Phase transition studies of BiMnO{sub 3}: Mean field theory approximations

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

Lakshmi Priya, K. B.; Natesan, Baskaran, E-mail: nbaski@nitt.edu

We studied the phase transition and magneto-electric coupling effect of BiMnO{sub 3} by employing mean field theory approximations. To capture the ferromagnetic and ferroelectric transitions of BiMnO{sub 3}, we construct an extended Ising model in a 2D square lattice, wherein, the magnetic (electric) interactions are described in terms of the direct interactions between the localized magnetic (electric dipole) moments of Mn ions with their nearest neighbors. To evaluate our model, we obtain magnetization, magnetic susceptibility and electric polarization using mean field approximation calculations. Our results reproduce both the ferromagnetic and the ferroelectric transitions, matching very well with the experimental reports.more » Furthermore, consistent with experimental observations, our mean field results suggest that there is indeed a coupling between the magnetic and electric ordering in BiMnO{sub 3}.« less

Collective orientational dynamics of pinned chemically-propelled nanorotors

NASA Astrophysics Data System (ADS)

Robertson, Bryan; Stark, Holger; Kapral, Raymond

2018-04-01

Collections of chemically propelled nanomotors free to move in solution can form dynamic clusters with diverse properties as a result of interactions through hydrodynamic flow and concentration fields, as well as direct intermolecular interactions between motors. Here, we study the collective rotational behavior of pinned sphere-dimer motors where direct motor-motor interactions play no role. Since the centers of mass of the motors are pinned, they cannot execute directed translational motion, but they can pump fluid and rotate; thus, the rotors remain coupled through hydrodynamic and chemical fields. Using a microscopic simulation method that accounts for coupling through both these fields, we show that different rotor configurations with a high degree of correlation exist and their forms depend on the nature of the fluid-rotor interactions. The correlations are greatly reduced or completely destroyed when the chemical interactions are removed, indicating that hydrodynamic coupling, while present, plays a lesser role in determining the collective rotor dynamics. These conclusions are supported by Langevin dynamics simulations that neglect hydrodynamics and include an approximate form of coupling through chemical fields.

Continuum Electrostatics Approaches to Calculating pKas and Ems in Proteins

PubMed Central

Gunner, MR; Baker, Nathan A.

2017-01-01

Proteins change their charge state through protonation and redox reactions as well as through binding charged ligands. The free energy of these reactions are dominated by solvation and electrostatic energies and modulated by protein conformational relaxation in response to the ionization state changes. Although computational methods for calculating these interactions can provide very powerful tools for predicting protein charge states, they include several critical approximations of which users should be aware. This chapter discusses the strengths, weaknesses, and approximations of popular computational methods for predicting charge states and understanding their underlying electrostatic interactions. The goal of this chapter is to inform users about applications and potential caveats of these methods as well as outline directions for future theoretical and computational research. PMID:27497160

Analytical solution and applications of three qubits in three coupled modes without rotating wave approximation

NASA Astrophysics Data System (ADS)

Zhang, Jian-Song; Zhang, Liu-Juan; Chen, Ai-Xi; Abdel-Aty, Mahmoud

2018-06-01

We study the dynamics of the three-qubit system interacting with multi-mode without rotating wave approximation (RWA). A physical realization of the system without direct qubits interactions with dephasing bath is proposed. It is shown that non-Markovian characters of the purity of the three qubits and the coupling strength of modes are stronger enough the RWA is no longer valid. The influences of the dephasing of qubits and interactions of modes on the dynamics of genuine multipartite entanglement and bipartite correlations of qubits are investigated. The multipartite and bipartite quantum correlations could be generated faster if we increase the coupling strength of modes and the RWA is not valid when the coupling strength is strong enough. The unitary transformations approach adopted here can be extended to other systems such as circuit or cavity quantum electrodynamic systems in the strong coupling regime.

A numerical analysis of the Born approximation for image formation modeling of differential interference contrast microscopy for human embryos

NASA Astrophysics Data System (ADS)

Trattner, Sigal; Feigin, Micha; Greenspan, Hayit; Sochen, Nir

2008-03-01

The differential interference contrast (DIC) microscope is commonly used for the visualization of live biological specimens. It enables the view of the transparent specimens while preserving their viability, being a non-invasive modality. Fertility clinics often use the DIC microscope for evaluation of human embryos quality. Towards quantification and reconstruction of the visualized specimens, an image formation model for DIC imaging is sought and the interaction of light waves with biological matter is examined. In many image formation models the light-matter interaction is expressed via the first Born approximation. The validity region of this approximation is defined in a theoretical bound which limits its use to very small specimens with low dielectric contrast. In this work the Born approximation is investigated via the Helmholtz equation, which describes the interaction between the specimen and light. A solution on the lens field is derived using the Gaussian Legendre quadrature formulation. This numerical scheme is considered both accurate and efficient and has shortened significantly the computation time as compared to integration methods that required a great amount of sampling for satisfying the Whittaker - Shannon sampling theorem. By comparing the numerical results with the theoretical values it is shown that the theoretical bound is not directly relevant to microscopic imaging and is far too limiting. The numerical exhaustive experiments show that the Born approximation is inappropriate for modeling the visualization of thick human embryos.

Oligomerization affects the kinetics and thermodynamics of the interaction of a Bowman-Birk inhibitor with proteases.

PubMed

Brand, G D; Pires, D A T; Furtado, J R; Cooper, A; Freitas, S M; Bloch, C

2017-03-15

The black-eyed pea trypsin/chymotrypsin inhibitor (BTCI) forms concentration dependent homomultimers, as previously demonstrated by Light scattering and Atomic Force Microscopy. Considering that these self-aggregates might influence their binding to cognate enzymes, we investigated the interaction of BTCI at picomolar concentrations using surface immobilized Chymotrypsin (α-CT) and Trypsin (T) by Surface Plasmon Resonance. Our results indicate that BTCI has subnanomolar affinity to both immobilized enzymes, which is approximately two orders of magnitude higher than previously reported. Moreover, we probed the influence of temperature on protein binding equilibria in order to investigate their interaction energetics. While the BTCI/T interaction concurs with the canonical entropy-driven mechanism described for BBI interactions with serine proteinases, the BTCI/α-CT interaction does not. Our measurements indicate that bimolecular BTCI/α-CT complexes form with a negative enthalpy change and a moderate entropic increase. Direct calorimetric evaluation is in accord with the van't Hoff approximation obtained by SPR. We demonstrate that as protein concentrations increase to the micromolar range, secondary endothermic events become prevalent and affect both the kinetics and thermodynamics of protein associations. Our study reinforces that BBI interactions with serine proteinases should be studied in dilute solutions to abridge often neglected secondary interactions. Copyright © 2017 Elsevier Inc. All rights reserved.

Telescopic multi-resolution augmented reality

NASA Astrophysics Data System (ADS)

Jenkins, Jeffrey; Frenchi, Christopher; Szu, Harold

2014-05-01

To ensure a self-consistent scaling approximation, the underlying microscopic fluctuation components can naturally influence macroscopic means, which may give rise to emergent observable phenomena. In this paper, we describe a consistent macroscopic (cm-scale), mesoscopic (micron-scale), and microscopic (nano-scale) approach to introduce Telescopic Multi-Resolution (TMR) into current Augmented Reality (AR) visualization technology. We propose to couple TMR-AR by introducing an energy-matter interaction engine framework that is based on known Physics, Biology, Chemistry principles. An immediate payoff of TMR-AR is a self-consistent approximation of the interaction between microscopic observables and their direct effect on the macroscopic system that is driven by real-world measurements. Such an interdisciplinary approach enables us to achieve more than multiple scale, telescopic visualization of real and virtual information but also conducting thought experiments through AR. As a result of the consistency, this framework allows us to explore a large dimensionality parameter space of measured and unmeasured regions. Towards this direction, we explore how to build learnable libraries of biological, physical, and chemical mechanisms. Fusing analytical sensors with TMR-AR libraries provides a robust framework to optimize testing and evaluation through data-driven or virtual synthetic simulations. Visualizing mechanisms of interactions requires identification of observable image features that can indicate the presence of information in multiple spatial and temporal scales of analog data. The AR methodology was originally developed to enhance pilot-training as well as `make believe' entertainment industries in a user-friendly digital environment We believe TMR-AR can someday help us conduct thought experiments scientifically, to be pedagogically visualized in a zoom-in-and-out, consistent, multi-scale approximations.

Continuum Electrostatics Approaches to Calculating pKas and Ems in Proteins.

PubMed

Gunner, M R; Baker, N A

2016-01-01

Proteins change their charge state through protonation and redox reactions as well as through binding charged ligands. The free energy of these reactions is dominated by solvation and electrostatic energies and modulated by protein conformational relaxation in response to the ionization state changes. Although computational methods for calculating these interactions can provide very powerful tools for predicting protein charge states, they include several critical approximations of which users should be aware. This chapter discusses the strengths, weaknesses, and approximations of popular computational methods for predicting charge states and understanding the underlying electrostatic interactions. The goal of this chapter is to inform users about applications and potential caveats of these methods as well as outline directions for future theoretical and computational research. © 2016 Elsevier Inc. All rights reserved.

The Effects of Videoconferencing, Class Size, and Learner Characteristics on Training Outcomes

ERIC Educational Resources Information Center

Brown, Kenneth G.; Rietz, Thomas A.; Sugrue, Brenda

2005-01-01

We examined direct and interaction effects of learners' characteristics (cognitive ability, prior knowledge, prior experience, and motivation to learn) and classroom characteristics (videoconferencing and class size) on learning from a 16-week course. A 2x2 quasi-experimental design varied the class size between large (approximately 60 students)…

Dark matter spin determination with directional direct detection experiments

NASA Astrophysics Data System (ADS)

Catena, Riccardo; Conrad, Jan; Döring, Christian; Ferella, Alfredo Davide; Krauss, Martin B.

2018-01-01

If dark matter has spin 0, only two WIMP-nucleon interaction operators can arise as leading operators from the nonrelativistic reduction of renormalizable single-mediator models for dark matter-quark interactions. Based on this crucial observation, we show that about 100 signal events at next generation directional detection experiments can be enough to enable a 2 σ rejection of the spin 0 dark matter hypothesis in favor of alternative hypotheses where the dark matter particle has spin 1 /2 or 1. In this context, directional sensitivity is crucial since anisotropy patterns in the sphere of nuclear recoil directions depend on the spin of the dark matter particle. For comparison, about 100 signal events are expected in a CF4 detector operating at a pressure of 30 torr with an exposure of approximately 26,000 cubic-meter-detector days for WIMPs of 100 GeV mass and a WIMP-fluorine scattering cross section of 0.25 pb. Comparable exposures require an array of cubic meter time projection chamber detectors.

Calculation of exchange integrals and Curie temperature for La-substituted barium hexaferrites.

PubMed

Wu, Chuanjian; Yu, Zhong; Sun, Ke; Nie, Jinlan; Guo, Rongdi; Liu, Hai; Jiang, Xiaona; Lan, Zhongwen

2016-10-31

As the macro behavior of the strength of exchange interaction, state of the art of Curie temperature T c , which is directly proportional to the exchange integrals, makes sense to the high-frequency and high-reliability microwave devices. Challenge remains as finding a quantitative way to reveal the relationship between the Curie temperature and the exchange integrals for doped barium hexaferrites. Here in this report, for La-substituted barium hexaferrites, the electronic structure has been determined by the density functional theory (DFT) and generalized gradient approximation (GGA). By means of the comparison between the ground and relative state, thirteen exchange integrals have been calculated as a function of the effective value U eff . Furthermore, based on the Heisenberg model, the molecular field approximation (MFA) and random phase approximation (RPA), which provide an upper and lower bound of the Curie temperature T c , have been adopted to deduce the Curie temperature T c . In addition, the Curie temperature T c derived from the MFA are coincided well with the experimental data. Finally, the strength of superexchange interaction mainly depends on 2b-4f 1 , 4f 2 -12k, 2a-4f 1 , and 4f 1 -12k interactions.

Revised direct radiocarbon dating of the Vindija G1 Upper Paleolithic Neandertals.

PubMed

Higham, Tom; Ramsey, Christopher Bronk; Karavanić, Ivor; Smith, Fred H; Trinkaus, Erik

2006-01-17

The 1998/1999 direct dating of two Neandertal specimens from level G(1) of Vindija Cave in Croatia to approximately 28,000 and approximately 29,000 radiocarbon ((14)C) years ago has led to interpretations concerning the late survival of Neandertals in south-central Europe, patterns of interaction between Neandertals and in-dispersing early modern humans in Europe, and complex biocultural scenarios for the earlier phases of the Upper Paleolithic. Given improvements, particularly in sample pretreatment techniques for bone radiocarbon samples, especially ultrafiltration of collagen samples, these Vindija G(1) Neandertal fossils are redated to approximately 32,000-33,000 (14)C years ago and possibly earlier. These results and the recent redating of a number of purportedly old modern human skeletal remains in Europe to younger time periods highlight the importance of fine chronological control when studying this biocultural time period and the tenuous nature of monolithic scenarios for the establishment of modern humans and earlier phases of the Upper Paleolithic in Europe.

