl-3-methylimidazolium bis(trifluoro-methylsulfonyl)-imide ionic liquid (IL) nanodroplets on surfaces with different strengths of van der Waals (VDW) interactions and in the presence of an electric field. By adjusting the depth of Lennard-Jones potential, the van der Waals interaction between the solid surface and ionic liquid was systematically varied. The shape of the droplets was analyzed to extract the corresponding contact angle utilized to characterize wetting states of the nanodroplets. The explored range of surface-IL interactions allowed contact angles ranging from complete IL spreading on the surface to poor wettability. The effect of the external electrical field was explored by adding point charges to the surface atoms. Systems with two charge densities (±0.002 e/atom and ±0.004 e/atom) that correspond to 1.36 V/nm and 2.72 V/nm electric fields were investigated. Asymmetrical wetting states were observed for both cases. At 1.36 V/nm electric field, contributions of IL-surface VDW interactions and Coulombic interactions to the wetting state were competitive. At 2.72 V/nm field, electrostatic interactions dominate the interaction between the nanodroplet and surface, leading to enhanced wettability on all surfaces.
Low-amplitude clustering in low-redshift 21-cm intensity maps cross-correlated with 2dF galaxy densities

NASA Astrophysics Data System (ADS)

Anderson, C. J.; Luciw, N. J.; Li, Y.-C.; Kuo, C. Y.; Yadav, J.; Masui, K. W.; Chang, T.-C.; Chen, X.; Oppermann, N.; Liao, Y.-W.; Pen, U.-L.; Price, D. C.; Staveley-Smith, L.; Switzer, E. R.; Timbie, P. T.; Wolz, L.

2018-05-01

We report results from 21-cm intensity maps acquired from the Parkes radio telescope and cross-correlated with galaxy maps from the 2dF galaxy survey. The data span the redshift range 0.057 < z < 0.098 and cover approximately 1300 deg2 over two long fields. Cross-correlation is detected at a significance of 5.7 σ. The amplitude of the cross-power spectrum is low relative to the expected dark matter power spectrum, assuming a neutral hydrogen (H I) bias and mass density equal to measurements from the ALFALFA survey. The decrement is pronounced and statistically significant at small scales. At k ˜ 1.5 h Mpc-1, the cross-power spectrum is more than a factor of 6 lower than expected, with a significance of 15.3 σ. This decrement indicates a lack of clustering of neutral hydrogen (H I), a small correlation coefficient between optical galaxies and H I, or some combination of the two. Separating 2dF into red and blue galaxies, we find that red galaxies are much more weakly correlated with H I on k ˜ 1.5 h Mpc-1 scales, suggesting that H I is more associated with blue star-forming galaxies and tends to avoid red galaxies.
Large-scale symmetry-adapted perturbation theory computations via density fitting and Laplace transformation techniques: investigating the fundamental forces of DNA-intercalator interactions.

PubMed

Hohenstein, Edward G; Parrish, Robert M; Sherrill, C David; Turney, Justin M; Schaefer, Henry F

2011-11-07

Symmetry-adapted perturbation theory (SAPT) provides a means of probing the fundamental nature of intermolecular interactions. Low-orders of SAPT (here, SAPT0) are especially attractive since they provide qualitative (sometimes quantitative) results while remaining tractable for large systems. The application of density fitting and Laplace transformation techniques to SAPT0 can significantly reduce the expense associated with these computations and make even larger systems accessible. We present new factorizations of the SAPT0 equations with density-fitted two-electron integrals and the first application of Laplace transformations of energy denominators to SAPT. The improved scalability of the DF-SAPT0 implementation allows it to be applied to systems with more than 200 atoms and 2800 basis functions. The Laplace-transformed energy denominators are compared to analogous partial Cholesky decompositions of the energy denominator tensor. Application of our new DF-SAPT0 program to the intercalation of DNA by proflavine has allowed us to determine the nature of the proflavine-DNA interaction. Overall, the proflavine-DNA interaction contains important contributions from both electrostatics and dispersion. The energetics of the intercalator interaction are are dominated by the stacking interactions (two-thirds of the total), but contain important contributions from the intercalator-backbone interactions. It is hypothesized that the geometry of the complex will be determined by the interactions of the intercalator with the backbone, because by shifting toward one side of the backbone, the intercalator can form two long hydrogen-bonding type interactions. The long-range interactions between the intercalator and the next-nearest base pairs appear to be negligible, justifying the use of truncated DNA models in computational studies of intercalation interaction energies.
Large-scale symmetry-adapted perturbation theory computations via density fitting and Laplace transformation techniques: Investigating the fundamental forces of DNA-intercalator interactions

NASA Astrophysics Data System (ADS)

Hohenstein, Edward G.; Parrish, Robert M.; Sherrill, C. David; Turney, Justin M.; Schaefer, Henry F.

2011-11-01

Symmetry-adapted perturbation theory (SAPT) provides a means of probing the fundamental nature of intermolecular interactions. Low-orders of SAPT (here, SAPT0) are especially attractive since they provide qualitative (sometimes quantitative) results while remaining tractable for large systems. The application of density fitting and Laplace transformation techniques to SAPT0 can significantly reduce the expense associated with these computations and make even larger systems accessible. We present new factorizations of the SAPT0 equations with density-fitted two-electron integrals and the first application of Laplace transformations of energy denominators to SAPT. The improved scalability of the DF-SAPT0 implementation allows it to be applied to systems with more than 200 atoms and 2800 basis functions. The Laplace-transformed energy denominators are compared to analogous partial Cholesky decompositions of the energy denominator tensor. Application of our new DF-SAPT0 program to the intercalation of DNA by proflavine has allowed us to determine the nature of the proflavine-DNA interaction. Overall, the proflavine-DNA interaction contains important contributions from both electrostatics and dispersion. The energetics of the intercalator interaction are are dominated by the stacking interactions (two-thirds of the total), but contain important contributions from the intercalator-backbone interactions. It is hypothesized that the geometry of the complex will be determined by the interactions of the intercalator with the backbone, because by shifting toward one side of the backbone, the intercalator can form two long hydrogen-bonding type interactions. The long-range interactions between the intercalator and the next-nearest base pairs appear to be negligible, justifying the use of truncated DNA models in computational studies of intercalation interaction energies.
A theoretical study of symmetry-breaking organic overlayers on single- and bi-layer graphene

NASA Astrophysics Data System (ADS)

Morales-Cifuentes, Josue; Einstein, T. L.

2013-03-01

An ``overlayer'' of molecules that breaks the AB symmetry of graphene can produce (modify) a band gap in single- (bi-) layer graphene.[2] Since the triangular shaped trimesic acid (TMA) molecule forms two familiar symmetry breaking configurations, we are motivated to model TMA physisorption on graphene surfaces in conjunction with experiments by Groce et al. at UMD. Using VASP, with ab initio van der Waals density functionals (vdW-DF), we simulate adsorption of TMA onto a graphene surface in several symmetry-breaking arrangements in order to predict/understand the effect of TMA adsorption on experimental observables. Supported by NSF-MRSEC Grant DMR 05-20471.
Lysobacter enzymogenes uses two distinct cell-cell signaling systems for differential regulation of secondary-metabolite biosynthesis and colony morphology.

PubMed

Qian, Guoliang; Wang, Yulan; Liu, Yiru; Xu, Feifei; He, Ya-Wen; Du, Liangcheng; Venturi, Vittorio; Fan, Jiaqin; Hu, Baishi; Liu, Fengquan

2013-11-01

Lysobacter enzymogenes is a ubiquitous environmental bacterium that is emerging as a potentially novel biological control agent and a new source of bioactive secondary metabolites, such as the heat-stable antifungal factor (HSAF) and photoprotective polyene pigments. Thus far, the regulatory mechanism(s) for biosynthesis of these bioactive secondary metabolites remains largely unknown in L. enzymogenes. In the present study, the diffusible signal factor (DSF) and diffusible factor (DF)-mediated cell-cell signaling systems were identified for the first time from L. enzymogenes. The results show that both Rpf/DSF and DF signaling systems played critical roles in modulating HSAF biosynthesis in L. enzymogenes. Rpf/DSF signaling and DF signaling played negative and positive effects in polyene pigment production, respectively, with DF playing a more important role in regulating this phenotype. Interestingly, only Rpf/DSF, but not the DF signaling system, regulated colony morphology of L. enzymgenes. Both Rpf/DSF and DF signaling systems were involved in the modulation of expression of genes with diverse functions in L. enzymogenes, and their own regulons exhibited only a few loci that were regulated by both systems. These findings unveil for the first time new roles of the Rpf/DSF and DF signaling systems in secondary metabolite biosynthesis of L. enzymogenes.
Lysobacter enzymogenes Uses Two Distinct Cell-Cell Signaling Systems for Differential Regulation of Secondary-Metabolite Biosynthesis and Colony Morphology

PubMed Central

Qian, Guoliang; Wang, Yulan; Liu, Yiru; Xu, Feifei; He, Ya-Wen; Du, Liangcheng; Venturi, Vittorio; Fan, Jiaqin; Hu, Baishi

2013-01-01

Lysobacter enzymogenes is a ubiquitous environmental bacterium that is emerging as a potentially novel biological control agent and a new source of bioactive secondary metabolites, such as the heat-stable antifungal factor (HSAF) and photoprotective polyene pigments. Thus far, the regulatory mechanism(s) for biosynthesis of these bioactive secondary metabolites remains largely unknown in L. enzymogenes. In the present study, the diffusible signal factor (DSF) and diffusible factor (DF)-mediated cell-cell signaling systems were identified for the first time from L. enzymogenes. The results show that both Rpf/DSF and DF signaling systems played critical roles in modulating HSAF biosynthesis in L. enzymogenes. Rpf/DSF signaling and DF signaling played negative and positive effects in polyene pigment production, respectively, with DF playing a more important role in regulating this phenotype. Interestingly, only Rpf/DSF, but not the DF signaling system, regulated colony morphology of L. enzymgenes. Both Rpf/DSF and DF signaling systems were involved in the modulation of expression of genes with diverse functions in L. enzymogenes, and their own regulons exhibited only a few loci that were regulated by both systems. These findings unveil for the first time new roles of the Rpf/DSF and DF signaling systems in secondary metabolite biosynthesis of L. enzymogenes. PMID:23974132
The detection of the imprint of filaments on cosmic microwave background lensing

NASA Astrophysics Data System (ADS)

He, Siyu; Alam, Shadab; Ferraro, Simone; Chen, Yen-Chi; Ho, Shirley

2018-05-01

Galaxy redshift surveys, such as the 2-Degree-Field Survey (2dF)1, Sloan Digital Sky Survey (SDSS)2, 6-Degree-Field Survey (6dF)3, Galaxy And Mass Assembly survey (GAMA)4 and VIMOS Public Extragalactic Redshift Survey (VIPERS)5, have shown that the spatial distribution of matter forms a rich web, known as the cosmic web6. Most galaxy survey analyses measure the amplitude of galaxy clustering as a function of scale, ignoring information beyond a small number of summary statistics. Because the matter density field becomes highly non-Gaussian as structure evolves under gravity, we expect other statistical descriptions of the field to provide us with additional information. One way to study the non-Gaussianity is to study filaments, which evolve non-linearly from the initial density fluctuations produced in the primordial Universe. In our study, we report the detection of lensing of the cosmic microwave background (CMB) by filaments, and we apply a null test to confirm our detection. Furthermore, we propose a phenomenological model to interpret the detected signal, and we measure how filaments trace the matter distribution on large scales through filament bias, which we measure to be around 1.5. Our study provides new scope to understand the environmental dependence of galaxy formation. In the future, the joint analysis of lensing and Sunyaev-Zel'dovich observations might reveal the properties of `missing baryons', the vast majority of the gas that resides in the intergalactic medium, which has so far evaded most observations.
Reconstruction of low-index graphite surfaces

NASA Astrophysics Data System (ADS)

Thinius, Sascha; Islam, Mazharul M.; Bredow, Thomas

2016-07-01

The low-index graphite surfaces (10 1 -0), (10 1 -1), (11 2 -0) and (11 2 - 1) have been studied by density functional theory (DFT) including van-der-Waals (vdW) corrections. Different from the (0001) surface which has been extensively investigated both experimentally and theoretically, there is no comprehensive study on the (10 1 -0)- (10 1 -1)-, (11 2 -0)- and (11 2 - 1)-surfaces available, although they are of relevance for Li insertion processes, e.g. in Li-ion batteries. In this study the structure and stability of all non-(0001) low-index surfaces were calculated with RPBE-D3 and converged slab models. In all cases reconstruction involving bond formation between unsaturated carbon atoms of two neighboring graphene sheets reduces the surface energy dramatically. Two possible reconstruction patterns have been considered. The first possibility leads to formation of oblong nanotubes. Alternatively, the graphene sheets form bonds to different neighboring sheets at the upper and lower sides and sinusoidal structures are formed. Both structure types have similar stabilities. Based on the calculated surface energies the Gibbs-Wulff theorem was applied to construct the macroscopic shape of graphite single crystals.
Sphingomonas wittichii Strain RW1 Genome-Wide Gene Expression Shifts in Response to Dioxins and Clay

PubMed Central

Tsoi, Tamara V.; Iwai, Shoko; Liu, Cun; Fish, Jordan A.; Gu, Cheng; Johnson, Timothy A.; Zylstra, Gerben; Teppen, Brian J.; Li, Hui; Hashsham, Syed A.; Boyd, Stephen A.; Cole, James R.; Tiedje, James M.

2016-01-01

Sphingomonas wittichii strain RW1 (RW1) is one of the few strains that can grow on dibenzo-p-dioxin (DD). We conducted a transcriptomic study of RW1 using RNA-Seq to outline transcriptional responses to DD, dibenzofuran (DF), and the smectite clay mineral saponite with succinate as carbon source. The ability to grow on DD is rare compared to growth on the chemically similar DF even though the same initial dioxygenase may be involved in oxidation of both substrates. Therefore, we hypothesized the reason for this lies beyond catabolic pathways and may concern genes involved in processes for cell-substrate interactions such as substrate recognition, transport, and detoxification. Compared to succinate (SUC) as control carbon source, DF caused over 240 protein-coding genes to be differentially expressed, whereas more than 300 were differentially expressed with DD. Stress response genes were up-regulated in response to both DD and DF. This effect was stronger with DD than DF, suggesting a higher toxicity of DD compared to DF. Both DD and DF caused changes in expression of genes involved in active cross-membrane transport such as TonB-dependent receptor proteins, but the patterns of change differed between the two substrates. Multiple transcription factor genes also displayed expression patterns distinct to DD and DF growth. DD and DF induced the catechol ortho- and the salicylate/gentisate pathways, respectively. Both DD and DF induced the shared down-stream aliphatic intermediate compound pathway. Clay caused category-wide down-regulation of genes for cell motility and chemotaxis, particularly those involved in the synthesis, assembly and functioning of flagella. This is an environmentally important finding because clay is a major component of soil microbes’ microenvironment influencing local chemistry and may serve as a geosorbent for toxic pollutants. Similar to clay, DD and DF also affected expression of genes involved in motility and chemotaxis. PMID:27309357
Functional Effects of Hyperthyroidism on Cardiac Papillary Muscle in Rats.

PubMed

Vieira, Fabricio Furtado; Olivoto, Robson Ruiz; Silva, Priscyla Oliveira da; Francisco, Julio Cesar; Fogaça, Rosalvo Tadeu Hochmuller

2016-12-01

Hyperthyroidism is currently recognized to affect the cardiovascular system, leading to a series of molecular and functional changes. However, little is known about the functional influence of hyperthyroidism in the regulation of cytoplasmic calcium and on the sodium/calcium exchanger (NCX) in the cardiac muscle. To evaluate the functional changes in papillary muscles isolated from animals with induced hyperthyroidism. We divided 36 Wistar rats into a group of controls and another of animals with hyperthyroidism induced by intraperitoneal T3 injection. We measured in the animals' papillary muscles the maximum contraction force, speed of contraction (+df/dt) and relaxation (-df/dt), contraction and relaxation time, contraction force at different concentrations of extracellular sodium, post-rest potentiation (PRP), and contraction force induced by caffeine. In hyperthyroid animals, we observed decreased PRP at all rest times (p < 0.05), increased +df/dt and -df/dt (p < 0.001), low positive inotropic response to decreased concentration of extracellular sodium (p < 0.001), reduction of the maximum force in caffeine-induced contraction (p < 0.003), and decreased total contraction time (p < 0.001). The maximal contraction force did not differ significantly between groups (p = 0.973). We hypothesize that the changes observed are likely due to a decrease in calcium content in the sarcoplasmic reticulum, caused by calcium leakage, decreased expression of NCX, and increased expression of a-MHC and SERCA2.
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.
Distribution of DNA in human Sertoli cell nucleoli.

PubMed

Mosgöller, W; Schöfer, C; Derenzini, M; Steiner, M; Maier, U; Wachtler, F

1993-10-01

For better understanding of nucleolar architecture, different techniques have been used to localize DNA within the dense fibrillar component (DF) or within the fibrillar centers (FC) by electron microscopy (EM). Since it still remains controversial which components contain DNA, we investigated the distribution of DNA in human Sertoli cells using various approaches. In situ hybridization (ISH) with human total genomic DNA as probe and the use of anti-DNA antibody were followed by immunogold detection. This allowed statistical evaluation of the signal density over individual components. The Feulgen-like osmium-ammine (OA) technique for the selective visualization of DNA was also applied. The anti-DNA antibodies detected DNA in mitochondria, in chromatin, and in the DF of the nucleolus. ISH using human total genomic DNA showed similar labeling patterns. The OA technique revealed DNA filaments in the FC and focal agglomerates of decondensed DNA within the DF. We conclude that (a) EM staining techniques that utilize colloidal gold appear to be less sensitive for DNA detection than the OA method, (b) the DF consists of different domains with different molecular composition, and (c) decondensed DNA is not necessarily confined to one particular nucleolar component.
Imaging exciton–polariton transport in MoSe2 waveguides

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

Hu, F.; Luan, Y.; Scott, M. E.

The exciton polariton (EP), a half-light and half-matter quasiparticle, is potentially an important element for future photonic and quantum technologies1-4. It provides both strong light-matter interactions and long-distance propagation that is necessary for applications associated with energy or information transfer. Recently, strongly-coupled cavity EPs at room temperature have been demonstrated in van der Waals (vdW) materials due to their strongly-bound excitons5-9. Here we report a nano-optical imaging study of waveguide EPs in MoSe2, a prototypical vdW semiconductor. The measured propagation length of the EPs is sensitive to the excitation photon energy and reaches over 12 μm. The polariton wavelength canmore » be conveniently altered from 600 nm down to 300 nm by controlling the waveguide thickness. Furthermore, we found an intriguing back-bending polariton dispersion close to the exciton resonance. The observed EPs in vdW semiconductors could be useful in future nanophotonic circuits operating in the near-infrared to visible spectral regions.« less
Imaging exciton–polariton transport in MoSe2 waveguides

DOE PAGES

Hu, F.; Luan, Y.; Scott, M. E.; ...

2017-05-08

The exciton polariton (EP), a half-light and half-matter quasiparticle, is potentially an important element for future photonic and quantum technologies1-4. It provides both strong light-matter interactions and long-distance propagation that is necessary for applications associated with energy or information transfer. Recently, strongly-coupled cavity EPs at room temperature have been demonstrated in van der Waals (vdW) materials due to their strongly-bound excitons5-9. Here we report a nano-optical imaging study of waveguide EPs in MoSe2, a prototypical vdW semiconductor. The measured propagation length of the EPs is sensitive to the excitation photon energy and reaches over 12 μm. The polariton wavelength canmore » be conveniently altered from 600 nm down to 300 nm by controlling the waveguide thickness. Furthermore, we found an intriguing back-bending polariton dispersion close to the exciton resonance. The observed EPs in vdW semiconductors could be useful in future nanophotonic circuits operating in the near-infrared to visible spectral regions.« less
Phonon-Assisted Ultrafast Charge Transfer at van der Waals Heterostructure Interface.

PubMed

Zheng, Qijing; Saidi, Wissam A; Xie, Yu; Lan, Zhenggang; Prezhdo, Oleg V; Petek, Hrvoje; Zhao, Jin

2017-10-11

The van der Waals (vdW) interfaces of two-dimensional (2D) semiconductor are central to new device concepts and emerging technologies in light-electricity transduction where the efficient charge separation is a key factor. Contrary to general expectation, efficient electron-hole separation can occur in vertically stacked transition-metal dichalcogenide heterostructure bilayers through ultrafast charge transfer between the neighboring layers despite their weak vdW bonding. In this report, we show by ab initio nonadiabatic molecular dynamics calculations, that instead of direct tunneling, the ultrafast interlayer hole transfer is strongly promoted by an adiabatic mechanism through phonon excitation occurring on 20 fs, which is in good agreement with the experiment. The atomic level picture of the phonon-assisted ultrafast mechanism revealed in our study is valuable both for the fundamental understanding of ultrafast charge carrier dynamics at vdW heterointerfaces as well as for the design of novel quasi-2D devices for optoelectronic and photovoltaic applications.

Can nonadditive dispersion forces explain chain formation of nanoparticles?

NASA Astrophysics Data System (ADS)

Kwaadgras, Bas W.; Verdult, Maarten W. J.; Dijkstra, Marjolein; van Roij, René

2013-03-01

We study to what extent dielectric nanoparticles prefer to self-assemble into linear chains or into more compact structures. To calculate the Van der Waals (VdW) attraction between the clusters we use the Coupled Dipole Method (CDM), which treats each atom in the nanoparticle as an inducible oscillating point dipole. The VdW attraction then results from the full many-body interactions between the dipoles. For non-capped nanoparticles, we calculate in which configuration the VdW attraction is maximal. We find that in virtually all cases we studied, many-body effects only result in local potential minima at the linear configuration, as opposed to global ones, and that these metastable minima are in most cases rather shallow compared to the thermal energy. In this work, we also compare the CDM results with those from Hamaker-de Boer and Axilrod-Teller theory to investigate the influence of the many-body effects and the accuracy of these two approximate methods.
Asymmetric van der Waals Forces Drive Orientation of Compositionally Anisotropic Nanocylinders within Smectic Arrays: Experiment and Simulation

PubMed Central

Smith, Benjamin D.; Fichthorn, Kristen A.; Kirby, David J.; Quimby, Lisa M.; Triplett, Derek A.; González, Pedro; Hernández, Darimar; Keating, Christine D.

2014-01-01

Understanding how micro- and nanoparticles interact is important for achieving bottom-up assembly of desired structures. Here, we examine the self-assembly of two-component, compositionally asymmetric nanocylinders that sediment from solution onto a solid surface. These particles spontaneously formed smectic arrays. Within the rows of an array, nanocylinders tended to assemble such that neighboring particles had the same orientation of their segments. As a probe of interparticle interactions, we classified nanocylinder alignments by measuring the segment orientations of many sets of neighboring particles. Monte Carlo simulations incorporating an exact expression for the van der Waals (vdW) energy indicate that differences in the vdW interactions, even when small, are the key factor in producing observed segment alignment. These results point to asymmetrical vdW interactions as a potentially powerful means of controlling orientation in multicomponent cylinder arrays, and suggest that designing for these interactions could yield new ways to control self-assembly. PMID:24308771
Effect of physisorbed molecules and an external external fields on the metallic Shockley surface state of Cu(111): A density functional theory study

NASA Astrophysics Data System (ADS)

Berland, Kristian; Einstein, T. L.; Hyldgaard, Per

2012-02-01

To manipulate the Cu(111) partially-filled Shockley surface state, we study its response to an external fieldootnotetextKB, TLE, PH; arXiv 1109:6706 E and physisorbed PAHs and quinone molecules. We use density-functional theory calculations with periodic-boundary conditions. The van der Waals density functional version vdW-DF2 accounts for the molecular adsorption. The issue that the Kohn-Sham wave functions couple to both sides of the Cu slab is handled with a decoupling scheme based on a rotation in Hilbert space. A convergence study reveals that to obtain a proper Shockley surface state, 6 Cu layers is sufficient, while 15 is optimal. We use 6 layers for the response to the molecules and 15 to external field. We find that the surface state displays isotropic dispersion (up to order k^6), free-electron like until the Fermi wave vector but with a significant quartic component beyond. The shift in band minimum and effective mass depend linearly on E, with a smaller fractional change in the latter. Charge transfer occurs beyond the outermost copper atoms, and most of the screening is due to bulk electrons. We find that the molecular physisorption increases the band minimum, with the effect the of a quinone being much stronger than the corresponding PAH.
Relativistic coupled-cluster and density-functional studies of argon at high pressure

NASA Astrophysics Data System (ADS)

Schwerdtfeger, Peter; Steenbergen, Krista G.; Pahl, Elke

2017-06-01

The equation of state P (V ,T ) for solid argon is determined by the calculation of accurate static and vibrational terms in the free energy. The static component comes from a quantum theoretical many-body expansion summing over all energetic contributions from two-, three-, and four-body fragments treated with relativistic coupled cluster theory, while the lattice vibrations are described at an anharmonic level including two- and three-body forces as well as temperature effects. The dynamic part is calculated within the Debye and Einstein approximation, as well as by a more accurate phonon treatment where the vibrational motions in the lattice are coupled. Our results are in good agreement with room-temperature high-pressure experimental data up to ˜20 GPa. In the 20-100 GPa pressure range, however, we see considerable deviations between experiment and theory, perhaps indicating missing four-body contributions (beyond the quadruple dipole terms included here), missing five and higher-body effects, and the need to go beyond the coupled cluster singles-doubles with perturbative triples treatment in such higher-body forces. This contrasts with the results for solid neon, where excellent agreement has been achieved taking only two- and three-body forces into account [P. Schwerdtfeger and A. Hermann, Phys. Rev. B 80, 064106 (2009), 10.1103/PhysRevB.80.064106]. We demonstrate that the phase transition from fcc to hcp cannot account for the large discrepancies observed. Density functional calculations give very mixed results in the high-pressure region, but some functionals such as optB88-vdW (proposed by Lundqvist and co-workers) describe the many-body forces in argon reasonably well over the range of pressures investigated. Theoretical investigations of the heavier rare gas solids reaching experimental accuracy in the high-pressure regime therefore remain a significant challenge.
Core executive functions are associated with success in young elite soccer players.

PubMed

Vestberg, Torbjörn; Reinebo, Gustaf; Maurex, Liselotte; Ingvar, Martin; Petrovic, Predrag

2017-01-01

Physical capacity and coordination cannot alone predict success in team sports such as soccer. Instead, more focus has been directed towards the importance of cognitive abilities, and it has been suggested that executive functions (EF) are fundamentally important for success in soccer. However, executive functions are going through a steep development from adolescence to adulthood. Moreover, more complex EF involving manipulation of information (higher level EF) develop later than simple executive functions such as those linked to simple working memory capacity (Core EF). The link between EF and success in young soccer players is therefore not obvious. In the present study we investigated whether EF are associated with success in soccer in young elite soccer players. We performed tests measuring core EF (a demanding working memory task involving a variable n-back task; dWM) and higher level EF (Design Fluency test; DF). Color-Word Interference Test and Trail Making Test were performed on an exploratory level as they contain a linguistic element. The lower level EF test (dWM) was taken from CogStateSport computerized concussion testing and the higher level EF test (DF) was from Delis-Kaplan Executive Function System test battery (D-KEFS). In a group of young elite soccer players (n = 30; aged 12-19 years) we show that they perform better than the norm in both the dWM (+0.49 SD) and DF (+0.86 SD). Moreover, we could show that both dWM and DF correlate with the number of goals the players perform during the season. The effect was more prominent for dWM (r = 0.437) than for DF (r = 0.349), but strongest for a combined measurement (r = 0.550). The effect was still present when we controlled for intelligence, length and age in a partial correlation analysis. Thus, our study suggests that both core and higher level EF may predict success in soccer also in young players.
Core executive functions are associated with success in young elite soccer players

PubMed Central

Reinebo, Gustaf; Maurex, Liselotte; Ingvar, Martin; Petrovic, Predrag

2017-01-01

Physical capacity and coordination cannot alone predict success in team sports such as soccer. Instead, more focus has been directed towards the importance of cognitive abilities, and it has been suggested that executive functions (EF) are fundamentally important for success in soccer. However, executive functions are going through a steep development from adolescence to adulthood. Moreover, more complex EF involving manipulation of information (higher level EF) develop later than simple executive functions such as those linked to simple working memory capacity (Core EF). The link between EF and success in young soccer players is therefore not obvious. In the present study we investigated whether EF are associated with success in soccer in young elite soccer players. We performed tests measuring core EF (a demanding working memory task involving a variable n-back task; dWM) and higher level EF (Design Fluency test; DF). Color-Word Interference Test and Trail Making Test were performed on an exploratory level as they contain a linguistic element. The lower level EF test (dWM) was taken from CogStateSport computerized concussion testing and the higher level EF test (DF) was from Delis-Kaplan Executive Function System test battery (D-KEFS). In a group of young elite soccer players (n = 30; aged 12–19 years) we show that they perform better than the norm in both the dWM (+0.49 SD) and DF (+0.86 SD). Moreover, we could show that both dWM and DF correlate with the number of goals the players perform during the season. The effect was more prominent for dWM (r = 0.437) than for DF (r = 0.349), but strongest for a combined measurement (r = 0.550). The effect was still present when we controlled for intelligence, length and age in a partial correlation analysis. Thus, our study suggests that both core and higher level EF may predict success in soccer also in young players. PMID:28178738
Epidemiology of dengue fever in Hanoi from 2002 to 2010 and its meteorological determinants.

PubMed

Minh An, Dao Thi; Rocklöv, Joacim

2014-01-01

Dengue fever (DF) is a growing public health problem in Vietnam. The disease burden in Vietnam has been increasing for decades. In Hanoi, in contrast to many other regions, extrinsic drivers such as weather have not been proved to be predictive of disease frequency, which limits the usefulness of such factors in an early warning system. The purpose of this research was to review the epidemiology of DF transmission and investigate the role of weather factors contributing to occurrence of DF cases. Monthly data from Hanoi (2002-2010) were used to test the proposed model. Descriptive time-series analysis was conducted. Stepwise multivariate linear regression analysis assuming a negative binomial distribution was established through several models. The predictors used were lags of 1-3 months previous observations of mean rainfall, mean temperature, DF cases, and their interactions. Descriptive analysis showed that DF occurred annually and seasonally with an increasing time trend in Hanoi. The annual low occurred from December to March followed by a gradual increase from April to July with a peak in September, October. The amplitude of the annual peak varied between years. Statistically significant relationships were estimated at lag 1-3 with rainfall, autocorrelation, and their interaction while temperature was estimated as influential at lag 3 only. For these relationships, the final model determined a correlation of 92% between predicted number of dengue cases and the observed dengue disease frequencies. Although the model performance was good, the findings suggest that other forces related to urbanization, density of population, globalization with increasing transport of people and goods, herd immunity, government vector control capacity, and changes in serotypes are also likely influencing the transmission of DF. Additional research taking into account all of these factors besides climatic factors is needed to help developing and developed countries find the right intervention for controlling DF epidemics, and to set up early warning systems with high sensitivity and specificity. Immediate action to control DF outbreak in Hanoi should include an information, communication, and education program that focuses on training Hanoi residents to more efficiently eliminate stagnant puddles and water containers after each rainfall to limit the vector population growth.
Preclinical Studies in Support of Defibrotide for the Treatment of Multiple Myeloma and Other Neoplasias

PubMed Central

Mitsiades, Constantine S.; Rouleau, Cecile; Echart, Cinara; Menon, Krishna; Teicher, Beverly; Distaso, Maria; Palumbo, Antonio; Boccadoro, Mario; Anderson, Kenneth C.; Iacobelli, Massimo; Richardson, Paul G.