Characteristics of Kinematics of a Coronal Mass Ejection During the 2010 August 1 CME-CME Interaction Event

NASA Technical Reports Server (NTRS)

Temmer, Manuela; Vrsnak, Bojan; Rollett, Tanja; Bein, Bianca; de Koning, Curt A.; Liu, Ying; Bosman, Eckhard; Davies, Jackie A.; Mostl, Christian; Zic, Tomislav;

The role of electronic dopant on full band in-plane RKKY coupling in armchair graphene nanoribbons-magnetic impurity system

NASA Astrophysics Data System (ADS)

Hoi, Bui Dinh; Yarmohammadi, Mohsen

2018-05-01

Motivated by the growing interest in solving the obstacles of spintronics applications, we study the Ruderman-Kittel-Kasuya-Yosida (RKKY) effective pairwise interaction between magnetic impurities interacting through the π -electrons embedded in both electronically doped-semiconducting and metallic armchair graphene nanoribbons. In terms of the Green's function formalism, treated in a tight-binding approximation with hopping beyond Dirac cone approximation, the RKKY coupling is an attraction or a repulsion depending on the magnetic impurities distances. Our results show that the RKKY coupling in semiconducting nanoribbons is much more affected by doping than metallic ones. Furthermore, we found that the RKKY coupling increases with ribbon width, while there exist some critical electronic concentrations in RKKY interaction oscillations. On the other hand, we find an unusual incoming wave-vector direction for electrons which describes more clearly the ferro- and antiferromagnetic spin configurations in such system. Also, the RKKY coupling at low and high-temperature regions has been addressed for both ferro- and antiferromagnetic spin arrangements.

Pressure-Induced Phase Transitions in the Cd-Yb Periodic Approximant to a Quasicrystal

NASA Astrophysics Data System (ADS)

Watanuki, Tetsu; Machida, Akihiko; Ikeda, Tomohiro; Aoki, Katsutoshi; Kaneko, Hiroshi; Shobu, Takahisa; Sato, Taku J.; Tsai, An Pang

2006-03-01

The phase study of a Cd-Yb 1/1 approximant crystal over a wide pressure and temperature range is crucial for the comparison study between periodic and quasiperiodic crystals. The Cd4 tetrahedra, the most inner part of the atomic clusters, exhibited various structural ordering in the orientation sensitive to pressure and temperature. Five ordered phases appeared in a P-T span up to 5.2 GPa and down to 10 K. The propagation direction of ordering alternated from [110] to ⟨111⟩ at about 1.0 GPa and again to [110] at 3.5 4.3 GPa. The primarily ordered phases that appeared by cooling to 210 250 K between 1.0 5.2 GPa further transformed to finely ordered ones at 120 155 K. Besides the original short-range type interaction, a long-range type interaction was likely developed under pressure to lead to the primary ordering of Cd4 tetrahedra. Coexistence of these interactions is responsible for the complicated phase behavior.

Quasi-static analysis of elastic behavior for some systems having higher fracture densities.

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

Berryman, J.G.; Aydin, A.

2009-10-15

Elastic behavior of geomechanical systems with interacting (but not intersecting) fractures is treated using generalizations of the Backus and the Schoenberg-Muir methods for analyzing layered systems whose layers are intrinsically anisotropic due to locally aligned fractures. By permitting the axis of symmetry of the locally anisotropic compliance matrix for individual layers to differ from that of the layering direction, we derive analytical formulas for interacting fractured regions with arbitrary orientations to each other. This procedure provides a systematic tool for studying how contiguous, but not yet intersecting, fractured domains interact, and provides a direct (though approximate) means of predicting whenmore » and how such interactions lead to more dramatic weakening effects and ultimately to failure of these complicated systems. The method permits decomposition of the system elastic behavior into specific eigenmodes that can all be analyzed, and provides a better understanding about which of these specific modes are expected to be most important to the evolving failure process.« less

Small-scale anisotropic intermittency in magnetohydrodynamic turbulence at low magnetic Reynolds numbers.

PubMed

Okamoto, Naoya; Yoshimatsu, Katsunori; Schneider, Kai; Farge, Marie

2014-03-01

Small-scale anisotropic intermittency is examined in three-dimensional incompressible magnetohydrodynamic turbulence subjected to a uniformly imposed magnetic field. Orthonormal wavelet analyses are applied to direct numerical simulation data at moderate Reynolds number and for different interaction parameters. The magnetic Reynolds number is sufficiently low such that the quasistatic approximation can be applied. Scale-dependent statistical measures are introduced to quantify anisotropy in terms of the flow components, either parallel or perpendicular to the imposed magnetic field, and in terms of the different directions. Moreover, the flow intermittency is shown to increase with increasing values of the interaction parameter, which is reflected in strongly growing flatness values when the scale decreases. The scale-dependent anisotropy of energy is found to be independent of scale for all considered values of the interaction parameter. The strength of the imposed magnetic field does amplify the anisotropy of the flow.

Impurity-induced anisotropic semiconductor-semimetal transition in monolayer biased black phosphorus

NASA Astrophysics Data System (ADS)

Bui, D. H.; Yarmohammadi, Mohsen

2018-07-01

Taking into account the electron-impurity interaction within the continuum approximation of tight-binding model, the Born approximation, and the Green's function method, the main features of anisotropic electronic phase transition are investigated in monolayer biased black phosphorus (BP). To this end, we concentrated on the disordered electronic density of states (DOS), which gives useful information for electro-optical devices. Increasing the impurity concentration in both unbiased and biased impurity-infected single-layer BP, in addition to the decrease of the band gap, independent of the direction, leads to the midgap states and an extra Van Hove singularity inside and outside of the band gap, respectively. Furthermore, strong impurity scattering potentials lead to a semiconductor-semimetal transition and one more Van Hove singularity in x-direction of unbiased BP and surprisingly, this transition does not occur in biased BP. We found that there is no phase transition in y-direction. Since real applications require structures with modulated band gaps, we have studied the influence of different bias voltages on the disordered DOS in both directions, resulting in the increase of the band gap.

Effective Mass Calculations for Two-dimensional Gas of Dipolar Fermions

NASA Astrophysics Data System (ADS)

Seydi, I.; Abedinpour, S. H.; Tanatar, B.

2017-06-01

We consider a two-dimensional system of ultracold dipolar fermions with dipole moments aligned in the perpendicular direction. We use the static structure factor information from Fermi-Hypernetted-Chain calculations to obtain the effective many-body dipole-dipole interaction and calculate the many-body effective mass of the system within the G0W approximation to the self-energy. A large cancellation between different contributions to the self-energy results in a weak dependence of the effective mass on the interaction strength over a large range of coupling constants.

Investigation of North Pond crustal fluids by poised potential methods

NASA Astrophysics Data System (ADS)

Jones, R. M.; Orcutt, B.

2017-12-01

Microbes are present in the deep subsurface but their rates of activity, potential metabolisms and roles in the environment are still largely unknown. The marine deep crustal subsurface accounts for approximately 2.3x1018 m2 of the earth's volume, making this environment potentially significant to earth processes despite low productivity inherent in resource limited conditions. This has implications for geochemical cycling and exploring limits of life, linking to the `follow the energy' approach for defining habitability on earth and further afield. Most resources for life in the marine deep crust originate from rock. One subset of lithotrophic interactions involves direct transfer between electron acceptors and donors embedded in minerals and microbes. In this investigation, poised potential methods such as chronoamperometry were used to investigate mineral-microbe electron transfer interactions in the context of North Pond, a Mid-Atlantic ridge site representative of cool, sediment-covered basalts that make up the majority of the deep marine subsurface. Electrodes were poised at potentials corresponding approximately to particular lithotrophic oxidation reactions to enrich for sub-sections of North Pond deep subsurface fluid communities that were associated with direct electron transfer at these potentials.

The binary protein-protein interaction landscape of Escherichia coli

PubMed Central

Rajagopala, Seesandra V.; Vlasblom, James; Arnold, Roland; Franca-Koh, Jonathan; Pakala, Suman B.; Phanse, Sadhna; Ceol, Arnaud; Häuser, Roman; Siszler, Gabriella; Wuchty, Stefan; Emili, Andrew; Babu, Mohan; Aloy, Patrick; Pieper, Rembert; Uetz, Peter

2014-01-01

Efforts to map the Escherichia coli interactome have identified several hundred macromolecular complexes, but direct binary protein-protein interactions (PPIs) have not been surveyed on a large scale. Here we performed yeast two-hybrid screens of 3,305 baits against 3,606 preys (~70% of the E. coli proteome) in duplicate to generate a map of 2,234 interactions, approximately doubling the number of known binary PPIs in E. coli. Integration of binary PPIs and genetic interactions revealed functional dependencies among components involved in cellular processes, including envelope integrity, flagellum assembly and protein quality control. Many of the binary interactions that could be mapped within multi-protein complexes were informative regarding internal topology and indicated that interactions within complexes are significantly more conserved than those interactions connecting different complexes. This resource will be useful for inferring bacterial gene function and provides a draft reference of the basic physical wiring network of this evolutionarily significant model microbe. PMID:24561554

Mammalian poly(A)-binding protein is a eukaryotic translation initiation factor, which acts via multiple mechanisms.

PubMed

Kahvejian, Avak; Svitkin, Yuri V; Sukarieh, Rami; M'Boutchou, Marie-Noël; Sonenberg, Nahum

2005-01-01

Translation initiation is a multistep process involving several canonical translation factors, which assemble at the 5'-end of the mRNA to promote the recruitment of the ribosome. Although the 3' poly(A) tail of eukaryotic mRNAs and its major bound protein, the poly(A)-binding protein (PABP), have been studied extensively, their mechanism of action in translation is not well understood and is confounded by differences between in vivo and in vitro systems. Here, we provide direct evidence for the involvement of PABP in key steps of the translation initiation pathway. Using a new technique to deplete PABP from mammalian cell extracts, we show that extracts lacking PABP exhibit dramatically reduced rates of translation, reduced efficiency of 48S and 80S ribosome initiation complex formation, and impaired interaction of eIF4E with the mRNA cap structure. Supplementing PABP-depleted extracts with wild-type PABP completely rectified these deficiencies, whereas a mutant of PABP, M161A, which is incapable of interacting with eIF4G, failed to restore translation. In addition, a stronger inhibition (approximately twofold) of 80S as compared to 48S ribosome complex formation (approximately 65% vs. approximately 35%, respectively) by PABP depletion suggests that PABP plays a direct role in 60S subunit joining. PABP can thus be considered a canonical translation initiation factor, integral to initiation complex formation at the 5'-end of mRNA.

The standard mean-field treatment of inter-particle attraction in classical DFT is better than one might expect

NASA Astrophysics Data System (ADS)

Archer, Andrew J.; Chacko, Blesson; Evans, Robert

2017-07-01

In classical density functional theory (DFT), the part of the Helmholtz free energy functional arising from attractive inter-particle interactions is often treated in a mean-field or van der Waals approximation. On the face of it, this is a somewhat crude treatment as the resulting functional generates the simple random phase approximation (RPA) for the bulk fluid pair direct correlation function. We explain why using standard mean-field DFT to describe inhomogeneous fluid structure and thermodynamics is more accurate than one might expect based on this observation. By considering the pair correlation function g(x) and structure factor S(k) of a one-dimensional model fluid, for which exact results are available, we show that the mean-field DFT, employed within the test-particle procedure, yields results much superior to those from the RPA closure of the bulk Ornstein-Zernike equation. We argue that one should not judge the quality of a DFT based solely on the approximation it generates for the bulk pair direct correlation function.

Genetic parameters for direct and maternal calving ease in Walloon dairy cattle based on linear and threshold models.

PubMed

Vanderick, S; Troch, T; Gillon, A; Glorieux, G; Gengler, N

2014-12-01

Calving ease scores from Holstein dairy cattle in the Walloon Region of Belgium were analysed using univariate linear and threshold animal models. Variance components and derived genetic parameters were estimated from a data set including 33,155 calving records. Included in the models were season, herd and sex of calf × age of dam classes × group of calvings interaction as fixed effects, herd × year of calving, maternal permanent environment and animal direct and maternal additive genetic as random effects. Models were fitted with the genetic correlation between direct and maternal additive genetic effects either estimated or constrained to zero. Direct heritability for calving ease was approximately 8% with linear models and approximately 12% with threshold models. Maternal heritabilities were approximately 2 and 4%, respectively. Genetic correlation between direct and maternal additive effects was found to be not significantly different from zero. Models were compared in terms of goodness of fit and predictive ability. Criteria of comparison such as mean squared error, correlation between observed and predicted calving ease scores as well as between estimated breeding values were estimated from 85,118 calving records. The results provided few differences between linear and threshold models even though correlations between estimated breeding values from subsets of data for sires with progeny from linear model were 17 and 23% greater for direct and maternal genetic effects, respectively, than from threshold model. For the purpose of genetic evaluation for calving ease in Walloon Holstein dairy cattle, the linear animal model without covariance between direct and maternal additive effects was found to be the best choice. © 2014 Blackwell Verlag GmbH.

Understanding the role of spin-motion coupling in Ramsey spectroscopy

NASA Astrophysics Data System (ADS)

Koller, Andrew; Beverland, Michael; Mundinger, Joshua; Gorshkov, Alexey; Rey, Ana Maria

2014-05-01

Ramsey spectroscopy has become a powerful technique for probing non-equilibrium dynamics of internal (pseudospin) degrees of freedom of interacting systems. In many theoretical treatments, the key to understanding the dynamics has been to assume the external (motional) degrees of freedom are decoupled from the pseudospin degrees of freedom. Determining the validity of this approximation - known as the spin model approximation - has not been addressed in detail. We shed light in this direction by calculating Ramsey dynamics exactly for two interacting spin-1/2 particles in a harmonic trap. We find that in 1D the spin model assumption works well over a wide range of experimentally-relevant conditions, but can fail at time scales longer than those set by the mean interaction energy. Surprisingly, in 2D a modified version of the spin model is exact to first order in the interaction strength. This analysis is important for a correct interpretation of Ramsey spectroscopy and has broad applications ranging from precision measurements to quantum information and to fundamental probes of many-body systems. Supported by NSF, ARO-DARPA-OLE, AFOSR, NIST, the Lee A. DuBridge and Gordon and Betty Moore Foundations, and the NDSEG program.

A More Accurate and Efficient Technique Developed for Using Computational Methods to Obtain Helical Traveling-Wave Tube Interaction Impedance

NASA Technical Reports Server (NTRS)

Kory, Carol L.

1999-01-01

The phenomenal growth of commercial communications has created a great demand for traveling-wave tube (TWT) amplifiers. Although the helix slow-wave circuit remains the mainstay of the TWT industry because of its exceptionally wide bandwidth, until recently it has been impossible to accurately analyze a helical TWT using its exact dimensions because of the complexity of its geometrical structure. For the first time, an accurate three-dimensional helical model was developed that allows accurate prediction of TWT cold-test characteristics including operating frequency, interaction impedance, and attenuation. This computational model, which was developed at the NASA Lewis Research Center, allows TWT designers to obtain a more accurate value of interaction impedance than is possible using experimental methods. Obtaining helical slow-wave circuit interaction impedance is an important part of the design process for a TWT because it is related to the gain and efficiency of the tube. This impedance cannot be measured directly; thus, conventional methods involve perturbing a helical circuit with a cylindrical dielectric rod placed on the central axis of the circuit and obtaining the difference in resonant frequency between the perturbed and unperturbed circuits. A mathematical relationship has been derived between this frequency difference and the interaction impedance (ref. 1). However, because of the complex configuration of the helical circuit, deriving this relationship involves several approximations. In addition, this experimental procedure is time-consuming and expensive, but until recently it was widely accepted as the most accurate means of determining interaction impedance. The advent of an accurate three-dimensional helical circuit model (ref. 2) made it possible for Lewis researchers to fully investigate standard approximations made in deriving the relationship between measured perturbation data and interaction impedance. The most prominent approximations made in the analysis were addressed and fully investigated for their accuracy by using the three-dimensional electromagnetic simulation code MAFIA (Solution of Maxwell's Equations by the Finite Integration Algorithm) (refs. 3 and 4). We found that several approximations introduced significant error (ref. 5).

Consider a non-spherical elephant: computational fluid dynamics simulations of heat transfer coefficients and drag verified using wind tunnel experiments.

PubMed

Dudley, Peter N; Bonazza, Riccardo; Porter, Warren P

2013-07-01

Animal momentum and heat transfer analysis has historically used direct animal measurements or approximations to calculate drag and heat transfer coefficients. Research can now use modern 3D rendering and computational fluid dynamics software to simulate animal-fluid interactions. Key questions are the level of agreement between simulations and experiments and how superior they are to classical approximations. In this paper we compared experimental and simulated heat transfer and drag calculations on a scale model solid aluminum African elephant casting. We found good agreement between experimental and simulated data and large differences from classical approximations. We used the simulation results to calculate coefficients for heat transfer and drag of the elephant geometry. Copyright © 2013 Wiley Periodicals, Inc.

Vorticity dynamics after the shock–turbulence interaction

DOE PAGES

Livescu, Daniel; Ryu, Jaiyoung

2015-07-23

In this article, the interaction of a shock wave with quasi-vortical isotropic turbulence (IT) represents a basic problem for studying some of the phenomena associated with high speed flows, such as hypersonic flight, supersonic combustion and Inertial Confinement Fusion (ICF). In general, in practical applications, the shock width is much smaller than the turbulence scales and the upstream turbulent Mach number is modest. In this case, recent high resolution shock-resolved Direct Numerical Simulations (DNS) (Ryu and Livescu, J Fluid Mech 756, R1, 2014) show that the interaction can be described by the Linear Interaction Approximation (LIA). Using LIA to alleviatemore » the need to resolve the shock, DNS post-shock data can be generated at much higher Reynolds numbers than previously possible. Here, such results with Taylor Reynolds number approximately 180 are used to investigate the changes in the vortical structure as a function of the shock Mach number, M s, up to M s = 10. It is shown that, as M s increases, the shock interaction induces a tendency towards a local axisymmetric state perpendicular to the shock front, which has a profound influence on the vortex-stretching mechanism and divergence of the Lamb vector and, ultimately, on the flow evolution away from the shock.« less

Final-state interactions in semi-inclusive deep inelastic scattering off the Deuteron

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

Wim Cosyn, Misak Sargsian

2011-07-01

Semi-inclusive deep inelastic scattering off the Deuteron with production of a slow nucleon in recoil kinematics is studied in the virtual nucleon approximation, in which the final state interaction (FSI) is calculated within general eikonal approximation. The cross section is derived in a factorized approach, with a factor describing the virtual photon interaction with the off-shell nucleon and a distorted spectral function accounting for the final-state interactions. One of the main goals of the study is to understand how much the general features of the diffractive high energy soft rescattering accounts for the observed features of FSI in deep inelasticmore » scattering (DIS). Comparison with the Jefferson Lab data shows good agreement in the covered range of kinematics. Most importantly, our calculation correctly reproduces the rise of the FSI in the forward direction of the slow nucleon production angle. By fitting our calculation to the data we extracted the W and Q{sup 2} dependences of the total cross section and slope factor of the interaction of DIS products, X, off the spectator nucleon. This analysis shows the XN scattering cross section rising with W and decreasing with an increase of Q{sup 2}. Finally, our analysis points at a largely suppressed off-shell part of the rescattering amplitude.« less

Relaxation approximation in the theory of shear turbulence

NASA Technical Reports Server (NTRS)

Rubinstein, Robert

1995-01-01

Leslie's perturbative treatment of the direct interaction approximation for shear turbulence (Modern Developments in the Theory of Turbulence, 1972) is applied to derive a time dependent model for the Reynolds stresses. The stresses are decomposed into tensor components which satisfy coupled linear relaxation equations; the present theory therefore differs from phenomenological Reynolds stress closures in which the time derivatives of the stresses are expressed in terms of the stresses themselves. The theory accounts naturally for the time dependence of the Reynolds normal stress ratios in simple shear flow. The distortion of wavenumber space by the mean shear plays a crucial role in this theory.

"And so They Ordered Me to Kill a Person": Conceptualizing the Impacts of Child Soldiering on the Development of Moral Agency

ERIC Educational Resources Information Center

Wainryb, Cecilia

2011-01-01

Approximately 300,000 child soldiers serve in various armed groups around the world, and become directly implicated in the perpetration of kidnappings, killings, and torture. Considering that children construct moral concepts and a sense of themselves as moral beings in the context of their everyday interactions with others, the concern with how…

New porphyrins bearing positively charged peripheral groups linked by a sulfonamide group to meso-tetraphenylporphyrin: interactions with calf thymus DNA.

PubMed

Manono, Janet; Marzilli, Patricia A; Marzilli, Luigi G

2009-07-06

New water-soluble cationic meso-tetraarylporphyrins (TArP, Ar = 4-C(6)H(4)) and some metal derivatives have been synthesized and characterized. One main goal was to assess if N-methylpyridinium (N-Mepy) groups must be directly attached to the porphyrin core for intercalative binding of porphyrins to DNA. The new porphyrins have the general formula, [T(R(2)R(1)NSO(2)Ar)P]X(4/8) (R(1) = CH(3) or H and R(2) = N-Mepy-n-CH(2) with n = 2, 3, or 4; or R(1) = R(2) = Et(3)NCH(2)CH(2)). Interactions of selected porphyrins and metalloporphyrins (Cu(II), Zn(II)) with calf thymus DNA were investigated by visible circular dichroism (CD), absorption, and fluorescence spectroscopies. The DNA-induced changes in the porphyrin Soret region (a positive induced CD feature and, at high DNA concentration, increases in the Soret band and fluorescence intensities) indicate that the new porphyrins interact with DNA in an outside, non-self-stacking binding mode. Several new metalloporphyrins did not increase DNA solution viscosity and thus do not intercalate, confirming the conclusion drawn from spectroscopic studies. Porphyrins known to intercalate typically bear two or more N-Mepy groups directly attached to the porphyrin ring, such as the prototypical meso-tetra(N-Mepy)porphyrin tetracation (TMpyP(4)). The distances between the nitrogens of the N-Mepy group are estimated to be approximately 11 A (cis) and 16 A (trans) for the relatively rigid TMpyP(4). For the new flexible porphyrin, [T(N-Mepy-4-CH(2)(CH(3))NSO(2)Ar)P]Cl(4), the distances between the nitrogens are estimated to be able to span the range from approximately 9 to approximately 25 A. Thus, the N-Mepy groups in the new porphyrins can adopt the same spacing as in known intercalators such as TMpyP(4). The absence of intercalation by the new porphyrins indicates that the propensity for the N-Mepy group to facilitate DNA intercalation of cationic porphyrins requires direct attachment of N-Mepy groups to the porphyrin core.

Measurement of SQUID noise levels for SuperCDMS SNOLAB detectors - Final Paper

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

Lee, Maxwell

SuperCDMS SNOLAB is a second generation direct dark matter search. In the SuperCDMS SNOLAB experiment, detectors are able to pick up from signals from dark matter nuclear recoil interactions which occur inside the bulk of the detectors. These interactions produce both phonon and charge signals. HEMTs read out charge signals whereas TES are used to detect phonon signals which are then read out by SQUID amplifiers. SQUID amplifiers must add negligible noise to the TES intrinsic noise which has been previously measured and is approximately 50pA/√Hz down to 100Hz for ease of signal distinguishability in dark matter nuclear interactions. Themore » intrinsic noise level of the SQUID was tested in the SLAC 300mK fridge and determined to provide adequately low levels of noise with a floor of approximately 3pA/√Hz. Furthermore, a 10x amplifier was tested for addition of extraneous noise. This noise was investigated with and without this amplifier, and it was found that it did not add a significant amount of noise to the intrinsic SQUID noise.« less

SAR by Oxime-Containing Peptide Libraries: Application to Tsg101 Ligand Optimization

PubMed Central

Liu, Fa; Stephen, Andrew G.; Waheed, Abdul A.; Aman, M. Javad; Freed, Eric O.; Fisher, Robert J.; Burke, Terrence R.

2008-01-01

HIV-1 viral assembly requires a direct interaction between a Pro-Thr-Ala-Pro (“PTAP”) motif in the viral protein Gag-p6 and the cellular endosomal sorting factor Tsg101. In an effort to develop competitive inhibitors of this interaction, an SAR study was conducted based on the application of post solid-phase oxime formation involving the sequential insertion of aminooxy-containing residues within a nonamer parent peptide followed by reaction with libraries of aldehydes. Approximately 15–20-fold enhancement in binding affinity was achieved by this approach. PMID:18655064

Computation of the shock-wave boundary layer interaction with flow separation

NASA Technical Reports Server (NTRS)

Ardonceau, P.; Alziary, T.; Aymer, D.

1980-01-01

The boundary layer concept is used to describe the flow near the wall. The external flow is approximated by a pressure displacement relationship (tangent wedge in linearized supersonic flow). The boundary layer equations are solved in finite difference form and the question of the presence and unicity of the solution is considered for the direct problem (assumed pressure) or converse problem (assumed displacement thickness, friction ratio). The coupling algorithm presented implicitly processes the downstream boundary condition necessary to correctly define the interacting boundary layer problem. The algorithm uses a Newton linearization technique to provide a fast convergence.

Roles of cations, electronegativity difference, and anionic interlayer interactions in the metallic versus nonmetallic character of Zintl phases related to arsenic.