2015-01-01

Purpose of the study Defibrotide (DF), an orally bioavailable polydisperse oligonucleotide has promising activity in hepatic veno-occlusive disease (VOD), a stem cell transplantation-related toxicity, characterized by microangiopathy. The anti-thrombotic properties of DF and its minimal hemorrhagic risk could serve for treatment of cancer-associated thrombotic complications. Given its cytoprotective effect on endothelium, we investigated whether DF protects tumor cells from cytotoxic anti-tumor agents. Further, given its anti-adhesive properties, we evaluated whether DF modulates the protection conferred to multiple myeloma (MM) cells by bone marrow stromal cells (BMSCs). Methods-Results DF lacks significant single-agent in vitro cytotoxicity on MM or solid tumor cells and does not attenuate their in vitro response to dexamethasone, bortezomib, immunomodulatory thalidomide derivatives, and conventional chemotherapeutics, including melphalan and cyclophosphamide. Importantly, DF enhances in vivo chemosensitivity of MM and mammary carcinoma xenografts in animal models. In co-cultures of MM cells with BMSCs in vitro, DF enhances the MM cell sensitivity to melphalan and dexamethasone, decreases MM-BMSC adhesion and its sequelae, including NF-κB activation in MM and BMSCs, and associated cytokine production. Moreover, DF inhibits expression and/or function of key mediators of MM interaction with BMSC and endothelium, including heparanase, angiogenic cytokines and adhesion molecules. Conclusion Defibrotide’s in vivo chemosensitizing properties and lack of direct in vitro activity against tumor cells suggest that it favorably modulates antitumor interactions between BMSC and endothelia in the tumor microenvironment. These data support clinical studies of DF in combination with conventional and novel therapies to potentially improve patient outcome in MM and other malignancies. PMID:19228727
DF-1, A Nontoxic Carbon Fullerene Based Antioxidant, is Effective as a Biomedical Countermeasure Against Radiation

NASA Technical Reports Server (NTRS)

Theriot, Corey A.; Casey, Rachael; Conyers, Jodie; Wu, Honglu

2010-01-01

A long-term goal of radiation research is the mitigation of inherent risks of radiation exposure. Thus the study and development of safe agents, whether biomedical or dietary, that act as effective radioprotectors is an important step in accomplishing this long-term goal. Some of the most effective agents to date have been aminothiols and their derivatives. Unfortunately, most of these agents have side effects such as nausea, vomiting, hypotension, weakness, and fatigability. For example, nausea and emesis occur in most patients treated with WR-2721 (Amifostine), requiring the use of effective antiemetics, with hypotension being the dose-limiting side effect in patients treated. Clearly, the need for a radioprotector that is both effective and safe still exists. Development of biocompatible nano-materials for radioprotection is a promising emerging technology that could be exploited to address the need to minimize biological effects when exposure is unavoidable. Testing free radical scavenging nanoparticles for potential use in radioprotection is exciting and highly relevant. Initial investigations presented here demonstrate the ability of a particular functionalized carbon fullerene nanoparticle, (DF-1), to act as an effective radioprotector. DF-1 was first identified as the most promising candidate in a screen of several functionalized carbon fullerenes based on lack of toxicity and antioxidant therapeutic potential against oxidative injuries (i.e. organ reperfusion and ionizing radiation). Subsequently, DF-1 has been shown to reduce chromosome aberration yield and cell death, as well as overall ROS levels in human lymphocytes and fibroblasts after exposure to gamma radiation and energetic protons while demonstrating no associated toxicity. The dose-reducing factor of DF-1 at LD50 is nearly 2.0 for gamma radiation. In addition, DF-1 treatment also significantly prevented cell cycle arrest after exposure. Finally, DF-1 markedly attenuated COX2 upregulation in cell culture after irradiation thus preventing an inflammatory response to irradiation. Taken together, these results suggest that DF-1 provides potent protection against several deleterious cellular consequences of irradiation in mammalian systems including oxidative stress, DNA damage, inflammation and cell death.
Molecular dynamics simulation and TDDFT study of the structures and UV-vis absorption spectra of MCT-β-CD and its inclusion complexes.

PubMed

Lu, Huijuan; Wang, Yujiao; Xie, Xiaomei; Chen, Feifei; Li, Wei

2015-01-01

In this research, the inclusion ratios and inclusion constants of MCT-β-CD/PERM and MCT-β-CD/CYPERM inclusion complexes were measured by UV-vis and fluorescence spectroscopy. The inclusion ratios are both 1:1, and the inclusion constants are 60 and 342.5 for MCT-β-CD/PERM and MCT-β-CD/CYPERM, respectively. The stabilities of inclusion complexes were investigated by MD simulation. MD shows that VDW energy plays a vital role in the stability of inclusion complex, and the destruction of inclusion complex is due to the increasing temperature. The UV-vis absorption spectra of MCT-β-CD and its inclusion complexes were studied by time-dependent density functional theory (TDDFT) method employing BLYP-D3, B3LYP-D3 and M06-2X-D3 functionals. BLYP-D3 well reproduces the UV-vis absorption spectrum and reveals that the absorption bands of MCT-β-CD mainly arise from n→π(∗) and n→σ(∗) transition, and those of inclusion complexes mainly arise from intramolecular charge transfer (ICT). ICT results in the shift of main absorption bands of MCT-β-CD. Copyright © 2015 Elsevier B.V. All rights reserved.
A decision-making framework for the grouping and testing of nanomaterials (DF4nanoGrouping).

PubMed

Arts, Josje H E; Hadi, Mackenzie; Irfan, Muhammad-Adeel; Keene, Athena M; Kreiling, Reinhard; Lyon, Delina; Maier, Monika; Michel, Karin; Petry, Thomas; Sauer, Ursula G; Warheit, David; Wiench, Karin; Wohlleben, Wendel; Landsiedel, Robert

2015-03-15

The European Centre for Ecotoxicology and Toxicology of Chemicals (ECETOC) 'Nano Task Force' proposes a Decision-making framework for the grouping and testing of nanomaterials (DF4nanoGrouping) that consists of 3 tiers to assign nanomaterials to 4 main groups, to perform sub-grouping within the main groups and to determine and refine specific information needs. The DF4nanoGrouping covers all relevant aspects of a nanomaterial's life cycle and biological pathways, i.e. intrinsic material and system-dependent properties, biopersistence, uptake and biodistribution, cellular and apical toxic effects. Use (including manufacture), release and route of exposure are applied as 'qualifiers' within the DF4nanoGrouping to determine if, e.g. nanomaterials cannot be released from a product matrix, which may justify the waiving of testing. The four main groups encompass (1) soluble nanomaterials, (2) biopersistent high aspect ratio nanomaterials, (3) passive nanomaterials, and (4) active nanomaterials. The DF4nanoGrouping aims to group nanomaterials by their specific mode-of-action that results in an apical toxic effect. This is eventually directed by a nanomaterial's intrinsic properties. However, since the exact correlation of intrinsic material properties and apical toxic effect is not yet established, the DF4nanoGrouping uses the 'functionality' of nanomaterials for grouping rather than relying on intrinsic material properties alone. Such functionalities include system-dependent material properties (such as dissolution rate in biologically relevant media), bio-physical interactions, in vitro effects and release and exposure. The DF4nanoGrouping is a hazard and risk assessment tool that applies modern toxicology and contributes to the sustainable development of nanotechnological products. It ensures that no studies are performed that do not provide crucial data and therefore saves animals and resources. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.
Computational Investigation of Graphene-Carbon Nanotube-Polymer Composite

NASA Astrophysics Data System (ADS)

Jha, Sanjiv; Roth, Michael; Todde, Guido; Subramanian, Gopinath; Shukla, Manoj; Univ of Southern Mississippi Collaboration; US Army Engineer Research; Development Center 3909 Halls Ferry Road Vicksburg, MS 39180, USA Collaboration

Graphene is a single atom thick two dimensional carbon sheet where sp2 -hybridized carbon atoms are arranged in a honeycomb structure. The functionalization of graphene and carbon nanotubes (CNTs) with polymer is a route for developing high performance nanocomposite materials. We study the interfacial interactions among graphene, CNT, and Nylon 6 polymer using computational methods based on density functional theory (DFT) and empirical force-field. Our DFT calculations are carried out using Quantum-ESPRESSO electronic structure code with van der Waals functional (vdW-DF2), whereas the empirical calculations are performed using LAMMPS with the COMPASS force-field. Our results demonstrated that the interactions between (8,8) CNT and graphene, and between CNT/graphene and Nylon 6 consist mostly of van der Waals type. The computed Young's moduli indicated that the mechanical properties of carbon nanostructures are enhanced by their interactions with polymer. The presence of Stone-Wales (SW) defects lowered the Young's moduli of carbon nanostructures.
Combined effect of plant sterols and dietary fiber for the treatment of hypercholesterolemia.

PubMed

Castellanos-Jankiewicz, Ashley; Del Bosque-Plata, Laura; Tejero, M Elizabeth

2014-06-01

Hypercholesterolemia is a major contributor for disease burden in both the developed and developing world and an important risk factor for cardiovascular diseases (CVD). Phytosterols (PhS) and dietary fiber (DF) act as low density lipoprotein cholesterol (LDL-C) lowering agents, offering an effective treatment against high blood cholesterol and CVD. The aim of this review was to consider clinical evidence that analyzed the combination of PhS and DF in a cereal carrier for lowering LDL-C. Electronic database searches were carried out to identify peer-reviewed journal articles, from which five intervention studies that combined both components in a cereal carrier were identified and included in the present review. LDL-C lowering effects varied widely among studies, due to large heterogeneity in study design, subject baseline characteristics, length of the interventions, PhS and DF dosage and type of DF used. In relation to a time of intake, three studies suggested a frequency or distribution of the product's consumption during the day, while two studies did not consider this factor. Overall, the selected studies found significant differences on LDL-C concentrations, although not all of them reached the expected outcomes. Future research should be conducted to explore the effect that different types of DF exert on LDL-C when combined with PhS, and to analyze the effect of the product's time of intake in order to suggest an optimal moment of the day for its consumption.
Calculation of Beach Change Under Interacting Cross-Shore and Longshore Processes

DTIC Science & Technology

2010-01-01

the dune toe , berm width, and shoreline position are calculated, while maintaining longshore transport rates representative of the regional long-term...during growth together with the dune shape, the seaward movement of the dune toe ΔyDw for a given increase in dune volume ΔVDw is: ΔyDw = ΔVDw DD ð2Þ...Expressing Eq. (1) in terms of dune toe advance yields: dyDw dt = qw DD ð3Þ It is assumed that sand transport to the dune is related to thewidth of the
Patient DF's visual brain in action: Visual feedforward control in visual form agnosia.

PubMed

Whitwell, Robert L; Milner, A David; Cavina-Pratesi, Cristiana; Barat, Masihullah; Goodale, Melvyn A

2015-05-01

Patient DF, who developed visual form agnosia following ventral-stream damage, is unable to discriminate the width of objects, performing at chance, for example, when asked to open her thumb and forefinger a matching amount. Remarkably, however, DF adjusts her hand aperture to accommodate the width of objects when reaching out to pick them up (grip scaling). While this spared ability to grasp objects is presumed to be mediated by visuomotor modules in her relatively intact dorsal stream, it is possible that it may rely abnormally on online visual or haptic feedback. We report here that DF's grip scaling remained intact when her vision was completely suppressed during grasp movements, and it still dissociated sharply from her poor perceptual estimates of target size. We then tested whether providing trial-by-trial haptic feedback after making such perceptual estimates might improve DF's performance, but found that they remained significantly impaired. In a final experiment, we re-examined whether DF's grip scaling depends on receiving veridical haptic feedback during grasping. In one condition, the haptic feedback was identical to the visual targets. In a second condition, the haptic feedback was of a constant intermediate width while the visual target varied trial by trial. Despite this incongruent feedback, DF still scaled her grip aperture to the visual widths of the target blocks, showing only normal adaptation to the false haptically-experienced width. Taken together, these results strengthen the view that DF's spared grasping relies on a normal mode of dorsal-stream functioning, based chiefly on visual feedforward processing. Copyright © 2014 Elsevier B.V. All rights reserved.
Effect of in vitro and in vivo organotin exposures on the immune functions of murray cod (Maccullochella peelii peelii).

PubMed

Harford, Andrew J; O'Halloran, Kathryn; Wright, Paul E A

2007-08-01

Murray cod (Maccullochella peelii peelii) is an iconic native Australian freshwater fish and an ideal species for ecotoxicological testing of environmental pollutants. The species is indigenous to the Murray-Darling basin, which is the largest river system in Australia but also the ultimate sink for many environmental pollutants. The organotins tributyltin (TBT) and dibutyltin (DBT) are common pollutants of both freshwater and marine environments and are also known for their immunotoxicity in both mammals and aquatic organisms. In this study, TBT and DBT were used as exemplar immunotoxins to assess the efficiency of immune function assays (i.e., mitogen-stimulated lymphoproliferation, phagocytosis in head kidney tissue, and serum lysozyme activity) and to compare the sensitivity of Murray cod to other fish species. The organotins were lethal to Murray cod at concentrations previously reported as sublethal in rainbow trout (i.e., intraperitoneal [i.p.] lethal dose to 75% of the Murray cod [LD75] = 2.5 mg/kg DBT and i.p. lethal dose to 100% of the Murray cod [LD100] = 12.5 mg/kg TBT and DBT). In vivo TBT exposure at 0.1 and 0.5 mg/kg stimulated the phagocytic function of Murray cod (F = 6.89, df = 18, p = 0.004), while the highest concentration of 2.5 mg/kg TBT decreased lymphocyte numbers (F = 7.92, df = 18, p = 0.02) and mitogenesis (F = 3.66, df = 18, p = 0.035). Dibutyltin was the more potent immunosuppressant in Murray cod, causing significant reductions in phagocytic activity (F = 5.34, df = 16, p = 0.013) and lymphocyte numbers (F = 10.63, df = 16, p = 0.001).
Thermochemistry analyses for transformation of C6 glucose compound into C9, C12 and C15 alkanes using density functional theory

NASA Astrophysics Data System (ADS)

Verma, Anand Mohan; Kishore, Nanda

2017-02-01

The hydrolysis of cellulose fraction of biomass yields C6 glucose which further can be transformed into long-chain hydrocarbons by C-C coupling. In this study, C6 glucose is transformed into three chain alkanes, namely, C9, C12 and C15 using C-C coupling reactions under the gas and aqueous phase milieus. The geometry optimisation and vibrational frequency calculations are carried out at well-known hybrid-GGA functional, B3LYP with the basis set of 6-31+g(d,p) under the density functional theory framework. The single point energetics are calculated at M05-2X/6-311+g(3df,2p) level of theory. All thermochemical properties are calculated over a wide range of temperature between 300 and 900 K at an interval of 100 K. The thermochemistry suggested that the aqueous phase behaviour is suitable for the hydrolysis of sugar into long-chain alkanes compared to gas-phase environment. The hydrodeoxygenation reactions under each reaction pathway are found as most favourable reactions in both phases; however, aqueous phase dominates over gas phase in all discussed thermodynamic parameters.
Communication: Infrared spectroscopy of protonated allyl-trimethylsilane: Evidence for the β-silyl effect

NASA Astrophysics Data System (ADS)

Chiavarino, Barbara; Crestoni, Maria Elisa; Lemaire, Joel; Maitre, Philippe; Fornarini, Simonetta

2013-08-01

β-trimethylsilyl-2-propyl cation has been formed by the gas phase protonation of allyl-trimethylsilane and characterized by infrared multiple photon dissociation spectroscopy. The experimental Cβ-Cα+ stretching feature at 1586 cm-1, remarkably blue-shifted with respect to a C-C single bond stretching mode, is indicative of high double bond character, a signature of β-stabilizing effect due to hyperconjugation of the trimethylsilyl group in the β-position with respect to the positively charged carbon. Density functional theory calculations at the B3LYP/6-311++G(2df,2p) level yield the optimized geometries and IR spectra for candidate isomeric cations and for neutral and charged reference species.
Dynamic surface electronic reconstruction as symmetry-protected topological orders in topological insulator Bi2Se3

NASA Astrophysics Data System (ADS)

Shu, G. J.; Liou, S. C.; Karna, S. K.; Sankar, R.; Hayashi, M.; Chou, F. C.

2018-04-01

The layered narrow-band-gap semiconductor Bi2Se3 is composed of heavy elements with strong spin-orbital coupling, which has been identified both as a good candidate for a thermoelectric material with high thermoelectric figure of merit (Z T ) and as a topological insulator of the Z2 type with a gapless surface band in a Dirac-cone shape. The existence of a conjugated π -bond system on the surface of each Bi2Se3 quintuple layer is proposed based on an extended valence bond model with valence electrons distributed in the hybridized orbitals. Supporting experimental evidence of a two-dimensional (2D) conjugated π -bond system on each quintuple layer of Bi2Se3 is provided using electron energy-loss spectroscopy and electron density mapping through inverse Fourier transform of x-ray diffraction data. Quantum chemistry calculations support the π -bond existence between partially filled 4 pz orbitals of Se via side-to-side orbital overlap positively. The conjugated π -bond system on the surface of each quintuple Bi2Se3 layer is proposed to be similar to that found in graphite (graphene) and responsible for the unique 2D conduction mechanism. The van der Waals (vdW) attractive force between quintuple layers is interpreted to be coming from the antiferroelectrically ordered effective electric dipoles, which are constructed with π -bond trimer pairs on Se layers across the vdW gap of minimized Coulomb repulsion.
Physical study of minced fish muscle with a white-grape by-product added as an ingredient.

PubMed

Sánchez-Alonso, I; Solas, M T; Borderías, A J

2007-03-01

Functional properties of a white grape dietary fiber concentrate (WGDF) obtained from wine industry residues were determined with a view to their use as potential functional ingredient in seafood products. The main features of interest of WGDF are that it is a natural product containing high concentrations of dietary fiber (DF) with a high-soluble DF (sDF)/insoluble DF (iDF) ratio and associated bioactive compounds; as such it is considered potentially suitable for use as dietary fiber in the enrichment of foods. WGDF was therefore added to minced fish muscle (MFM) of horse mackerel (Trachurus trachurus) to take advantage of its technological properties, and also to enrich a food product that is a functional product in itself but does not contain dietary fiber. WGDF was added (2% and 4%) to MFM, which was stored for 6 mo at -20 degrees C, and a further lot was vacuum packed. Physical and mechanical properties, sensory and color analyses, microscopy, and electrophoretic profiles were all done in samples every month. The results indicate that WGDF had good functional properties, high water and oil retention capacity, and considerable swelling properties, which would make it useful as a natural ingredient in foods. The addition of WGDF to MFM augmented aggregation of myofibrillar proteins in the course of frozen storage, although electrophoretic profiles were very similar in samples with and without WGDF. The addition of WGDF to MFM made samples softer and less springy and cohesive. SEM showed good dispersion of WGDF in MFM but the matrix was more discontinuous than in the control. Water retention was significantly enhanced when WGDF was added, and the cooking yield improved. In sensory evaluation, samples containing 2% of WGDF scored highest in overall acceptance as compared with the control. Vacuum packing did not significantly affect the properties considered during frozen storage.

Epidemiology of malaria in pregnancy in central India.

PubMed Central

Singh, N.; Shukla, M. M.; Sharma, V. P.

1999-01-01

Analysis of three years of data from a malaria clinic operated by the Indian Council of Medical Research (ICMR) in the Government Medical College Hospital in Jabalpur, central India, showed a high malaria prevalence among pregnant women, which was statistically highly significant (P < 0.0001) compared with the situation among nonpregnant women. Cerebral malaria was a common complication of severe Plasmodium falciparum infection, with a high mortality during pregnancy, requiring immediate attention. The study also showed that malaria infection was more frequent in primigravidae, falling progressively with increasing parity. Mean parasite densities were significantly higher in pregnant women compared with nonpregnant women for both P. falciparum (P < 0.001; df = 137) and P. vivax (P < 0.05; df = 72) infection. Pregnant women with falciparum or vivax malaria were significantly more anaemic than noninfected pregnant women or infected nonpregnant women. The average weight of 155 neonates from infected mothers was 350 g less than that of 175 neonates from noninfected mothers. This difference in birth weight was statistically significant for both P. falciparum (P < 0.0001; df = 278) and P. vivax (P < 0.0001; df = 223) infection. Congenital malaria was not recorded. We conclude that pregnant women from this geographical area require systematic intervention owing to their high susceptibility to malaria during pregnancy and the puerperium. PMID:10444880
Effects of consuming diets containing Agave tequilana dietary fibre and jamaica calyces on body weight gain and redox status in hypercholesterolemic rats.

PubMed

Sáyago-Ayerdi, Sonia G; Mateos, Raquel; Ortiz-Basurto, Rosa I; Largo, Carlota; Serrano, José; Granado-Serrano, Ana Belén; Sarriá, Beatriz; Bravo, Laura; Tabernero, María

2014-04-01

Dietary fibre (DF) obtained from Agave tequilana, which is rich in fructans and insoluble DF, and jamaica calyces (Hibiscus sabdariffa), which is rich in DF and phenolic compounds, were assessed as new potential functional ingredients using the hypercholesterolemic animal model. Wistar rats (200-250 g) were divided into 3 groups (n=8) and fed with cholesterol-rich diets supplemented with cellulose (CC, control), agave DF (ADF) or ADF with jamaica calyces (ADF-JC). After consuming the test diets for 5 weeks, weight gain in the ADF-JC group was significantly lower than in the other groups. The ADF and ADF-JC groups had a reduced concentration of cholesterol transporters in the caecum tissue, although no changes were observed in the plasma lipid profile. Both treatments improved the redox status by reducing the malondialdehyde serum levels and protein oxidative damage, compared to the CC group. DF from A. tequilana alone, or in combination with jamaica calyces, shows promising potential as a bioactive ingredient. Copyright © 2013 Elsevier Ltd. All rights reserved.
Reframing the action and perception dissociation in DF: haptics matters, but how?

PubMed

Whitwell, Robert L; Buckingham, Gavin

2013-02-01

Goodale and Milner's (1992) "vision-for-action" and "vision-for-perception" account of the division of labor between the dorsal and ventral "streams" has come to dominate contemporary views of the functional roles of these two pathways. Nevertheless, some lines of evidence for the model remain controversial. Recently, Thomas Schenk reexamined visual form agnosic patient DF's spared anticipatory grip scaling to object size, one of the principal empirical pillars of the model. Based on this new evidence, Schenk rejects the original interpretation of DF's spared ability that was based on segregated processing of object size and argues that DF's spared grip scaling relies on haptic feedback to calibrate visual egocentric cues that relate the posture of the hand to the visible edges of the goal-object. However, a careful consideration of the tasks that Schenk employed reveals some problems with his claim. We suspect that the core issues of this controversy will require a closer examination of the role that cognition plays in the operation of the dorsal and ventral streams in healthy controls and in patient DF.
Rational-operator-based depth-from-defocus approach to scene reconstruction.

PubMed

Li, Ang; Staunton, Richard; Tjahjadi, Tardi

2013-09-01

This paper presents a rational-operator-based approach to depth from defocus (DfD) for the reconstruction of three-dimensional scenes from two-dimensional images, which enables fast DfD computation that is independent of scene textures. Two variants of the approach, one using the Gaussian rational operators (ROs) that are based on the Gaussian point spread function (PSF) and the second based on the generalized Gaussian PSF, are considered. A novel DfD correction method is also presented to further improve the performance of the approach. Experimental results are considered for real scenes and show that both approaches outperform existing RO-based methods.
Modelling a 3D structure for EgDf1 from shape Echinococcus granulosus: putative epitopes, phosphorylation motifs and ligand

NASA Astrophysics Data System (ADS)

Paulino, M.; Esteves, A.; Vega, M.; Tabares, G.; Ehrlich, R.; Tapia, O.

1998-07-01

EgDf1 is a developmentally regulated protein from the parasite Echinococcus granulosus related to a family of hydrophobic ligand binding proteins. This protein could play a crucial role during the parasite life cycle development since this organism is unable to synthetize most of their own lipids de novo. Furthermore, it has been shown that two related protein from other parasitic platyhelminths (Fh15 from Fasciola hepatica and Sm14 from Schistosoma mansoni) are able to confer protective inmunity against experimental infection in animal models. A three-dimensional structure would help establishing structure/function relationships on a knowledge based manner. 3D structures for EgDf1 protein were modelled by using myelin P2 (mP2) and intestine fatty acid binding protein (I-FABP) as templates. Molecular dynamics techniques were used to validate the models. Template mP2 yielded the best 3D structure for EgDf1. Palmitic and oleic acids were docked inside EgDf1. The present theoretical results suggest definite location in the secondary structure of the epitopic regions, consensus phosphorylation motifs and oleic acid as a good ligand candidate to EgDf1. This protein might well be involved in the process of supplying hydrophobic metabolites for membrane biosynthesis and for signaling pathways.
Three-particle annihilation in a 2D heterostructure revealed through data-hypercubic photoresponse microscopy (Conference Presentation)

NASA Astrophysics Data System (ADS)

Gabor, Nathaniel M.

2017-05-01

Van de Waals (vdW) heterostructures - which consist of precisely assembled atomically thin electronic materials - exhibit unusual quantum behavior. These quantum materials-by-design are of fundamental interest in basic scientific research and hold tremendous potential in advanced technological applications. Problematically, the fundamental optoelectronic response in these heterostructures is difficult to access using the standard techniques within the traditions of materials science and condensed matter physics. In the standard approach, characterization is based on the measurement of a small amount of one-dimensional data, which is used to gain a precise picture of the material properties of the sample. However, these techniques are fundamentally lacking in describing the complex interdependency of experimental degrees of freedom in vdW heterostructures. In this talk, I will present our recent experiments that utilize a highly data-intensive approach to gain deep understanding of the infrared photoresponse in vdW heterostructure photodetectors. These measurements, which combine state-of-the-art data analytics and measurement design with fundamentally new device structures and experimental parameters, give a clear picture of electron-hole pair interactions at ultrafast time scales.
Controllable Schottky barrier in GaSe/graphene heterostructure: the role of interface dipole

NASA Astrophysics Data System (ADS)

Si, Chen; Lin, Zuzhang; Zhou, Jian; Sun, Zhimei

2017-03-01

The discoveries of graphene and other related two-dimensional crystals have recently led to a new technology: van der Waals (vdW) heterostructures based on these atomically thin materials. Such a paradigm has been proved promising for a wide range of applications from nanoelectronics to optoelectronics and spintronics. Here, using first-principles calculations, we investigate the electronic structure and interface characteristics of a newly synthesized GaSe/graphene (GaSe/g) vdW heterostructure. We show that the intrinsic electronic properties of GaSe and graphene are both well preserved in the heterostructure, with a Schottky barrier formed at the GaSe/g interface. More interestingly, the band alignment between graphene and GaSe can be effectively modulated by tuning the interfacial distance or applying an external electric filed. This makes the Schottky barrier height (SBH) controllable, which is highly desirable in the electronic and optoelectronic devices based on vdW heterostructures. In particular, the tunability of the interface dipole and potential step is further uncovered to be the underlying mechanism that ensures this controllable tuning of SBH.
Ambient noise levels and characterization in Aegean region, Turkey

NASA Astrophysics Data System (ADS)

Sevim, Fatih; Zor, Ekrem; Açıkgöz, Cem; Tarancıoğlu, Adil

2018-03-01

We assessed the ambient noise level in the Aegean region and analyzed its diurnal variation and its relation to the earthquake detection capability of the Aegean Region Seismic Network (ARSN). We prepared probability density functions (PDFs) for 19 broadband stations in the Aegean region operated by the Earth and Marine Sciences Institute (EMSI) of the Marmara Research Center (MRC) of the Turkish Scientific Research Council (TÜBİTAK). The power spectral densities (PSDs) used to construct PDFs for each station were computed for the periods between 0.02 and 180 s. In addition, we generated noise map of the Aegean region for different periods using the PDFs to assess the origin of the noise. We analyzed earthquake activity in the region and found that there are more local events recorded at night than during the day for each station. This difference is strongly related to diurnal variation of background noise level for the period range mostly covering the frequency range for the local events. We observed daytime noise level 15 to 20 dB higher than that at the nighttime in high frequencies for almost all stations caused by its proximity to settled areas and roads. Additionally, we observed a splitting peak within the Double Frequency (DF) microseism band; it showed a clear noise increase around the short period DF band at all the stations, decreasing inland. This peak may be related to sea waves locally generated in the Aegean Sea. We also identified a prominent increase related to marble saw companies in some stations' noise PDFs.
Tunable Schottky barrier in van der Waals heterostructures of graphene and g-GaN

NASA Astrophysics Data System (ADS)

Sun, Minglei; Chou, Jyh-Pin; Ren, Qingqiang; Zhao, Yiming; Yu, Jin; Tang, Wencheng

2017-04-01

Using first-principles calculations, we systematically investigated the electronic properties of graphene/g-GaN van der Waals (vdW) heterostructures. We discovered that the Dirac cone of graphene could be quite well preserved in the vdW heterostructures. Moreover, a transition from an n-type to p-type Schottky contact at the graphene/g-GaN interface was induced with a decreased interlayer distance from 4.5 to 2.5 Å. This relationship is expected to enable effective control of the Schottky barrier, which is an important development in the design of Schottky devices.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Makarewicz, Jan, E-mail: jama@amu.edu.pl; Shirkov, Leonid

The pyridine-Ar (PAr) van der Waals (vdW) complex is studied using a high level ab initio method. Its structure, binding energy, and intermolecular vibrational states are determined from the analytical potential energy surface constructed from interaction energy (IE) values computed at the coupled cluster level of theory with single, double, and perturbatively included triple excitations with the augmented correlation consistent polarized valence double-ζ (aug-cc-pVDZ) basis set complemented by midbond functions. The structure of the complex at its global minimum with Ar at a distance of 3.509 Å from the pyridine plane and shifted by 0.218 Å from the center ofmore » mass towards nitrogen agrees well with the corresponding equilibrium structure derived previously from the rotational spectrum of PAr. The PAr binding energy D{sub e} of 392 cm{sup −1} is close to that of 387 cm{sup −1} calculated earlier at the same ab initio level for the prototypical benzene-Ar (BAr) complex. However, under an extension of the basis set, D{sub e} for PAr becomes slightly lower than D{sub e} for BAr. The ab initio vdW vibrational energy levels allow us to estimate the reliability of the methods for the determination of the vdW fundamentals from the rotational spectra. To disclose the character of the intermolecular interaction in PAr, the symmetry-adapted perturbation theory (SAPT) is employed for the analysis of different physical contributions to IE. It is found that SAPT components of IE can be approximately expressed in the binding region by only two of them: the exchange repulsion and dispersion energy. The total induction effect is negligible. The interrelations between various SAPT components found for PAr are fulfilled for a few other complexes involving aromatic molecules and Ar or Ne, which indicates that they are valid for all rare gas (Rg) atoms and aromatics.« less
Character of intermolecular interaction in pyridine-argon complex: Ab initio potential energy surface, internal dynamics, and interrelations between SAPT energy components.

PubMed

Makarewicz, Jan; Shirkov, Leonid

2016-05-28

The pyridine-Ar (PAr) van der Waals (vdW) complex is studied using a high level ab initio method. Its structure, binding energy, and intermolecular vibrational states are determined from the analytical potential energy surface constructed from interaction energy (IE) values computed at the coupled cluster level of theory with single, double, and perturbatively included triple excitations with the augmented correlation consistent polarized valence double-ζ (aug-cc-pVDZ) basis set complemented by midbond functions. The structure of the complex at its global minimum with Ar at a distance of 3.509 Å from the pyridine plane and shifted by 0.218 Å from the center of mass towards nitrogen agrees well with the corresponding equilibrium structure derived previously from the rotational spectrum of PAr. The PAr binding energy De of 392 cm(-1) is close to that of 387 cm(-1) calculated earlier at the same ab initio level for the prototypical benzene-Ar (BAr) complex. However, under an extension of the basis set, De for PAr becomes slightly lower than De for BAr. The ab initio vdW vibrational energy levels allow us to estimate the reliability of the methods for the determination of the vdW fundamentals from the rotational spectra. To disclose the character of the intermolecular interaction in PAr, the symmetry-adapted perturbation theory (SAPT) is employed for the analysis of different physical contributions to IE. It is found that SAPT components of IE can be approximately expressed in the binding region by only two of them: the exchange repulsion and dispersion energy. The total induction effect is negligible. The interrelations between various SAPT components found for PAr are fulfilled for a few other complexes involving aromatic molecules and Ar or Ne, which indicates that they are valid for all rare gas (Rg) atoms and aromatics.
X-ray variability of Pleiades late-type stars as observed with the ROSAT-PSPC

NASA Astrophysics Data System (ADS)

Marino, A.; Micela, G.; Peres, G.; Sciortino, S.