PubMed

Alemany, Pere; Llunell, Miquel; Canadell, Enric

2008-10-01

A first-principles Density Functional Theory study of several layered solids structurally related to rhombohedral arsenic has been carried out. The electronic structures of rhombohedral arsenic, CaSi(2), CaAl(2)Si(2), KSnSb, and SrSn(2)As(2) are discussed in detail, emphasizing on the origins of their metallic or nonmetallic behaviours. It is found that all of these systems are metallic except KSnSb. Electronegativity differences between the elements in the anionic sublattice and/or direct interlayer interactions play the main role in controlling the conductivity behavior. CaSi(2) exhibits a peculiar feature since the cation directly influences the conductivity but is not essential for its appearance. Cation-anion interactions are shown to have an important covalent contribution, but despite this fact and the metallic character found for most of these phases, the Zintl approach still provides a valid approximation to their electronic structure. (c) 2008 Wiley Periodicals, Inc.

On the Scattering of Sound by a Rectilinear Vortex

NASA Astrophysics Data System (ADS)

HOWE, M. S.

1999-11-01

A re-examination is made of the two-dimensional interaction of a plane, time-harmonic sound wave with a rectilinear vortex of small core diameter at low Mach number. Sakov [1] and Ford and Smith [2] have independently resolved the “infinite forward scatter” paradox encountered in earlier applications of the Born approximation to this problem. The first order scattered field (Born approximation) has nulls in the forward and back scattering directions, but the interaction of the wave with non-acoustically compact components of the vortex velocity field causes wavefront distortion, and the phase of the incident wave to undergo a significant variation across a parabolic domain whose axis extends along the direction of forward scatter from the vortex core. The transmitted wave crests of the incident wave become concave and convex, respectively, on opposite sides of the axis of the parabola, and focusing and defocusing of wave energy produces corresponding increases and decreases in wave amplitude. Wave front curvature decreases with increasing distance from the vortex core, with the result that the wave amplitude and phase are asymptotically equal to the respective values they would have attained in the absence of the vortex. The transverse acoustic dipole generated by translational motion of the vortex at the incident wave acoustic particle velocity, and the interaction of the incident wave with acoustically compact components of the vortex velocity field, are responsible for a system of cylindrically spreading, scattered waves outside the parabolic domain.

Investigation of the radiation background in the interaction region of the medium-energy electron relativisitic heavy ion collider (MeRHIC)

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

Beebe-Wang,J.

There are three main sources of the radiation background in MeRHIC: forward synchrotron radiation generated upstream of the detector, the direct backward radiation caused by the photons hitting beampipe downstream of the detector, and the indirect secondary radiation caused by hard photons hitting vacuum systems, masks, collimators, absorbers or any other elements in the interaction region. In this paper, we first calculate the primary radiation distribution by employing electromagnetic theory. Then we obtain the direct backward scattering rate by applying the kinematic Born approximation deduced from scattering dynamics. The diffuse scattering cross section is calculated as a function of themore » surface properties of the MeRHIC vacuum system. Finally, the dominating physical processes and minimization of indirect secondary radiation is presented and discussed.« less

Energy Deposition Processes in Titan's Upper Atmosphere

NASA Technical Reports Server (NTRS)

Sittler, Edward C., Jr.; Bertucci, Cesar; Coates, Andrew; Cravens, Tom; Dandouras, Iannis; Shemansky, Don

2008-01-01

Most of Titan's atmospheric organic and nitrogen chemistry, aerosol formation, and atmospheric loss are driven from external energy sources such as Solar UV, Saturn's magnetosphere, solar wind and galactic cosmic rays. The Solar UV tends to dominate the energy input at lower altitudes of approximately 1100 km but which can extend down to approximately 400 km, while the plasma interaction from Saturn's magnetosphere, Saturn's magnetosheath or solar wind are more important at higher altitudes of approximately 1400 km, but the heavy ion plasma [O(+)] of approximately 2 keV and energetic ions [H(+)] of approximately 30 keV or higher from Saturn's magnetosphere can penetrate below 950km. Cosmic rays with energies of greater than 1 GeV can penetrate much deeper into Titan's atmosphere with most of its energy deposited at approximately 100 km altitude. The haze layer tends to dominate between 100 km and 300 km. The induced magnetic field from Titan's interaction with the external plasma can be very complex and will tend to channel the flow of energy into Titan's upper atmosphere. Cassini observations combined with advanced hybrid simulations of the plasma interaction with Titan's upper atmosphere show significant changes in the character of the interaction with Saturn local time at Titan's orbit where the magnetosphere displays large and systematic changes with local time. The external solar wind can also drive sub-storms within the magnetosphere which can then modify the magnetospheric interaction with Titan. Another important parameter is solar zenith angle (SZA) with respect to the co-rotation direction of the magnetospheric flow. Titan's interaction can contribute to atmospheric loss via pickup ion loss, scavenging of Titan's ionospheric plasma, loss of ionospheric plasma down its induced magnetotail via an ionospheric wind, and non-thermal loss of the atmosphere via heating and sputtering induced by the bombardment of magnetospheric keV ions and electrons. This energy input evidently drives the large positive and negative ions observed below approximately 1100 km altitude with ion masses exceeding 10,000 daltons. We refer to these ions as seed particles for the aerosols observed below 300 km altitude. These seed particles can be formed, for example, from the polymerization of acetylene (C2H2) and benzene (C6H6) molecules in Titan's upper atmosphere to form polycyclic aromatic hydrocarbons (PAH) and/or fullerenes (C60). In the case of fullerenes, which are hollow spherical carbon shells, magnetospheric keV [O(+)] ions can become trapped inside the fullerenes and eventually find themselves inside the aerosols as free oxygen. The aerosols are then expected to fall to Titan's surface as polymerized hydrocarbons with trapped free oxygen where unknown surface chemistry can take place.

Environment and genotype effects on the content of dietary fiber and its components in wheat in the HEALTHGRAIN diversity screen.

PubMed

Gebruers, Kurt; Dornez, Emmie; Bedõ, Zoltan; Rakszegi, Mariann; Frás, Anna; Boros, Danuta; Courtin, Christophe M; Delcour, Jan A

2010-09-08

Within the HEALTHGRAIN diversity screen, the variability of the contents of dietary fiber (DF) and components thereof was studied in wheat. Furthermore, the contribution of genotype and environment to this variability was estimated. The levels of total DF (TDF), total nonstarch polysaccharide (TOTNSP), water-extractable nonstarch polysaccharide (WENSP), total arabinoxylan (TOTAX), lignin, and beta-glucan in whole meal, flour, and/or bran varied approximately 1.8-fold. The highest variability was observed for the water-extractable arabinoxylan (WEAX) level in flour and bran (approximately 3.7-fold). Genotype and environment contributed to a similar extent to the variability in TDF, TOTNSP, and TOTAX content in wheat. The observed relatively high impact of genotype-environment interaction suggests that the levels of these constituents are weak breeding parameters. The WENSP level is a more stable parameter as the effect of the interaction term was much less than the impact of genotype. For TOTAX and WEAX in flour, WEAX in bran, beta-glucan in whole meal, and extract viscosity, wheat genotype determined approximately 50% or higher of the variation observed, whereas the impact of the genotype-environment interaction was relatively low. These findings suggest that the health-related and technological functionality of wheat can be directed to a certain extent by selection of appropriate wheat varieties.

Fast and Accurate Multivariate Gaussian Modeling of Protein Families: Predicting Residue Contacts and Protein-Interaction Partners

PubMed Central

Feinauer, Christoph; Procaccini, Andrea; Zecchina, Riccardo; Weigt, Martin; Pagnani, Andrea

2014-01-01

In the course of evolution, proteins show a remarkable conservation of their three-dimensional structure and their biological function, leading to strong evolutionary constraints on the sequence variability between homologous proteins. Our method aims at extracting such constraints from rapidly accumulating sequence data, and thereby at inferring protein structure and function from sequence information alone. Recently, global statistical inference methods (e.g. direct-coupling analysis, sparse inverse covariance estimation) have achieved a breakthrough towards this aim, and their predictions have been successfully implemented into tertiary and quaternary protein structure prediction methods. However, due to the discrete nature of the underlying variable (amino-acids), exact inference requires exponential time in the protein length, and efficient approximations are needed for practical applicability. Here we propose a very efficient multivariate Gaussian modeling approach as a variant of direct-coupling analysis: the discrete amino-acid variables are replaced by continuous Gaussian random variables. The resulting statistical inference problem is efficiently and exactly solvable. We show that the quality of inference is comparable or superior to the one achieved by mean-field approximations to inference with discrete variables, as done by direct-coupling analysis. This is true for (i) the prediction of residue-residue contacts in proteins, and (ii) the identification of protein-protein interaction partner in bacterial signal transduction. An implementation of our multivariate Gaussian approach is available at the website http://areeweb.polito.it/ricerca/cmp/code. PMID:24663061

On-tissue Direct Monitoring of Global Hydrogen/Deuterium Exchange by MALDI Mass Spectrometry: Tissue Deuterium Exchange Mass Spectrometry (TDXMS)*

PubMed Central

Quanico, Jusal; Franck, Julien

2016-01-01

Hydrogen/deuterium exchange mass spectrometric (H/DXMS) methods for protein structural analysis are conventionally performed in solution. We present Tissue Deuterium Exchange Mass Spectrometry (TDXMS), a method to directly monitor deuterium uptake on tissue, as a means to better approximate the deuterium exchange behavior of proteins in their native microenvironment. Using this method, a difference in deuterium uptake behavior was observed when the same proteins were monitored in solution and on tissue. The higher maximum deuterium uptake at equilibrium for all proteins analyzed in solution suggests a more open conformation in the absence of interacting partners normally observed on tissue. We also demonstrate a difference in the deuterium uptake behavior of a few proteins across different morphological regions of the same tissue section. Modifications of the total number of hydrogens exchanged, as well as the kinetics of exchange, were both observed. These results provide information on the implication of protein interactions with partners as well as on the conformational changes related to these interactions, and illustrate the importance of examining protein deuterium exchange behavior in the presence of its specific microenvironment directly at the level of tissues. PMID:27512083

Recognition of the Xenopus ribosomal core promoter by the transcription factor xUBF involves multiple HMG box domains and leads to an xUBF interdomain interaction.

PubMed

Leblanc, B; Read, C; Moss, T

1993-02-01

The interaction of the ribosomal transcription factor xUBF with the RNA polymerase I core promoter of Xenopus laevis has been studied both at the DNA and protein levels. It is shown that a single xUBF-DNA complex forms over the 40S initiation site (+1) and involves at least the DNA sequences between -20 and +60 bp. DNA sequences upstream of +10 and downstream of +18 are each sufficient to direct complex formation independently. HMG box 1 of xUBF independently recognizes the sequences -20 to -1 and +1 to +22 and the addition of the N-terminal dimerization domain to HMG box 1 stabilizes its interaction with these sequences approximately 10-fold. HMG boxes 2/3 interact with the DNA downstream of +22 and can independently position xUBF across the initiation site. The C-terminal segment of xUBF, HMG boxes 4, 5 or the acidic domain, directly or indirectly interact with HMG box 1, making the core promoter sequences between -11 and -15 hypersensitive to DNase. This interaction also requires the DNA sequences between +17 and +32, i.e. the HMG box 2/3 binding site. The data suggest extensive folding of the core promoter within the xUBF complex.

Asymptotic form for the cross section for the Coulomb interacting rearrangement collisions.

NASA Technical Reports Server (NTRS)

Omidvar, K.

1973-01-01

It is shown that in a rearrangement collision leading to the formation of highly excited hydrogenlike states the cross section at high energies behaves as 1/n-squared, with n the principal quantum number, thus invalidating the Brinkman-Kramers approximation for large n. Similarly, in high-energy inelastic electron-hydrogenlike-atom collisions the exchange cross section for sufficiently large n dominates the direct excitation cross section.

Correlation between Satellite-Derived Aerosol Characteristics and Oceanic Dimethylsulfide (DMS)

DTIC Science & Technology

1988-12-01

intensity gained by multiple scattering into the beam from all directions and the beam addition term accounting for single scattering events. The physical...the extinction and scattering coefficients are the integracion over radius of the product of the cross sectional area of aerosol particles, the...the same photon more than once is small. Therefore, the multiple interaction term can be neglected and a single scattering approximation is made. The

Laser/Materials Interaction Studies for Enhanced Sensitivity of Laser Ultrasonic Systems.

DTIC Science & Technology

1998-05-01

laser wavelengths is given. Graphite is birefrengent , and hence, the index of refraction and the skin depth depend on the polarization direction...Another development in the model would be the inclusion of processes occurring in the air under atmospheric conditions. The vacuum model presented... atmospheric pressure. 279 74 The jump conditions for cases where this approximation breaks down are treated by Knight (1979). Vaporization in the

Ionization energies and electron affinities from a random-phase-approximation many-body Green's-function method including exchange interactions

NASA Astrophysics Data System (ADS)

Heßelmann, Andreas

2017-06-01

A many-body Green's-function method employing an infinite order summation of ring and exchange-ring contributions to the self-energy is presented. The individual correlation and relaxation contributions to the quasiparticle energies are calculated using an iterative scheme which utilizes density fitting of the particle-hole, particle-particle and hole-hole densities. It is shown that the ionization energies and electron affinities of this approach agree better with highly accurate coupled-cluster singles and doubles with perturbative triples energy difference results than those obtained with second-order Green's-function approaches. An analysis of the correlation and relaxation terms of the self-energy for the direct- and exchange-random-phase-approximation (RPA) Green's-function methods shows that the inclusion of exchange interactions leads to a reduction of the two contributions in magnitude. These differences, however, strongly cancel each other when summing the individual terms to the quasiparticle energies. Due to this, the direct- and exchange-RPA methods perform similarly for the description of ionization energies (IPs) and electron affinities (EAs). The coupled-cluster reference IPs and EAs, if corrected to the adiabatic energy differences between the neutral and charged molecules, were shown to be in very good agreement with experimental measurements.