2003-08-01

We present a comprehensive analysis of X-ray variability of the late-type (dF7-dM) Pleiades stars, detected in all ROSAT-PSPC observations; X-ray variations on short (hours) and medium (months) time scales have been explored. We have grouped the stars in two samples: 89 observations of 42 distinct dF7-dK2 stars and 108 observations of 61 dK3-dM stars. The Kolmogorov-Smirnov test applied on all X-ray photon time series show that the percentage of cases of significant variability is quite similar on both samples, suggesting that the presence of variability does not depend on mass for the time scales and mass range explored. The comparison between the Time X-ray Amplitude Distribution functions (XAD) of the set of dF7-dK2 and of the dK3-dM show that, on short time scales, dK3-dM stars show larger variations than dF7-dK2. A subsample of eleven dF7-dK2 and eleven dK3-dM Pleiades stars allows the study of variability on longer time scales: we found that variability on medium - long time scales is relatively more common among dF7-dK2 stars than among dK3-dM ones. For both dF7-dK2 Pleiades stars and dF7-dK2 field stars, the variability on short time scales depends on Lx while this dependence has not been observed among dK3-dM stars. It may be that the variability among dK3-dM stars is dominated by flares that have a similar luminosity distribution for stars of different Lx, while flaring distribution in dF7-dK2 stars may depend on X-ray luminosity. The lowest mass stars show significant rapid variability (flares?) and no evidence of rotation modulation or cycles. On the contrary, dF7-dK2 Pleiades stars show both rapid variability and variations on longer time scales, likely associated with rotational modulation or cycles.
Free vibration of multiwall carbon nanotubes

NASA Astrophysics Data System (ADS)

Wang, C. Y.; Ru, C. Q.; Mioduchowski, A.

2005-06-01

A multiple-elastic shell model is applied to systematically study free vibration of multiwall carbon nanotubes (MWNTs). Using Flugge [Stresses in Shells (Springer, Berlin, 1960)] equations of elastic shells, vibrational frequencies and associated modes are calculated for MWNTs of innermost radii 5 and 0.65 nm, respectively. The emphasis is placed on the effect of interlayer van der Waals (vdW) interaction on free vibration of MWNTs. Our results show that the interlayer vdW interaction has a crucial effect on radial (R) modes of large-radius MWNTs (e.g., of the innermost radius 5 nm), but is less pronounced for R modes of small-radius MWNTs (e.g., of the innermost radius 0.65 nm), and usually negligible for torsional (T) and longitudinal (L) modes of MWNTs. This is attributed to the fact that the interlayer vdW interaction, characterized by a radius-independent vdW interaction coefficient, depends on radial deflections only, and is dominant only for large-radius MWNTs of lower radial rigidity but less pronounced for small-radius MWNTs of much higher radial rigidity. As a result, the R modes of large-radius MWNTs are typically collective motions of almost all nested tubes, and the R modes of small-radius MWNTs, as well as the T and L modes of MWNTs, are basically vibrations of individual tubes. In particular, an approximate single-shell model is suggested to replace the multiple-shell model in calculating the lowest frequency of R mode of thin MWNTs (defined by the innermost radius-to-thickness ratio not less than 4) with relative errors less than 10%. In addition, the simplified Flugge single equation is adopted to substitute the exact Flugge equations in determining the R-mode frequencies of MWNTs with relative errors less than 10%.
Computations of Lifshitz-van der Waals interaction energies between irregular particles and surfaces at all separations for resuspension modelling

NASA Astrophysics Data System (ADS)

Priye, Aashish; Marlow, William H.

2013-10-01

The phenomenon of particle resuspension plays a vital role in numerous fields. Among many aspects of particle resuspension dynamics, a dominant concern is the accurate description and formulation of the van der Waals (vdW) interactions between the particle and substrate. Current models treat adhesion by incorporating a material-dependent Hamaker's constant which relies on the heuristic Hamaker's two-body interactions. However, this assumption of pairwise summation of interaction energies can lead to significant errors in condensed matter as it does not take into account the many-body interaction and retardation effects. To address these issues, an approach based on Lifshitz continuum theory of vdW interactions has been developed to calculate the principal many-body interactions between arbitrary geometries at all separation distances to a high degree of accuracy through Lifshitz's theory. We have applied this numerical implementation to calculate the many-body vdW interactions between spherical particles and surfaces with sinusoidally varying roughness profile and also to non-spherical particles (cubes, cylinders, tetrahedron etc) orientated differently with respect to the surface. Our calculations revealed that increasing the surface roughness amplitude decreases the adhesion force and non-spherical particles adhere to the surfaces more strongly when their flatter sides are oriented towards the surface. Such practical shapes and structures of particle-surface systems have not been previously considered in resuspension models and this rigorous treatment of vdW interactions provides more realistic adhesion forces between the particle and the surface which can then be coupled with computational fluid dynamics models to improve the predictive capabilities of particle resuspension dynamics.
Quantification of functional brace forces for posterior cruciate ligament injuries on the knee joint: an in vivo investigation.

PubMed

LaPrade, Robert F; Smith, Sean D; Wilson, Katharine J; Wijdicks, Coen A

2015-10-01

Counteracting posterior translation of the tibia with an anterior force on the posterior proximal tibia has been demonstrated clinically to improve posterior knee laxity following posterior cruciate ligament (PCL) injury. This study quantified forces applied to the posterior proximal tibia by two knee braces designed for treatment of PCL injuries. The forces applied by two knee braces to the posterior proximal tibia and in vivo three-dimensional knee kinematics of six adult, male, healthy volunteer subjects (mean ± standard deviation: height, 182.5 ± 5.2 cm; body mass, 83.2 ± 9.3 kg; body mass index, 24.9 ± 1.5 kg/m(2); age, 25.8 ± 2.9 years) were measured using a custom pressure mapping technique and traditional surface marker motion capture techniques, while subjects performed three functional activities. The activities included seated unloaded knee flexion, squatting, and stair descent in a new generation dynamic force (DF) PCL brace and a static force (SF) PCL brace. During unloaded flexion at the lowest force level setting, the force applied by the DF brace increased as a function of flexion angle (slope = 0.7 N/°; p < 0.001) compared to the SF brace effect. Force applied by the SF brace did not significantly change as a function of flexion angle (slope = 0.0 N/°; n.s.). By 45° of flexion, the average force applied by the DF brace (48.1 N) was significantly larger (p < 0.001) than the average force applied by the SF brace (25.0 N). The difference in force continued to increase as flexion angle increased. During stair descent, average force (mean ± standard deviation) at toe off was significantly higher (p = 0.013) for the DF brace (78.7 ± 21.6 N) than the SF brace (37.3 ± 7.2 N). Similar trends were observed for squatting and for the higher force level settings. The DF brace applied forces to the posterior proximal tibia that dynamically increased with increased flexion angle. Additionally, the DF brace applied significantly larger forces at higher flexion angles compared to the SF brace where the PCL is known to experience larger in situ forces. Clinical studies are necessary to determine whether the loading characteristics of the DF brace, which more closely replicated the in situ loading profile of the native PCL, results in long-term improved posterior knee laxity following PCL injury. II.
The galaxy luminosity function around groups

NASA Astrophysics Data System (ADS)

González, R. E.; Padilla, N. D.; Galaz, G.; Infante, L.

2005-11-01

We present a study on the variations of the luminosity function of galaxies around clusters in a numerical simulation with semi-analytic galaxies, attempting to detect these variations in the 2dF Galaxy Redshift Survey. We subdivide the simulation box into equal-density regions around clusters, which we assume can be achieved by selecting objects at a given normalized distance (r/rrms, where rrms is an estimate of the halo radius) from the group centre. The semi-analytic model predicts important variations in the luminosity function out to r/rrms~= 5. In brief, variations in the mass function of haloes around clusters (large dark matter haloes with M > 1012h-1Msolar) lead to cluster central regions that present a high abundance of bright galaxies (high M* values) as well as low-luminosity galaxies (high α) at r/rrms~= 3 there is a lack of bright galaxies, which shows the depletion of galaxies in the regions surrounding clusters (minimum in M* and α), and a tendency to constant luminosity function parameters at larger cluster-centric distances. We take into account the observational biases present in the real data by reproducing the peculiar velocity effect on the redshifts of galaxies in the simulation box, and also by producing mock catalogues. We find that excluding from the analysis galaxies which in projection are close to the centres of the groups provides results that are qualitatively consistent with the full simulation box results. When we apply this method to mock catalogues of the 2dF Galaxy Redshift Survey (2dFGRS) and the 2PIGG catalogue of groups, we find that the variations in the luminosity function are almost completely erased by the Finger of God effect; only a lack of bright galaxies at r/rrms~= 3 can be marginally detected in the mock catalogues. The results from the real 2dFGRS data show a clearer detection of a dip in M* and α for r/rrms= 3, consistent with the semi-analytic predictions.
Effects of van der Waals density functional corrections on trends in furfural adsorption and hydrogenation on close-packed transition metal surfaces

NASA Astrophysics Data System (ADS)

Liu, Bin; Cheng, Lei; Curtiss, Larry; Greeley, Jeffrey

2014-04-01

The hydrogenation of furfural to furfuryl alcohol on Pd(111), Cu(111) and Pt(111) is studied with both standard Density Functional Theory (DFT)-GGA functionals and with van der Waals-corrected density functionals. VdW-DF functionals, including optPBE, optB88, optB86b, and Grimme's method, are used to optimize the adsorption configurations of furfural, furfuryl alcohol, and related intermediates resulting from hydrogenation of furfural, and the results are compared to corresponding values determined with GGA functionals, including PW91 and PBE. On Pd(111) and Pt(111), the adsorption geometries of the intermediates are not noticeably different between the two classes of functionals, while on Cu(111), modest changes are seen in both the perpendicular distance and the orientation of the aromatic ring with respect to the planar surface. In general, the binding energies increase substantially in magnitude as a result of van der Waals contributions on all metals. In contrast, however, dispersion effects on the kinetics of hydrogenation are relatively small. It is found that activation barriers are not significantly affected by the inclusion of dispersion effects, and a Brønsted-Evans-Polanyi relationship developed solely from PW91 calculations on Pd(111) is capable of describing corresponding results on Cu(111) and Pt(111), even when the dispersion effects are included. Finally, the reaction energies and barriers derived from the dispersion-corrected and pure GGA calculations are used to plot simple potential energy profiles for furfural hydrogenation to furfuryl alcohol on the three considered metals, and an approximately constant downshift of the energetics due to the dispersion corrections is observed.
Comparative evaluation of four mosquitoes sampling methods in rice irrigation schemes of lower Moshi, northern Tanzania.

PubMed

Kweka, Eliningaya J; Mahande, Aneth M

2009-07-06

Adult malaria vector sampling is the most important parameter for setting up an intervention and understanding disease dynamics in malaria endemic areas. The intervention will ideally be species-specific according to sampling output. It was the objective of this study to evaluate four sampling techniques, namely human landing catch, pit shelter, indoor resting collection and odour-baited entry trap. These four sampling methods were evaluated simultaneously for thirty days during October 2008, a season of low mosquitoes density and malaria transmission. These trapping methods were performed in one village for maximizing homogeneity in mosquito density. The cattle and man used in odour-baited entry trap were rotated between the chambers to avoid bias. A total of 3,074 mosquitoes were collected. Among these 1,780 (57.9%) were Anopheles arabiensis and 1,294 (42.1%) were Culex quinquefasciatus. Each trap sampled different number of mosquitoes, Indoor resting collection collected 335 (10.9%), Odour-baited entry trap-cow 1,404 (45.7%), Odour-baited entry trap-human 378 (12.3%), Pit shelter 562 (18.3%) and HLC 395 (12.8%). General linear model univariate analysis method was used, position of the trapping method had no effect on mosquito density catch (DF = 4, F = 35.596, P = 0.78). Days variation had no effect on the collected density too (DF = 29, F = 4.789, P = 0.09). The sampling techniques had significant impact on the caught mosquito densities (DF = 4, F = 34.636, P < 0.0001). The Wilcoxon pair-wise comparison between mosquitoes collected in human landing catch and pit shelter was significant (Z = -3.849, P < 0.0001), human landing catch versus Indoor resting collection was not significant (Z = -0.502, P = 0.615), human landing catch versus odour-baited entry trap-man was significant (Z = -2.687, P = 0.007), human landing catch versus odour-baited entry trap-cow was significant (Z = -3.127, P = 0.002). Odour-baited traps with different baits and pit shelter have shown high productivity in collecting higher densities of mosquitoes than human landing catch. These abilities are the possibilities of replacing the human landing catch practices for sampling malaria vectors in areas with An. arabiensis as malaria vectors. Further evaluations of these sampling methods need to be investigated is other areas with different species.
Effect of dispersion correction on the Au(1 1 1)-H2O interface: A first-principles study

NASA Astrophysics Data System (ADS)

Nadler, Roger; Sanz, Javier Fdez.

2012-09-01

A theoretical study of the H2O-Au(1 1 1) interface based on first principles density functional theory (DFT) calculations with and without inclusion of dispersion correction is reported. Three different computational approaches are considered. First, the standard generalized gradient approximation (GGA) functional PBE is employed. Second, an additional energy term is further included that adds a semi-empirically derived dispersion correction (PBE-D2), and, finally, a recently proposed functional that includes van der Waals (vdW) interactions directly in its functional form (optB86b-vdW) was used to represent the state-of-the art of DFT functionals. The monomeric water adsorption was first considered in order to explore the dependency of geometry on the details of the model slab used to represent it (size, thickness, coverage). When the dispersion corrections are included the Au-H2O interaction is stronger, as manifested by the smaller dAu-O and stronger adsorption energies. Additionally, the interfacial region between Au(1 1 1) slab surfaces and a liquid water layer was investigated with Born-Oppenheimer molecular dynamics (BOMD) using the same functionals. Two or three interfacial orientations can be determined, depending on the theoretical methodology applied. Closest to the surface, H2O is adsorbed O-down, whereas further away it is oriented with one OH bond pointing to the surface and the molecular plane parallel to the normal direction. For the optB86b-vdW functional a third orientation is found where one H atom points into the bulk water layer and the second OH bond is oriented parallel to the metal surface. As for the water density in the first adsorption layer we find a very small increase of roughly 8%. From the analysis of vibrational spectra a weakening of the H-bond network is observed upon the inclusion of the Au(1 1 1) slab, however, no disruption of H-bonds is observed. While the PBE and PBE-D2 spectra are very similar, the optB86b-vdW spectrum shows that the H-bonds are even more weakened.
Hydroxyethyl cellulose doped with copper(II) phthalocyanine-tetrasulfonic acid tetrasodium salt as an effective dual functional hole-blocking layer for polymer light-emitting diodes

NASA Astrophysics Data System (ADS)

Wu, Cheng-Liang; Chen, Yun

2017-07-01

We report a doping method to improve the performance of solution-processed polymer light-emitting diodes (PLEDs). Doping 12 wt% copper(II) phthalocyanine-tetrasulfonated acid tetrasodium salt (TS-CuPc) into hydroxyethyl cellulose (HEC) as a dual functional hole-blocking layer (df-HBL) of multilayer PLED (glass/ITO/PEDOT:PSS/HY-PPV/TS-CuPc-doped HEC/LiF/Al) significantly enhanced maximum luminance, maximum current and power efficiency over that without the df-HBL (10,319 cd/m2, 2.98 cd/A and 1.24 lm/W) to (29,205 cd/m2, 13.27 cd/A and 9.56 lm/W). CV measurements reveal that HEC possesses a powerful hole-blocking capability. Topography and conductivity AFM images show that doping TS-CuPc increases the interfacial contact area and interfacial conductivity, which can overcome the insulating nature of HEC and thus further facilitate electron injection. Enhancements in device performance are attributed to the improved carrier balance and recombination in the presence of df-HBL, confirmed in electron-only and hole-only devices. Moreover, apparently raised open-circuit voltages provide further evidence that enhanced electron injection is indeed realized by the df-HBL. This study demonstrates an effective approach to develop highly efficient PLEDs.

Determination of early diastolic LV vortex formation time (T*) via the PDF formalism: a kinematic model of filling.

PubMed

Ghosh, Erina; Shmuylovich, Leonid; Kovacs, Sandor J

2009-01-01

The filling (diastolic) function of the human left ventricle is most commonly assessed by echocardiography, a non-invasive imaging modality. To quantify diastolic function (DF) empiric indices are obtained from the features (height, duration, area) of transmitral flow velocity contour, obtained by echocardiography. The parameterized diastolic filling (PDF) formalism is a kinematic model developed by Kovács et. al. which incorporates the suction pump attribute of the left ventricle and facilitates DF quantitation by analysis of echocardiographic transmitral flow velocity contours in terms of stiffness (k), relaxation (c) and load (x(0)). A complementary approach developed by Gharib et. al., uses fluid mechanics and characterizes DF in terms of vortex formation time (T*) derived from streamline features formed by the jet of blood aspirated into the ventricle. Both of these methods characterize DF using a causality-based approach. In this paper, we derive T*'s kinematic analogue T*(kinematic) in terms of k, c and x(0). A comparison between T*(kinematic) and T*(fluid) (mechanic) obtained from averaged transmitral velocity and mitral annulus diameter, is presented. We found that T* calculated by the two methods were comparable and T*(kinematic) correlated with the peak LV recoil driving force kx(0).
Spatial and Temporal Variation in Tadpole Communities in Neotropical Montane Streams.

NASA Astrophysics Data System (ADS)

Brenes, R.; Lips, K. R.

2005-05-01

Tadpoles transfer nutrients and energy between environments and amphibian declines are likely to affect this process. As the first step in determining amphibian production, we quantified seasonal and microhabitat variation in abundance and diversity of tadpoles at two sites: pre and post-decline. We quantified density of all tadpole species in riffles, runs, and pools monthly for a year. Three species occurred at the decline site (average density = 0.0026 ± 0.0034 m-2), and 10 of 11 species occurred year-round at the healthy site (2.80 ± 4.37 m-2). Tadpole abundance varied seasonally, with more tadpoles (X2=270.23, 10 d.f., p<0.001) at lower densities (0.50 m-2 ± 0.58) during the rainy season than during the dry season (5.10 m-2 ± 5.31; t = 3.079, 10 d.f., P= 0.01). Microhabitats differed in overall density (leaf packs, 1.044 ± 1.17 m-2; riffles, 0.04 ± 0.013 m-2, pools 0.38 ± 0.005 m-2; isolated pools 2.09 ± 1.03 m-2). Riffles and pools had a diverse tadpole assemblage, but leaf packs and isolated pools were dominated by Hyalinobatrachium colymbiphyllum (3.74 ± 1.86 m-2, F= 13.47, p=0.01) and Colostethus flotator (9.35 ± 4.56 m-2, F=32.77, p=0.002), respectively. High abundance, density, prevalence, and persistence suggest an important role for tadpoles in these ecosystems.
Dispersion corrected hartree-fock and density functional theory for organic crystal structure prediction.

PubMed

Brandenburg, Jan Gerit; Grimme, Stefan

2014-01-01

We present and evaluate dispersion corrected Hartree-Fock (HF) and Density Functional Theory (DFT) based quantum chemical methods for organic crystal structure prediction. The necessity of correcting for missing long-range electron correlation, also known as van der Waals (vdW) interaction, is pointed out and some methodological issues such as inclusion of three-body dispersion terms are discussed. One of the most efficient and widely used methods is the semi-classical dispersion correction D3. Its applicability for the calculation of sublimation energies is investigated for the benchmark set X23 consisting of 23 small organic crystals. For PBE-D3 the mean absolute deviation (MAD) is below the estimated experimental uncertainty of 1.3 kcal/mol. For two larger π-systems, the equilibrium crystal geometry is investigated and very good agreement with experimental data is found. Since these calculations are carried out with huge plane-wave basis sets they are rather time consuming and routinely applicable only to systems with less than about 200 atoms in the unit cell. Aiming at crystal structure prediction, which involves screening of many structures, a pre-sorting with faster methods is mandatory. Small, atom-centered basis sets can speed up the computation significantly but they suffer greatly from basis set errors. We present the recently developed geometrical counterpoise correction gCP. It is a fast semi-empirical method which corrects for most of the inter- and intramolecular basis set superposition error. For HF calculations with nearly minimal basis sets, we additionally correct for short-range basis incompleteness. We combine all three terms in the HF-3c denoted scheme which performs very well for the X23 sublimation energies with an MAD of only 1.5 kcal/mol, which is close to the huge basis set DFT-D3 result.
A density functional theory computational study of adsorption of Di-Meta-Cyano Azobenzene molecules on Si (111) surfaces

NASA Astrophysics Data System (ADS)

Motevalli, Benyamin; Taherifar, Neda; Wu, Bisheng; Tang, Wenxin; Liu, Jefferson Zhe

2017-11-01

The adsorption of di-meta-cyano azobenzene (DMC) cis and trans isomers on non-passivated and passivated Si (111) (7 × 7) surfaces is studied using density functional theory (DFT) calculations. Our results reveal that on the non-passivated surface the 12 Si adatoms are accessible to form chemical bonds with DMC molecules. Interestingly, the trans isomer forms two chemical bonds near the corner hole atom in Si (111) (7 × 7) surface, which is not observed in the widely studied metallic surfaces. The DMC isomers show significant structural distortion in the chemisorption case. The strong chemical bonds (and high bonding energy) could be detrimental to conformation switching between these two isomers under external stimuli. The physisorption case is also examined. Monte Carlo (MC) simulations with empirical force fields were employed to search about 106 different adsorption positions and DMC molecule orientations to identify the stable adsorption sites (up to six). The DFT-PBE and DFT-D2 calculations were then carried out to obtain the relaxed atomistic structures and accurate adsorption energy. We find that it is imperative to take van der Waals (vdW) interaction into account in DFT calculations. Our results show that the adsorption sites generally are encompassed by either the Si adatoms or the passivated H atoms, which could enhance the long-range dispersion interaction between DMC molecules and Si surfaces. The molecular structures of both isomers remain unchanged compared with gas phase. The obtained adsorption energy results ΔEads are moderate (0.2-0.8 eV). At some adsorption sites on the passivated surface, both isomers have similar moderate ΔEads (0.4-0.6 eV), implying promises of molecular switching that should be examined in experiments.
[Effect of grain-bean package, grain-bean package dietary fiber and single whole grain dietary fiber on dyslipidemia rats].

PubMed

Liu, Yang; Zhai, Chengkai; Sun, Guiju; Zhang, Hong; Jiang, Mingxia; Zhang, Haifeng; Guo, Junling; Lan, Xi

2014-05-01

To observe and compare the effects of grain-bean package, dietary fiber (DF) extracted from grain-bean package, and DF from grain corn on the blood lipids and fatty acid synthase (FAS) activity in high-fat, high-cholesterol feeding induced dyslipidemia rats, and observe its effects on regulation of sterol regulatory element protein-1c (SREBP-1c) mRNA expression in rat liver. Consolidation 50 SD rats of clean grade feeding adaptation for one week, randomly assigned into normal control group, hyperlipidemia model group, grain-bean package group, grain-bean package DF group and grain corn group. Feed with corresponding diets for 8 weeks, and measure the total cholesterol (TC), triglyceridaemia (TG), high density lipoprotein cholesterol (HDL-C), fasting blood glucose (FBG), FAS, SREBP-1c mRNA of all groups. Compared with control group, TC, TG, FBG levels of hyperlipidemia model group were significantly increased (P < 0.05). Compared with model group, TC, TG, FBG levels of grain-bean package group, grain-bean package DF group were significantly decreased, HDL-C levels significantly increased, and activity of FAS, regulation of SREBP-1c were significantly decreased (P < 0.05). The Grain-bean package dietary fiber can improve blood lipids levels of dyslipidemia rats, and decrease FAS activity and SREBP-1c mRNA expression.
Nonadditivity of van der Waals forces on liquid surfaces

NASA Astrophysics Data System (ADS)

Venkataram, Prashanth S.; Whitton, Jeremy D.; Rodriguez, Alejandro W.

2016-09-01

We present an approach for modeling nanoscale wetting and dewetting of textured solid surfaces that exploits recently developed, sophisticated techniques for computing exact long-range dispersive van der Waals (vdW) or (more generally) Casimir forces in arbitrary geometries. We apply these techniques to solve the variational formulation of the Young-Laplace equation and predict the equilibrium shapes of liquid-vacuum interfaces near solid gratings. We show that commonly employed methods of computing vdW interactions based on additive Hamaker or Derjaguin approximations, which neglect important electromagnetic boundary effects, can result in large discrepancies in the shapes and behaviors of liquid surfaces compared to exact methods.
Communication: Many-body stabilization of non-covalent interactions: Structure, stability, and mechanics of Ag3Co(CN)6 framework.

PubMed

Liu, Xiaofei; Hermann, Jan; Tkatchenko, Alexandre

2016-12-28

Stimuli-responsive metal-organic frameworks (MOFs) and other framework materials exhibit a broad variety of useful properties, which mainly stem from an interplay of strong covalent bonds within the organic linkers with presumably weak van der Waals (vdW) interactions which determine the overall packing of the framework constituents. Using Ag 3 Co(CN) 6 as a fundamental test case-a system with a colossal positive and negative thermal expansion [A. L. Goodwin et al., Science 319, 794 (2008)]-we demonstrate that its structure, stability, dielectric, vibrational, and mechanical properties are critically influenced by many-body electronic correlation contributions to non-covalent vdW interactions. The Ag 3 Co(CN) 6 framework is a remarkable molecular crystal, being visibly stabilized, rather than destabilized, by many-body vdW correlations. A detailed comparison with H 3 Co(CN) 6 highlights the crucial role of strongly polarized metallophilic interactions in dictating the exceptional properties of denser MOFs. Beyond MOFs, our findings indicate that many-body electronic correlations can substantially stabilize polarizable materials, providing a novel mechanism for tuning the properties of nanomaterials with intricate structural motifs.
Molecular Self-Assembly Driven by London Dispersion Forces

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

Li, Guo; Cooper, Valentino R; Cho, Jun-Hyung

2011-01-01

The nature and strength of intermolecular interactions are crucial to a variety of kinetic and dynamic processes at surfaces. Whereas strong chemisorption bonds are known to facilitate molecular binding, the importance of the weaker yet ubiquitous van der Waals (vdW) interactions remains elusive in most cases. Here we use first-principles calculations combined with kinetic Monte Carlo simulations to unambiguously demonstrate the vital role that vdW interactions play in molecular self-assembly, using styrene nanowire growth on silicon as a prototypical example. We find that, only when the London dispersion forces are included, accounting for the attractive parts of vdW interactions, canmore » the effective intermolecular interaction be reversed from being repulsive to attractive. Such attractive interactions, in turn, ensure the preferred growth of long wires under physically realistic conditions as observed experimentally. We further propose a cooperative scheme, invoking the application of an electric field and the selective creation of Si dangling bonds, to drastically improve the ordered arrangement of the molecular structures. The present study represents a significant step forward in the fundamental understanding and precise control of molecular self-assembly guided by London dispersion forces.« less
Tunneling Diode Based on WSe2 /SnS2 Heterostructure Incorporating High Detectivity and Responsivity.

PubMed

Zhou, Xing; Hu, Xiaozong; Zhou, Shasha; Song, Hongyue; Zhang, Qi; Pi, Lejing; Li, Liang; Li, Huiqiao; Lü, Jingtao; Zhai, Tianyou

2018-02-01

van der Waals (vdW) heterostructures based on atomically thin 2D materials have led to a new era in next-generation optoelectronics due to their tailored energy band alignments and ultrathin morphological features, especially in photodetectors. However, these photodetectors often show an inevitable compromise between photodetectivity and photoresponsivity with one high and the other low. Herein, a highly sensitive WSe 2 /SnS 2 photodiode is constructed on BN thin film by exfoliating each material and manually stacking them. The WSe 2 /SnS 2 vdW heterostructure shows ultralow dark currents resulting from the depletion region at the junction and high direct tunneling current when illuminated, which is confirmed by the energy band structures and electrical characteristics fitted with direct tunneling. Thus, the distinctive WSe 2 /SnS 2 vdW heterostructure exhibits both ultrahigh photodetectivity of 1.29 × 10 13 Jones (I ph /I dark ratio of ≈10 6 ) and photoresponsivity of 244 A W -1 at a reverse bias under the illumination of 550 nm light (3.77 mW cm -2 ). © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Theory of coherent van der Waals matter.

PubMed

Kulić, Igor M; Kulić, Miodrag L

2014-12-01

We explain in depth the previously proposed theory of the coherent van der Waals (cvdW) interaction, the counterpart of van der Waals (vdW) force, emerging in spatially coherently fluctuating electromagnetic fields. We show that cvdW driven matter is dominated by many-body interactions, which are significantly stronger than those found in standard van der Waals (vdW) systems. Remarkably, the leading two- and three-body interactions are of the same order with respect to the distance (∝R(-6)), in contrast to the usually weak vdW three-body effects (∝R(-9)). From a microscopic theory we show that the anisotropic cvdW many-body interactions drive the formation of low-dimensional structures such as chains, membranes, and vesicles with very unusual, nonlocal properties. In particular, cvdW chains display a logarithmically growing stiffness with the chain length, while cvdW membranes have a bending modulus growing linearly with their size. We argue that the cvdW anisotropic many-body forces cause local cohesion but also a negative effective "surface tension." We conclude by deriving the equation of state for cvdW materials and propose experiments to test the theory, in particular the unusual three-body nature of cvdW.
Theory of coherent van der Waals matter

NASA Astrophysics Data System (ADS)

Kulić, Igor M.; Kulić, Miodrag L.

2014-12-01

We explain in depth the previously proposed theory of the coherent van der Waals (cvdW) interaction, the counterpart of van der Waals (vdW) force, emerging in spatially coherently fluctuating electromagnetic fields. We show that cvdW driven matter is dominated by many-body interactions, which are significantly stronger than those found in standard van der Waals (vdW) systems. Remarkably, the leading two- and three-body interactions are of the same order with respect to the distance (∝R-6) , in contrast to the usually weak vdW three-body effects (∝R-9 ). From a microscopic theory we show that the anisotropic cvdW many-body interactions drive the formation of low-dimensional structures such as chains, membranes, and vesicles with very unusual, nonlocal properties. In particular, cvdW chains display a logarithmically growing stiffness with the chain length, while cvdW membranes have a bending modulus growing linearly with their size. We argue that the cvdW anisotropic many-body forces cause local cohesion but also a negative effective "surface tension." We conclude by deriving the equation of state for cvdW materials and propose experiments to test the theory, in particular the unusual three-body nature of cvdW.
Reaction mechanism of molybdoenzyme formate dehydrogenase.

PubMed

Leopoldini, Monica; Chiodo, Sandro G; Toscano, Marirosa; Russo, Nino

2008-01-01

Formate dehydrogenase is a molybdoenzyme of the anaerobic formate hydrogen lyase complex of the Escherichia coli microorganism that catalyzes the oxidation of formate to carbon dioxide. The two proposed mechanisms of reaction, which differ in the occurrence of a direct coordination or not of a SeCys residue to the molybdenum metal during catalysis were analyzed at the density functional level in both vacuum and protein environments. Some DF functionals, in addition to the very popular B3LYP one, were employed to compute barrier heights. Results revealed the role played by the SeCys residue in performing the abstraction of the proton from the formate substrate. The computation of the energetic profiles for both mechanisms indicated that the reaction barriers are higher when the selenium is directly coordinated to the metal, whereas less energy is required when SeCys is not a ligand at the molybdenum site.
Halo-substituted azobenzenes adsorbed at Ag(111) and Au(111) interfaces: Structures and optical properties

NASA Astrophysics Data System (ADS)

Hughes, Zak E.; Baev, Alexander; Prasad, Paras N.; Walsh, Tiffany R.

2017-05-01

The adsorption of azobenzene (AB), ortho fluoro-azobenzene (FAB) and ortho chlor-azobenzol (ClAB), in both the cis and trans isomers, at the Au(111) and Ag(111) surfaces is investigated using plane-wave density functional calculations with the revPBE-vdW-DF functional. The resulting adsorption energies and internal structures of AB adsorbed to both metal surfaces are in broad agreement with available experimental data. In the gas phase, FAB and ClAB feature a significant reduction in the energy difference between the two isomeric states, compared with AB. This relative reduction in the energy difference is still significant for the adsorbed form of FAB but is only weakly apparent for ClAB. The absorption spectra of the molecules have also been calculated, with the halogen substituents generating significant changes in the gas phase, but only a modest difference for the adsorbed molecules.
The structure elucidation of mequindox and 1,4-bisdesoxymequindox: NMR analyses, FT-IR spectra, DFT calculations and thermochemical studies

NASA Astrophysics Data System (ADS)

Zhang, Jiaheng; He, Xin; Gao, Haixiang

2011-10-01

In the current work, we report a combined experimental and theoretical study on the molecular conformation, vibrational spectra, and nuclear magnetic resonance (NMR) spectra of mequindox (MEQ) and 1,4-bisdesoxymequindox (1,4-BDM). The geometric structure and vibrational frequencies of MEQ and 1,4-BDM have been calculated by density functional theory employing the B3LYP functional and 6-311++G(d,p) basis set. The 1H and 13C NMR chemical shifts have been calculated by gauge-including atomic orbital method with B3LYP 6-311++G(2df,2pd) approach. The calculation results have been applied to simulate the infrared and NMR spectra of the compounds. The theoretical results agree well with the observed spectra. The bond dissociation enthalpy of MEQ and the heat of formation of MEQ and 1,4-BDM have also been computed.
INFRARED SPECTRUM OF POTASSIUM-CATIONIZED TRIETHYLPHOSPHATE GENERATED USING TANDEM MASS SPECTROMETRY AND INFRARED MULTIPLE PHOTON DISSOCIATION

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

Gary S. Groenewold; Christopher M. Leavitt; Ryan P. Dain

2009-09-01

Tandem mass spectrometry and wavelength selective infrared photodissociation was used to generate an infrared spectrum of gas-phase triethylphosphate cationized by attachment of K+. Prominent absorptions were observed in the region of 900 to 1300 cm-1 that are characteristic of phosphate P=O and P-O-R stretches. The relative positions and intensities of the IR absorptions were reproduced well by density functional theory (DFT) calculations performed using the B3LYP functional and the 6-31+g(d), 6-311+g(d,p) and 6-311++G(3df,2pd) basis sets. Because of good correspondence between experiment and theory for the cation, DFT was then used to generate a theoretical spectrum for neutral triethylphosphate, which inmore » turn accurately reproduces the IR spectrum of the neat liquid when solvent effects are included in the calculations.« less
Soot superaggregates from flaming wildfires and their direct radiative forcing.

PubMed

Chakrabarty, Rajan K; Beres, Nicholas D; Moosmüller, Hans; China, Swarup; Mazzoleni, Claudio; Dubey, Manvendra K; Liu, Li; Mishchenko, Michael I

2014-07-01

Wildfires contribute significantly to global soot emissions, yet their aerosol formation mechanisms and resulting particle properties are poorly understood and parameterized in climate models. The conventional view holds that soot is formed via the cluster-dilute aggregation mechanism in wildfires and emitted as aggregates with fractal dimension Df ≈ 1.8 mobility diameter Dm ≤ 1 μm, and aerodynamic diameter Da ≤ 300 nm. Here we report the ubiquitous presence of soot superaggregates (SAs) in the outflow from a major wildfire in India. SAs are porous, low-density aggregates of cluster-dilute aggregates with characteristic Df ≈ 2.6, Dm > 1 μm, and Da ≤ 300 nm that form via the cluster-dense aggregation mechanism. We present additional observations of soot SAs in wildfire smoke-laden air masses over Northern California, New Mexico, and Mexico City. At 550 nm wavelength, [corrected] we estimate that SAs contribute, per unit optical depth, up to 35% less atmospheric warming than freshly-emitted (D(f) ≈ 1.8) [corrected] aggregates, and ≈90% more warming than the volume-equivalent spherical soot particles simulated in climate models.
Soot superaggregates from flaming wildfires and their direct radiative forcing

PubMed Central

Chakrabarty, Rajan K.; Beres, Nicholas D.; Moosmüller, Hans; China, Swarup; Mazzoleni, Claudio; Dubey, Manvendra K.; Liu, Li; Mishchenko, Michael I.

2014-01-01

Wildfires contribute significantly to global soot emissions, yet their aerosol formation mechanisms and resulting particle properties are poorly understood and parameterized in climate models. The conventional view holds that soot is formed via the cluster-dilute aggregation mechanism in wildfires and emitted as aggregates with fractal dimension Df ≈ 1.8 mobility diameter Dm ≤ 1 μm, and aerodynamic diameter Da ≤ 300 nm. Here we report the ubiquitous presence of soot superaggregates (SAs) in the outflow from a major wildfire in India. SAs are porous, low-density aggregates of cluster-dilute aggregates with characteristic Df ≈ 2.6, Dm > 1 μm, and Da ≤ 300 nm that form via the cluster-dense aggregation mechanism. We present additional observations of soot SAs in wildfire smoke-laden air masses over Northern California, New Mexico, and Mexico City. We estimate that SAs contribute, per unit optical depth, up to 35% less atmospheric warming than freshly-emitted (Df ≈ 1.8) aggregates, and ≈90% more warming than the volume-equivalent spherical soot particles simulated in climate models. PMID:24981204
Adsorption structures and energetics of molecules on metal surfaces: Bridging experiment and theory

NASA Astrophysics Data System (ADS)

Maurer, Reinhard J.; Ruiz, Victor G.; Camarillo-Cisneros, Javier; Liu, Wei; Ferri, Nicola; Reuter, Karsten; Tkatchenko, Alexandre

2016-05-01

Adsorption geometry and stability of organic molecules on surfaces are key parameters that determine the observable properties and functions of hybrid inorganic/organic systems (HIOSs). Despite many recent advances in precise experimental characterization and improvements in first-principles electronic structure methods, reliable databases of structures and energetics for large adsorbed molecules are largely amiss. In this review, we present such a database for a range of molecules adsorbed on metal single-crystal surfaces. The systems we analyze include noble-gas atoms, conjugated aromatic molecules, carbon nanostructures, and heteroaromatic compounds adsorbed on five different metal surfaces. The overall objective is to establish a diverse benchmark dataset that enables an assessment of current and future electronic structure methods, and motivates further experimental studies that provide ever more reliable data. Specifically, the benchmark structures and energetics from experiment are here compared with the recently developed van der Waals (vdW) inclusive density-functional theory (DFT) method, DFT + vdWsurf. In comparison to 23 adsorption heights and 17 adsorption energies from experiment we find a mean average deviation of 0.06 Å and 0.16 eV, respectively. This confirms the DFT + vdWsurf method as an accurate and efficient approach to treat HIOSs. A detailed discussion identifies remaining challenges to be addressed in future development of electronic structure methods, for which the here presented benchmark database may serve as an important reference.
2-Pyridinethiol/2-pyridinethione tautomeric equilibrium. A comparative experimental and computational study.

PubMed

Moran, Damian; Sukcharoenphon, Kengkaj; Puchta, Ralph; Schaefer, Henry F; Schleyer, Paul V R; Hoff, Carl D

2002-12-13

The gas phase and solvent dependent preference of the tautomerization between 2-pyridinethiol (2SH) and 2-pyridinethione (2S) has been assessed using variable temperature Fourier transform infrared (FTIR) experiments, as well as ab initio and density functional theory computations. No spectroscopic evidence (nu(S)(-)(H) stretch) for 2SH was observed in toluene, C(6)D(6), heptane, or methylene chloride solutions. Although, C(s)() 2SH is 2.61 kcal/mol more stable than C(s)() 2S (CCSD(T)/cc-pVTZ//B3LYP/6-311+G(3df,2p)+ZPE), cyclohexane solvent-field relative energies (IPCM-MP2/6-311+G(3df,2p)) favor 2S by 1.96 kcal/mol. This is in accord with the FTIR observations and in quantitative agreement with the -2.6 kcal/mol solution (toluene or C(6)D(6)) calorimetric enthalpy for the 2S/2SH tautomerization favoring the thione. As the intramolecular transition state for the 2S, 2SH tautomerization (2TS) lies 25 (CBS-Q) to 30 kcal/mol (CCSD/cc-pVTZ) higher in energy than either tautomer, tautomerization probably occurs in the hydrogen bonded dimer. The B3LYP/6-311+G(3df,2p) optimized C(2) 2SH dimer is 10.23 kcal/mol + ZPE higher in energy than the C(2)(h)() 2S dimer and is only 2.95 kcal/mol + ZPE lower in energy than the C(2) 2TS dimer transition state. Dimerization equilibrium measurements (FTIR, C(6)D(6)) over the temperature range 22-63 degrees C agree: K(eq)(298) = 165 +/- 40 M(-)(1), DeltaH = -7.0 +/- 0.7 kcal/mol, and DeltaS = -13.4 +/- 3.0 cal/(mol deg). The difference between experimental and B3LYP/6-311+G(3df,2p) [-34.62 cal/(mol deg)] entropy changes is due to solvent effects. The B3LYP/6-311+G(3df,2p) nucleus independent chemical shifts (NICS) are -8.8 and -3.5 ppm 1 A above the 2SH and 2S ring centers, respectively, and the thiol is aromatic. Although the thione is not aromatic, it is stabilized by the thioamide resonance. In solvent, the large 2S dipole, 2-3 times greater than 2SH, favors the thione tautomer and, in conclusion, 2S is thermodynamically more stable than 2SH in solution.
Rapid estimation of the electron correlation energy for van der Waals complexes RgX (Rg = Kr, Xe, X = Br, I)

NASA Astrophysics Data System (ADS)

Xinying, Li; Yongfang, Zhao; Xiaogong, Jing; Fengli, Liu; Fengyou, Hao

2006-01-01

We present the rules of electron correlation energies for RgX (Rg = Kr, Xe, X = Br, I) van der Waals (vdW) complex systems at CCSD(T) theoretical level with SDB-cc-pVQZ basis set by the Gaussian 98 program. A new method to derive the dispersion coefficient C6 by fitting the intermonomer electron correlation energies to C6R-6 function is introduced. The present C6 values are compared with the corresponding theoretical ones.

Epitaxial graphene-encapsulated surface reconstruction of Ge(110)

NASA Astrophysics Data System (ADS)

Campbell, Gavin P.; Kiraly, Brian; Jacobberger, Robert M.; Mannix, Andrew J.; Arnold, Michael S.; Hersam, Mark C.; Guisinger, Nathan P.; Bedzyk, Michael J.

2018-04-01

Understanding and engineering the properties of crystalline surfaces has been critical in achieving functional electronics at the nanoscale. Employing scanning tunneling microscopy, surface x-ray diffraction, and high-resolution x-ray reflectivity experiments, we present a thorough study of epitaxial graphene (EG)/Ge(110) and report a Ge(110) "6 × 2" reconstruction stabilized by the presence of epitaxial graphene unseen in group-IV semiconductor surfaces. X-ray studies reveal that graphene resides atop the surface reconstruction with a 0.34 nm van der Waals (vdW) gap and provides protection from ambient degradation.
Anomalous van der Waals-Casimir interactions on graphene: A concerted effect of temperature, retardation, and non-locality

NASA Astrophysics Data System (ADS)

Ambrosetti, Alberto; Silvestrelli, Pier Luigi

2018-04-01

Dispersion forces play a major role in graphene, largely influencing adhesion of adsorbate moieties and stabilization of functional multilayered structures. However, the reliable prediction of dispersion interactions on graphene up to the relevant ˜10 nm scale is an extremely challenging task: in fact, electromagnetic retardation effects and the highly non-local character of π electrons can imply sizeable qualitative variations of the interaction with respect to known pairwise approaches. Here we address both issues, determining the finite-temperature van der Waals (vdW)-Casimir interaction for point-like and extended adsorbates on graphene, explicitly accounting for the non-local dielectric permittivity. We find that temperature, retardation, and non-locality play a crucial role in determining the actual vdW scaling laws and the stability of both atomic and larger molecular adsorbates. Our results highlight the importance of these effects for a proper description of systems of current high interest, such as graphene interacting with biomolecules, and self-assembly of complex nanoscale structures. Due to the generality of our approach and the observed non-locality of other 2D materials, our results suggest non-trivial vdW interactions from hexagonal mono-layered materials from group 14 of the periodic table, to transition metal dichalcogenides.
Anomalous van der Waals-Casimir interactions on graphene: A concerted effect of temperature, retardation, and non-locality.

PubMed

Ambrosetti, Alberto; Silvestrelli, Pier Luigi

2018-04-07

Dispersion forces play a major role in graphene, largely influencing adhesion of adsorbate moieties and stabilization of functional multilayered structures. However, the reliable prediction of dispersion interactions on graphene up to the relevant ∼10 nm scale is an extremely challenging task: in fact, electromagnetic retardation effects and the highly non-local character of π electrons can imply sizeable qualitative variations of the interaction with respect to known pairwise approaches. Here we address both issues, determining the finite-temperature van der Waals (vdW)-Casimir interaction for point-like and extended adsorbates on graphene, explicitly accounting for the non-local dielectric permittivity. We find that temperature, retardation, and non-locality play a crucial role in determining the actual vdW scaling laws and the stability of both atomic and larger molecular adsorbates. Our results highlight the importance of these effects for a proper description of systems of current high interest, such as graphene interacting with biomolecules, and self-assembly of complex nanoscale structures. Due to the generality of our approach and the observed non-locality of other 2D materials, our results suggest non-trivial vdW interactions from hexagonal mono-layered materials from group 14 of the periodic table, to transition metal dichalcogenides.
Combinatorial screening of organic electronic materials: thin film stability

NASA Astrophysics Data System (ADS)

Chattopadhyay, Santanu; Carson Meredith, J.

2005-01-01

Dewetting of thin polymeric semiconducting-insulating (and conducting-insulating) bilayers is a serious fundamental problem facing the fabrication of organic electronic devices such as transistors, light-emitting diodes and supercapacitors. This paper describes a high-throughput characterization method that utilizes orthogonal thickness-gradient libraries of the bilayer components poly(3-octylthiophene) (semiconductor) and poly(styrene) (insulator). The technique allows simultaneous observation of hundreds of combinations of thicknesses and has permitted rapid discovery of a previously-unknown VDW instability transition. We observe that the onset of VDW instability in the PS-P3OT bilayer is a complex function of P3OT thickness that cannot be predicted by Hamaker constant models for free energy. At low P3OT thickness, the semiconductor acts to stabilize the PS insulator. But above a P3OT thickness of 175 nm, this behaviour is switched and P3OT destabilizes the PS. These thickness-dependent effects are correlated very well with dramatic transitions in P3OT optical spectra and the P3OT-AFM tip interaction forces. This unusual behaviour places critical limitations on practical device thicknesses and interfacial combinations, and points to the need for a thin-film stability theory that accounts for thickness-dependent molecular-electronic effects.
Van der Waals MoS2/VO2 heterostructure junction with tunable rectifier behavior and efficient photoresponse.

PubMed

Oliva, Nicoló; Casu, Emanuele Andrea; Yan, Chen; Krammer, Anna; Rosca, Teodor; Magrez, Arnaud; Stolichnov, Igor; Schueler, Andreas; Martin, Olivier J F; Ionescu, Adrian Mihai

2017-10-27

Junctions between n-type semiconductors of different electron affinity show rectification if the junction is abrupt enough. With the advent of 2D materials, we are able to realize thin van der Waals (vdW) heterostructures based on a large diversity of materials. In parallel, strongly correlated functional oxides have emerged, having the ability to show reversible insulator-to-metal (IMT) phase transition by collapsing their electronic bandgap under a certain external stimulus. Here, we report for the first time the electronic and optoelectronic characterization of ultra-thin n-n heterojunctions fabricated using deterministic assembly of multilayer molybdenum disulphide (MoS 2 ) on a phase transition material, vanadium dioxide (VO 2 ). The vdW MoS 2 /VO 2 heterojunction combines the excellent blocking capability of an n-n junction with a high conductivity in on-state, and it can be turned into a Schottky rectifier at high applied voltage or at temperatures higher than 68 °C, exploiting the metal state of VO 2 . We report tunable diode-like current rectification with a good diode ideality factor of 1.75 and excellent conductance swing of 120 mV/dec. Finally, we demonstrate unique tunable photosensitivity and excellent junction photoresponse in the 500/650 nm wavelength range.
MicroRNA-134 Contributes to Glucose-Induced Endothelial Cell Dysfunction and This Effect Can Be Reversed by Far-Infrared Irradiation

PubMed Central

Wang, Yen-Li; Chang, Shih-Ting; Liao, Ko-Hsun; Lo, Hung-Hao; Chiu, Ya-Lin; Hsieh, Tsung-Han; Huang, Tse-Shun; Lin, Chin-Sheng; Cheng, Shu-Meng; Cheng, Cheng-Chung

2016-01-01

Diabetes mellitus (DM) is a metabolic disease that is increasing worldwide. Furthermore, it is associated with the deregulation of vascular-related functions, which can develop into major complications among DM patients. Endothelial colony forming cells (ECFCs) have the potential to bring about medical repairs because of their post-natal angiogenic activities; however, such activities are impaired by high glucose- (HG) and the DM-associated conditions. Far-infrared radiation (FIR) transfers energy as heat that is perceived by the thermoreceptors in human skin. Several studies have revealed that FIR improves vascular endothelial functioning and boost angiogenesis. FIR has been used as anti-inflammatory therapy and as a clinical treatment for peripheral circulation improvement. In addition to vascular repair, there is increasing evidence to show that FIR can be applied to a variety of diseases, including cardiovascular disorders, hypertension and arthritis. Yet mechanism of action of FIR and the biomarkers that indicate FIR effects remain unclear. MicroRNA-134 (miR-134-5p) was identified by small RNA sequencing as being increased in high glucose (HG) treated dfECFCs (HG-dfECFCs). Highly expressed miR-134 was also validated in dmECFCs by RT-qPCR and it is associated with impaired angiogenic activities of ECFCs. The functioning of ECFCs is improved by FIR treatment and this occurs via a reduction in the level of miR-134 and an increase in the NRIP1 transcript, a direct target of miR-134. Using a mouse ischemic hindlimb model, the recovery of impaired blood flow in the presence of HG-dfECFCs was improved by FIR pretreatment and this enhanced functionality was decreased when there was miR-134 overexpression in the FIR pretreated HG-dfECFCs. In conclusion, our results reveal that the deregulation of miR-134 is involved in angiogenic defects found in DM patients. FIR treatment improves the angiogenic activity of HG-dfECFCs and dmECFCs and FIR has potential as a treatment for DM. Detection of miR-134 expression in FIR-treated ECFCs should help us to explore further the effectiveness of FIR therapy. PMID:26799933
MicroRNA-134 Contributes to Glucose-Induced Endothelial Cell Dysfunction and This Effect Can Be Reversed by Far-Infrared Irradiation.

PubMed

Wang, Hsei-Wei; Su, Shu-Han; Wang, Yen-Li; Chang, Shih-Ting; Liao, Ko-Hsun; Lo, Hung-Hao; Chiu, Ya-Lin; Hsieh, Tsung-Han; Huang, Tse-Shun; Lin, Chin-Sheng; Cheng, Shu-Meng; Cheng, Cheng-Chung

2016-01-01

Diabetes mellitus (DM) is a metabolic disease that is increasing worldwide. Furthermore, it is associated with the deregulation of vascular-related functions, which can develop into major complications among DM patients. Endothelial colony forming cells (ECFCs) have the potential to bring about medical repairs because of their post-natal angiogenic activities; however, such activities are impaired by high glucose- (HG) and the DM-associated conditions. Far-infrared radiation (FIR) transfers energy as heat that is perceived by the thermoreceptors in human skin. Several studies have revealed that FIR improves vascular endothelial functioning and boost angiogenesis. FIR has been used as anti-inflammatory therapy and as a clinical treatment for peripheral circulation improvement. In addition to vascular repair, there is increasing evidence to show that FIR can be applied to a variety of diseases, including cardiovascular disorders, hypertension and arthritis. Yet mechanism of action of FIR and the biomarkers that indicate FIR effects remain unclear. MicroRNA-134 (miR-134-5p) was identified by small RNA sequencing as being increased in high glucose (HG) treated dfECFCs (HG-dfECFCs). Highly expressed miR-134 was also validated in dmECFCs by RT-qPCR and it is associated with impaired angiogenic activities of ECFCs. The functioning of ECFCs is improved by FIR treatment and this occurs via a reduction in the level of miR-134 and an increase in the NRIP1 transcript, a direct target of miR-134. Using a mouse ischemic hindlimb model, the recovery of impaired blood flow in the presence of HG-dfECFCs was improved by FIR pretreatment and this enhanced functionality was decreased when there was miR-134 overexpression in the FIR pretreated HG-dfECFCs. In conclusion, our results reveal that the deregulation of miR-134 is involved in angiogenic defects found in DM patients. FIR treatment improves the angiogenic activity of HG-dfECFCs and dmECFCs and FIR has potential as a treatment for DM. Detection of miR-134 expression in FIR-treated ECFCs should help us to explore further the effectiveness of FIR therapy.
Systematic study on the isotopic behavior of fusion barrier using the density-dependent nucleon-nucleon interactions

NASA Astrophysics Data System (ADS)

Ghodsi, O. N.; Khalaj, M.

By changing the neutron and nuclear matter incompressibility constant K, we investigate the isotopic behavior of the fusion barriers for the collision of large number of different isotopes with condition of 0.7 ≤ N/Z ≤ 1.36. Here, the double folding (DF) model which is accompanied by density-dependent (DD) versions of M3Y interactions is adopted as a basic heavy ion-ion potential. We show that the selected DD potentials predict a linear behavior for the calculated fusion barrier heights as a function of (N/Z - 1) for both proton- and neutron-rich systems. Moreover, the results indicate that the isotopic behavior of these values depend linearly on the change in the K constant. The isotopic studies conducted on the fusion cross-section also shows that the properties of the nuclear matter in the range of energy which is below the fusion barrier will quite affect the fusion process.
Triamcinolone Acetonide Selectively Inhibits Angiogenesis in Small Blood Vessels and Decreases Vessel Diameter within the Vascular Tree

NASA Technical Reports Server (NTRS)

McKay, Terri L.; Gredeon, Dan J.; Vickerman, Mary B.; Hylton, alan G.; Ribita, Daniela; Olar, Harry H.; Kaiser, Peter K.; Parsons-Wingerter, Patricia

2007-01-01

The steroid triamcinolone acetonide (TA) is a potent anti-angiogenesis drug used to treat retinal vascular diseases that include diabetic retinopathy, vascular occlusions and choroidal neovascularization. To quantify the effects of TA on branching morphology within the angiogenic microvascular tree of the chorioallantoic membrane (CAM) of quail embryos. Increasing concentrations of TA (0-16 ng/ml) were applied topically on embryonic day 7 (E7) to the chorioallantoic membrane (CAM) of quail embryos cultured in Petri dishes, and incubated for an additional 24 or 48 hours until fixation. Binary (black/white) microscopic images of arterial end points were quantified by VESGEN software (for Generational Analysis of Vessel Branching) to obtain major vascular parameters that include vessel diameter (Dv), fractal dimension (Df), tortuosity (Tv) and densities of vessel area, length, number and branch point (Av, Lv, Nv and Brv). For assessment of specific changes in vascular morphology induced by TA, the VESGEN software automatically segmented the vascular tree into branching generations (G1...G10) according to changes in vessel diameter and branching. Vessel density decreased significantly up to 34% as the function of increasing concentration of TA according to Av, Lv, Brv, Nv and Df. TA selectively inhibited the growth of new, small vessels, because Lv decreased from 13.14plus or minus 0.61 cm/cm2 for controls to 8.012 plus or minus 0.82 cm/cm2 at 16 ng TA/ml in smaller branching generations (G7-G10), and for Nv from 473.83 plus or minus 29.85 cm(-)2 to 302.32 plus or minus 33.09 cm-()2. In contrast, vessel diameter (Dv) decreased throughout the vascular tree (G1-G10).
The spectroscopic (FTIR, FT-IR gas phase and FT-Raman), first order hyperpolarizabilities, NMR analysis of 2,4-dichloroaniline by ab initio HF and density functional methods.

PubMed

Sundaraganesan, N; Karpagam, J; Sebastian, S; Cornard, J P

2009-07-01

In this work, the experimental and theoretical study on molecular structure and vibrational spectra of 2,4-dichloroaniline (2,4-DCA) were studied. The Fourier transform infrared (gas phase) and Fourier transform Raman spectra of 2,4-DCA were recorded. The molecular geometry and vibrational frequencies of 2,4-DCA in the ground state were calculated by using the Hartree-Fock (HF) and density functional (DF) methods (BLYP, B3LYP and SVWN) with 6-31G(d,p) as basis set. Comparison of the observed fundamental vibrational frequencies of 2,4-DCA with calculated results by HF and density functional methods indicates that BLYP is superior to other methods for molecular vibrational problems. The difference between the observed and scaled wave number values of most of the fundamentals is very small. The electric dipole moment (micro) and the first hyperpolarizability (beta) values of the investigated molecule were computed using ab initio quantum mechanical calculations. The calculated results also show that the 2,4-DCA molecule might have microscopic nonlinear optical (NLO) behavior with non-zero values. Natural atomic charges of 2,4-DCA and 4-chloroaniline was calculated and compared. The isotropic chemical shift computed by (13)C NMR analyses also shows good agreement with experimental observations. The theoretically predicted FTIR and FT-Raman spectra of the title molecule have been constructed.
The influence of ankle dorsiflexion and self-reported patient outcomes on dynamic postural control in participants with chronic ankle instability.

PubMed

Terada, Masafumi; Harkey, Matthew S; Wells, Ashley M; Pietrosimone, Brian G; Gribble, Phillip A

2014-01-01

We investigated the influence of ankle dorsiflexion range of motion (DF-ROM) and self-reported patient outcomes on dynamic postural control assessed with the Star Excursion Balance Test (SEBT) in individuals with chronic ankle instability (CAI). Twenty-nine participants with self-reported CAI volunteered. The primary outcome measurements were categorized into clinician-and patient-generated. Clinician-generated outcome measurements included anterior (SEBT-A), posteriormedial (SEBT-PM) and posteriorlateral (SEBT-PL) reach distances (cm) normalized by leg length (cm) of the SEBT, maximum weight-bearing dorsiflexion (WB-DF) (cm), and open-chain DF-ROM (°). Self-reported patient-generated outcome measures included the foot and ankle ability measure and the level of perceived pain, stiffness, stability, and function of their involved ankle on a 10-cm visual analog scale (VAS). Pearson product moment correlations were used to examine the relationship of the SEBT performances with DF-ROM and self-reported patient outcome measures. A multiple linear regression was performed to determine the influence of patient- and clinician-generated measures on the SEBT. SEBT-A performance was significantly and fairly correlated with WB-DF (r=0.410, p=0.014), perceived ankle stiffness (r=0.477, p=0.014), and open-chain DF-ROM (r=0.404, p=0.015). The strongest predictor of the variance in SEBT-A was the combination of the variance in WB-DF and VAS-stiffness (R2=0.348, p=0.004). There were no significant correlations with the SEBT-PM and SEBT-PL. WB-DF and VAS-stiffness may represent targets for intervention that need to be addressed to produce the best outcome in participants with CAI when altered dynamic postural control is detected on the SEBT-A. Copyright © 2014 Elsevier B.V. All rights reserved.
Mitochondrial-targeted DNA delivery using a DF-MITO-Porter, an innovative nano carrier with cytoplasmic and mitochondrial fusogenic envelopes

NASA Astrophysics Data System (ADS)

Yamada, Yuma; Kawamura, Eriko; Harashima, Hideyoshi

2012-08-01

Mitochondrial gene therapy has the potential for curing a variety of diseases that are associated with mitochondrial DNA mutations and/or defects. To achieve this, it will be necessary to deliver therapeutic agents into the mitochondria in diseased cells. A number of mitochondrial drug delivery systems have been reported to date. However, reports of mitochondrial-targeted DNA delivery are limited. To achieve this, the therapeutic agent must be taken up by the cell (1), after which, the multi-processes associated with intracellular trafficking must be sophisticatedly regulated so as to release the agent from the endosome and deliver it to the cytosol (2) and to pass through the mitochondrial membrane (3). We report herein on the mitochondrial delivery of oligo DNA as a model therapeutic using a Dual Function (DF)-MITO-Porter, an innovative nano carrier designed for mitochondrial delivery. The critical structural elements of the DF-MITO-Porter include mitochondria-fusogenic inner envelopes and endosome-fusogenic outer envelopes, modified with octaarginine which greatly assists in cellular uptake. Inside the cell, the carrier passes through the endosomal and mitochondrial membranes via step-wise membrane fusion. When the oligo DNA was packaged in the DF-MITO-Porter, cellular uptake efficiency was strongly enhanced. Intracellular observation using confocal laser scanning microscopy showed that the DF-MITO-Porter was effectively released from endosomes. Moreover, the findings confirmed that the mitochondrial targeting activity of the DF-MITO-Porter was significantly higher than that of a carrier without outer endosome-fusogenic envelopes. These results support the conclusion that mitochondrial-targeted DNA delivery using a DF-MITO-Porter can be achieved when intracellular trafficking is optimally regulated.
Profile of hepatic involvement in dengue infections in adult Pakistani population.

PubMed

Iqtadar, Somia; Akbar, Nabeel; Huma, Naima; Randhawa, Fawad Ahmad

2017-01-01

To estimate the range of hepatic involvement in dengue infections by assessing clinical and biochemical profile of adult dengue infected patients. Serologically confirmed 220 adult cases of dengue infections admitted to Mayo hospital from June 2013 to November 2013 were classified as having dengue fever, dengue haemorragic fever and dengue shock syndrome. The frequency and range of bilirubin, liver enzymes derangement and presence of liver enlargement in each group was calculated and further stratified according to age and gender. Patients with positive viral serology, chronic liver disease, malaria and typhoid were excluded from the study. About 60% of DHF patients had hepatomegaly compared to 40% of DF patients. Liver dysfunction was more common in DF compared to DHF (38.15 vs 18.6%). Hyperbilirubinemia was noted in 40 (18.2%) patients, 28 (12.7%) in DF and 12(5.5%) in DHF. The mean serum bilirubin was higher in DHF [0.87+0.33] compared to DF [0.74+0.27]. Bilirubin was higher in male patients and in younger (<20 years) age group. ALT was elevated more frequently in male patients in age group of 31-40 years and in DF patients as compared to DHF [72(32.7% vs 40(18.2%)]. The mean serum ALT level was 103.7 U/l in DHF and 69.2U/l in DF. AST was raised in all DHF patients as compared to DF in which 40% patients had normal AST levels. Alkaline Phosphate was high in all DHF patients with a mean of 278.7. It was raised in most of the DF patients as well and majority of patients were in age group of 31-40 years. Liver involvement is very common in dengue infections and is not limited to elevation of transaminases only. Bilirubin and Alkaline phosphatase are also raised in considerable number of patients. Therefore in adults with fever, jaundice, hepatomegaly and altered liver function tests, the diagnosis of dengue infection should be strongly considered in areas where dengue infection is endemic. List of abbreviations: DF: Dengue Fever DHF: Dengue Hemorrhagic Fever DSS: Dengue Shock Syndrome DIC: Disseminated intravascular coagulation ALT: Alanine transaminase AST: Aspartate aminotransferase.
[Density functional theory studies on structure and spectrum of Cu3 Ti cluster].

PubMed

Wei, Yong-Hui; Cheng, Jian-Bo; Zhao, Bing; Lombardi, John R

2008-07-01

Bulk intermetallic Ti-Cu compounds have been found to possess special properties, including increased hardness, as well as displaying enhanced sound absorption and e shape memory. Since only one Raman progression is observed, there is not sufficient information to determine the structure of TiCu3. The different structures and vibrational frequencies of the Cu3 Ti cluster were studied by means of the density functional theory with SVWN5, B3LYP and BPW91 methods at basis sets of lanl2dz, 6-31g, 6-311g, 6-311g(d), 6-311 +/- g(2df) and 6-311 +/- g(3d2f). The calculated results show that the ground state of the Cu3 Ti cluster is a e-type structure with the C2v point group symmetry, and the bond lengths and vibrational frequencies of Cu3 T are considerably dependent on the variation of basis sets. We observed only a single Raman progression in approximately 300 cm(-1). This progression is most likely the totally symmetric stretch. The computed and observed Raman spectra were also compared with each other.
Thermal stability of mullite RMn₂O₅ (R = Bi, Y, Pr, Sm or Gd): combined density functional theory and experimental study.