Combinations of coupled cluster, density functionals, and the random phase approximation for describing static and dynamic correlation, and van der Waals interactions

NASA Astrophysics Data System (ADS)

Garza, Alejandro J.; Bulik, Ireneusz W.; Alencar, Ana G. Sousa; Sun, Jianwei; Perdew, John P.; Scuseria, Gustavo E.

2016-04-01

Contrary to standard coupled cluster doubles (CCD) and Brueckner doubles (BD), singlet-paired analogues of CCD and BD (denoted here as CCD0 and BD0) do not break down when static correlation is present, but neglect substantial amounts of dynamic correlation. In fact, CCD0 and BD0 do not account for any contributions from multielectron excitations involving only same-spin electrons at all. We exploit this feature to add - without introducing double counting, self-interaction, or increase in cost - the missing correlation to these methods via meta-GGA (generalised gradient approximation) density functionals (Tao-Perdew-Staroverov-Scuseria and strongly constrained and appropriately normed). Furthermore, we improve upon these CCD0+DFT blends by invoking range separation: the short- and long-range correlations absent in CCD0/BD0 are evaluated with density functional theory and the direct random phase approximation, respectively. This corrects the description of long-range van der Waals forces. Comprehensive benchmarking shows that the combinations presented here are very accurate for weakly correlated systems, while also providing a reasonable description of strongly correlated problems without resorting to symmetry breaking.

Fermi orbital self-interaction corrected electronic structure of molecules beyond local density approximation

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

Hahn, T., E-mail: torsten.hahn@physik.tu-freiberg.de; Liebing, S.; Kortus, J.

2015-12-14

The correction of the self-interaction error that is inherent to all standard density functional theory calculations is an object of increasing interest. In this article, we apply the very recently developed Fermi-orbital based approach for the self-interaction correction [M. R. Pederson et al., J. Chem. Phys. 140, 121103 (2014) and M. R. Pederson, J. Chem. Phys. 142, 064112 (2015)] to a set of different molecular systems. Our study covers systems ranging from simple diatomic to large organic molecules. We focus our analysis on the direct estimation of the ionization potential from orbital eigenvalues. Further, we show that the Fermi orbitalmore » positions in structurally similar molecules appear to be transferable.« less

A behaviour study on the potential for direct transmission of tuberculosis from possums (Trichosurus vulpecula) to alpacas (Lama pacos), and the converse from alpacas to possums.

PubMed

Black, H; Simper, J M; Bloom, D; Bloom, K

1999-12-01

To evaluate the potential for the direct transmission of tuberculosis from possums to alpacas, and vice versa. A field study was conducted on an alpaca farm in Northland, New Zealand on 7 January 1999. Observations were recorded on the interaction of one group of male alpacas with a simulated dead possum, one male and one female alpaca group with a simulated terminally tuberculous possum, and one group of male alpacas with a normal possum in an enclosure from which the animals could not escape. The possum was sedated with ketamine as hydrochloride to simulate death (inactive; no movement), and terminal illness (active, inco-ordinated movement around the paddock). The observations were based on the focal animal sampling technique, they were un-replicated, and recorded visually and manually with intermittent still photography. Both male and female alpacas showed strongly inquisitive interaction with the possum. They clustered around the possum (focal animal) very soon after it was observed by the first member of the group. The interest of the majority of both sex groups remained high for the observation periods of approximately 30 minutes, and most individuals remained within 5 metres of the possum for that time. Approximately 50% of the alpacas were within possible aerosol transmission distance of 2 metres from the sedated, erratically mobile possum with their heads towards it for approximately 50% of the two observation periods. Aggressive behaviour was recorded for a young male with stamping on the moving possum. Similar, but more vigorous and prolonged stamping behaviour was recorded for a female with a young (<1 week) offspring (cria). The stamping behaviour was accompanied by very close nose to nose contact of the alpaca and possum. At one point the female threw the possum approximately 1.5 metres in the air with her teeth. The group of male alpacas placed in an enclosure with an unsedated normal possum generally moved away from the possum during its rapid active attempts to escape. When it became inactive their approaches were cautious and only once elicited a defence reaction from the possum, from which they recoiled. One male made one attempt to stamp on the active possum. Soon after the possum became inactive in a small loose hay pile, the alpacas lost interest in it. The alpaca / possum behavioural interactions show there is potential for direct aerosol transmission of tuberculosis from possums to alpacas, but probably not from alpacas to possums.

Transport Coefficients in weakly compressible turbulence

NASA Technical Reports Server (NTRS)

Rubinstein, Robert; Erlebacher, Gordon

1996-01-01

A theory of transport coefficients in weakly compressible turbulence is derived by applying Yoshizawa's two-scale direct interaction approximation to the compressible equations of motion linearized about a state of incompressible turbulence. The result is a generalization of the eddy viscosity representation of incompressible turbulence. In addition to the usual incompressible eddy viscosity, the calculation generates eddy diffusivities for entropy and pressure, and an effective bulk viscosity acting on the mean flow. The compressible fluctuations also generate an effective turbulent mean pressure and corrections to the speed of sound. Finally, a prediction unique to Yoshizawa's two-scale approximation is that terms containing gradients of incompressible turbulence quantities also appear in the mean flow equations. The form these terms take is described.

Sound-turbulence interaction in transonic boundary layers

NASA Astrophysics Data System (ADS)

Lelostec, Ludovic; Scalo, Carlo; Lele, Sanjiva

2014-11-01

Acoustic wave scattering in a transonic boundary layer is investigated through a novel approach. Instead of simulating directly the interaction of an incoming oblique acoustic wave with a turbulent boundary layer, suitable Dirichlet conditions are imposed at the wall to reproduce only the reflected wave resulting from the interaction of the incident wave with the boundary layer. The method is first validated using the laminar boundary layer profiles in a parallel flow approximation. For this scattering problem an exact inviscid solution can be found in the frequency domain which requires numerical solution of an ODE. The Dirichlet conditions are imposed in a high-fidelity unstructured compressible flow solver for Large Eddy Simulation (LES), CharLESx. The acoustic field of the reflected wave is then solved and the interaction between the boundary layer and sound scattering can be studied.

Two-parametric {\\delta'} -interactions: approximation by Schrödinger operators with localized rank-two perturbations

NASA Astrophysics Data System (ADS)

Golovaty, Yuriy

2018-06-01

We construct a norm resolvent approximation to the family of point interactions , by Schrödinger operators with localized rank-two perturbations coupled with short range potentials. In particular, a new approximation to the -interactions is obtained.

Linear Elastic Waves - Series: Cambridge Texts in Applied Mathematics (No. 26)

NASA Astrophysics Data System (ADS)

Harris, John G.

2001-10-01

Wave propagation and scattering are among the most fundamental processes that we use to comprehend the world around us. While these processes are often very complex, one way to begin to understand them is to study wave propagation in the linear approximation. This is a book describing such propagation using, as a context, the equations of elasticity. Two unifying themes are used. The first is that an understanding of plane wave interactions is fundamental to understanding more complex wave interactions. The second is that waves are best understood in an asymptotic approximation where they are free of the complications of their excitation and are governed primarily by their propagation environments. The topics covered include reflection, refraction, the propagation of interfacial waves, integral representations, radiation and diffraction, and propagation in closed and open waveguides. Linear Elastic Waves is an advanced level textbook directed at applied mathematicians, seismologists, and engineers. Aimed at beginning graduate students Includes examples and exercises Has application in a wide range of disciplines

Analysis of fluid-structure interaction in a frame pipe undergoing plastic deformations

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

Khamlichi, A.; Jezequel, L.; Jacques, Y.

1995-11-01

Water hammer pressure waves of sufficiently large magnitude can cause plastic flexural deformations in a frame pipe. In this study, the authors propose a modelization of this problem based on plane wave approximation for the fluid equations and approximation of the structure motion by a single-degree-of-freedom elastic-plastic oscillator. Direct analytical integration of elastic-plastic equations through pipe sections, then over the pipe length is performed in order to identify the oscillator parameters. Comparison of the global load-displacement relationship obtained with the finite element solution was considered and has shown good agreement. Fluid-structure coupling is achieved by assuming elbows to act likemore » plane monopole sources, where localized jumps of fluid velocity occur and where net pressure forces are exerted on the structure. The authors have applied this method to analyze the fluid-structure interaction in this range of deformations. Energy exchange between the fluid and the structure and energy dissipation are quantified.« less

LEOrbit: A program to calculate parameters relevant to modeling Low Earth Orbit spacecraft-plasma interaction

NASA Astrophysics Data System (ADS)

Marchand, R.; Purschke, D.; Samson, J.

2013-03-01

Understanding the physics of interaction between satellites and the space environment is essential in planning and exploiting space missions. Several computer models have been developed over the years to study this interaction. In all cases, simulations are carried out in the reference frame of the spacecraft and effects such as charging, the formation of electrostatic sheaths and wakes are calculated for given conditions of the space environment. In this paper we present a program used to compute magnetic fields and a number of space plasma and space environment parameters relevant to Low Earth Orbits (LEO) spacecraft-plasma interaction modeling. Magnetic fields are obtained from the International Geophysical Reference Field (IGRF) and plasma parameters are obtained from the International Reference Ionosphere (IRI) model. All parameters are computed in the spacecraft frame of reference as a function of its six Keplerian elements. They are presented in a format that can be used directly in most spacecraft-plasma interaction models. Catalogue identifier: AENY_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AENY_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 270308 No. of bytes in distributed program, including test data, etc.: 2323222 Distribution format: tar.gz Programming language: FORTRAN 90. Computer: Non specific. Operating system: Non specific. RAM: 7.1 MB Classification: 19, 4.14. External routines: IRI, IGRF (included in the package). Nature of problem: Compute magnetic field components, direction of the sun, sun visibility factor and approximate plasma parameters in the reference frame of a Low Earth Orbit satellite. Solution method: Orbit integration, calls to IGRF and IRI libraries and transformation of coordinates from geocentric to spacecraft frame reference. Restrictions: Low Earth orbits, altitudes between 150 and 2000 km. Running time: Approximately two seconds to parameterize a full orbit with 1000 points.

Accurate, precise, and efficient theoretical methods to calculate anion-π interaction energies in model structures.

PubMed

Mezei, Pál D; Csonka, Gábor I; Ruzsinszky, Adrienn; Sun, Jianwei

2015-01-13

A correct description of the anion-π interaction is essential for the design of selective anion receptors and channels and important for advances in the field of supramolecular chemistry. However, it is challenging to do accurate, precise, and efficient calculations of this interaction, which are lacking in the literature. In this article, by testing sets of 20 binary anion-π complexes of fluoride, chloride, bromide, nitrate, or carbonate ions with hexafluorobenzene, 1,3,5-trifluorobenzene, 2,4,6-trifluoro-1,3,5-triazine, or 1,3,5-triazine and 30 ternary π-anion-π' sandwich complexes composed from the same monomers, we suggest domain-based local-pair natural orbital coupled cluster energies extrapolated to the complete basis-set limit as reference values. We give a detailed explanation of the origin of anion-π interactions, using the permanent quadrupole moments, static dipole polarizabilities, and electrostatic potential maps. We use symmetry-adapted perturbation theory (SAPT) to calculate the components of the anion-π interaction energies. We examine the performance of the direct random phase approximation (dRPA), the second-order screened exchange (SOSEX), local-pair natural-orbital (LPNO) coupled electron pair approximation (CEPA), and several dispersion-corrected density functionals (including generalized gradient approximation (GGA), meta-GGA, and double hybrid density functional). The LPNO-CEPA/1 results show the best agreement with the reference results. The dRPA method is only slightly less accurate and precise than the LPNO-CEPA/1, but it is considerably more efficient (6-17 times faster) for the binary complexes studied in this paper. For 30 ternary π-anion-π' sandwich complexes, we give dRPA interaction energies as reference values. The double hybrid functionals are much more efficient but less accurate and precise than dRPA. The dispersion-corrected double hybrid PWPB95-D3(BJ) and B2PLYP-D3(BJ) functionals perform better than the GGA and meta-GGA functionals for the present test set.

Resonant electronic excitation energy transfer by exchange mechanism in the quantum dot system

NASA Astrophysics Data System (ADS)

Chikalova-Luzina, O. P.; Samosvat, D. M.; Vyatkin, V. M.; Zegrya, G. G.