PubMed

Li, Chenzhe; Thampy, Sampreetha; Zheng, Yongping; Kweun, Joshua M; Ren, Yixin; Chan, Julia Y; Kim, Hanchul; Cho, Maenghyo; Kim, Yoon Young; Hsu, Julia W P; Cho, Kyeongjae

2016-03-31

Understanding and effectively predicting the thermal stability of ternary transition metal oxides with heavy elements using first principle simulations are vital for understanding performance of advanced materials. In this work, we have investigated the thermal stability of mullite RMn2O5 (R = Bi, Pr, Sm, or Gd) structures by constructing temperature phase diagrams using an efficient mixed generalized gradient approximation (GGA) and the GGA + U method. Simulation predicted stability regions without corrections on heavy elements show a 4-200 K underestimation compared to our experimental results. We have found the number of d/f electrons in the heavy elements shows a linear relationship with the prediction deviation. Further correction on the strongly correlated electrons in heavy elements could significantly reduce the prediction deviations. Our corrected simulation results demonstrate that further correction of R-site elements in RMn2O5 could effectively reduce the underestimation of the density functional theory-predicted decomposition temperature to within 30 K. Therefore, it could produce an accurate thermal stability prediction for complex ternary transition metal oxide compounds with heavy elements.
Evidence for a π junction in Nb/Ni 0.96V0.04/Nb trilayers revealed by superfluid density measurements

NASA Astrophysics Data System (ADS)

Hinton, M. J.; Steers, Stanley; Peters, Bryan; Yang, F. Y.; Lemberger, T. R.

2016-07-01

We report measurements of the superfluid density, λ-2(T ) , in ferromagnet-on-superconductor (F/S) bilayers and S/F/S' trilayers comprising Nb with Ni, Py, CoFe, and NiV ferromagnets. Bilayers provide information about F/S interface transparency and the T dependence of λ-2 that inform interpretation of trilayer data. The Houzet-Meyer theory accounts well for the measured dependence of λ-2(0 ) and Tc of F/S bilayers on thickness of F layer, dF, except that λ-2(0 ) is slightly under expectations for CoFe/Nb bilayers. For Nb/F/Nb' trilayers, we are able to extract Tc and and λ-2 for both Nb layers when F is thick enough to weaken interlayer coupling. The lower "Tc" is actually a crossover identified by onset of superfluid in the lower-Tc Nb layer. For Nb/NiV/Nb' trilayers, λ-2(0 ) versus dF for both Nb layers has a minimum followed by a recovery, suggestive of a π junction.
Quantifying Diastolic Function: From E-Waves as Triangles to Physiologic Contours via the 'Geometric Method'.

PubMed

Golman, Mikhail; Padovano, William; Shmuylovich, Leonid; Kovács, Sándor J

2018-03-01

Conventional echocardiographic diastolic function (DF) assessment approximates transmitral flow velocity contours (Doppler E-waves) as triangles, with peak (E peak ), acceleration time (AT), and deceleration time (DT) as indexes. These metrics have limited value because they are unable to characterize the underlying physiology. The parametrized diastolic filling (PDF) formalism provides a physiologic, kinematic mechanism based characterization of DF by extracting chamber stiffness (k), relaxation (c), and load (x o ) from E-wave contours. We derive the mathematical relationship between the PDF parameters and E peak , AT, DT and thereby introduce the geometric method (GM) that computes the PDF parameters using E peak , AT, and DT as input. Numerical experiments validated GM by analysis of 208 E-waves from 31 datasets spanning the full range of clinical diastolic function. GM yielded indistinguishable average parameter values per subject vs. the gold-standard PDF method (k: R 2 = 0.94, c: R 2 = 0.95, x o : R 2 = 0.95, p < 0.01 all parameters). Additionally, inter-rater reliability for GM-determined parameters was excellent (k: ICC = 0.956 c: ICC = 0.944, x o : ICC = 0.993). Results indicate that E-wave symmetry (AT/DT) may comprise a new index of DF. By employing indexes (E peak , AT, DT) that are already in standard clinical use the GM capitalizes on the power of the PDF method to quantify DF in terms of physiologic chamber properties.
Trait Neuroticism, Depression, and Cognitive Function in Older Primary Care Patients

PubMed Central

Boyle, Lisa L.; Lyness, Jeffrey M.; Duberstein, Paul R.; Karuza, Jurgis; King, Deborah A.; Messing, Susan; Tu, Xin

2010-01-01

Objective Prior studies on the association of trait neuroticism and cognitive function in older adults have yielded mixed findings. We tested hypotheses that neuroticism is associated with measures of cognition and that depression moderates these relationships. Design Cross-sectional observational study. Setting Primary care offices. Participants Primary care patients age ≥65 years. Measurements Trait neuroticism was assessed by the NEO-Five Factor Inventory. Major and minor depression (MDD, MinD) were determined by the Structured Clinical Interview for DSM-IV, and depressive symptom severity by the Hamilton Depression Rating Scale (Ham-D). Cognitive measures included the Mini-Mental State Examination (MMSE), Initiation-Perseveration subscale of the Mattis Dementia Rating Scale, and Trail-Making Tests A and B. Results In multiple regression analyses, neuroticism was associated with MMSE score independent of depression diagnosis (β = −0.04, χ2 = 14.2, df = 1, p = 0.0002, 95% CI = −0.07, −0.02) and Ham-D score (β = −0.04, χ2 = 8.97, df = 1, p = 0.003, 95% CI = −0.06, −0.01). Interactions between neuroticism and depression diagnosis (χ2 = 7.21, df = 2, p = 0.03) and Ham-D scores (χ2 = 0.55, df = 1, p = 0.46) failed to lend strong support to the moderation hypothesis. Conclusion Neuroticism is associated with lower MMSE scores. Findings do not confirm a moderating role for depression, but suggest that depression diagnosis may confer additional risk for poorer global cognitive function in patients with high neuroticism. Further study is necessary. PMID:20220585
Vocalization behavior and response of black rails

USGS Publications Warehouse

Legare, M.L.; Eddleman, W.R.; Buckley, P.A.; Kelly, C.

1999-01-01

We measured the vocal responses and movements of radio-tagged black rails (Laterallus jamaicensis) (n = 43, 26 males, 17 females) to playback of vocalizations at 2 sites in Florida during the breeding seasons of 1992-95. We used regression coefficients from logistic regression equations to model the probability of a response conditional to the birds' sex, nesting status, distance to playback source, and the time of survey. With a probability of 0.811, non-nesting male black rails were most likely to respond to playback, while nesting females were the least likely to respond (probability = 0.189). Linear regression was used to determine daily, monthly, and annual variation in response from weekly playback surveys along a fixed route during the breeding seasons of 1993-95. Significant sources of variation in the linear regression model were month (F = 3.89, df = 3, p = 0.0140), year (F = 9.37, df = 2, p = 0.0003), temperature (F = 5.44, df=1, p = 0.0236), and month*year (F = 2.69, df = 5, p = 0.0311). The model was highly significant (p < 0.0001) and explained 53% of the variation of mean response per survey period (R2 = 0.5353). Response probability data obtained from the radio-tagged black rails and data from the weekly playback survey route were combined to provide a density estimate of 0.25 birds/ha for the St. Johns National Wildlife Refuge. Density estimates for black rails may be obtained from playback surveys, and fixed radius circular plots. Circular plots should be considered as having a radius of 80 m and be located so the plot centers are 150 m apart. Playback tapes should contain one series of Kic-kic-kerr and Growl vocalizations recorded within the same geographic region as the study area. Surveys should be conducted from 0-2 hours after sunrise or 0-2 hours before sunset, during the pre-nesting season, and when wind velocity is < 20 kph. Observers should listen for 3-4 minutes after playing the survey tape and record responses heard during that time. Observers should be trained to identify black rail vocalizations and should have acceptable hearing ability. Given the number of variables that may have large effects on the response behavior of black rails to tape playback, we recommend that future studies using playback surveys should be cautious when presenting estimates of 'absolute' density. Though results did account for variation in response behavior, we believe that additional variation in vocal response between sites, with breeding status, and bird density remains in question. Playback surveys along fixed routes providing a simple index of abundance would be useful to monitor populations over large geographic areas, and over time. Considering the limitations of most agency resources for webless waterbirds, index surveys may be more appropriate. Future telemetry studies of this type on other species and at other sites would be useful to calibrate information obtained from playback surveys whether reporting an index of abundance or density estimate.
Visual processing of words in a patient with visual form agnosia: a behavioural and fMRI study.

PubMed

Cavina-Pratesi, Cristiana; Large, Mary-Ellen; Milner, A David

2015-03-01

Patient D.F. has a profound and enduring visual form agnosia due to a carbon monoxide poisoning episode suffered in 1988. Her inability to distinguish simple geometric shapes or single alphanumeric characters can be attributed to a bilateral loss of cortical area LO, a loss that has been well established through structural and functional fMRI. Yet despite this severe perceptual deficit, D.F. is able to "guess" remarkably well the identity of whole words. This paradoxical finding, which we were able to replicate more than 20 years following her initial testing, raises the question as to whether D.F. has retained specialized brain circuitry for word recognition that is able to function to some degree without the benefit of inputs from area LO. We used fMRI to investigate this, and found regions in the left fusiform gyrus, left inferior frontal gyrus, and left middle temporal cortex that responded selectively to words. A group of healthy control subjects showed similar activations. The left fusiform activations appear to coincide with the area commonly named the visual word form area (VWFA) in studies of healthy individuals, and appear to be quite separate from the fusiform face area (FFA). We hypothesize that there is a route to this area that lies outside area LO, and which remains relatively unscathed in D.F. Copyright © 2014 Elsevier Ltd. All rights reserved.

Prediction of radial breathing-like modes of double-walled carbon nanotubes with arbitrary chirality

NASA Astrophysics Data System (ADS)

Ghavanloo, Esmaeal; Fazelzadeh, S. Ahmad

2014-10-01

The radial breathing-like modes (RBLMs) of double-walled carbon nanotubes (DWCNTs) with arbitrary chirality are investigated by a simple analytical model. For this purpose, DWCNT is considered as double concentric elastic thin cylindrical shells, which are coupled through van der Waals (vdW) forces between two adjacent tubes. Lennard-Jones potential and a molecular mechanics model are used to calculate the vdW forces and to predict the mechanical properties, respectively. The validity of these theoretical results is confirmed through the comparison of the experimental results. Finally, a new approach is proposed to determine the diameters and the chiral indices of the inner and outer tubes of the DWCNTs with high precision.
Activation of Noble Metals on Metal-Carbide Surfaces: Novel Catalysts for CO Oxidation, Desulfurization and Hydrogenation Reactions

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

Rodriguez J. A.; Illas, F.

2012-01-01

This perspective article focuses on the physical and chemical properties of highly active catalysts for CO oxidation, desulfurization and hydrogenation reactions generated by depositing noble metals on metal-carbide surfaces. To rationalize structure-reactivity relationships for these novel catalysts, well-defined systems are required. High-resolution photoemission, scanning tunneling microscopy (STM) and first-principles periodic density-functional (DF) calculations have been used to study the interaction of metals of Groups 9, 10 and 11 with MC(001) (M = Ti, Zr, V, Mo) surfaces. DF calculations give adsorption energies that range from 2 eV (Cu, Ag, Au) to 6 eV (Co, Rh, Ir). STM images show thatmore » Au, Cu, Ni and Pt grow on the carbide substrates forming two-dimensional islands at very low coverage, and three-dimensional islands at medium and large coverages. In many systems, the results of DF calculations point to the preferential formation of admetal-C bonds with significant electronic perturbations in the admetal. TiC(001) and ZrC(001) transfer some electron density to the admetals facilitating bonding of the adatom with electron-acceptor molecules (CO, O{sub 2}, C{sub 2}H{sub 4}, SO{sub 2}, thiophene, etc.). For example, the Cu/TiC(001) and Au/TiC(001) systems are able to cleave both S-O bonds of SO{sub 2} at a temperature as low as 150 K, displaying a reactivity much larger than that of TiC(001) or extended surfaces of bulk copper and gold. At temperatures below 200 K, Au/TiC is able to dissociate O{sub 2} and perform the 2CO + O{sub 2} {yields} 2CO{sub 2} reaction. Furthermore, in spite of the very poor hydrodesulfurization performance of TiC(001) or Au(111), a Au/TiC(001) surface displays an activity for the hydrodesulfurization of thiophene higher than that of conventional Ni/MoS{sub x} catalysts. In general, the Au/TiC system is more chemically active than systems generated by depositing Au nanoparticles on oxide surfaces. Thus, metal carbides are excellent supports for enhancing the chemical reactivity of noble metals.« less
Mass spectrometric analysis and aerodynamic properties of various types of combustion-related aerosol particles

NASA Astrophysics Data System (ADS)

Schneider, J.; Weimer, S.; Drewnick, F.; Borrmann, S.; Helas, G.; Gwaze, P.; Schmid, O.; Andreae, M. O.; Kirchner, U.

2006-12-01

Various types of combustion-related particles in the size range between 100 and 850 nm were analyzed with an aerosol mass spectrometer and a differential mobility analyzer. The measurements were performed with particles originating from biomass burning, diesel engine exhaust, laboratory combustion of diesel fuel and gasoline, as well as from spark soot generation. Physical and morphological parameters like fractal dimension, effective density, bulk density and dynamic shape factor were derived or at least approximated from the measurements of electrical mobility diameter and vacuum aerodynamic diameter. The relative intensities of the mass peaks in the mass spectra obtained from particles generated by a commercial diesel passenger car, by diesel combustion in a laboratory burner, and by evaporating and re-condensing lubrication oil were found to be very similar. The mass spectra from biomass burning particles show signatures identified as organic compounds like levoglucosan but also others which are yet unidentified. The aerodynamic behavior yielded a fractal dimension (Df) of 2.09 +/- 0.06 for biomass burning particles from the combustion of dry beech sticks, but showed values around three, and hence more compact particle morphologies, for particles from combustion of more natural oak. Scanning electron microscope images confirmed the finding that the beech combustion particles were fractal-like aggregates, while the oak combustion particles displayed a much more compact shape. For particles from laboratory combusted diesel fuel, a Df value of 2.35 was found, for spark soot particles, Df [approximate] 2.10. The aerodynamic properties of fractal-like particles from dry beech wood combustion indicate an aerodynamic shape factor [chi] that increases with electrical mobility diameter, and a bulk density of 1.92 g cm-3. An upper limit of [chi] [approximate] 1.2 was inferred for the shape factor of the more compact particles from oak combustion.
Electrostatic contribution to the binding stability of protein-protein complexes.

PubMed

Dong, Feng; Zhou, Huan-Xiang

2006-10-01

To investigate roles of electrostatic interactions in protein binding stability, electrostatic calculations were carried out on a set of 64 mutations over six protein-protein complexes. These mutations alter polar interactions across the interface and were selected for putative dominance of electrostatic contributions to the binding stability. Three protocols of implementing the Poisson-Boltzmann model were tested. In vdW4 the dielectric boundary between the protein low dielectric and the solvent high dielectric is defined as the protein van der Waals surface and the protein dielectric constant is set to 4. In SE4 and SE20, the dielectric boundary is defined as the surface of the protein interior inaccessible to a 1.4-A solvent probe, and the protein dielectric constant is set to 4 and 20, respectively. In line with earlier studies on the barnase-barstar complex, the vdW4 results on the large set of mutations showed the closest agreement with experimental data. The agreement between vdW4 and experiment supports the contention of dominant electrostatic contributions for the mutations, but their differences also suggest van der Waals and hydrophobic contributions. The results presented here will serve as a guide for future refinement in electrostatic calculation and inclusion of nonelectrostatic effects. Proteins 2006. (c) 2006 Wiley-Liss, Inc.
Nitrogen Doping Enables Covalent-Like π–π Bonding between Graphenes

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

Tian, Yong-Hui; Huang, Jingsong; Sheng, Xiaolan

In neighboring layers of bilayer (and few-layer) graphenes, both AA and AB stacking motifs are known to be separated at a distance corresponding to van der Waals (vdW) interactions. In this Letter, we present for the first time a new aspect of graphene chemistry in terms of a special chemical bonding between the giant graphene "molecules". Through rigorous theoretical calculations, we demonstrate that the N-doped graphenes (NGPs) with various doping levels can form an unusual two-dimensional (2D) pi-pi bonding in bilayer NGPs bringing the neighboring NGPs to significantly reduced interlayer separations. The interlayer binding energies can be enhanced by upmore » to 50% compared to the pristine graphene bilayers that are characterized by only vdW interactions. Such an unusual chemical bonding arises from the pi-pi overlap across the vdW gap while the individual layers maintain their in-plane pi-conjugation and are accordingly planar. Moreover, the existence of the resulting interlayer covalent-like bonding is corroborated by electronic structure calculations and crystal orbital overlap population (COOP) analyses. In NGP-based graphite with the optimal doping level, the NGP layers are uniformly stacked and the 3D bulk exhibits metallic characteristics both in the in-plane and along the stacking directions.« less
Analytical solution for static and dynamic analysis of magnetically affected viscoelastic orthotropic double-layered graphene sheets resting on viscoelastic foundation

NASA Astrophysics Data System (ADS)

Jalaei, M. H.; Arani, A. Ghorbanpour

2018-02-01

By considering the small scale effect based on the nonlocal Eringen's theory, the static and dynamic analysis of viscoelastic orthotropic double-layered graphene sheets subjected to longitudinal magnetic field and mechanical load is investigated analytically. For this objective, first order shear deformation theory (FSDT) is proposed. The surrounding medium is simulated by visco-Pasternak foundation model in which damping, normal and transverse shear loads are taken into account. The governing equations of motion are obtained via energy method and Hamilton's principle which are then solved analytically by means of Navier's approach and Laplace inversion technique in the space and time domains, respectively. Through various parametric studies, the influences of the nonlocal parameter, structural damping, van der Waals (vdW) interaction, stiffness and damping coefficient of the foundation, magnetic parameter, aspect ratio and length to thickness ratio on the static and dynamic response of the nanoplates are examined. The results depict that when the vdW interaction is considered to be zero, the upper layer deflection reaches a maximum point whereas the lower layer deflection becomes zero. In addition, it is observed that with growing the vdW interaction, the effect of magnetic field on the deflection of the lower layer increases while this effect reduces for the upper layer deflection.
Nitrogen-Doping Enables Covalent-Like pi-pi Bonding between Graphenes

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

Tian, Yong-Hui; Huang, Jingsong; Sumpter, Bobby G

The neighboring layers in bi-layer (and few-layer) graphenes of both AA and AB stacking motifs are known to be separated at a distance corresponding to van der Waals (vdW) interactions. In this Letter, we present for the first time a new aspect of graphene chemistry in terms of a special chemical bonding between the giant graphene molecules . Through rigorous theoretical calculations, we demonstrate that the N-doped graphenes (NGPs) with various doping levels can form an unusual two-dimensional (2D) pi pi bonding in bi-layer NGPs bringing the neighboring NGPs to significantly reduced interlayer separations. The interlayer binding energies can bemore » enhanced by up to 50% compared to the pristine graphene bi-layers that are characterized by only vdW interactions. Such an unusual chemical bonding arises from the pi pi overlap across the vdW gap while the individual layers maintain their in-plane pi-conjugation and are accordingly planar. The existence of the resulting interlayer covalent-like bonding is corroborated by electronic structure calculations and crystal orbital overlap population (COOP) analyses. In NGP-based graphite with the optimal doping level, the NGP layers are uniformly stacked and the 3D bulk exhibits metallic characteristics both in the in-plane and along the stacking directions.« less
Nitrogen Doping Enables Covalent-Like π–π Bonding between Graphenes

DOE PAGES

Tian, Yong-Hui; Huang, Jingsong; Sheng, Xiaolan; ...

2015-07-07

In neighboring layers of bilayer (and few-layer) graphenes, both AA and AB stacking motifs are known to be separated at a distance corresponding to van der Waals (vdW) interactions. In this Letter, we present for the first time a new aspect of graphene chemistry in terms of a special chemical bonding between the giant graphene "molecules". Through rigorous theoretical calculations, we demonstrate that the N-doped graphenes (NGPs) with various doping levels can form an unusual two-dimensional (2D) pi-pi bonding in bilayer NGPs bringing the neighboring NGPs to significantly reduced interlayer separations. The interlayer binding energies can be enhanced by upmore » to 50% compared to the pristine graphene bilayers that are characterized by only vdW interactions. Such an unusual chemical bonding arises from the pi-pi overlap across the vdW gap while the individual layers maintain their in-plane pi-conjugation and are accordingly planar. Moreover, the existence of the resulting interlayer covalent-like bonding is corroborated by electronic structure calculations and crystal orbital overlap population (COOP) analyses. In NGP-based graphite with the optimal doping level, the NGP layers are uniformly stacked and the 3D bulk exhibits metallic characteristics both in the in-plane and along the stacking directions.« less
FLIS Procedures Manual. Materiel Management Decision Rule Tables.

DTIC Science & Technology

1996-10-01

U5 C PA FAPA DF PA 06 TA 67 PA PA TU PA TU PA FEPA DF PA 06 SE 67 PA PA TU PA TU PA FGPA DF PA 06 TG 67 PA PA TU PA TU PA FJPA DF PA 06 SJ 67 PA PA SJ...AJ TU AJ TU TA FAJ4 DF AJ 22 TA 97 AJ AJ TU AJ TU TA FAKE DF KE 06 TA 67 KE KE TU KE TU TA FAKZ DF KZ 01 TA 5D KZ KZ TU KZ TU I TA FAPA DF PA 06 TA...AJ TU TU FAJ5 DF AJ 22 TG 97 AJ AJ TU AJ TU TU FAKE DF KE 06 TA 67 KE KE TU KE TU TU FAPA DF PA 01 TA 67 PA PA TU PA TU TU FATC DF AZ 22 TA 8D AZ AZ
Nanoparticle interaction potentials constructed by multiscale computation

NASA Astrophysics Data System (ADS)

Lee, Cheng K.; Hua, Chi C.

2010-06-01

The van der Waals (vdW) potentials governing macroscopic objects have long been formulated in the context of classical theories, such as Hamaker's microscopic theory and Lifshitz's continuum theory. This work addresses the possibility of constructing the vdW interaction potentials of nanoparticle species using multiscale simulation schemes. Amorphous silica nanoparticles were considered as a benchmark example for which a series of (SiO2)n (n being an integer) has been systematically surveyed as the potential candidates of the packing units that reproduce known bulk material properties in atomistic molecular dynamics simulations. This strategy led to the identification of spherical Si6O12 molecules, later utilized as the elementary coarse-grained (CG) particles to compute the pair interaction potentials of silica nanoparticles ranging from 0.62 to 100 nm in diameter. The model nanoparticles so built may, in turn, serve as the children CG particles to construct nanoparticles assuming arbitrary sizes and shapes. Major observations are as follows. The pair interaction potentials for all the investigated spherical silica nanoparticles can be cast into a semiempirical, generalized Lennard-Jones 2α-α potential (α being a size-dependent, large integral number). In its reduced form, we discuss the implied universalities for the vdW potentials governing a certain range of amorphous nanoparticle species as well as how thermodynamic transferability can be fulfilled automatically. In view of future applications with colloidal suspensions, we briefly evaluated the vdW potential in the presence of a "screening" medium mimicking the effects of electrical double layers or grafting materials atop the nanoparticle core. The general observations shed new light on strategies to attain a microscopic control over interparticle attractions. In future perspectives, the proposed multiscale computation scheme shall help bridge the current gap between the modeling of polymer chains and macroscopic objects by introducing molecular models coarse-grained at a similar level so that the interactions between these two can be treated in a consistent and faithful way.
Low-coverage surface diffusion in complex periodic energy landscapes: Analytical solution for systems with symmetric hops and application to intercalation in topological insulators

NASA Astrophysics Data System (ADS)

Gosálvez, Miguel A.; Otrokov, Mikhail M.; Ferrando, Nestor; Ryabishchenkova, Anastasia G.; Ayuela, Andres; Echenique, Pedro M.; Chulkov, Evgueni V.

2016-02-01

This is the first of two papers that introduce a general expression for the tracer diffusivity in complex, periodic energy landscapes with M distinct hop rates in one-, two-, and three-dimensional diluted systems (low-coverage, single-tracer limit). The present report focuses on the analysis of diffusion in systems where the end sites of the hops are located symmetrically with respect to the hop origins (symmetric hops), as encountered in many ideal surfaces and bulk materials. For diffusion in two dimensions, a number of formulas are presented for complex combinations of the different hops in systems with triangular, rectangular, and square symmetry. The formulas provide values in excellent agreement with kinetic Monte Carlo simulations, concluding that the diffusion coefficient can be directly determined from the proposed expressions without performing the simulations. Based on the diffusion barriers obtained from first-principles calculations and a physically meaningful estimate of the attempt frequencies, the proposed formulas are used to analyze the diffusion of Cu, Ag, and Rb adatoms on the surface and within the van der Waals (vdW) gap of a model topological insulator, Bi2Se3 . Considering the possibility of adsorbate intercalation from the terraces to the vdW gaps at morphological steps, we infer that, at low coverage and room temperature, (i) a majority of the Rb atoms bounce back at the steps and remain on the terraces, (ii) Cu atoms mostly intercalate into the vdW gap, the remaining fraction staying at the steps, and (iii) Ag atoms essentially accumulate at the steps and gradually intercalate into the vdW gap. These conclusions are in good qualitative agreement with previous experiments. The companion report (M. A. Gosálvez et al., Phys. Rev. B, submitted] extends the present study to the description of systems that contain asymmetric hops.
Investigation of verbal and visual working memory by multi-channel time-resolved functional near-infrared spectroscopy

NASA Astrophysics Data System (ADS)

Contini, D.; Caffini, M.; Re, R.; Zucchelli, L.; Spinelli, L.; Basso Moro, S.; Bisconti, S.; Ferrari, M.; Quaresima, V.; Cutini, S.; Torricelli, A.

2013-03-01

Working memory (WM) is fundamental for a number of cognitive processes, such as comprehension, reasoning and learning. WM allows the short-term maintenance and manipulation of the information selected by attentional processes. The goal of this study was to examine by time-resolved fNIRS neural correlates of the verbal and visual WM during forward and backward digit span (DF and DB, respectively) tasks, and symbol span (SS) task. A neural dissociation was hypothesised between the maintenance and manipulation processes. In particular, a dorsolateral/ventrolateral prefrontal cortex (DLPFC/VLPFC) recruitment was expected during the DB task, whilst a lateralised involvement of Brodmann Area (BA) 10 was expected during the execution of the DF task. Thirteen subjects were monitored by a multi-channel, dual-wavelength (690 and 829 nm) time-resolved fNIRS system during 3 minutes long DF and DB tasks and 4 minutes long SS task. The participants' mean memory span was calculated for each task: DF: 6.46+/-1.05 digits; DB: 5.62+/-1.26 digits; SS: 4.69+/-1.32 symbols. No correlation was found between the span level and the heart rate data (measured by pulse oximeter). As expected, DB elicited a broad activated area, in the bilateral VLPFC and the right DLPFC, whereas a more localised activation was observed over the right hemisphere during either DF (BA 10) or SS (BA 10 and 44). The robust involvement of the DLPFC during DB, compared to DF, is compatible with previous findings and with the key role of the central executive subserving in manipulating processes.
Potential of New Isolates of Dunaliella Salina for Natural β-Carotene Production.

PubMed

Xu, Yanan; Ibrahim, Iskander M; Wosu, Chiziezi I; Ben-Amotz, Ami; Harvey, Patricia J

2018-02-01

The halotolerant microalga Dunaliella salina has been widely studied for natural β-carotene production. This work shows biochemical characterization of three newly isolated Dunaliella salina strains, DF15, DF17, and DF40, compared with D. salina CCAP 19/30 and D. salina UTEX 2538 (also known as D. bardawil ). Although all three new strains have been genetically characterized as Dunaliella salina strains, their ability to accumulate carotenoids and their capacity for photoprotection against high light stress are different. DF15 and UTEX 2538 reveal great potential for producing a large amount of β-carotene and maintained a high rate of photosynthesis under light of high intensity; however, DF17, DF40, and CCAP 19/30 showed increasing photoinhibition with increasing light intensity, and reduced contents of carotenoids, in particular β-carotene, suggesting that the capacity of photoprotection is dependent on the cellular content of carotenoids, in particular β-carotene. Strong positive correlations were found between the cellular content of all-trans β-carotene, 9- cis β-carotene, all-trans α-carotene and zeaxanthin but not lutein in the D. salina strains. Lutein was strongly correlated with respiration in photosynthetic cells and strongly related to photosynthesis, chlorophyll and respiration, suggesting an important and not hitherto identified role for lutein in coordinated control of the cellular functions of photosynthesis and respiration in response to changes in light conditions, which is broadly conserved in Dunaliella strains. Statistical analysis based on biochemical data revealed a different grouping strategy from the genetic classification of the strains. The significance of these data for strain selection for commercial carotenoid production is discussed.
Dietary fibers from mushroom sclerotia: 1. Preparation and physicochemical and functional properties.

PubMed

Wong, Ka-Hing; Cheung, Peter C K

2005-11-30

Preparation of three novel dietary fibers (DFs) from mushroom sclerotia, namely, Pleurotus tuberregium, Polyporous rhinocerus, and Wolfiporia cocos, by a scale-up modified AOAC procedure using industrial enzymes was investigated. A remarkably high level of total dietary fiber (TDF) ranging from 81.7 to 96.3% sample dry matter (DM), in which a content of nonstarch polysaccharide (NSP) ranging from 86.6 to 94.3% sclerotial TDF DM, was obtained from the three sclerotia. All sclerotial DFs were rich in beta-glucan (the glucose residue ranged from 89.7 to 94.5% NSP DM) with a very low level of resistant glycogen (ranged from 3.77 to 3.94% sclerotial TDF DM). All three novel sclerotial DFs also exhibited similar, if not better, physicochemical and functional properties (pH, color, water binding capacity, oil holding capacity, and emulsifying properties) as those of barely DF control and commercial DF-rich ingredients. The potential use of the three mushroom sclerotial DFs as a new beta-glucan type DF-rich ingredient in the food industry was discussed.
Unconventional Magnetism and Band Gap Formation in LiFePO4: Consequence of Polyanion Induced Non-planarity.

PubMed

Jena, Ajit; Nanda, B R K

2016-01-21

Oxygen plays a critical role in strongly correlated transition metal oxides as crystal field effect is one of the key factors that determine the degree of localization of the valence d/f states. Based on the localization, a set of conventional mechanisms such as Mott-Hubbard, Charge-transfer and Slater were formulated to explain the antiferromagnetic and insulating (AFI) phenomena in many of these correlated systems. From the case study on LiFePO4, through density-functional calculations, we demonstrate that none of these mechanisms are strictly applicable to explain the AFI behavior when the transition metal oxides have polyanions such as (PO4)(3-). The symmetry-lowering of the metal-oxygen complex, to stabilize the polyanion, creates an asymmetric crystal field for d/f states. In LiFePO4 this field creates completely non-degenerate Fe-d states which, with negligible p-d and d-d covalent interactions, become atomically localized to ensure a gap at the Fermi level. Due to large exchange splitting, high spin state is favored and an antiferromagnetic configuration is stabilized. For the prototype LiFePO4, independent electron approximation is good enough to obtain the AFI ground state. Inclusion of additional correlation measures like Hubbard U simply amplifies the gap and therefore LiFePO4 can be preferably called as weakly coupled Mott insulator.
Unconventional Magnetism and Band Gap Formation in LiFePO4: Consequence of Polyanion Induced Non-planarity

PubMed Central

Jena, Ajit; Nanda, B. R. K.

2016-01-01

Oxygen plays a critical role in strongly correlated transition metal oxides as crystal field effect is one of the key factors that determine the degree of localization of the valence d/f states. Based on the localization, a set of conventional mechanisms such as Mott-Hubbard, Charge-transfer and Slater were formulated to explain the antiferromagnetic and insulating (AFI) phenomena in many of these correlated systems. From the case study on LiFePO4, through density-functional calculations, we demonstrate that none of these mechanisms are strictly applicable to explain the AFI behavior when the transition metal oxides have polyanions such as (PO4)3−. The symmetry-lowering of the metal-oxygen complex, to stabilize the polyanion, creates an asymmetric crystal field for d/f states. In LiFePO4 this field creates completely non-degenerate Fe-d states which, with negligible p-d and d-d covalent interactions, become atomically localized to ensure a gap at the Fermi level. Due to large exchange splitting, high spin state is favored and an antiferromagnetic configuration is stabilized. For the prototype LiFePO4, independent electron approximation is good enough to obtain the AFI ground state. Inclusion of additional correlation measures like Hubbard U simply amplifies the gap and therefore LiFePO4 can be preferably called as weakly coupled Mott insulator. PMID:26791249
Odd-frequency pairing in superconducting heterostructures .

NASA Astrophysics Data System (ADS)

Golubov, A. A.; Tanaka, Y.; Yokoyama, T.; Asano, Y.

2007-03-01

We present a general theory of the proximity effect in junctions between unconventional superconductors and diffusive normal metals (DN) or ferromagnets (DF). We consider all possible symmetry classes in a superconductor allowed by the Pauli principle: even-frequency spin-singlet even-parity state, even-frequency spin-triplet odd-parity state, odd-frequency spin-triplet even-parity state and odd-frequency spin-singlet odd-parity state. For each of the above states, symmetry and spectral properties of the induced pair amplitude in the DN (DF) are determined. The cases of junctions with spin-singlet s- and d-wave superconductors and spin-triplet p-wave superconductors are adressed in detail. We discuss the interplay between the proximity effect and midgap Andreev bound states arising at interfaces in unconventional (d- or p-wave) junctions. The most striking property is the odd-frequency symmetry of the pairing amplitude induced in DN (DF) in contacts with p-wave superconductors. This leads to zero-energy singularity in the density of states and to anomalous screening of an external magnetic field. Peculiarities of Josephson effect in d- or p-wave junctions are discussed. Experiments are suggested to detect an order parameter symmetry using heterostructures with unconventional superconductors.
Localization of the panhypopituitary dwarf mutation (df) on mouse chromosome 11 in an intersubspecific backcross.

PubMed

Buckwalter, M S; Katz, R W; Camper, S A

1991-07-01

Ames dwarf (df) is an autosomal recessive mutation characterized by severe dwarfism and infertility. This mutation provides a mouse model for panhypopituitarism. The dwarf phenotype results from failure in the differentiation of the cells which produce growth hormone, prolactin, and thyroid stimulating hormone. Using the backcross (DF/B-df/df X CASA/Rk) X DF/B-df/df, we confirmed the assignment of df to mouse chromosome 11 and demonstrated recombination between df and the growth hormone gene. This backcross is an invaluable resource for screening candidate genes for the df mutation. The df locus maps to less than 1 cM distal to Pad-1 (0.85 +/- 0.85 cM). Two new genes localized on mouse chromosome 11, Rpo2-1, and Edp-1, map to a region of conserved synteny with human chromosome 17. The localization of the alpha 1 adrenergic receptor, Adra-1, extends a known region of synteny conservation between mouse chromosome 11 and human chromosome 5, and suggests that a human counterpart to df would map to human chromosome 5.
Probing Behavior of Dichelops furcatus (F.) (Heteroptera: Pentatomidae) on Wheat Plants Characterized by Electropenetrography (EPG) and Histological Studies

PubMed Central

Lucini, Tiago

2017-01-01

The stink bug Dichelops furcatus (F.) (Heteroptera: Pentatomidae) has increased in abundance in recent years on the wheat, Triticum aestivum L., crop cultivated in the southern region of Brazil. To investigate the probing (stylet penetration) behaviors and nonprobing behaviors of D. furcatus on wheat plants, the electrical penetration graph or electropenetrography (EPG) technique was applied. Nine EPG waveforms (types/subtypes) were identified and described on stem and on ear head of wheat plants, as follows: Z, Np, Df1a, Df1b, Df2, Df3a, Df3b, Df4a, and Df4b. For the waveforms Df1, Df2, Df3, and Df4, stylets were severed to determine, via histological studies, the location of the stylet tip and/or salivary sheath tip in plant tissue. Waveform Z was visually correlated with the bug standing still on the plant surface, whereas during Np the bug was walking. Df1a and Df1b represent initial stylet insertion, deep penetration of the stylets into the plant tissue, and secretion of salivary sheath. Df2 represents xylem sap ingestion on stem and on ear head. Waveforms Df3a and Df4a were related to the cell rupturing feeding strategy (laceration and maceration tactics) on stem and on ear head (seed endosperm), respectively. Waveforms Df3b and Df4b represent ingestion of cellular contents derived from cell rupturing activities on stem and on ear head (seed endosperm), respectively. With this fundamental knowledge in hand, future studies can use EPG to develop novel pest management solutions. PMID:28931161
Effect of dual-focus soft contact lens wear on axial myopia progression in children.

PubMed

Anstice, Nicola S; Phillips, John R

2011-06-01

To test the efficacy of an experimental Dual-Focus (DF) soft contact lens in reducing myopia progression. Prospective, randomized, paired-eye control, investigator-masked trial with cross-over. Forty children, 11-14 years old, with mean spherical equivalent refraction (SER) of -2.71 ± 1.10 diopters (D). Dual-Focus lenses had a central zone that corrected refractive error and concentric treatment zones that created 2.00 D of simultaneous myopic retinal defocus during distance and near viewing. Control was a single vision distance (SVD) lens with the same parameters but without treatment zones. Children wore a DF lens in 1 randomly assigned eye and an SVD lens in the fellow eye for 10 months (period 1). Lens assignment was then swapped between eyes, and lenses were worn for a further 10 months (period 2). Primary outcome was change in SER measured by cycloplegic autorefraction over 10 months. Secondary outcome was a change in axial eye length (AXL) measured by partial coherence interferometry over 10 months. Accommodation wearing DF lenses was assessed using an open-field autorefractor. In period 1, the mean change in SER with DF lenses (-0.44 ± 0.33 D) was less than with SVD lenses (-0.69 ± 0.38 D; P < 0.001); mean increase in AXL was also less with DF lenses (0.11 ± 0.09 mm) than with SVD lenses (0.22 ± 0.10 mm; P < 0.001). In 70% of the children, myopia progression was reduced by 30% or more in the eye wearing the DF lens relative to that wearing the SVD lens. Similar reductions in myopia progression and axial eye elongation were also observed with DF lens wear during period 2. Visual acuity and contrast sensitivity with DF lenses were not significantly different than with SVD lenses. Accommodation to a target at 40 cm was driven through the central distance-correction zone of the DF lens. Dual-Focus lenses provided normal acuity and contrast sensitivity and allowed accommodation to near targets. Myopia progression and eye elongation were reduced significantly in eyes wearing DF lenses. The data suggest that sustained myopic defocus, even when presented to the retina simultaneously with a clear image, can act to slow myopia progression without compromising visual function. Proprietary or commercial disclosure may be found after the references. Copyright © 2011 American Academy of Ophthalmology. Published by Elsevier Inc. All rights reserved.

Federal Logistics Information System (FLIS) Procedures Manual. Volume 13. Change 1.

DTIC Science & Technology

1997-01-01

BD 06 TA 67 BD BD TU BD TU BD FBDA DF BD 06 TA 96 BD BD TU BD TU BD FBDD DF BD 06 TD 96 BD BD TU BD TU BD FBDE DF BD 06 SE 96 BD BD TU BD TU BD FBDG...XN TD FAZD DF AZ 06 TD 96 AZ AZ TU AZ TU TD FAZ7 DF AZ 22 TD 97 AZ AZ TU AZ TU TD FBDD DF BD 06 TD 96 BD BD TU BD TU TD FBD7 DF BD 22 TD 97 BD BD TU...48 TU TU FBDA DF BD 06 TA 96 BD BD TU BD TU TU FBDD DF BD 06 TD 96 BD BD TU BD TU TU FBDE DF BD 06 SE 96 BD BD TU BD TU TU FBDG DF BD 06 TG 96 BD BD TU
Profile of hepatic involvement in dengue infections in adult Pakistani population

PubMed Central

Iqtadar, Somia; Akbar, Nabeel; Huma, Naima; Randhawa, Fawad Ahmad

2017-01-01

Objectives: To estimate the range of hepatic involvement in dengue infections by assessing clinical and biochemical profile of adult dengue infected patients. Methods: Serologically confirmed 220 adult cases of dengue infections admitted to Mayo hospital from June 2013 to November 2013 were classified as having dengue fever, dengue haemorragic fever and dengue shock syndrome. The frequency and range of bilirubin, liver enzymes derangement and presence of liver enlargement in each group was calculated and further stratified according to age and gender. Patients with positive viral serology, chronic liver disease, malaria and typhoid were excluded from the study. Results: About 60% of DHF patients had hepatomegaly compared to 40% of DF patients. Liver dysfunction was more common in DF compared to DHF (38.15 vs 18.6%). Hyperbilirubinemia was noted in 40 (18.2%) patients, 28 (12.7%) in DF and 12(5.5%) in DHF. The mean serum bilirubin was higher in DHF [0.87+0.33] compared to DF [0.74+0.27]. Bilirubin was higher in male patients and in younger (<20 years) age group. ALT was elevated more frequently in male patients in age group of 31-40 years and in DF patients as compared to DHF [72(32.7% vs 40(18.2%)]. The mean serum ALT level was 103.7 U/l in DHF and 69.2U/l in DF. AST was raised in all DHF patients as compared to DF in which 40% patients had normal AST levels. Alkaline Phosphate was high in all DHF patients with a mean of 278.7. It was raised in most of the DF patients as well and majority of patients were in age group of 31-40 years. Conclusion: Liver involvement is very common in dengue infections and is not limited to elevation of transaminases only. Bilirubin and Alkaline phosphatase are also raised in considerable number of patients. Therefore in adults with fever, jaundice, hepatomegaly and altered liver function tests, the diagnosis of dengue infection should be strongly considered in areas where dengue infection is endemic. List of abbreviations: DF: Dengue Fever DHF: Dengue Hemorrhagic Fever DSS: Dengue Shock Syndrome DIC: Disseminated intravascular coagulation ALT: Alanine transaminase AST: Aspartate aminotransferase PMID:29067074
Supercooling of Hydrogen on Template Materials to Deterministically Seed Ignition-Quality Solid Fuel Layers

DOE PAGES

Shin, S. J.; Zepeda-Ruiz, L. A.; Lee, J. R. I.; ...

2016-09-01

In this study, we explored templating effects of various materials for hydrogen (H 2 and D 2) solidification by measuring the degree of supercooling required for liquid hydrogen to solidify below each triple point. The results show high supercooling (>100 mK) for most metallic, covalent, and ionic solids, and low supercooling (<100 mK) for van der Waals (vdW) solids. We attribute the low supercooling of vdW solids to the weak interaction of the substrate and hydrogen. Highly ordered pyrolytic graphite showed the lowest supercooling among materials that are solid at room temperature, but did not exhibit a templating effect withinmore » a fill-tube and capsule assembly.« less
van der Waals heterostructures of germanene, stanene, and silicene with hexagonal boron nitride and their topological domain walls

NASA Astrophysics Data System (ADS)

Wang, Maoyuan; Liu, Liping; Liu, Cheng-Cheng; Yao, Yugui

2016-04-01

We investigate van der Waals (vdW) heterostructures made of germanene, stanene, or silicene with hexagonal boron nitride (h-BN). The intriguing topological properties of these buckled honeycomb materials can be maintained and further engineered in the heterostructures, where the competition between the substrate effect and external electric fields can be used to control the tunable topological phase transitions. Using such heterostructures as building blocks, various vdW topological domain walls (DW) are designed, along which there exist valley polarized quantum spin Hall edge states or valley-contrasting edge states which are protected by valley(spin)- resolved topological charges and can be tailored by the patterning of the heterojunctions and by external fields.
Left-right asymmetry is formed in individual cells by intrinsic cell chirality.

PubMed

Hatori, Ryo; Ando, Tadashi; Sasamura, Takeshi; Nakazawa, Naotaka; Nakamura, Mitsutoshi; Taniguchi, Kiichiro; Hozumi, Shunya; Kikuta, Junichi; Ishii, Masaru; Matsuno, Kenji

2014-08-01

Many animals show left-right (LR) asymmetric morphology. The mechanisms of LR asymmetric development are evolutionarily divergent, and they remain elusive in invertebrates. Various organs in Drosophila melanogaster show stereotypic LR asymmetry, including the embryonic gut. The Drosophila embryonic hindgut twists 90° left-handedly, thereby generating directional LR asymmetry. We recently revealed that the hindgut epithelial cell is chiral in shape and other properties; this is termed planar cell chirality (PCC). We previously showed by computer modeling that PCC is sufficient to induce the hindgut rotation. In addition, both the PCC and the direction of hindgut twisting are reversed in Myosin31DF (Myo31DF) mutants. Myo31DF encodes Drosophila MyosinID, an actin-based motor protein, whose molecular functions in LR asymmetric development are largely unknown. Here, to understand how PCC directs the asymmetric cell-shape, we analyzed PCC in genetic mosaics composed of cells homozygous for mutant Myo31DF, some of which also overexpressed wild-type Myo31DF. Wild-type cell-shape chirality only formed in the Myo31DF-overexpressing cells, suggesting that cell-shape chirality was established in each cell and reflects intrinsic PCC. A computer model recapitulating the development of this genetic mosaic suggested that mechanical interactions between cells are required for the cell-shape behavior seen in vivo. Our mosaic analysis also suggested that during hindgut rotation in vivo, wild-type Myo31DF suppresses the elongation of cell boundaries, supporting the idea that cell-shape chirality is an intrinsic property determined in each cell. However, the amount and distribution of F-actin and Myosin II, which are known to help generate the contraction force on cell boundaries, did not show differences between Myo31DF mutant cells and wild-type cells, suggesting that the static amount and distribution of these proteins are not involved in the suppression of cell-boundary elongation. Taken together, our results suggest that cell-shape chirality is intrinsically formed in each cell, and that mechanical force from intercellular interactions contributes to its formation and/or maintenance. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.
Psychosis of Alzheimer disease: prevalence, incidence, persistence, risk factors, and mortality.

PubMed

Vilalta-Franch, Joan; López-Pousa, Secundino; Calvó-Perxas, Laia; Garre-Olmo, Josep

2013-11-01

To establish the prevalence, incidence, persistence, risk factors, and mortality risk increase of psychosis of Alzheimer disease (PoAD) in a clinical sample. Cross-sectional, observational study of 491 patients with probable AD who, at baseline visit, were evaluated with the Cambridge Examination for Mental Disorders of the Elderly, the Neuropsychiatric Inventory-10, the Rapid Disability Rating Scale-2, and the Zarit Burden Interview. All participants were reevaluated at 6, 12, 18, and 24 months. PoAD diagnoses were made using specific criteria. PoAD prevalence was 7.3%, and the cumulative incidence at 6, 12, 18, and 24 months was 5.8%, 10.6%, 13.5%, and 15.1%, respectively. After 1 year, psychotic symptoms persisted in 68.7% of the patients with initial PoAD. At baseline, patients with PoAD scored lower in the Cambridge Cognitive Examination and Mini-Mental State Examination and higher in the Rapid Disability Rating Scale-2 and Zarit Burden Interview tests. Both low scores in the Cambridge Cognitive Examination subscale of learning memory (hazard ratio [HR] = 0.874; 95% CI: 0.788-0.969; Wald χ2 = 6.515; df = 1) and perception (HR = 0.743; 95% CI: 0.610-0.904; Wald χ2 = 8.778; df = 1), and high scores in expressive language (HR = 1.179; 95% CI: 1.024-1.358; Wald χ2 = 5.261; df = 1) and calculation skills (HR = 1.763; 95% CI: 1.067-2.913; Wald χ2 = 4.905; df = 1) were found to be associated with PoAD. PoAD leads to a faster functional impairment, and it increases mortality risk (HR = 2.191; 95% CI: 1.136-4.228; Wald χ2 = 5.471; df = 1) after controlling for age, gender, cognitive and functional disability, general health status, and antipsychotic treatment. PoAD seems to define a phenotype of AD of greater severity, with worsened functional progression and increased mortality risk. Copyright © 2013 American Association for Geriatric Psychiatry. Published by Elsevier Inc. All rights reserved.
Expression of EMAP-II in the rat dental follicle and its potential role in tooth eruption

PubMed Central

Liu, Dawen; Wise, Gary E.

2008-01-01

Endothelial monocyte-activating polypeptide II (EMAP-II) is an inflammatory cytokine with chemotactic activity. Because the dental follicle (DF) recruits mononuclear cells (osteoclast precursors) to promote the osteoclastogenesis needed for tooth eruption, it was the aim of this study to determine if EMAP-II may contribute to this recruitment. Using a DNA microarray, EMAP-II was found to be highly expressed in vivo in the DFs of day 1 to day 11 postnatal rats, with its expression elevated at days 1 and 3. Using a siRNA to knock down EMAP-II expression also resulted in a reduction in expression of CSF-1 and MCP-1 in the DF cells. Addition of EMAP-II protein to the DF cells partially restored the expression of CSF-1 and MCP-1. In chemotaxis assays using either conditioned medium of the DF cells with anti-EMAP-II antibody added or conditioned medium of DF cells with EMAP-II knocked down by siRNA, migration indexes of bone marrow mononuclear cells were significantly reduced. These results suggest that EMAP-II is another chemotactic molecule in the dental follicle involved in recruitment of mononuclear cells, and that EMAP-II may exert its chemotactic function directly by recruiting mononuclear cells and indirectly by enhancing the expression of other chemotactic molecules (CSF-1 and MCP-1). PMID:18705801
Oxygen acceleration in magnetotail reconnection

NASA Astrophysics Data System (ADS)

Liang, Haoming; Lapenta, Giovanni; Walker, Raymond J.; Schriver, David; El-Alaoui, Mostafa; Berchem, Jean

2017-01-01

Motivated by the observed high concentration of oxygen ions in the magnetotail during enhanced geomagnetic activity, we investigated the oxygen acceleration in magnetotail reconnection by using 2.5-D implicit particle-in-cell simulations. We found that lobe oxygen ions can enter the downstream outflow region, i.e., the outflow region downstream of the dipolarization fronts (DFs) or the reconnection jet fronts. Without entering the reconnection exhaust, they are accelerated by the Hall electric field. They can populate the downstream outflow region before the DFs arrive there. This acceleration is in addition to acceleration in the exhaust by the Hall and reconnection electric fields. Oxygen ions in the preexisting current sheet are reflected by the propagating DF creating a reflected beam with a hook shape in phase space. This feature can be applied to deduce a history of the DF speed. However, it is difficult to observe for protons because their typical thermal velocity in the plasma sheet is comparable those of the DF and the reflection speed. The oxygen ions from the lobes and the preexisting current sheet form multiple beams in the distribution function in front of the DF. By comparing oxygen concentrations of 50%, 5%, and 0% with the same current sheet thickness, we found that the DF thickness is proportional to the oxygen concentration in the preexisting current sheet. All the simulation results can be used to compare with the observations from the Magnetospheric Multiscale mission.
Bandgap engineering and charge separation in two-dimensional GaS-based van der Waals heterostructures for photocatalytic water splitting

NASA Astrophysics Data System (ADS)

Wang, Biao; Kuang, Anlong; Luo, Xukai; Wang, Guangzhao; Yuan, Hongkuan; Chen, Hong

2018-05-01

Two-dimensional (2D) gallium sulfide (GaS), hexagonal boron nitride (h-BN) and graphitic carbon nitride (g-C3N4) have been fabricated and expected to be promising photocatalysts under ultraviolet irradiation. Here, we employ hybrid density functional calculations to explore the potential of the 2D GaS-based heterojunctions GaS/h-BN (g-C3N4) for the design of efficient water redox photocatalysts. Both heterostructures can be formed via van der Waals (vdW) interaction and are direct bandgap semiconductors, whose bandgaps are reduced comparing with isolated GaS, h-BN or g-C3N4 monolayers and whose bandedges straddle water redox potentials. Furthermore, the optical absorption of GaS/h-BN (g-C3N4) heterostructures is observably enhanced in the ultraviolet-visible (UV-vis) light range. The electron-hole pairs in GaS/h-BN (g-C3N4) heterostructures are completely separated from different layers. In addition, the in-plane biaxial strain can effectively modulate the electronic properties of GaS/h-BN (g-C3N4) heterostructures. Thus the GaS/h-BN (g-C3N4) heterostructures are anticipated to be promising candidates for photocatalytic water splitting to produce hydrogen.
Sensing properties of pristine boron nitride nanostructures towards alkaloids: A first principles dispersion corrected study

NASA Astrophysics Data System (ADS)

Roondhe, Basant; Dabhi, Shweta D.; Jha, Prafulla K.

2018-05-01

To understand the underlying physics behind the interaction of biomolecules with the nanomaterials to use them practically as bio-nanomaterials is very crucial. A first principles calculation under the frame work of density functional theory is executed to investigate the electronic structures and binding properties of alkaloids (Caffeine and Nicotine) over single walled boron nitride nanotube (BNNT) and boron nitride nanoribbon (BNNR) to determine their suitability towards filtration or sensing of these molecules. We have also used GGA-PBE scheme with the inclusion of Van der Waals (vdW) interaction based on DFT-D2. Increase in the accuracy by incorporating the dispersion correction in the calculation is observed for the long range Van der Waals interaction. Binding energy range of BNNT and BNNR with both alkaloids have been found to be -0.35 to -0.76 eV and -0.45 to -0.91 eV respectively which together with the binding distance shows physisorption binding of these molecules to the both nanostructures. The transfer of charge between the BN nanostructures and the adsorbed molecule has also been analysed by using Lowdin charge analysis. The sensitivity of both nanostructures BNNT and BNNR towards both alkaloids is observed through electronic structure calculations, density of states and quantum conductance. The binding of both alkaloids with BNNR is stronger. The analysis of the calculated properties suggests absence of covalent interaction between the considered species (BNNT/BNNR) and alkaloids. The study may be useful in designing the boron nitride nanostructure based sensing device for alkaloids.
Utility of DF-1 for Radioprotection in Lymphocytes

NASA Technical Reports Server (NTRS)

Reynolds, Julia; Casey, Rachael; Wu, Honglu; Huff, Janice; Emami, Kamal; Moore, Valerie; Jeevarajan, Antony

2007-01-01

The development of degenerative changes in the vasculature, such as atherosclerosis, is a known consequence of exposure to ionizing radiation, and is thus a concern for astronaut health following long duration space flight. Cellular damage caused by radiation is due to free radical generation and DNA damage. The goal of this project was to assess the ability of a C60-derivative, DF-1, to mitigate cellular damage resulting from radiation exposure in primary human lymphocytes. DF-1 is a water-soluble C60 fullerene encapsulated in dendrimeric functional groups that is proposed to exhibit antioxidant properties. Human lymphocytes are radiosensitive and travel throughout the body potentially causing bystander effects in any tissues they contact. These cells were subjected to varying doses of gamma radiation in the presence or absence of DF-1. Cells were collected at 48 hours post-irradiation for chromosomal aberration studies and at 72 hours post-irradiation for micronuclei studies. These studies showed that the irradiated cells contained more chromosomal aberrations and micronuclei than the control cells. Addition of the DF-1 reduced the amount of observed DNA damage in the irradiated cells. Growth curves were measured for the lymphocytes exposed to 0 and 4 Gray gamma irradiations, and we observed less growth in the cells irradiated at 4 Gy. 2,7-dichlorofluorescein diacetate was used to detect reactive oxygen species production, and increased production of ROS was observed in the irradiated lymphocytes. Human lymphocytes were subjected to varying doses of gamma or photon radiation in the presence and absence of DF-1 and a known radioprotectant, amifostine. After irradiation, the production of reactive oxygen species, growth curves and cell viability were measured. These cells were also collected to quantify chromosomal aberrations and micronuclei formation. We predict that irradiated cells will show the most damage and that DF-1 will provide protective effects similar to those of amifostine, an established radioprotectant.
Computational studies on the crystal structure, thermodynamic properties, detonation performance, and pyrolysis mechanism of 2,4,6,8-tetranitro-1,3,5,7-tetraazacubane as a novel high energy density material.

PubMed

Wang, Fang; Du, Hongchen; Zhang, Jianying; Gong, Xuedong

2011-10-27

Studies have suggested that octanitrocubane (ONC) is one of the most powerful non-nuclear high energy density material (HEDM) currently known. 2,4,6,8-Tetranitro-1,3,5,7-tetraazacubane (TNTAC) studied in this work may also be a novel HEDM due to its high nitrogen content and crystal density. Density functional theory and molecular mechanics methods have been employed to study the crystal structure, IR spectrum, electronic structure, thermodynamic properties, gas-phase and condensed-phase heat of formation, detonation performance, and pyrolysis mechanism of TNTAC. The TNTAC has a predicted density of about 2.12 g/cm(3), and its detonation velocity (10.42 km/s) and detonation pressure (52.82 GPa) are higher than that of ONC. The crystalline packing is P2(1)2(1)2(1), and the corresponding cell parameters are Z = 4, a = 8.87 Å, b = 8.87 Å, and c = 11.47 Å. Both the density of states of the predicted crystal and the bond dissociation energy of the molecule in gas phase show that the cage C-N bond is the trigger bond during thermolysis. The activation energy of the pyrolysis initiation reaction obtained from the B3LYP/6-311++G(2df,2p) level is 125.98 kJ/mol, which indicates that TNTAC meets the thermal stability request as an exploitable HEDM.
Income and race/ethnicity influence dietary fiber intake and vegetable consumption.

PubMed

Storey, Maureen; Anderson, Patricia

2014-10-01

Grains, fruits, and vegetables are the primary sources of dietary fiber (DF), with the white potato contributing nearly 7% of the DF to the US food supply. The DF composition of the white potato-with or without the skin and regardless of cooking method-compares well with the DF content of other vegetables. Many health benefits, including improved gastrointestinal health, are attributed to greater DF consumption; however, less than 3% of males and females have an adequate intake of DF. Because of this population-wide shortfall, DF is considered to be a nutrient of concern. In this study, using data from the National Health and Nutrition Examination Survey 2009 to 2010, we examined the mean intake of DF across sex, age, race/ethnicity, family income, and poverty threshold. This study shows that mean intake of DF is far below recommendations, with children and adolescents aged 2 to 19 years consuming an average of less than 14 g of DF per day. Adults 20+ years old consume, on average, about 17 g of DF per day, and men consume significantly more DF than women. Non-Hispanic black adults consume significantly less DF compared with other race/ethnic groups. Lower family income and living at less than 131% of poverty were associated with lower DF intakes among adults. Federal and local government policies should encourage consumption of all vegetables, including the white potato, as an important source of DF. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.
Quantum molecular dynamics study on the proton exchange, ionic structures, and transport properties of warm dense hydrogen-deuterium mixtures

NASA Astrophysics Data System (ADS)

Liu, Lei; Li, Zhi-Guo; Dai, Jia-Yu; Chen, Qi-Feng; Chen, Xiang-Rong

2018-06-01

Comprehensive knowledge of physical properties such as equation of state (EOS), proton exchange, dynamic structures, diffusion coefficients, and viscosities of hydrogen-deuterium mixtures with densities from 0.1 to 5 g /cm3 and temperatures from 1 to 50 kK has been presented via quantum molecular dynamics (QMD) simulations. The existing multi-shock experimental EOS provides an important benchmark to evaluate exchange-correlation functionals. The comparison of simulations with experiments indicates that a nonlocal van der Waals density functional (vdW-DF1) produces excellent results. Fraction analysis of molecules using a weighted integral over pair distribution functions was performed. A dissociation diagram together with a boundary where the proton exchange (H2+D2⇌2 HD ) occurs was generated, which shows evidence that the HD molecules form as the H2 and D2 molecules are almost 50% dissociated. The mechanism of proton exchange can be interpreted as a process of dissociation followed by recombination. The ionic structures at extreme conditions were analyzed by the effective coordination number model. High-order cluster, circle, and chain structures can be founded in the strongly coupled warm dense regime. The present QMD diffusion coefficient and viscosity can be used to benchmark two analytical one-component plasma (OCP) models: the Coulomb and Yukawa OCP models.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Einasto, Jaan; Einasto, M.; Saar, E.

We investigate properties of superclusters of galaxies found on the basis of the 2dF Galaxy Redshift Survey, and compare them with properties of superclusters from the Millennium Simulation.We study the dependence of various characteristics of superclusters on their distance from the observer, on their total luminosity, and on their multiplicity. The multiplicity is defined by the number of Density Field (DF) clusters in superclusters. Using the multiplicity we divide superclusters into four richness classes: poor, medium, rich and extremely rich.We show that superclusters are asymmetrical and have multi-branching filamentary structure, with the degree of asymmetry and filamentarity being higher formore » the more luminous and richer superclusters. The comparison of real superclusters with Millennium superclusters shows that most properties of simulated superclusters agree very well with real data, the main differences being in the luminosity and multiplicity distributions.« less
Electron acceleration behind a wavy dipolarization front

NASA Astrophysics Data System (ADS)

Wu, Mingyu; Lu, Quanming; Volwerk, Martin; Nakamura, Rumi; Zhang, Tielong

2018-02-01

In this paper, with the in-situ observations from the Time History of Events and Macroscale Interactions during Substorms (THEMIS) probes we report a wavy dipolarization front (DF) event, where the DF has different magnetic structures and electron distributions at different y positions in the Geocentric Solar Magnetospheric (GSM) coordinates. At y ˜2.1RE (RE is the radius of Earth), the DF has a relatively simple structure, which is similar to that of a conventional DF. At y ˜3.0RE, the DF is revealed to have a multiple DF structure, where the plasma exhibits a vortex flow. Such a wavy DF could be the results of the interchange instability. The different structure of such a wavy DF at different sites has a great effect on electron acceleration. Fermi acceleration can occur at the site of the DF with a simple or multiple DF structure, while betatron acceleration as a local process has the contribution to energetic electrons only at the site of the DF with a simple structure.
Does defibrotide prophylaxis decrease the risk of acute graft versus host disease following allogeneic hematopoietic cell transplantation?

PubMed

Tekgündüz, Emre; Kaya, Ali Hakan; Bozdağ, Sinem Civriz; Koçubaba, Şerife; Kayıkçı, Ömür; Namdaroğlu, Sinem; Uğur, Bilge; Akpınar, Seval; Batgi, Hikmetullah; Bekdemir, Filiz; Altuntaş, Fevzi

2016-02-01

There is some preliminary evidence, that veno-occlusive disease prophylaxis with defibrotide (DF) may also have a role in decreasing risk of acute graft-versus-host disease (aGvHD) by preventing tissue damage. In this study, we aimed to investigate the role of DF prophylaxis on the development of aGvHD at D+180. One hundred ninety-five consecutive adult patients receiving allogeneic HCT were retrospectively evaluated in 3 groups: no DF, DF/post-HCT (DF D+1 to D+14) and DF/pre-HCT (DF for 14 days concurrently with conditioning). The total (p: 0.057) and grades III/IV (p: 0.051) aGvHD rates at D+180 were 46.5%, 40%, 25.5% and 15.5%, 11.2%, 0% in patients on no DF, DF/post-HCT and DF/pre-HCT. DF may have a role in decreasing incidence and severity of aGvHD, especially if used concurrently with conditioning regimen. Copyright © 2016 Elsevier Ltd. All rights reserved.
Climate change and dengue fever transmission in China: Evidences and challenges.

PubMed

Li, Chenlu; Lu, Yongmei; Liu, Jianing; Wu, Xiaoxu

2018-05-01

Dengue Fever (DF) has become one of the most serious infectious diseases in China. Dengue virus and its vector (Aedes mosquito) are known to be sensitive to climate condition. Climate impacts DF through affecting three essential bioecological aspects: DF virus, vector (mosquito) and DF transmission environment. Weather-based DF model, mosquito model and climate model are the three pillars to help the prediction of DF distribution. Through a systematic review of literature between 1980 and 2017, this paper summarizes empirical evidences in China on the impact of climate change on DF; it further reviews the related DF incidence models and their findings on how changes in weather factors may impact DF occurrences in China. Compared with some well-known research projects in the western countries, there is a lack of knowledge in China regarding how the spatiotemporal distribution of DF will respond to climate change. However, being able to predict DF distribution is key to China's efforts to prevent and control DF transmission. We conclude this paper by recommending four focused areas for China: promoting more advanced research on the relationship between extreme weather events and DF, developing regional-specific models for the high risk regions of DF in south China, encouraging interdisciplinary collaboration between climate studies and health services, and enhancing public health education and management at national, regional and local levels. Copyright © 2017 Elsevier B.V. All rights reserved.
Design for Occupational Safety and Health of Workers in Construction in Developing Countries: A Study of Architects in Nigeria.