2017-11-01

A microscopic theory of nonradiative resonance energy transfer between spherical A3B5 semiconductor quantum dots by the exchange mechanism is suggested. The interdot Coulomb interaction is taken into consideration. It is assumed that the quantum dot-donor and the quantum dot-acceptor are made from the same A3B5 compound and are embedded in the matrix of another material that produces potential barriers for electrons and holes. The dependences of the energy transfer rate on the quantum-dot system parameters are found in the frame of the Kane model that provides the most adequate description of the real spectra of A3B5 semiconductors. The analytical treatment is carried out with using the density matrix method, which enabled us to perform an energy transfer analysis both in the weak-interaction approximation and in the strong-interaction approximation. The numerical calculations showed the saturation of the energy transfer rate at the distances between the donor and the acceptor approaching the contact one. The contributions of the exchange and direct Coulomb intractions can be of the same order at the small distances and can have the same value in the saturation range.

Pulling adsorbed polymers at an angle: A low temperature theory

NASA Astrophysics Data System (ADS)

Iliev, Gerasim; Whittington, Stuart

2012-02-01

We consider several partially-directed walk models in two- and three-dimensions to study the problem of a homopolymer interacting with a surface while subject to a force at the terminal monomer. The force is applied with a component parallel to the surface as well as a component perpendicular to the surface. Depending on the relative values of the force in each direction, the force can either enhance the adsorption transition or lead to desorption in an adsorbed polymer. For each model, we determine the associated generating function and extract the phase diagram, identifying states where the polymer is thermally desorbed, adsorbed, and under the influence of the force. We note the different regimes that appear in the problem and provide a low temperature approximation to describe them. The approximation is exact at T=0 and models the exact results extremely well for small values of T. This work is an extension of a model considered by S. Whittington and E. Orlandini.

Coulomb couplings in solubilised light harvesting complex II (LHCII): challenging the ideal dipole approximation from TDDFT calculations.

PubMed

López-Tarifa, P; Liguori, Nicoletta; van den Heuvel, Naudin; Croce, Roberta; Visscher, Lucas

2017-07-19

The light harvesting complex II (LHCII), is a pigment-protein complex responsible for most of the light harvesting in plants. LHCII harvests sunlight and transfers excitation energy to the reaction centre of the photo-system, where the water oxidation process takes place. The energetics of LHCII can be modulated by means of conformational changes allowing a switch from a harvesting to a quenched state. In this state, the excitation energy is no longer transferred but converted into thermal energy to prevent photooxidation. Based on molecular dynamics simulations at the microsecond time scale, we have recently proposed that the switch between different fluorescent states can be probed by correlating shifts in the chromophore-chromophore Coulomb interactions to particular protein movements. However, these findings are based upon calculations in the ideal point dipole approximation (IDA) where the Coulomb couplings are simplified as first order dipole-dipole interactions, also assuming that the chromophore transition dipole moments lay in particular directions of space with constant moduli (FIX-IDA). In this work, we challenge this approximation using the time-dependent density functional theory (TDDFT) combined with the frozen density embedding (FDE) approach. Our aim is to establish up to which limit FIX-IDA can be applied and which chromophore types are better described under this approximation. For that purpose, we use the classical trajectories of solubilised light harvesting complex II (LHCII) we have recently reported [Liguori et al., Sci. Rep., 2015, 5, 15661] and selected three pairs of chromophores containing chlorophyll and carotenoids (Chl and Car): Chla611-Chla612, Chlb606-Chlb607 and Chla612-Lut620. Using the FDE in the Tamm-Dancoff approximation (FDEc-TDA), we show that IDA is accurate enough for predicting Chl-Chl Coulomb couplings. However, the FIX-IDA largely overestimates Chl-Car interactions mainly because the transition dipole for the Cars is not trivially oriented on the polyene chain.

Energetics of the magnetosphere

NASA Technical Reports Server (NTRS)

Stern, D. P.

1980-01-01

The approximate magnitudes of several power inputs and energies associated with the Earth's magnetosphere will be derived. They include: Solar wind power impinging on the dayside magnetopause approximately 1.4 10 to the 13th power watt; power input to cross tail current approximately 3 10 to the 11th power watt; energy of moderate magnetic storm approximately 2 10 to the 15th power joule; power related to the flow of j approximately 1 to 3 10 to the 11th power watt; average power deposited by the aurora approximately 2 10 to the 10th power watt. Stored magnetic energy: released in a substorm approximately 1.5 10 to the 14th power joule. Compared to the above, the rate at which energy is released locally in magnetospheric regions where magnetic merging occurs is probably small. Merging is essential, however, for the existence of open field lines, which provide the most likely explanation for some major energy inputs listed here. Merging is also required if part of the open flux of the tail lobes is converted into closed flux, as seems to happen during substorms. Again, most of the energy release becomes evident only beyond the merging region, though some particles may gain appreciable energy in that region itself, if the plasma sheet is completely squeezed out and the high latitude lobes interact directly.

Social Interactions of Juvenile Brown Boobies at Sea as Observed with Animal-Borne Video Cameras

PubMed Central

Yoda, Ken; Murakoshi, Miku; Tsutsui, Kota; Kohno, Hiroyoshi

2011-01-01

While social interactions play a crucial role on the development of young individuals, those of highly mobile juvenile birds in inaccessible environments are difficult to observe. In this study, we deployed miniaturised video recorders on juvenile brown boobies Sula leucogaster, which had been hand-fed beginning a few days after hatching, to examine how social interactions between tagged juveniles and other birds affected their flight and foraging behaviour. Juveniles flew longer with congeners, especially with adult birds, than solitarily. In addition, approximately 40% of foraging occurred close to aggregations of congeners and other species. Young seabirds voluntarily followed other birds, which may directly enhance their foraging success and improve foraging and flying skills during their developmental stage, or both. PMID:21573196

Magic tilt angle for stabilizing two-dimensional solitons by dipole-dipole interactions

NASA Astrophysics Data System (ADS)

Chen, Xing-You; Chuang, You-Lin; Lin, Chun-Yan; Wu, Chien-Ming; Li, Yongyao; Malomed, Boris A.; Lee, Ray-Kuang

2017-10-01

In the framework of the Gross-Pitaevskii equation, we study the formation and stability of effectively two-dimensional solitons in dipolar Bose-Einstein condensates (BECs), with dipole moments polarized at an arbitrary angle θ relative to the direction normal to the system's plane. Using numerical methods and the variational approximation, we demonstrate that unstable Townes solitons, created by the contact attractive interaction, may be completely stabilized (with an anisotropic shape) by the dipole-dipole interaction (DDI), in the interval θcr<θ ≤π /2 . The stability boundary θcr weakly depends on the relative strength of the DDI, remaining close to the magic angle θm=arccos(1 /√{3 }) . The results suggest that DDIs provide a generic mechanism for the creation of stable BEC solitons in higher dimensions.

Molecular links among the causative genes for ocular malformation: Otx2 and Sox2 coregulate Rax expression.

PubMed

Danno, Hiroki; Michiue, Tatsuo; Hitachi, Keisuke; Yukita, Akira; Ishiura, Shoichi; Asashima, Makoto

2008-04-08

The neural-related genes Sox2, Pax6, Otx2, and Rax have been associated with severe ocular malformations such as anophthalmia and microphthalmia, but it remains unclear as to how these genes are linked functionally. We analyzed the upstream signaling of Xenopus Rax (also known as Rx1) and identified the Otx2 and Sox2 proteins as direct upstream regulators of Rax. We revealed that endogenous Otx2 and Sox2 proteins bound to the conserved noncoding sequence (CNS1) located approximately 2 kb upstream of the Rax promoter. This sequence is conserved among vertebrates and is required for potent transcriptional activity. Reporter assays showed that Otx2 and Sox2 synergistically activated transcription via CNS1. Furthermore, the Otx2 and Sox2 proteins physically interacted with each other, and this interaction was affected by the Sox2-missense mutations identified in these ocular disorders. These results demonstrate that the direct interaction and interdependence between the Otx2 and Sox2 proteins coordinate Rax expression in eye development, providing molecular linkages among the genes responsible for ocular malformation.

Subaru SCExAO First-Light Direct Imaging of a Young Debris Disk around HD 36546

NASA Technical Reports Server (NTRS)

Currie, Thayne; Guyon, Olivier; Tamura, Motohide; Kudo, Tomoyuki; Jovanovic, Nemanja; Lozi, Julien; Schlieder, Joshua E.; Brandt, TImothy D.; Kuhn, Jonasa; Serabyn, Eugene;

Quantitative analysis of optical properties of flowing blood using a photon-cell interactive Monte Carlo code: effects of red blood cells' orientation on light scattering.

PubMed

Sakota, Daisuke; Takatani, Setsuo

2012-05-01

Optical properties of flowing blood were analyzed using a photon-cell interactive Monte Carlo (pciMC) model with the physical properties of the flowing red blood cells (RBCs) such as cell size, shape, refractive index, distribution, and orientation as the parameters. The scattering of light by flowing blood at the He-Ne laser wavelength of 632.8 nm was significantly affected by the shear rate. The light was scattered more in the direction of flow as the flow rate increased. Therefore, the light intensity transmitted forward in the direction perpendicular to flow axis decreased. The pciMC model can duplicate the changes in the photon propagation due to moving RBCs with various orientations. The resulting RBC's orientation that best simulated the experimental results was with their long axis perpendicular to the direction of blood flow. Moreover, the scattering probability was dependent on the orientation of the RBCs. Finally, the pciMC code was used to predict the hematocrit of flowing blood with accuracy of approximately 1.0 HCT%. The photon-cell interactive Monte Carlo (pciMC) model can provide optical properties of flowing blood and will facilitate the development of the non-invasive monitoring of blood in extra corporeal circulatory systems.

An activation switch in the rhodopsin family of G protein-coupled receptors: the thyrotropin receptor.

PubMed

Urizar, Eneko; Claeysen, Sylvie; Deupí, Xavier; Govaerts, Cedric; Costagliola, Sabine; Vassart, Gilbert; Pardo, Leonardo

2005-04-29

We aimed at understanding molecular events involved in the activation of a member of the G protein-coupled receptor family, the thyrotropin receptor. We have focused on the transmembrane region and in particular on a network of polar interactions between highly conserved residues. Using molecular dynamics simulations and site-directed mutagenesis techniques we have identified residue Asn-7.49, of the NPxxY motif of TM 7, as a molecular switch in the mechanism of thyrotropin receptor (TSHr) activation. Asn-7.49 appears to adopt two different conformations in the inactive and active states. These two states are characterized by specific interactions between this Asn and polar residues in the transmembrane domain. The inactive gauche+ conformation is maintained by interactions with residues Thr-6.43 and Asp-6.44. Mutation of these residues into Ala increases the constitutive activity of the receptor by factors of approximately 14 and approximately 10 relative to wild type TSHr, respectively. Upon receptor activation Asn-7.49 adopts the trans conformation to interact with Asp-2.50 and a putatively charged residue that remains to be identified. In addition, the conserved Leu-2.46 of the (N/S)LxxxD motif also plays a significant role in restraining the receptor in the inactive state because the L2.46A mutation increases constitutive activity by a factor of approximately 13 relative to wild type TSHr. As residues Leu-2.46, Asp-2.50, and Asn-7.49 are strongly conserved, this molecular mechanism of TSHr activation can be extended to other members of the rhodopsin-like family of G protein-coupled receptors.

Numerical simulation of interaction between chemically active exhaust and a jet blast deflector

NASA Astrophysics Data System (ADS)

Korotaeva, T. A.; Turchinovich, A. O.

2017-10-01

The interaction of chemically active exhausts of aircraft engines with jet blast deflector (JBD) of various configurations has been considered at the stage of ground run procedure. The problem is modeled in the 3-D approximation in the framework of the numerical solution of the Navier-Stokes equations taking into account the kinetic model of the interaction of between the components of engine exhaust and air. A complex field of gasdynamic flow that is realized when jets emerge from nozzles and interact with each other, with air, with a gas deflector has been studied. The main purpose of the study is to prove the concept that it is possible to generate a vortex flow that can not only change the direction of the jets, but also contribute to the lifting of the mass of pollutants and their dispersion in the atmosphere using a gas deflector shape.

Predicting the properties of the lead alloys from DFT calculations

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

Buimaga-Iarinca, L., E-mail: luiza.iarinca@itim-cj.ro; Calborean, A.

2015-12-23

We provide qualitative results for the physical properties of the lead alloys at atomic scale by using DFT calculations. Our approach is based on the two assumptions: (i) the geometric structure of lead atoms provides a matrix where the alloying elements can take their positions in the structure as substitutions and (ii) there is a small probability of a direct interaction between the alloying elements, thus the interactions of each alloying element may be approximated by the interactions to the lead matrix. DFT calculations are used to investigate the interaction between several types of impurities and the lead matrix formore » low concentrations of the alloying element. We report results such as the enthalpy of formation, charge transfer and mechanical stress induced by the impurities in the lead matrix; these results can be used as qualitative guide in tuning the physico-chemical properties of the lead alloys.« less

Laboratory modeling and analysis of aircraft-lightning interactions

NASA Technical Reports Server (NTRS)

Turner, C. D.; Trost, T. F.