PubMed

Manu, Patrick; Poghosyan, Anush; Mshelia, Ibrahim Mark; Iwo, Samuel Tekena; Mahamadu, Abdul-Majeed; Dziekonski, Krzysztof

2018-06-14

Design for safety (DfS) of workers is amongst the prominent ways of tackling poor occupational safety and health (OSH) performance in construction. However, in developing countries there is an extremely limited research on DfS. This study thus makes an important contribution to the subject of DfS in developing countries by specifically examining the awareness and practice of DfS amongst architects within the construction sector of Nigeria. A survey of architects, yielding 161 valid responses, was conducted. While there is a high awareness of the concept of DfS, the actual practice is low. Additionally, although there is high interest in DfS training, the engagement in DfS training is low. Significantly, awareness of DfS, training and education related to DfS, and membership of a design professional body have very limited bearing on the practice of DfS by architects. The findings are thus symptomatic of the prevalence of influential DfS implementation barriers within the construction sector. Industry stakeholders should seek to raise the profile of DfS practice within the sector. Furthermore, similar empirical studies in the construction sector of other developing countries would be useful in shedding light on the status of DfS in these countries.
Ellagic Acid Derivatives from Rubus ulmifolius Inhibit Staphylococcus aureus Biofilm Formation and Improve Response to Antibiotics

PubMed Central

Quave, Cassandra L.; Estévez-Carmona, Miriam; Compadre, Cesar M.; Hobby, Gerren; Hendrickson, Howard; Beenken, Karen E.; Smeltzer, Mark S.

2012-01-01

Background Biofilms contribute to the pathogenesis of many forms of Staphylococcus aureus infection. Treatment of these infections is complicated by intrinsic resistance to conventional antibiotics, thus creating an urgent need for strategies that can be used for the prevention and treatment of biofilm-associated infections. Methodology/Principal Findings This study demonstrates that a botanical natural product composition (220D-F2) rich in ellagic acid and its derivatives can limit S. aureus biofilm formation to a degree that can be correlated with increased antibiotic susceptibility. The source of this composition is Rubus ulmifolius Schott. (Rosaceae), a plant used in complementary and alternative medicine in southern Italy for the treatment of skin and soft tissue infections. All S. aureus clonal lineages tested exhibited a reduced capacity to form a biofilm at 220D-F2 concentrations ranging from 50–200 µg/mL, which were well below the concentrations required to limit bacterial growth (530–1040 µg/mL). This limitation was therapeutically relevant in that inclusion of 220D-F2 resulted in enhanced susceptibility to the functionally-distinct antibiotics daptomycin, clindamycin and oxacillin. Testing with kidney and liver cell lines also demonstrated a lack of host cell cytotoxicity at concentrations of 220D-F2 required to achieve these effects. Conclusions/Significance These results demonstrate that extract 220D-F2 from the root of Rubus ulmifolius can be used to inhibit S. aureus biofilm formation to a degree that can be correlated with increased antibiotic susceptibility without toxic effects on normal mammalian cells. Hence, 220D-F2 is a strong candidate for development as a botanical drug for use in the prevention and treatment of S. aureus biofilm-associated infections. PMID:22242149

Centrifugo-pneumatic valving utilizing dissolvable films.

PubMed

Gorkin, Robert; Nwankire, Charles E; Gaughran, Jennifer; Zhang, Xin; Donohoe, Gerard G; Rook, Martha; O'Kennedy, Richard; Ducrée, Jens

2012-08-21

In this article we introduce a novel technology that utilizes specialized water dissolvable thin films for valving in centrifugal microfluidic systems. In previous work (William Meathrel and Cathy Moritz, IVD Technologies, 2007), dissolvable films (DFs) have been assembled in laminar flow devices to form efficient sacrificial valves where DFs simply open by direct contact with liquid. Here, we build on the original DF valving scheme to leverage sophisticated, merely rotationally actuated vapour barriers and flow control for enabling comprehensive assay integration with low-complexity instrumentation on "lab-on-a-disc" platforms. The advanced sacrificial valving function is achieved by creating an inverted gas-liquid stack upstream of the DF during priming of the system. At low rotational speeds, a pocket of trapped air prevents a surface-tension stabilized liquid plug from wetting the DF membrane. However, high-speed rotation disrupts the metastable gas/liquid interface to wet the DF and thus opens the valve. By judicious choice of the radial position and geometry of the valve, the burst frequency can be tuned over a wide range of rotational speeds nearly 10 times greater than those attained by common capillary burst valves based on hydrophobic constrictions. The broad range of reproducible burst frequencies of the DF valves bears the potential for full integration and automation of comprehensive, multi-step biochemical assay protocols. In this report we demonstrate DF valving, discuss the biocompatibility of using the films, and show a potential sequential valving system including the on-demand release of on-board stored liquid reagents, fast centrifugal sedimentation and vigorous mixing; thus providing a viable basis for use in lab-on-a-disc platforms for point-of-care diagnostics and other life science applications.
Potential of New Isolates of Dunaliella Salina for Natural β-Carotene Production

PubMed Central

Xu, Yanan; Wosu, Chiziezi I.; Ben-Amotz, Ami

2018-01-01

The halotolerant microalga Dunaliella salina has been widely studied for natural β-carotene production. This work shows biochemical characterization of three newly isolated Dunaliella salina strains, DF15, DF17, and DF40, compared with D. salina CCAP 19/30 and D. salina UTEX 2538 (also known as D. bardawil). Although all three new strains have been genetically characterized as Dunaliella salina strains, their ability to accumulate carotenoids and their capacity for photoprotection against high light stress are different. DF15 and UTEX 2538 reveal great potential for producing a large amount of β-carotene and maintained a high rate of photosynthesis under light of high intensity; however, DF17, DF40, and CCAP 19/30 showed increasing photoinhibition with increasing light intensity, and reduced contents of carotenoids, in particular β-carotene, suggesting that the capacity of photoprotection is dependent on the cellular content of carotenoids, in particular β-carotene. Strong positive correlations were found between the cellular content of all-trans β-carotene, 9-cis β-carotene, all-trans α-carotene and zeaxanthin but not lutein in the D. salina strains. Lutein was strongly correlated with respiration in photosynthetic cells and strongly related to photosynthesis, chlorophyll and respiration, suggesting an important and not hitherto identified role for lutein in coordinated control of the cellular functions of photosynthesis and respiration in response to changes in light conditions, which is broadly conserved in Dunaliella strains. Statistical analysis based on biochemical data revealed a different grouping strategy from the genetic classification of the strains. The significance of these data for strain selection for commercial carotenoid production is discussed. PMID:29389891
Differentiation between pine woods according to species and growing location using FTIR-ATR.

PubMed

Traoré, Mohamed; Kaal, Joeri; Martínez Cortizas, Antonio

2018-01-01

Attenuated total reflectance-Fourier transform infrared (FTIR-ATR) spectroscopy was applied to 120 samples of heartwood rings from eight individual pine trees from different locations in Spain. Pinus sylvestris cores were collected at the Artikutza natural park (Ps-ART). Pinus nigra cores were collected in Sierra de Cazorla (Pn-LIN) and in La Sagra Mountain (Pn-LSA). Three discriminant analysis tests were performed using all bands (DF T ), lignin bands only (DF L ) and polysaccharides bands only (DF P ), to explore the ability of FTIR-ATR to separate between species and growing location. The DF L model enabled a good separation between pine species, whereas the DF P model enabled differentiation for both species and growing location. The DF T model enabled virtually perfect separation, based on two functions involving twelve FTIR bands. Discrimination between species was related to bands at 860 and 1655 cm -1 , which were more intense in P. sylvestris samples, and bands at 1425 and 1635 cm -1 , more intense in P. nigra samples. These vibrations were related to differences in lignin structure and polysaccharide linear chains. Discrimination between growing locations was mainly related to polysaccharide absorptions: at 900, 1085 and 1335 cm -1 more representative of Pn-LIN samples, and at 1105 and 1315 cm -1 mostly associated to Pn-LSA samples. These absorptions are related to β-glycosidic linkages (900 cm -1 ), cellulose and hemicellulose (C-O bonds, 1085 and 1105 cm -1 ) and content in amorphous/crystalline cellulose (1315 and 1335 cm -1 ). These results show that FTIR-ATR in combination with multivariate statistics can be a useful tool for species identification and provenancing for pine wood samples of unknown origin.
Memory-guided reaching in a patient with visual hemiagnosia.

PubMed

Cornelsen, Sonja; Rennig, Johannes; Himmelbach, Marc

2016-06-01

The two-visual-systems hypothesis (TVSH) postulates that memory-guided movements rely on intact functions of the ventral stream. Its particular importance for memory-guided actions was initially inferred from behavioral dissociations in the well-known patient DF. Despite of rather accurate reaching and grasping movements to visible targets, she demonstrated grossly impaired memory-guided grasping as much as impaired memory-guided reaching. These dissociations were later complemented by apparently reversed dissociations in patients with dorsal damage and optic ataxia. However, grasping studies in DF and optic ataxia patients differed with respect to the retinotopic position of target objects, questioning the interpretation of the respective findings as a double dissociation. In contrast, the findings for reaching errors in both types of patients came from similar peripheral target presentations. However, new data on brain structural changes and visuomotor deficits in DF also questioned the validity of a double dissociation in reaching. A severe visuospatial short-term memory deficit in DF further questioned the specificity of her memory-guided reaching deficit. Therefore, we compared movement accuracy in visually-guided and memory-guided reaching in a new patient who suffered a confined unilateral damage to the ventral visual system due to stroke. Our results indeed support previous descriptions of memory-guided movements' inaccuracies in DF. Furthermore, our data suggest that recently discovered optic-ataxia like misreaching in DF is most likely caused by her parieto-occipital and not by her ventral stream damage. Finally, multiple visuospatial memory measurements in HWS suggest that inaccuracies in memory-guided reaching tasks in patients with ventral damage cannot be explained by visuospatial short-term memory or perceptual deficits, but by a specific deficit in visuomotor processing. Copyright © 2016 Elsevier Ltd. All rights reserved.
Necrotic cell death by hydrogen peroxide in immortal DF-1 chicken embryo fibroblast cells expressing deregulated MnSOD and catalase.

PubMed

Kim, H; You, S; Kong, B W; Foster, L K; Farris, J; Foster, D N

2001-08-22

The reactive oxygen species are known as endogenous toxic oxidant damaging factors in a variety of cell types, and in response, the antioxidant genes have been implicated in cell proliferation, senescence, immortalization, and tumorigenesis. The expression of manganese superoxide dismutase mRNA was shown to increase in most of the immortal chicken embryo fibroblast (CEF) cells tested, while expression of catalase mRNA appeared to be dramatically decreased in all immortal CEF cells compared to their primary counterparts. The expression of copper-zinc superoxide dismutase mRNA was shown to increase slightly in some immortal CEF cells. The glutathione peroxidase expressed relatively similar levels in both primary and immortal CEF cells. As primary and immortal DF-1 CEF cells were treated with 10-100 microM of hydrogen peroxide (concentrations known to be sublethal in human diploid fibroblasts), immortal DF-1 CEF cells were shown to be more sensitive to hydrogen peroxide, and total cell numbers were dramatically reduced when compared with primary cell counterparts. This increased sensitivity to hydrogen peroxide in immortal DF-1 cells occurred without evident changes in either antioxidant gene expression, mitochondrial membrane potential, cell cycle distribution or chromatin condensation. However, the total number of dead cells without chromatin condensation was dramatically elevated in immortal DF-1 CEFs treated with hydrogen peroxide, indicating that the inhibition of immortal DF-1 cell growth by low concentrations of hydrogen peroxide is due to increased necrotic cell death, but not apoptosis. Taken together, our observation suggests that the balanced antioxidant function might be important for cell proliferation in response to toxic oxidative damage by hydrogen peroxide.
Fractal dimension of trabecular bone projection texture is related to three-dimensional microarchitecture.

PubMed

Pothuaud, L; Benhamou, C L; Porion, P; Lespessailles, E; Harba, R; Levitz, P

2000-04-01

The purpose of this work was to understand how fractal dimension of two-dimensional (2D) trabecular bone projection images could be related to three-dimensional (3D) trabecular bone properties such as porosity or connectivity. Two alteration processes were applied to trabecular bone images obtained by magnetic resonance imaging: a trabeculae dilation process and a trabeculae removal process. The trabeculae dilation process was applied from the 3D skeleton graph to the 3D initial structure with constant connectivity. The trabeculae removal process was applied from the initial structure to an altered structure having 99% of porosity, in which both porosity and connectivity were modified during this second process. Gray-level projection images of each of the altered structures were simply obtained by summation of voxels, and fractal dimension (Df) was calculated. Porosity (phi) and connectivity per unit volume (Cv) were calculated from the 3D structure. Significant relationships were found between Df, phi, and Cv. Df values increased when porosity increased (dilation and removal processes) and when connectivity decreased (only removal process). These variations were in accordance with all previous clinical studies, suggesting that fractal evaluation of trabecular bone projection has real meaning in terms of porosity and connectivity of the 3D architecture. Furthermore, there was a statistically significant linear dependence between Df and Cv when phi remained constant. Porosity is directly related to bone mineral density and fractal dimension can be easily evaluated in clinical routine. These two parameters could be associated to evaluate the connectivity of the structure.
Small-scale heterogeneity spectra in the Earth mantle resolved by PKP-ab,-bc and -df waves

NASA Astrophysics Data System (ADS)

Zheng, Y.

2016-12-01

Plate tectonics creates heterogeneities at mid ocean ridges and subducts the heterogeneities back to the mantle at subduction zones. Heterogeneities manifest themselves by different densities and seismic wave speeds. The length scales and spatial distribution of the heterogeneities measure the mixing mechanism of the plate tectonics. This information can be mathematically captured as the heterogeneity spatial Fourier spectrum. Since most heterogeneities created are on the order of 10s of km, global seismic tomography is not able to resolve them directly. Here, we use seismic P-waves that transmit through the outer core (phases: PKP-ab and PKP-bc) and through the inner core (PKP-df) to probe the lower-mantle heterogeneities. The differential traveltimes (PKP-ab versus PKP-df; PKP-bc versus PKP-df) are sensitive to lower mantle structures. We have collected more than 10,000 PKP phases recorded by Japan Hi-Net short-period seismic network. We found that the lower mantle was filled with seismic heterogeneities from scale 20km to 200km. The heterogeneity spectrum is similar to an exponential distribution but is more enriched in small-scale heterogeneities at the high-wavenumber end. The spectrum is "red" meaning large scales have more power and heterogeneities show a multiscale nature: small-scale heterogeneities are embedded in large-scale heterogeneities. These small-scale heterogeneities cannot be due to thermal origin and they must be compositional. If all these heterogeneities were located in the D" layer, statistically, it would have a root-mean-square P-wave velocity fluctuation of 1% (i.e., -3% to 3%).
Reproduction and population dynamics of Mastomys natalensis Smith, 1834 in an agricultural landscape in the Western Usambara Mountains, Tanzania.

PubMed

Makundi, Rhodes H; Massawe, Apia W; Mulungu, Loth S

2007-12-01

The multimammate rat, Mastomys natalensis Smith 1834, is a dominant species in agro-ecosystems in Sub-Saharan Africa, but adapts quickly to changes in non-agricultural landscape, particularly woodlands and forests. In this study we report on reproduction and population dynamics of M. natalensis in deforested high elevation localities in the Usambara Mountains, north-east Tanzania. We conducted Capture-Mark-Recapture studies in 2002-2004, and established that reproduction of M. natalensis takes place in the extended wet season between February and June, and the population density peaks in June-August. Reproduction cease in July to January and population density drops from July onwards. Reproduction and population density fluctuations are linked to the duration and amount of rainfall. In years when rainfall was below average and the wet season was short, the population density was significantly lower (below 10 animals/ha and 60 animals/ha in 2003 and 2004 respectively, compared to >100 animals/ha in 2002 when rainfall was above the seasonal average) (F(df 2,13)= 9.092, p < 0.01 for in between years variations and F(df 12,15)= 5.389, p < 0.01 for effect of cumulative annual rainfall on population density). These densities were much lower than in the lowland savannah habitats in central and southwest Tanzania. A comparison between the farmland/fallow mosaic fields and agro-forestry areas showed higher population densities in the former, which have similarities to the preferred habitats in the lowland savannahs. The increasing abundance of M. natalensis in the Usambara could have some consequences: M. natalensis is major pest and is involved in the plague cycle in the western Usambara Mountains. Mastomys natalensis is also a strong competitor and the impact on endemic rodent species, e.g. Lophuromys flavopunctatus and Praomys delectorum is unknown.
Inclusion of particle-vibration coupling in the Fayans functional: Odd-even mass differences of semimagic nuclei

NASA Astrophysics Data System (ADS)

Saperstein, E. E.; Baldo, M.; Pankratov, S. S.; Tolokonnikov, S. V.

2018-05-01

A method is presented to evaluate the particle-phonon coupling (PC) corrections to the single-particle energies in semimagic nuclei, based on the direct solution of the Dyson equation with PC-corrected mass operator. It is used for finding the odd-even mass difference between even Pb and Sn isotopes and their odd-proton neighbors. The Fayans energy density functional DF3-a is used, which gives rather highly accurate predictions for these mass differences already at the mean-field level. In the case of the lead chain, account for the PC corrections induced by the low-lying phonons 21+ and 31- makes agreement of the theory with the experimental data significantly better. For the tin chain, the situation is not so definite. In this case, the PC corrections make agreement better in the case of the addition mode but they spoil the agreement for the removal mode. We discuss the reason for such a discrepancy.
Accurate and computationally efficient prediction of thermochemical properties of biomolecules using the generalized connectivity-based hierarchy.

PubMed

Sengupta, Arkajyoti; Ramabhadran, Raghunath O; Raghavachari, Krishnan

2014-08-14

In this study we have used the connectivity-based hierarchy (CBH) method to derive accurate heats of formation of a range of biomolecules, 18 amino acids and 10 barbituric acid/uracil derivatives. The hierarchy is based on the connectivity of the different atoms in a large molecule. It results in error-cancellation reaction schemes that are automated, general, and can be readily used for a broad range of organic molecules and biomolecules. Herein, we first locate stable conformational and tautomeric forms of these biomolecules using an accurate level of theory (viz. CCSD(T)/6-311++G(3df,2p)). Subsequently, the heats of formation of the amino acids are evaluated using the CBH-1 and CBH-2 schemes and routinely employed density functionals or wave function-based methods. The calculated heats of formation obtained herein using modest levels of theory and are in very good agreement with those obtained using more expensive W1-F12 and W2-F12 methods on amino acids and G3 results on barbituric acid derivatives. Overall, the present study (a) highlights the small effect of including multiple conformers in determining the heats of formation of biomolecules and (b) in concurrence with previous CBH studies, proves that use of the more effective error-cancelling isoatomic scheme (CBH-2) results in more accurate heats of formation with modestly sized basis sets along with common density functionals or wave function-based methods.
Effects of dose, flow rate, and bile acid on diclofenac disposition in the perfused rat liver.

PubMed

Uraki, Misato; Kawase, Atsushi; Matsushima, Yuka; Iwaki, Masahiro

2016-06-01

An in situ perfused rat liver system is useful for studying the hepatic disposition of drugs and their metabolites. However, the effects of the perfusion conditions on drug disposition are unclear. We examined the effects of conditions such as flow rate (13 or 26 mL/min) and bile acid on disposition of diclofenac (DF) as a model drug and DF metabolites [diclofenac-1-O-acyl glucuronide (DF-Glu) or 4'-hydroxydiclofenac (DF-4'OH)] in the absence of albumin. DF, DF-Glu, and DF-4'OH concentrations in the perfusate and cumulative amounts of DF-Glu excreted in bile were measured using high-performance liquid chromatography methods. DF in the perfusate was rapidly eliminated as the perfusate flow rate increased. The area under the plasma concentration-time curve from 0 to 60 min (AUC0-60) for DF-Glu and DF-4'OH in a perfusate containing bile acid was lower at a flow rate of 26 and 13 mL/min, respectively. The bile flow rate at 26 mL/min with 24 μM of bile acid in the perfusate was significantly higher (ca. 3.5 times) compared with that at 13 mL/min without bile acid. Cumulative biliary DF-Glu excretion was also dramatically affected by the flow rate and addition of bile acid. This study indicated that the flow rate and bile acid in the perfused rat liver were key factors for bile flow rate and DF, DF-Glu, and DF-4'OH disposition in the absence of albumin.
Efficient band structure modulations in two-dimensional MnPSe3/CrSiTe3 van der Waals heterostructures

NASA Astrophysics Data System (ADS)

Pei, Qi; Wang, Xiaocha; Zou, Jijun; Mi, Wenbo

2018-05-01

As a research upsurge, van der Waals (vdW) heterostructures give rise to numerous combined merits and novel applications in nanoelectronics fields. Here, we systematically investigate the electronic structure of MnPSe3/CrSiTe3 vdW heterostructures with various stacking patterns. Then, particular attention of this work is paid on the band structure modulations in MnPSe3/CrSiTe3 vdW heterostructures via biaxial strain or electric field. Under a tensile strain, the relative band edge positions of heterostructures transform from type-I (nested) to type-II (staggered). The relocation of conduction band minimum also brings about a transition from indirect to direct band gap. Under a compressive strain, the electronic properties change from semiconducting to metallic. The physical mechanism of strain-dependent band structure may be ascribed to the shifts of the energy bands impelled by different superposition of atomic orbitals. Meanwhile, our calculations manifest that band gap values of MnPSe3/CrSiTe3 heterostructures are insensitive to the electric field. Even so, by applying a suitable intensity of negative electric field, the band alignment transition from type-I to type-II can also be realized. The efficient band structure modulations via external factors endow MnPSe3/CrSiTe3 heterostructures with great potential in novel applications, such as strain sensors, photocatalysis, spintronic and photoelectronic devices.
Comparison of calculation and experiment implicates significant electrostatic contributions to the binding stability of barnase and barstar.

PubMed

Dong, Feng; Vijayakumar, M; Zhou, Huan-Xiang

2003-07-01

The contributions of electrostatic interactions to the binding stability of barnase and barstar were studied by the Poisson-Boltzmann model with three different protocols: a), the dielectric boundary specified as the van der Waals (vdW) surface of the protein along with a protein dielectric constant (epsilon (p)) of 4; b), the dielectric boundary specified as the molecular (i.e., solvent-exclusion (SE)) surface along with epsilon (p) = 4; and c), "SE + epsilon (p) = 20." The "vdW + epsilon (p) = 4" and "SE + epsilon (p) = 20" protocols predicted an overall electrostatic stabilization whereas the "SE + epsilon (p) = 4" protocol predicted an overall electrostatic destabilization. The "vdW + epsilon (p) = 4" protocol was most consistent with experiment. It quantitatively reproduced the observed effects of 17 mutations neutralizing charged residues lining the binding interface and the measured coupling energies of six charge pairs across the interface and reasonably rationalized the experimental ionic strength and pH dependences of the binding constant. In contrast, the "SE + epsilon (p) = 4" protocol predicted significantly larger coupling energies of charge pairs whereas the "SE + epsilon (p) = 20" protocol did not predict any pH dependence. This study calls for further scrutiny of the different Poisson-Boltzmann protocols and demonstrates potential danger in drawing conclusions on electrostatic contributions based on a particular calculation protocol.
Efficient band structure modulations in two-dimensional MnPSe3/CrSiTe3 van der Waals heterostructures.

PubMed

Pei, Qi; Wang, Xiaocha; Zou, Jijun; Mi, Wenbo

2018-05-25

As a research upsurge, van der Waals (vdW) heterostructures give rise to numerous combined merits and novel applications in nanoelectronics fields. Here, we systematically investigate the electronic structure of MnPSe 3 /CrSiTe 3 vdW heterostructures with various stacking patterns. Then, particular attention of this work is paid on the band structure modulations in MnPSe 3 /CrSiTe 3 vdW heterostructures via biaxial strain or electric field. Under a tensile strain, the relative band edge positions of heterostructures transform from type-I (nested) to type-II (staggered). The relocation of conduction band minimum also brings about a transition from indirect to direct band gap. Under a compressive strain, the electronic properties change from semiconducting to metallic. The physical mechanism of strain-dependent band structure may be ascribed to the shifts of the energy bands impelled by different superposition of atomic orbitals. Meanwhile, our calculations manifest that band gap values of MnPSe 3 /CrSiTe 3 heterostructures are insensitive to the electric field. Even so, by applying a suitable intensity of negative electric field, the band alignment transition from type-I to type-II can also be realized. The efficient band structure modulations via external factors endow MnPSe 3 /CrSiTe 3 heterostructures with great potential in novel applications, such as strain sensors, photocatalysis, spintronic and photoelectronic devices.
Theoretical and experimental NMR studies on muscimol from fly agaric mushroom (Amanita muscaria)

NASA Astrophysics Data System (ADS)

Kupka, Teobald; Wieczorek, Piotr P.

2016-01-01

In this article we report results of combined theoretical and experimental NMR studies on muscimol, the bioactive alkaloid from fly agaric mushroom (Amanita muscaria). The assignment of 1H and 13C NMR spectra of muscimol in DMSO-d6 was supported by additional two-dimensional heteronuclear correlated spectra (2D NMR) and gauge independent atomic orbital (GIAO) NMR calculations using density functional theory (DFT). The effect of solvent in theoretical calculations was included via polarized continuum model (PCM) and the hybrid three-parameter B3LYP density functional in combination with 6-311++G(3df,2pd) basis set enabled calculation of reliable structures of non-ionized (neutral) molecule and its NH and zwitterionic forms in the gas phase, chloroform, DMSO and water. GIAO NMR calculations, using equilibrium and rovibrationally averaged geometry, at B3LYP/6-31G* and B3LYP/aug-cc-pVTZ-J levels of theory provided muscimol nuclear magnetic shieldings. The theoretical proton and carbon chemical shifts were critically compared with experimental NMR spectra measured in DMSO. Our results provide useful information on its structure in solution. We believe that such data could improve the understanding of basic features of muscimol at atomistic level and provide another tool in studies related to GABA analogs.
Electronic and Crystalline Structure, Magnetic Response, and Optical Characterization of Rare-Earth Ruthenate Sr2HoRuO6

NASA Astrophysics Data System (ADS)

Velásquez Moya, X. A.; Cardona, R.; Villa Hernández, J. I.; Landínez Téllez, D. A.; Roa-Rojas, J.

2018-03-01

Sr2HoRuO6 ceramic has been synthesized and its structural, morphological, magnetic, optical, and electronic properties studied. Rietveld refinement of x-ray diffraction patterns revealed that this oxide material crystallizes in monoclinic perovskite structure in space group P2 1 /n (no. 14). Scanning electron microscopy revealed polycrystalline surface morphology. x-Ray dispersive spectroscopy suggested that Sr2HoRuO6 was obtained with expected stoichiometry. Magnetic susceptibility curves as a function of temperature revealed ferrimagnetic feature of this material below the Néel temperature T N of 14 K. Evidence of magnetic disorder was provided by the irreversibility observed in the zero-field-cooled and field-cooled responses of the susceptibility below T irr = 169 K. Analysis of the diffuse reflectance spectrum suggested that this material behaves as a semiconductor with energy gap E g of 1.38 eV. Results of band structure and density-of-states calculations are in agreement with the interpretation of Sr2HoRuO6 as a semiconductor. The ferrimagnetic behavior is interpreted as due to exchange mechanisms of d-f (Ru-O-Ho) electrons. The effective magnetic moment calculated from density functional theory was 93.5% of the experimental value obtained from Curie-Weiss fitting of the susceptibility curve.
What is going on between defibrotide and endothelial cells? Snapshots reveal the hot spots of their romance

PubMed Central

Mir, Enrique; Rovira, Montse; Escolar, Ginés; Carreras, Enric; Diaz-Ricart, Maribel

2016-01-01

Defibrotide (DF) has received European Medicines Agency authorization to treat sinusoidal obstruction syndrome, an early complication after hematopoietic cell transplantation. DF has a recognized role as an endothelial protective agent, although its precise mechanism of action remains to be elucidated. The aim of the present study was to investigate the interaction of DF with endothelial cells (ECs). A human hepatic EC line was exposed to different DF concentrations, previously labeled. Using inhibitory assays and flow cytometry techniques along with confocal microscopy, we explored: DF-EC interaction, endocytic pathways, and internalization kinetics. Moreover, we evaluated the potential role of adenosine receptors in DF-EC interaction and if DF effects on endothelium were dependent of its internalization. Confocal microscopy showed interaction of DF with EC membranes followed by internalization, though DF did not reach the cell nucleus even after 24 hours. Flow cytometry revealed concentration, temperature, and time dependent uptake of DF in 2 EC models but not in other cell types. Moreover, inhibitory assays indicated that entrance of DF into ECs occurs primarily through macropinocytosis. Our experimental approach did not show any evidence of the involvement of adenosine receptors in DF-EC interaction. The antiinflammatory and antioxidant properties of DF seem to be caused by the interaction of the drug with the cell membrane. Our findings contribute to a better understanding of the precise mechanisms of action of DF as a therapeutic and potential preventive agent on the endothelial damage underlying different pathologic situations. PMID:26755708
Acetylene chain reaction on hydrogenated boron nitride monolayers: a density functional theory study.

PubMed

Ponce-Pérez, R; Cocoletzi, Gregorio H; Takeuchi, Noboru

2017-11-28

Spin-polarized first-principles total-energy calculations have been performed to investigate the possible chain reaction of acetylene molecules mediated by hydrogen abstraction on hydrogenated hexagonal boron nitride monolayers. Calculations have been done within the periodic density functional theory (DFT), employing the PBE exchange correlation potential, with van der Waals corrections (vdW-DF). Reactions at two different sites have been considered: hydrogen vacancies on top of boron and on top of nitrogen atoms. As previously calculated, at the intermediate state of the reaction, when the acetylene molecule is attached to the surface, the adsorption energy is of the order of -0.82 eV and -0.20 eV (measured with respect to the energy of the non interacting molecule-substrate system) for adsorption on top of boron and nitrogen atoms, respectively. After the hydrogen abstraction takes place, the system gains additional energy, resulting in adsorption energies of -1.52 eV and -1.30 eV, respectively. These results suggest that the chain reaction is energetically favorable. The calculated minimum energy path (MEP) for hydrogen abstraction shows very small energy barriers of the order of 5 meV and 22 meV for the reaction on top of boron and nitrogen atoms, respectively. Finally, the density of states (DOS) evolution study helps to understand the chain reaction mechanism. Graphical abstract Acetylene chain reaction on hydrogenated boron nitride monolayers.
Carbon chemistry of the Apollo 15 and 16 deep drill cores

NASA Technical Reports Server (NTRS)

Wszolek, P. C.; Burlingame, A. L.

1973-01-01

The carbon chemistry of the Apollo 15 and 16 deep drill cores is a function of the surface exposure plus the chemical and mineralogical composition of the individual samples. The depth profiles of carbide and methane yields in the Apollo 15 core show a general decline with depth and correlate with the solar wind noble gas content, percentage agglutinates, track densities, and metallic iron. All horizons examined were exposed for a considerable time on the lunar surface. The Apollo 16 core samples show that chemical and mineralogical composition plays an important role in determining the nature of carbide-like material present in the fines. The higher aluminum and calcium contents and lower iron contents of highlands material result in carbide-like material yielding less CD4 and more C2D2 (deuteroacetylene) upon DF acid dissolution.
cDF Theory Software for mesoscopic modeling of equilibrium and transport phenomena

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

2015-12-01

The approach is based on classical Density Functional Theory ((cDFT) coupled with the Poisson-Nernst-Planck (PNP) transport kinetics model and quantum mechanical description of short-range interaction and elementary transport processes. The model we proposed and implemented is fully atomistic, taking into account pairwise short-range and manybody long-range interactions. But in contrast to standard molecular dynamics (MD) simulations, where long-range manybody interactions are evaluated as a sum of pair-wise atom-atom contributions, we include them analytically based on wellestablished theories of electrostatic and excluded volume interactions in multicomponent systems. This feature of the PNP/cDFT approach allows us to reach well beyond the length-scalesmore » accessible to MD simulations, while retaining the essential physics of interatomic interactions from first principles and in a parameter-free fashion.« less

Hydrolysis reaction of 2,4-dichlorophenoxyacetic acid. A kinetic and computational study

NASA Astrophysics Data System (ADS)

Romero, Jorge Marcelo; Jorge, Nelly Lidia; Grand, André; Hernández-Laguna, Alfonso

2015-10-01

The degradation of the 2,4-dichlorophenoxyacetic acid in aqueous solution is an hydrolysis reaction. Two products are identified: 2,4-dichlorophenol and glycolic acid. Reaction is investigated as a function of pH and temperature, and it is first-order kinetics and pH-dependent. Reaction is modeled in gas phase, where a proton catalyses the reaction. Critical points of PES are calculated at B3LYP/6-311++G(3df,2p), and aug-cc-pvqz//6-311++G(3df,2p) levels plus ZPE at 6-311++G(3df,2p) level. The activation barrier is 21.2 kcal/mol. Theoretical results agree with the experimental results. A second mechanism related with a Cl2Phsbnd Osbnd CH2sbnd COOH⋯H2O complex is found, but with a rate limiting step of 38.4 kcal/mol.
Physicochemical Properties of Dietary Fibers from Artocarpus camansi Fruit

NASA Astrophysics Data System (ADS)

Suryanti, V.; Kusumaningsih, T.; Rumingtyas, Y. S.

2017-04-01

The objective of this work was to investigate the dietary fiber (DF) contents of Artocorpus camansi (breadnut) fruit and examine their physicochemical properties, such as water-holding capacity (WAC), oil-holding capacity (OHC) and water absorption capacity (WAC). This fruit flour contained of both water soluble fibers (SDF), such as pectin (1.95%) and gum (0.4%), and water insoluble fibers (IDF) (89.25%). The IDF content of this fruit was significantly high in respect to other DF sources. The WHC, OHC and WAC of IDF were 4.10, 2.60 and 4.0%, respectively. Moreover, the WHC, OHC and WHC of total dietary fibers (TDF) were 4.2, 4.3 and 4.6%, respectively. The results showed that the DF of fruit flour had good physicochemical properties. The findings suggested that there is a potential application of A. camansi of fruit as functional ingredients in the food industry.
Electromagnetically induced grating with Rydberg atoms

NASA Astrophysics Data System (ADS)

Asghar, Sobia; Ziauddin, Qamar, Shahid; Qamar, Sajid

2016-09-01

We present a scheme to realize electromagnetically induced grating in an ensemble of strongly interacting Rydberg atoms, which act as superatoms due to the dipole blockade mechanism. The ensemble of three-level cold Rydberg-dressed (87Rb) atoms follows a cascade configuration where a strong standing-wave control field and a weak probe pulse are employed. The diffraction intensity is influenced by the strength of the probe intensity, the control field strength, and the van der Waals (vdW) interaction. It is noticed that relatively large first-order diffraction can be obtained for low-input intensity with a small vdW shift and a strong control field. The scheme can be considered as an amicable solution to realize the atomic grating at the microscopic level, which can provide background- and dark-current-free diffraction.
Linseed dietary fibers reduce apparent digestibility of energy and fat and weight gain in growing rats.

PubMed

Kristensen, Mette; Knudsen, Knud Erik Bach; Jørgensen, Henry; Oomah, David; Bügel, Susanne; Toubro, Søren; Tetens, Inge; Astrup, Arne

2013-08-19

Dietary fibers (DF) may affect energy balance, an effect often ascribed to the viscous nature of some water soluble DF, which affect luminal viscosity and thus multiple physiological processes. We have tested the hypothesis that viscous linseed DF reduce apparent nutrient digestibility, and limit weight gain, in a randomized feeding trial where 60 male, growing, Wistar rats, with an initial weight of ~200 g, were fed different diets (n = 10 per group): low DF control (C), 5% DF from cellulose (5-CEL), CEL + 5% DF from whole (5-WL) or ground linseed (5-GL), CEL + 5% DF from linseed DF extract (5-LDF), and CEL + 10% DF from linseed DF extract (10-LDF). Diets were provided ad libitum for 21 days. Feed intake and faecal output were measured during days 17-21. Faecal fat excretion increased with increasing DF content and was highest in the 10-LDF group. Apparent fat digestibility was highest with the C diet (94.9% ± 0.8%) and lowest (74.3% ± 0.6%) with the 10-LDF diet, and decreased in a non-linear manner with increasing DF (p < 0.001). Apparent fat digestibility also decreased with increased accessibility of DF (5-WL vs. 5-GL) and when the proportion of viscous DF increased (5-GL vs. 5-LDF). The 10-LDF resulted in a lower final body weight (258 ± 6.2 g) compared to C (282 ± 5.9 g), 5-CEL (281 ± 5.9 g), and 5-WL (285 ± 5.9 g) (p < 0.05). The 10-LDF diet reduced body fat compared to 5-CEL (p < 0.01). In conclusion, DF extracted from linseed reduced apparent energy and fat digestibility and resulted in restriction of body weight gain in growing rats.
The Ames dwarf mutation attenuates Alzheimer's disease phenotype of APP/PS1 mice.

PubMed

Puig, Kendra L; Kulas, Joshua A; Franklin, Whitney; Rakoczy, Sharlene G; Taglialatela, Giulio; Brown-Borg, Holly M; Combs, Colin K

2016-04-01

APP/PS1 double transgenic mice expressing human mutant amyloid precursor protein (APP) and presenilin-1 (PS1) demonstrate robust brain amyloid beta (Aβ) peptide containing plaque deposition, increased markers of oxidative stress, behavioral dysfunction, and proinflammatory gliosis. On the other hand, lack of growth hormone, prolactin, and thyroid-stimulating hormone due to a recessive mutation in the Prop 1 gene (Prop1df) in Ames dwarf mice results in a phenotype characterized by potentiated antioxidant mechanisms, improved learning and memory, and significantly increased longevity in homozygous mice. Based on this, we hypothesized that a similar hormone deficiency might attenuate disease changes in the brains of APP/PS1 mice. To test this idea, APP/PS1 mice were crossed to the Ames dwarf mouse line. APP/PS1, wild-type, df/+, df/df, df/+/APP/PS1, and df/df/APP/PS1 mice were compared at 6 months of age through behavioral testing and assessing amyloid burden, reactive gliosis, and brain cytokine levels. df/df mice demonstrated lower brain growth hormone and insulin-like growth factor 1 concentrations. This correlated with decreased astrogliosis and microgliosis in the df/df/APP/PS1 mice and, surprisingly, reduced Aβ plaque deposition and Aβ 1-40 and Aβ 1-42 concentrations. The df/df/APP/PS1 mice also demonstrated significantly elevated brain levels of multiple cytokines in spite of the attenuated gliosis. These data indicate that the df/df/APP/PS1 line is a unique resource in which to study aging and resistance to disease and suggest that the affected pituitary hormones may have a role in regulating disease progression. Copyright © 2016 Elsevier Inc. All rights reserved.
Globular Clusters Shine in a Galaxy Lacking Dark Matter

NASA Astrophysics Data System (ADS)

Kohler, Susanna

2018-04-01

You may have seen recent news about NGC 1052DF2, a galaxy that was discovered to have little or no dark matter. Now, a new study explores what NGC 1052DF2 does have: an enigmatic population of unusually large and luminous globular clusters.Keck/LRIS spectra (left and right) and HST images (center) of the 11 clusters associated with NGC 1052DF2. The color images each span 1 1. [van Dokkum et al. 2018]An Unusual DwarfThe ultra-diffuse galaxy NGC 1052DF2, originally identified with the Dragonfly Telescope Array, has puzzled astronomers since the discovery that its dynamical mass determined by the motions of globular-cluster-like objects spotted within it is essentially the same as its stellar mass. This equivalence implies that the galaxy is strangely lacking dark matter; the upper limit set on its dark matter halo is 400 times smaller than what we would expect for such a dwarf galaxy.Led by Pieter van Dokkum (Yale University), the team that made this discovery has now followed up with detailed Hubble Space Telescope imaging and Keck spectroscopy. Their goal? To explore the objects that allowed them to make the dynamical-mass measurement: the oddly bright globular clusters of NGC 1052DF2.Sizes (circularized half-light radii) vs. absolute magnitudes for globular clusters in NGC1052DF2 (black) and the Milky Way (red). [Adapted from van Dokkum et al. 2018]Whats Up with the Globular Clusters?Van Dokkum and collaborators spectroscopically confirmed 11 compact objects associated with the faint galaxy. These objects are globular-cluster-like in their appearance, but the peak of their luminosity distribution is offset by a factor of four from globular clusters of other galaxies; these globular clusters are significantly brighter than is typical.Using the Hubble imaging, the authors determined that NGC 1052DF2s globular clusters are more than twice the size of the Milky Ways globular clusters in the same luminosity range. As is typical for globular clusters, they are an old ( 9.3 billion years) population and metal-poor.Rethinking Formation TheoriesThe long-standing picture of galaxies has closely connected old, metal-poor globular clusters to the galaxies dark-matter halos. Past studies have found that the ratio between the total globular-cluster mass and the overall mass of a galaxy (i.e., all dark + baryonic matter) holds remarkably constant across galaxies its typically 3 x 10-5. This has led researchers to believe that properties of the dark-matter halo may determine globular-cluster formation.The luminosity function of the compact objects in NGC 1052DF2. The red and blue curves show the luminosity functions of globular clusters in the Milky Way and in the typical ultra-diffuse galaxies of the Coma cluster, respectively. NGC 1052DF2s globular clusters peak at a significantly higher luminosity. [Adapted from van Dokkum et al. 2018]NGC 1052DF2, with a globular-cluster mass thats 3% of the mass of the galaxy ( 1000 times the expected ratio!), defies this picture. This unusual galaxy therefore demonstrates that the usual relation between globular-cluster mass and total galaxy mass probably isnt due to a fundamental connection between the dark-matter halo and globular-cluster formation. Instead, van Dokkum and collaborators suggest, globular-cluster formation may ultimately be a baryon-driven process.As with all unexpected discoveries in astronomy, we must now determine whether NGC 1052DF2 is simply a fluke, or whether it represents a new class of object we can expect to find more of. Either way, this unusual galaxy is forcing us to rethink what we know about galaxies and the star clusters they host.CitationPieter van Dokkum et al 2018 ApJL 856 L30. doi:10.3847/2041-8213/aab60b
Functional properties and dietary fiber characterization of mango processing by-products (Mangifera indica L., cv Ataulfo and Tommy Atkins).

PubMed

García-Magaña, María de Lourdes; García, Hugo S; Bello-Pérez, Luis A; Sáyago-Ayerdi, Sonia G; de Oca, Miguel Mata-Montes

2013-09-01

Several reports have focused on utilization of post-harvest residues of crops, while neglecting those residues produced by mango processing. These residues represent a waste of nutrients and a source of environmental contaminants. Such by-products could be valuable sources of dietary fiber (DF), antioxidant compounds, and single carbohydrates. The aim of this study was to evaluate some functional properties (FP), and the content of DF and polyphenols (PP) of the peel and coarse material obtained from residues during the industrial processing of Ataulfo and Tommy Atkins mangoes. The total dietary fiber (TDF) content was about 225 mg/g and 387 mg/g (dry weight) for the coarse material and the peel, respectively, from which soluble dietary fiber represented 23 and 42%, respectively. The main neutral sugar identified was rhamnose, especially in peels; the klason lignin (KL) content was 92 mg/g, which highlights the Ataulfo peel (Ataulfo-P) and the Tommy Atkins peel (Tommy Atkins-P). The extractable PP content in Ataulfo-P was higher than in Tommy-Atkins-P, and interesting data for non-extractable PP were obtained in the residues. FP as swelling, water holding, oil holding, and glucose absorption in the residues was studied, obtaining better functional properties when compared to cellulose fiber. The results show that mango industrial by-products, mainly from the Ataulfo-P variety, could be used as ingredients in food products because of their functional properties as well as their DF and PP content.
Population-Based Questionnaire Survey on Health Effects of Aircraft Noise on Residents Living around U.S. Airfields in the RYUKYUS—PART II: AN Analysis of the Discriminant Score and the Factor Score

NASA Astrophysics Data System (ADS)

HIRAMATSU, K.; MATSUI, T.; MIYAKITA, T.; ITO, A.; TOKUYAMA, T.; OSADA, Y.; YAMAMOTO, T.

2002-02-01

Discriminant function values of psychosomatics and neurosis are calculated using the 12 scale scores of the Todai Health Index, a general health questionnaire, obtained in the survey done around the Kadena and Futenma U.S. airfields in Okinawa, Japan. The total number of answers available for the analysis is 6301. Factor analysis is applied to the 12 scale scores by means of the principal factor method, and Oblimin rotation is done because the factors extracted are considered likely to correlate with each other to a greater or lesser extent. The logistic regression analysis is made with the independent variables of discriminant function (DF) values and factor scores and with the dependent variables of Ldn, age (six levels), sex, occupation (four categories) and the interaction of age and sex. Results indicate that the odds ratio of the DF values regarding psychosomatic disorder and of the score of somatic factor have clear dose-response relationship. The odds ratios of the DF value of neurosis and of the score of the mental factor increase in the area where noise exposure is very intense.
What is going on between defibrotide and endothelial cells? Snapshots reveal the hot spots of their romance.

PubMed

Palomo, Marta; Mir, Enrique; Rovira, Montse; Escolar, Ginés; Carreras, Enric; Diaz-Ricart, Maribel

2016-03-31

Defibrotide (DF) has received European Medicines Agency authorization to treat sinusoidal obstruction syndrome, an early complication after hematopoietic cell transplantation. DF has a recognized role as an endothelial protective agent, although its precise mechanism of action remains to be elucidated. The aim of the present study was to investigate the interaction of DF with endothelial cells (ECs). A human hepatic EC line was exposed to different DF concentrations, previously labeled. Using inhibitory assays and flow cytometry techniques along with confocal microscopy, we explored: DF-EC interaction, endocytic pathways, and internalization kinetics. Moreover, we evaluated the potential role of adenosine receptors in DF-EC interaction and if DF effects on endothelium were dependent of its internalization. Confocal microscopy showed interaction of DF with EC membranes followed by internalization, though DF did not reach the cell nucleus even after 24 hours. Flow cytometry revealed concentration, temperature, and time dependent uptake of DF in 2 EC models but not in other cell types. Moreover, inhibitory assays indicated that entrance of DF into ECs occurs primarily through macropinocytosis. Our experimental approach did not show any evidence of the involvement of adenosine receptors in DF-EC interaction. The antiinflammatory and antioxidant properties of DF seem to be caused by the interaction of the drug with the cell membrane. Our findings contribute to a better understanding of the precise mechanisms of action of DF as a therapeutic and potential preventive agent on the endothelial damage underlying different pathologic situations. © 2016 by The American Society of Hematology.
The role of a combined coagulation and disk filtration process as a pre-treatment to microfiltration and reverse osmosis membranes in a municipal wastewater pilot plant.

PubMed

Chon, Kangmin; Cho, Jaeweon; Kim, Seung Joon; Jang, Am

2014-12-01

A pilot study was conducted to assess the performance of a municipal wastewater reclamation plant consisting of a combined coagulation-disk filtration (CC-DF) process, microfiltration (MF) and reverse osmosis (RO) membranes, in terms of the removal of water contaminants and changes in characteristics of effluent organic matter (EfOM). The CC-DF and MF membranes were not effective for the removal of dissolved water contaminants. However, they could partially reduce the turbidity associated with the cake layer formation by particulate materials on the membrane surfaces. Furthermore, most of water contaminants were completely removed by the RO membranes. Although the CC-DF process could remove approximately 20% of turbidity, the aluminium concentrations considerably increased after the CC-DF process due to the residual coagulants complexed with both carboxylic acid and alcohol functional groups of EfOM. Those aluminium-EfOM complexes had a lower negative charge and higher molecular weight (>0.1 μm pore size of the MF membranes) compared to non-complexed EfOM. These results indicate that the control of the formation of the aluminium-EfOM complexes should be considered as a key step to use the CC-DF process as a pre-treatment of the MF and RO membranes for mitigation of membrane fouling in the tested pilot plant. Copyright © 2014 Elsevier Ltd. All rights reserved.
Using Baidu Search Index to Predict Dengue Outbreak in China

NASA Astrophysics Data System (ADS)

Liu, Kangkang; Wang, Tao; Yang, Zhicong; Huang, Xiaodong; Milinovich, Gabriel J.; Lu, Yi; Jing, Qinlong; Xia, Yao; Zhao, Zhengyang; Yang, Yang; Tong, Shilu; Hu, Wenbiao; Lu, Jiahai

2016-12-01

This study identified the possible threshold to predict dengue fever (DF) outbreaks using Baidu Search Index (BSI). Time-series classification and regression tree models based on BSI were used to develop a predictive model for DF outbreak in Guangzhou and Zhongshan, China. In the regression tree models, the mean autochthonous DF incidence rate increased approximately 30-fold in Guangzhou when the weekly BSI for DF at the lagged moving average of 1-3 weeks was more than 382. When the weekly BSI for DF at the lagged moving average of 1-5 weeks was more than 91.8, there was approximately 9-fold increase of the mean autochthonous DF incidence rate in Zhongshan. In the classification tree models, the results showed that when the weekly BSI for DF at the lagged moving average of 1-3 weeks was more than 99.3, there was 89.28% chance of DF outbreak in Guangzhou, while, in Zhongshan, when the weekly BSI for DF at the lagged moving average of 1-5 weeks was more than 68.1, the chance of DF outbreak rose up to 100%. The study indicated that less cost internet-based surveillance systems can be the valuable complement to traditional DF surveillance in China.
Oral support measures used in feeding the preterm infant.

PubMed

Hill, A S; Kurkowski, T B; Garcia, J

2000-01-01

Evidence that bottle-feeding is a stressor for inefficient preterm infant feeders is seen in untoward changes in the physiologic system and nutritive sucking patterns. To determine whether a therapeutic technique, oral support (cheek and jaw support), would influence the cardiopulmonary functions or nutritive sucking patterns of preterm infants during feeding. A crossover repeated measures design was used with 20 preterm infants for a total of 40 bottle-feeding sessions. The Whitney Mercury Strain Gage and a Nonin Cardiopulmonary monitor were used to observe sucking characteristics and cardiopulmonary functions during feeding. Infants not receiving support paused longer (F= 6.37, df= 5, p < .001) and more frequently (F= 5.01, df= 5, p < .001) than supported infants. There were no differences between the groups in the number of sucks and bursts, the burst duration, the stability of the total sucking activity, or the rate of sucking. Oxygen saturation (SaO2) values, heart rate, and respiratory rate did not differ between the groups during feeding. Postfeeding SaO2 levels were lower than prefeeding levels for infants not receiving oral support (t= 0.96, df= 19, p= .03). Oral support provided stability for the jaw and fostered the return of the infant's prefeeding SaO2 values, but it did not interfere with cardiopulmonary function during feeding. Further research is needed to determine whether there is a cumulative effect of oral support, and whether it influences state behavior.
Two-dimensional Topology of the Two-Degree Field Galaxy Redshift Survey

NASA Astrophysics Data System (ADS)

Hoyle, Fiona; Vogeley, Michael S.; Gott, J. Richard, III

2002-05-01

We study the topology of the publicly available data released by the Two Degree Field Galaxy Redshift Survey team (2dF GRS). The 2dF GRS data contain over 100,000 galaxy redshifts with a magnitude limit of bJ=19.45 and is the largest such survey to date. The data lie over a wide range of right ascension (75° strips) but only within a narrow range of declination (10° and 15° strips). This allows measurements of the two-dimensional genus to be made. We find that the genus curves of the north Galactic pole (NGP) and south Galactic pole (SGP) are slightly different. The NGP displays a slight meatball shift topology, whereas the SGP displays a bubble-like topology. The current SGP data also have a slightly higher genus amplitude. In both cases, a slight excess of overdense regions is found over underdense regions. We assess the significance of these features using mock catalogs drawn from the Virgo Consortium's Hubble volume ΛCDM z=0 simulation. We find that differences between the NGP and SGP genus curves are only significant at the 1 σ level. The average genus curve of the 2dF GRS agrees well with that extracted from the ΛCDM mock catalogs. We also use the simulations to assess how the current incompleteness of the survey (the strips are not completely filled in) affects the measurement of the genus and find that we are not sensitive to the geometry; there are enough data in the current sample to trace the isolated high- and low-density regions. We compare the amplitude of the 2dF GRS genus curve to the amplitude of the genus curve of a Gaussian random field that we construct to have the same power spectrum as the 2dF GRS. In previous three-dimensional analyses, it was found that the genus curve of observed samples was lower than the Gaussian random field curve, presumably because of high-order correlations present in the data. However, we find that the 2dF GRS genus curve has an amplitude that is slightly higher than that of the power-spectrum-matched Gaussian random field. We suggest that in two dimensions the genus measurement is less sensitive to nonlinear effects because of the effective smoothing over the thickness of the slice.
Progranulin expression in breast cancer with different intrinsic subtypes.

PubMed

Li, Li Qin; Min, Li Shan; Jiang, Qun; Ping, Jin Liang; Li, Jing; Dai, Li Cheng

2012-04-15

Progranulin is a newly discovered 88-kDa glycoprotein originally purified from the highly tumorigenic mouse teratoma-derived cell line PC. We found that high progranulin expression was associated with higher breast carcinoma angiogenesis, reflected by increased vascular endothelial growth factor expression and higher microvessel density. However, no immunohistochemical evidence currently exists to correlate progranulin expression with clinicopathological features in different intrinsic subtypes of breast carcinoma biopsies. The aim of this study was to investigate the progranulin expression profiles in the intrinsic subtypes of breast carcinomas and their relevance to histopathological and clinicopathological features. Tissue blocks containing 264 cases of breast carcinomas from 2006 to 2009 were classified as different intrinsic subtypes. Tissues of four intrinsic subtypes were immunostained for progranulin, vascular endothelial growth factor and CD105. Their relevance to histopathological and clinicopathological features was also analyzed. Twenty tissue samples from breast fibroadenomas were included in this study. Progranulin expression showed no significant differences in different intrinsic subtypes, although an increasing tendency could be found in the triple-negative breast cancer (TNBC) subgroup (χ(2)=5.00, df=3, p=0.17). However, differences were significant when pathologically node metastasis-positive (pN(+)) TNBC were excluded (χ(2)=17.84, df=3, p<0.01). Some clinicopathological parameters, including CK5/6 (χ(2)=0.08, df=3, p=0.78), E-cadherin (χ(2)=0.71, df=3, p=0.40) and P53 (χ(2)=0.05, df=3, p=0.83), displayed no correlation with activity of progranulin in pathologically node metastasis-negative (pN(-)) TNBC. It was noted that the EGFR expression level of the pN(-) TNBC subtype was significantly higher in cases with strong progranulin expression than in cases with weak progranulin expression (χ(2)=11.26, df=1, p<0.01). A significantly higher expression level of progranulin in pN(-) TNBC suggests that progranulin is a promising new target for pN(-) TNBC treatment. Strong expression of progranulin correlates with positive EGFR expression in the pN(-) TNBC subtype. The close relationship between EGFR and progranulin/VEGF/CD105 expression may partly play a role in high angiogenesis levels in the pN(-) TNBC subtype. Copyright © 2012 Elsevier GmbH. All rights reserved.
The behavior of dietary fiber in the gastrointestinal tract determines its physiological effect.

PubMed

Capuano, Edoardo

2017-11-02

A diet rich in dietary fiber (DF) is considered healthy and recommended dietary intake of DF is established all over the world. The physiological effect of DF is mostly related to its behavior during digestion. In this review, the behavior of DF in the human digestive tract is discussed and linked to its physiological effect with special attention to four aspects of such behavior: (i) the modulation of bioavailability by the plant cell walls, (ii) the effect of DF on the rheological and colloidal state of digesta, (iii) the binding of DF with phenolic compounds, bile salts, mineral ions, and digestive enzymes, and (iv) DF fermentation in the large intestine and the corresponding effect on microbiota composition. It is stressed that the detailed chemical characterization of DF is crucial to explain its effect on health and that DF behavior in the digestive tract can be modulated by interactions with other food and meal components so that information of the bare content in DF of food is not sufficient to predict its physiological effect.
Kinetic feature of dipolarization fronts produced by interchange instability in the magnetotail

NASA Astrophysics Data System (ADS)

Lyu, Haoyu

2017-04-01

A two-dimensional extended MHD simulation is performed to study the kinetic feature of depolarization fronts (DF) in the scale of the ion inertial length / ion Larmor radius. The interchange instability, arising due to the force imbalance between the tailward gradient of thermal pressure and Earthward magnetic curvature force, self-consistently produces the DF in the near-Earth region. Numerical investigations indicate that the DF is a tangential discontinuity, which means that the normal plasma velocity across the DF should be zero in the reference system that is static with the DF structure. The electric system, including electric field and current, is determined by Hall effect arising in the scale of ion inertial length. Hall effect not only mainly contributes on the electric field normal to the tangent plane of the DF, increases the current along the tangent plane of the DF, but also makes the DF structure asymmetric. The drifting motion of the large-scale DF structure is determined by the FLR effect arising in the scale of ion Larmor radius. The ion magnetization velocity induced by the FLR effect is towards to duskward at the subsolar point of the DF, but the y component of velocity in the region after the DF, which dominantly results in the drifting motion of the whole mushroom structure towards the dawn.
Altered Knee and Ankle Kinematics During Squatting in Those With Limited Weight-Bearing–Lunge Ankle-Dorsiflexion Range of Motion

PubMed Central

Dill, Karli E.; Begalle, Rebecca L.; Frank, Barnett S.; Zinder, Steven M.; Padua, Darin A.

2014-01-01

Context: Ankle-dorsiflexion (DF) range of motion (ROM) may influence movement variables that are known to affect anterior cruciate ligament loading, such as knee valgus and knee flexion. To our knowledge, researchers have not studied individuals with limited or normal ankle DF-ROM to investigate the relationship between those factors and the lower extremity movement patterns associated with anterior cruciate ligament injury. Objective: To determine, using 2 different measurement techniques, whether knee- and ankle-joint kinematics differ between participants with limited and normal ankle DF-ROM. Design: Cross-sectional study. Setting: Sports medicine research laboratory. Patients or Other Participants: Forty physically active adults (20 with limited ankle DF-ROM, 20 with normal ankle DF-ROM). Main Outcome Measure(s): Ankle DF-ROM was assessed using 2 techniques: (1) nonweight-bearing ankle DF-ROM with the knee straight, and (2) weight-bearing lunge (WBL). Knee flexion, knee valgus-varus, knee internal-external rotation, and ankle DF displacements were assessed during the overhead-squat, single-legged squat, and jump-landing tasks. Separate 1-way analyses of variance were performed to determine whether differences in knee- and ankle-joint kinematics existed between the normal and limited groups for each assessment. Results: We observed no differences between the normal and limited groups when classifying groups based on nonweight-bearing passive-ankle DF-ROM. However, individuals with greater ankle DF-ROM during the WBL displayed greater knee-flexion and ankle-DF displacement and peak knee flexion during the overhead-squat and single-legged squat tasks. In addition, those individuals also demonstrated greater knee-varus displacement during the single-legged squat. Conclusions: Greater ankle DF-ROM assessed during the WBL was associated with greater knee-flexion and ankle-DF displacement during both squatting tasks as well as greater knee-varus displacement during the single-legged squat. Assessment of ankle DF-ROM using the WBL provided important insight into compensatory movement patterns during squatting, whereas nonweight-bearing passive ankle DF-ROM did not. Improving ankle DF-ROM during the WBL may be an important intervention for altering high-risk movement patterns commonly associated with noncontact anterior cruciate ligament injury. PMID:25144599
Altered knee and ankle kinematics during squatting in those with limited weight-bearing-lunge ankle-dorsiflexion range of motion.

PubMed

Dill, Karli E; Begalle, Rebecca L; Frank, Barnett S; Zinder, Steven M; Padua, Darin A

2014-01-01

Ankle-dorsiflexion (DF) range of motion (ROM) may influence movement variables that are known to affect anterior cruciate ligament loading, such as knee valgus and knee flexion. To our knowledge, researchers have not studied individuals with limited or normal ankle DF-ROM to investigate the relationship between those factors and the lower extremity movement patterns associated with anterior cruciate ligament injury. To determine, using 2 different measurement techniques, whether knee- and ankle-joint kinematics differ between participants with limited and normal ankle DF-ROM. Cross-sectional study. Sports medicine research laboratory. Forty physically active adults (20 with limited ankle DF-ROM, 20 with normal ankle DF-ROM). Ankle DF-ROM was assessed using 2 techniques: (1) nonweight-bearing ankle DF-ROM with the knee straight, and (2) weight-bearing lunge (WBL). Knee flexion, knee valgus-varus, knee internal-external rotation, and ankle DF displacements were assessed during the overhead-squat, single-legged squat, and jump-landing tasks. Separate 1-way analyses of variance were performed to determine whether differences in knee- and ankle-joint kinematics existed between the normal and limited groups for each assessment. We observed no differences between the normal and limited groups when classifying groups based on nonweight-bearing passive-ankle DF-ROM. However, individuals with greater ankle DF-ROM during the WBL displayed greater knee-flexion and ankle-DF displacement and peak knee flexion during the overhead-squat and single-legged squat tasks. In addition, those individuals also demonstrated greater knee-varus displacement during the single-legged squat. Greater ankle DF-ROM assessed during the WBL was associated with greater knee-flexion and ankle-DF displacement during both squatting tasks as well as greater knee-varus displacement during the single-legged squat. Assessment of ankle DF-ROM using the WBL provided important insight into compensatory movement patterns during squatting, whereas nonweight-bearing passive ankle DF-ROM did not. Improving ankle DF-ROM during the WBL may be an important intervention for altering high-risk movement patterns commonly associated with noncontact anterior cruciate ligament injury.
The role of particle-to-cell interactions in dictating nanoparticle aided magnetophoretic separation of microalgal cells.

PubMed

Toh, Pey Yi; Ng, Bee Wah; Ahmad, Abdul Latif; Chieh, Derek Chan Juinn; Lim, JitKang

2014-11-07

Successful application of a magnetophoretic separation technique for harvesting biological cells often relies on the need to tag the cells with magnetic nanoparticles. This study investigates the underlying principle behind the attachment of iron oxide nanoparticles (IONPs) onto microalgal cells, Chlorella sp. and Nannochloropsis sp., in both freshwater and seawater, by taking into account the contributions of various colloidal forces involved. The complex interplay between van der Waals (vdW), electrostatic (ES) and Lewis acid-base interactions (AB) in dictating IONP attachment was studied under the framework of extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) analysis. Our results showed that ES interaction plays an important role in determining the net interaction between the Chlorella sp. cells and IONPs in freshwater, while the AB and vdW interactions play a more dominant role in dictating the net particle-to-cell interaction in high ionic strength media (≥100 mM NaCl), such as seawater. XDLVO predicted effective attachment between cells and surface functionalized IONPs (SF-IONPs) with an estimated secondary minimum of -3.12 kT in freshwater. This prediction is in accordance with the experimental observation in which 98.89% of cells can be magnetophoretically separated from freshwater with SF-IONPs. We have observed successful magnetophoretic separation of microalgal cells from freshwater and/or seawater for all the cases as long as XDLVO analysis predicts particle attachment. For both the conditions, no pH adjustment is required for particle-to-cell attachment.
The one-electron oxidation of a dithiolate molecule: the importance of chemical intuition.

PubMed

Bushnell, Eric A C; Burns, Thomas D; Boyd, Russell J

2014-05-14

A series of nine commonly used density functional methods were assessed to accurately predict the oxidation potential of the (C2H2S2(-2)/C2H2S2(•-)) redox couple. It was found that due to their greater tendency for charge delocalization the GGA functionals predict a structure where the radical electron is delocalized within the alkene backbone of C2H2S2(•-), whereas the hybrid functionals and the reference QCISD/cc-pVTZ predict that the radical electron remains localized on the sulfurs. However, chemical intuition suggests that the results obtained with the GGA functionals should be correct. Indeed, with the use of the geometries obtained at the HCTH/6-311++G(3df,3pd) level of theory both the QCISD and hybrid DFT methods yield a molecule with a delocalized electron. Notably, this new molecule lies at least 53 kJ mol(-1) lower in energy than the previously optimized one that had a localized radical. Using these new structures the calculated oxidation potential was found to be 2.71-2.97 V for the nine DFT functionals tested. The M06-L functional provided the best agreement with the QCISD/cc-pVTZ reference oxidation potential of 3.28 V.

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