1982-01-01

Modeling studies of the interaction of a delta wing aircraft with direct lightning strikes were carried out using an approximate scale model of an F-106B. The model, which is three feet in length, is subjected to direct injection of fast current pulses supplied by wires, which simulate the lightning channel and are attached at various locations on the model. Measurements are made of the resulting transient electromagnetic fields using time derivative sensors. The sensor outputs are sampled and digitized by computer. The noise level is reduced by averaging the sensor output from ten input pulses at each sample time. Computer analysis of the measured fields includes Fourier transformation and the computation of transfer functions for the model. Prony analysis is also used to determine the natural frequencies of the model. Comparisons of model natural frequencies extracted by Prony analysis with those for in flight direct strike data usually show lower damping in the in flight case. This is indicative of either a lightning channel with a higher impedance than the wires on the model, only one attachment point, or short streamers instead of a long channel.

Rho0 production and possible modification in Au+Au and p+p collisions at square root [sNN] = 200 GeV.

PubMed

Adams, J; Adler, C; Aggarwal, M M; Ahammed, Z; Amonett, J; Anderson, B D; Arkhipkin, D; Averichev, G S; Badyal, S K; Balewski, J; Barannikova, O; Barnby, L S; Baudot, J; Bekele, S; Belaga, V V; Bellwied, R; Berger, J; Bezverkhny, B I; Bhardwaj, S; Bhati, A K; Bichsel, H; Billmeier, A; Bland, L C; Blyth, C O; Bonner, B E; Botje, M; Boucham, A; Brandin, A; Bravar, A; Cadman, R V; Cai, X Z; Caines, H; Calderón de la Barca Sánchez, M; Carroll, J; Castillo, J; Cebra, D; Chaloupka, P; Chattopadhyay, S; Chen, H F; Chen, Y; Chernenko, S P; Cherney, M; Chikanian, A; Christie, W; Coffin, J P; Cormier, T M; Cramer, J G; Crawford, H J; Das, D; Das, S; Derevschikov, A A; Didenko, L; Dietel, T; Dong, W J; Dong, X; Draper, J E; Du, F; Dubey, A K; Dunin, V B; Dunlop, J C; Dutta Majumdar, M R; Eckardt, V; Efimov, L G; Emelianov, V; Engelage, J; Eppley, G; Erazmus, B; Estienne, M; Fachini, P; Faine, V; Faivre, J; Fatemi, R; Filimonov, K; Filip, P; Finch, E; Fisyak, Y; Flierl, D; Foley, K J; Fu, J; Gagliardi, C A; Gagunashvili, N; Gans, J; Ganti, M S; Gaudichet, L; Geurts, F; Ghazikhanian, V; Ghosh, P; Gonzalez, J E; Grachov, O; Grebenyuk, O; Gronstal, S; Grosnick, D; Guertin, S M; Gupta, A; Gutierrez, T D; Hallman, T J; Hamed, A; Hardtke, D; Harris, J W; Heinz, M; Henry, T W; Heppelmann, S; Hippolyte, B; Hirsch, A; Hjort, E; Hoffmann, G W; Horsley, M; Huang, H Z; Huang, S L; Hughes, E; Humanic, T J; Igo, G; Ishihara, A; Jacobs, P; Jacobs, W W; Janik, M; Jiang, H; Johnson, I; Jones, P G; Judd, E G; Kabana, S; Kaplan, M; Keane, D; Khodyrev, V Yu; Kiryluk, J; Kisiel, A; Klay, J; Klein, S R; Klyachko, A; Koetke, D D; Kollegger, T; Kopytine, M; Kotchenda, L; Kovalenko, A D; Kramer, M; Kravtsov, P; Kravtsov, V I; Krueger, K; Kuhn, C; Kulikov, A I; Kumar, A; Kunde, G J; Kunz, C L; Kutuev, R Kh; Kuznetsov, A A; Lamont, M A C; Landgraf, J M; Lange, S; Lasiuk, B; Laue, F; Lauret, J; Lebedev, A; Lednický, R; LeVine, M J; Li, C; Li, Q; Lindenbaum, S J; Lisa, M A; Liu, F; Liu, L; Liu, Z; Liu, Q J; Ljubicic, T; Llope, W J; Long, H; Longacre, R S; Lopez-Noriega, M; Love, W A; Ludlam, T; Lynn, D; Ma, J; Ma, Y G; Magestro, D; Mahajan, S; Mangotra, L K; Mahapatra, D P; Majka, R; Manweiler, R; Margetis, S; Markert, C; Martin, L; Marx, J; Matis, H S; Matulenko, Yu A; McClain, C J; McShane, T S; Meissner, F; Melnick, Yu; Meschanin, A; Miller, M L; Milosevich, Z; Minaev, N G; Mironov, C; Mischke, A; Mishra, D; Mitchell, J; Mohanty, B; Molnar, L; Moore, C F; Mora-Corral, M J; Morozov, D A; Morozov, V; De Moura, M M; Munhoz, M G; Nandi, B K; Nayak, S K; Nayak, T K; Nelson, J M; Netrakanti, P K; Nikitin, V A; Nogach, L V; Norman, B; Nurushev, S B; Odyniec, G; Ogawa, A; Okorokov, V; Oldenburg, M; Olson, D; Paic, G; Pal, S K; Panebratsev, Y; Panitkin, S Y; Pavlinov, A I; Pawlak, T; Peitzmann, T; Perevoztchikov, V; Perkins, C; Peryt, W; Petrov, V A; Phatak, S C; Picha, R; Planinic, M; Pluta, J; Porile, N; Porter, J; Poskanzer, A M; Potekhin, M; Potrebenikova, E; Potukuchi, B V K S; Prindle, D; Pruneau, C; Putschke, J; Rai, G; Rakness, G; Raniwala, R; Raniwala, S; Ravel, O; Ray, R L; Razin, S V; Reichhold, D; Reid, J G; Renault, G; Retiere, F; Ridiger, A; Ritter, H G; Roberts, J B; Rogachevski, O V; Romero, J L; Rose, A; Roy, C; Ruan, L J; Sahoo, R; Sakrejda, I; Salur, S; Sandweiss, J; Savin, I; Schambach, J; Scharenberg, R P; Schmitz, N; Schroeder, L S; Schweda, K; Seger, J; Seyboth, P; Shahaliev, E; Shao, M; Shao, W; Sharma, M; Shestermanov, K E; Shimanskii, S S; Singaraju, R N; Simon, F; Skoro, G; Smirnov, N; Snellings, R; Sood, G; Sorensen, P; Sowinski, J; Speltz, J; Spinka, H M; Srivastava, B; Stanislaus, T D S; Stock, R; Stolpovsky, A; Strikhanov, M; Stringfellow, B; Struck, C; Suaide, A A P; Sugarbaker, E; Suire, C; Sumbera, M; Surrow, B; Symons, T J M; Szanto de Toledo, A; Szarwas, P; Tai, A; Takahashi, J; Tang, A H; Thein, D; Thomas, J H; Timoshenko, S; Tokarev, M; Tonjes, M B; Trainor, T A; Trentalange, S; Tribble, R E; Tsai, O; Ullrich, T; Underwood, D G; Van Buren, G; VanderMolen, A M; Varma, R; Vasilevski, I; Vasiliev, A N; Vernet, R; Vigdor, S E; Viyogi, Y P; Voloshin, S A; Vznuzdaev, M; Waggoner, W; Wang, F; Wang, G; Wang, G; Wang, X L; Wang, Y; Wang, Z M; Ward, H; Watson, J W; Webb, J C; Wells, R; Westfall, G D; Whitten, C; Wieman, H; Willson, R; Wissink, S W; Witt, R; Wood, J; Wu, J; Xu, N; Xu, Z; Xu, Z Z; Yamamoto, E; Yepes, P; Yurevich, V I; Yuting, B; Zanevski, Y V; Zhang, H; Zhang, W M; Zhang, Z P; Zhaomin, Z P; Zizong, Z P; Zołnierczuk, P A; Zoulkarneev, R; Zoulkarneeva, J; Zubarev, A N

2004-03-05

We report results on rho(770)(0)-->pi(+)pi(-) production at midrapidity in p+p and peripheral Au+Au collisions at sqrt[s(NN)]=200 GeV. This is the first direct measurement of rho(770)(0)-->pi(+)pi(-) in heavy-ion collisions. The measured rho(0) peak in the invariant mass distribution is shifted by approximately 40 MeV/c(2) in minimum bias p+p interactions and approximately 70 MeV/c(2) in peripheral Au+Au collisions. The rho(0) mass shift is dependent on transverse momentum and multiplicity. The modification of the rho(0) meson mass, width, and shape due to phase space and dynamical effects are discussed.

Direct Measurement of Pyroelectric and Electrocaloric Effects in Thin Films

NASA Astrophysics Data System (ADS)

Pandya, Shishir; Wilbur, Joshua D.; Bhatia, Bikram; Damodaran, Anoop R.; Monachon, Christian; Dasgupta, Arvind; King, William P.; Dames, Chris; Martin, Lane W.

2017-03-01

An understanding of polarization-heat interactions in pyroelectric and electrocaloric thin-film materials requires that the electrothermal response is reliably characterized. While most work, particularly in electrocalorics, has relied on indirect measurement protocols, here we report a direct technique for measuring both pyroelectric and electrocaloric effects in epitaxial ferroelectric thin films. We demonstrate an electrothermal test platform where localized high-frequency (approximately 1 kHz) periodic heating and highly sensitive thin-film resistance thermometry allow the direct measurement of pyrocurrents (<10 pA ) and electrocaloric temperature changes (<2 mK ) using the "2-omega" and an adapted "3-omega" technique, respectively. Frequency-domain, phase-sensitive detection permits the extraction of the pyrocurrent from the total current, which is often convoluted by thermally-stimulated currents. The wide-frequency-range measurements employed in this study further show the effect of secondary contributions to pyroelectricity due to the mechanical constraints of the substrate. Similarly, measurement of the electrocaloric effect on the same device in the frequency domain (at approximately 100 kHz) allows for the decoupling of Joule heating from the electrocaloric effect. Using one-dimensional, analytical heat-transport models, the transient temperature profile of the heterostructure is characterized to extract pyroelectric and electrocaloric coefficients.

Direct Push Optical Screening Tool for High Resolution, Real-Time Mapping of Chlorinated Solvent DNAPL Architecture

DTIC Science & Technology

2016-07-01

petroleum hydrocarbon fuels due to higher densities, lower viscosities , and increased weathering (mass depletion) of residual chlorinated solvent DNAPL...generally classified as stratified layers of fine sand and silt with few clay layers. A silt layer was penetrated consistently at a depth of about 45...e.g., stiff clays ) there is potential for the thickness of the dye interaction zone to increase to approximately 1-2 mm. Intuition suggests that this

Modeling Kelvin Wave Cascades in Superfluid Helium

NASA Astrophysics Data System (ADS)

Boffetta, G.; Celani, A.; Dezzani, D.; Laurie, J.; Nazarenko, S.

2009-09-01

We study two different types of simplified models for Kelvin wave turbulence on quantized vortex lines in superfluids near zero temperature. Our first model is obtained from a truncated expansion of the Local Induction Approximation (Truncated-LIA) and it is shown to possess the same scalings and the essential behaviour as the full Biot-Savart model, being much simpler than the later and, therefore, more amenable to theoretical and numerical investigations. The Truncated-LIA model supports six-wave interactions and dual cascades, which are clearly demonstrated via the direct numerical simulation of this model in the present paper. In particular, our simulations confirm presence of the weak turbulence regime and the theoretically predicted spectra for the direct energy cascade and the inverse wave action cascade. The second type of model we study, the Differential Approximation Model (DAM), takes a further drastic simplification by assuming locality of interactions in k-space via using a differential closure that preserves the main scalings of the Kelvin wave dynamics. DAMs are even more amenable to study and they form a useful tool by providing simple analytical solutions in the cases when extra physical effects are present, e.g. forcing by reconnections, friction dissipation and phonon radiation. We study these models numerically and test their theoretical predictions, in particular the formation of the stationary spectra, and closeness of numerics for the higher-order DAM to the analytical predictions for the lower-order DAM.

Hybrid Simulation of the Shock Wave Trailing the Moon

NASA Technical Reports Server (NTRS)

Israelevich, P.; Ofman, Leon

2012-01-01

A standing shock wave behind the Moon was predicted by Michel (1967) but never observed nor simulated. We use 1D hybrid code in order to simulate the collapse of the plasma-free cavity behind the Moon and for the first time to model the formation of this shock. Starting immediately downstream of the obstacle we consider the evolution of plasma expansion into the cavity in the frame of reference moving along with the solar wind. Well-known effects as electric charging of the cavity affecting the plasma flow and counterstreaming ion beams in the wake are reproduced. Near the apex of the inner Mach cone where the plasma flows from the opposite sides of the obstacle meet, a shock wave arises. We expect the shock to be produced at periods of high electron temperature solar wind streams (T(sub i) much less than T(sub e) approximately 100 eV). The shock is produced by the interaction of oppositely directed proton beams in the plane containing solar wind velocity and interplanetary magnetic field vectors. In the direction across the magnetic field and the solar wind velocity, the shock results from the interaction of the plasma flow with the region of the enhanced magnetic field inside the cavity that plays the role of the magnetic barrier. The appearance of the standing shock wave is expected at the distance of approximately 7R(sub M) downstream of the Moon.

The Three-dimensional Structure of the Eta Carinae Homunculus

NASA Technical Reports Server (NTRS)

Steffen, W.; Teodoro, M.; Madura, T.I.; Groh, J.H.; Gull, T.R.; Mehner, A.; Corcoran, M.F.; Damineli, A.; Hamaguchi, K.

2014-01-01

We investigate, using the modeling code SHAPE, the three-dimensional structure of the bipolar Homunculus nebula surrounding Eta Carinae as mapped by new ESO VLT/X-Shooter observations of the H2 (lambda) = 2.12125 micrometers emission line. Our results reveal for the first time important deviations from the axisymmetric bipolar morphology: 1) circumpolar trenches in each lobe positioned point-symmetrically from the center and 2) offplanar protrusions in the equatorial region from each lobe at longitudinal (approximately 55 degrees) and latitudinal (10 degrees to 20 degrees) distances from the projected apastron direction of the binary orbit. The angular distance between the protrusions (approximately 110 degrees) is similar to the angular extent of each polar trench (approximately 130 degrees) and nearly equal to the opening angle of the wind-wind collision cavity (approximately 110 degrees). As in previous studies, we confirm a hole near the centre of each polar lobe and no detectable near-IR H2 emission from the thin optical skirt seen prominently in visible imagery. We conclude that the interaction between the outflows and/or radiation from the central binary stars and their orientation in space has had, and possibly still has, a strong influence on the Homunculus. This implies that prevailing theoretical models of the Homunculus are incomplete as most assume a single star origin that produces an axisymmetric nebula.We discuss how the newly found features might be related to the Homunculus ejection, the central binary and the interacting stellar winds.

Astrophysical uncertainties on the local dark matter distribution and direct detection experiments

NASA Astrophysics Data System (ADS)

Green, Anne M.

2017-08-01

The differential event rate in weakly interacting massive particle (WIMP) direct detection experiments depends on the local dark matter density and velocity distribution. Accurate modelling of the local dark matter distribution is therefore required to obtain reliable constraints on the WIMP particle physics properties. Data analyses typically use a simple standard halo model which might not be a good approximation to the real Milky Way (MW) halo. We review observational determinations of the local dark matter density, circular speed and escape speed and also studies of the local dark matter distribution in simulated MW-like galaxies. We discuss the effects of the uncertainties in these quantities on the energy spectrum and its time and direction dependence. Finally, we conclude with an overview of various methods for handling these astrophysical uncertainties.

A force-based, parallel assay for the quantification of protein-DNA interactions.

PubMed

Limmer, Katja; Pippig, Diana A; Aschenbrenner, Daniela; Gaub, Hermann E

2014-01-01

Analysis of transcription factor binding to DNA sequences is of utmost importance to understand the intricate regulatory mechanisms that underlie gene expression. Several techniques exist that quantify DNA-protein affinity, but they are either very time-consuming or suffer from possible misinterpretation due to complicated algorithms or approximations like many high-throughput techniques. We present a more direct method to quantify DNA-protein interaction in a force-based assay. In contrast to single-molecule force spectroscopy, our technique, the Molecular Force Assay (MFA), parallelizes force measurements so that it can test one or multiple proteins against several DNA sequences in a single experiment. The interaction strength is quantified by comparison to the well-defined rupture stability of different DNA duplexes. As a proof-of-principle, we measured the interaction of the zinc finger construct Zif268/NRE against six different DNA constructs. We could show the specificity of our approach and quantify the strength of the protein-DNA interaction.

Gender differences in teacher-student interactions in science classrooms

NASA Astrophysics Data System (ADS)

Jones, M. Gail; Wheatley, Jack

1990-12-01

Thirty physical science and 30 chemistry classes, which contained a total of 1332 students, were observed using the Brophy-Good Teacher-Child Dyadic Interaction System. Classroom interactions were examined for gender differences that may contribute to the underrepresentation of women in physics and engineering courses and subsequent careers. The Brophy-Good coding process allows for examination of patterns of interactions for individuals and groups of pupils. An analysis of variance of the data yielded a significant main effect for teacher praise, call outs, procedural questions, and behavioral warnings based on the sex of the student and a significant teacher-sex main effect for direct questions. Significant two-way interactions were found for the behavioral warning variable for teacher sex and subject by student sex. Female teachers warned male students significantly more than female students. Male teachers warned both genders with similar frequency. Male students also received significantly more behavioral warnings in physical science classes than female students. In chemistry classes, both male and female students received approximately the same number of behavioral warnings.

Tuning the phase diagram of colloid-polymer mixtures via Yukawa interactions

NASA Astrophysics Data System (ADS)

González García, Álvaro; Tuinier, Remco

2016-12-01

Theory that predicts the phase behavior of interacting Yukawa spheres in a solution containing nonadsorbing polymer is presented. Our approach accounts for multiple overlap of depletion zones. It is found that additional Yukawa interactions beyond hard core interactions strongly affect the location and presence of coexistence regions and phase states. The theoretical phase diagrams are compared with Monte Carlo simulations. The agreement between the two approaches supports the validity of the theoretical approximations made and confirms that, by choosing the parameters of the interaction potentials, tuning of the binodals is possible. The critical end point characterizes the phase diagram topology. It is demonstrated how an additional Yukawa interaction shifts this point with respect to the hard sphere case. Provided a certain depletant-to-colloid size ratio for which a stable colloidal gas-liquid phase coexistence takes place for hard spheres, added direct interactions turn this into a metastable gas-liquid equilibrium. The opposite case, the induction of a stable gas-liquid coexistence where only fluid-solid was present for hard spheres, is also reported.

Gaussian theory for spatially distributed self-propelled particles

NASA Astrophysics Data System (ADS)

Seyed-Allaei, Hamid; Schimansky-Geier, Lutz; Ejtehadi, Mohammad Reza

2016-12-01

Obtaining a reduced description with particle and momentum flux densities outgoing from the microscopic equations of motion of the particles requires approximations. The usual method, we refer to as truncation method, is to zero Fourier modes of the orientation distribution starting from a given number. Here we propose another method to derive continuum equations for interacting self-propelled particles. The derivation is based on a Gaussian approximation (GA) of the distribution of the direction of particles. First, by means of simulation of the microscopic model, we justify that the distribution of individual directions fits well to a wrapped Gaussian distribution. Second, we numerically integrate the continuum equations derived in the GA in order to compare with results of simulations. We obtain that the global polarization in the GA exhibits a hysteresis in dependence on the noise intensity. It shows qualitatively the same behavior as we find in particles simulations. Moreover, both global polarizations agree perfectly for low noise intensities. The spatiotemporal structures of the GA are also in agreement with simulations. We conclude that the GA shows qualitative agreement for a wide range of noise intensities. In particular, for low noise intensities the agreement with simulations is better as other approximations, making the GA to an acceptable candidates of describing spatially distributed self-propelled particles.

MEANS: python package for Moment Expansion Approximation, iNference and Simulation

PubMed Central

Fan, Sisi; Geissmann, Quentin; Lakatos, Eszter; Lukauskas, Saulius; Ale, Angelique; Babtie, Ann C.; Kirk, Paul D. W.; Stumpf, Michael P. H.

2016-01-01

Motivation: Many biochemical systems require stochastic descriptions. Unfortunately these can only be solved for the simplest cases and their direct simulation can become prohibitively expensive, precluding thorough analysis. As an alternative, moment closure approximation methods generate equations for the time-evolution of the system’s moments and apply a closure ansatz to obtain a closed set of differential equations; that can become the basis for the deterministic analysis of the moments of the outputs of stochastic systems. Results: We present a free, user-friendly tool implementing an efficient moment expansion approximation with parametric closures that integrates well with the IPython interactive environment. Our package enables the analysis of complex stochastic systems without any constraints on the number of species and moments studied and the type of rate laws in the system. In addition to the approximation method our package provides numerous tools to help non-expert users in stochastic analysis. Availability and implementation: https://github.com/theosysbio/means Contacts: m.stumpf@imperial.ac.uk or e.lakatos13@imperial.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153663

MEANS: python package for Moment Expansion Approximation, iNference and Simulation.

PubMed

Fan, Sisi; Geissmann, Quentin; Lakatos, Eszter; Lukauskas, Saulius; Ale, Angelique; Babtie, Ann C; Kirk, Paul D W; Stumpf, Michael P H

2016-09-15

Many biochemical systems require stochastic descriptions. Unfortunately these can only be solved for the simplest cases and their direct simulation can become prohibitively expensive, precluding thorough analysis. As an alternative, moment closure approximation methods generate equations for the time-evolution of the system's moments and apply a closure ansatz to obtain a closed set of differential equations; that can become the basis for the deterministic analysis of the moments of the outputs of stochastic systems. We present a free, user-friendly tool implementing an efficient moment expansion approximation with parametric closures that integrates well with the IPython interactive environment. Our package enables the analysis of complex stochastic systems without any constraints on the number of species and moments studied and the type of rate laws in the system. In addition to the approximation method our package provides numerous tools to help non-expert users in stochastic analysis. https://github.com/theosysbio/means m.stumpf@imperial.ac.uk or e.lakatos13@imperial.ac.uk Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Including fluid shear viscosity in a structural acoustic finite element model using a scalar fluid representation

PubMed Central

Cheng, Lei; Li, Yizeng; Grosh, Karl

2013-01-01

An approximate boundary condition is developed in this paper to model fluid shear viscosity at boundaries of coupled fluid-structure system. The effect of shear viscosity is approximated by a correction term to the inviscid boundary condition, written in terms of second order in-plane derivatives of pressure. Both thin and thick viscous boundary layer approximations are formulated; the latter subsumes the former. These approximations are used to develop a variational formation, upon which a viscous finite element method (FEM) model is based, requiring only minor modifications to the boundary integral contributions of an existing inviscid FEM model. Since this FEM formulation has only one degree of freedom for pressure, it holds a great computational advantage over the conventional viscous FEM formulation which requires discretization of the full set of linearized Navier-Stokes equations. The results from thick viscous boundary layer approximation are found to be in good agreement with the prediction from a Navier-Stokes model. When applicable, thin viscous boundary layer approximation also gives accurate results with computational simplicity compared to the thick boundary layer formulation. Direct comparison of simulation results using the boundary layer approximations and a full, linearized Navier-Stokes model are made and used to evaluate the accuracy of the approximate technique. Guidelines are given for the parameter ranges over which the accurate application of the thick and thin boundary approximations can be used for a fluid-structure interaction problem. PMID:23729844

Including fluid shear viscosity in a structural acoustic finite element model using a scalar fluid representation.

PubMed

Cheng, Lei; Li, Yizeng; Grosh, Karl

2013-08-15

An approximate boundary condition is developed in this paper to model fluid shear viscosity at boundaries of coupled fluid-structure system. The effect of shear viscosity is approximated by a correction term to the inviscid boundary condition, written in terms of second order in-plane derivatives of pressure. Both thin and thick viscous boundary layer approximations are formulated; the latter subsumes the former. These approximations are used to develop a variational formation, upon which a viscous finite element method (FEM) model is based, requiring only minor modifications to the boundary integral contributions of an existing inviscid FEM model. Since this FEM formulation has only one degree of freedom for pressure, it holds a great computational advantage over the conventional viscous FEM formulation which requires discretization of the full set of linearized Navier-Stokes equations. The results from thick viscous boundary layer approximation are found to be in good agreement with the prediction from a Navier-Stokes model. When applicable, thin viscous boundary layer approximation also gives accurate results with computational simplicity compared to the thick boundary layer formulation. Direct comparison of simulation results using the boundary layer approximations and a full, linearized Navier-Stokes model are made and used to evaluate the accuracy of the approximate technique. Guidelines are given for the parameter ranges over which the accurate application of the thick and thin boundary approximations can be used for a fluid-structure interaction problem.

An additional role for the Brønsted acid-base catalysts of mandelate racemase in transition state stabilization.

PubMed

Nagar, Mitesh; Bearne, Stephen L

2015-11-10

Mandelate racemase (MR) catalyzes the interconversion of the enantiomers of mandelate and serves as a paradigm for understanding the enzyme-catalyzed abstraction of an α-proton from a carbon acid substrate with a high pKa. The enzyme utilizes a two-base mechanism with Lys 166 and His 297 acting as Brønsted acid and base catalysts, respectively, in the R → S reaction direction. In the S → R reaction direction, their roles are reversed. Using isothermal titration calorimetry (ITC), MR is shown to bind the intermediate/transition state (TS) analogue inhibitor benzohydroxamate (BzH) in an entropy-driven process with a value of ΔCp equal to -358 ± 3 cal mol(-1) K(-1), consistent with an increased number of hydrophobic interactions. However, MR binds BzH with an affinity that is ∼2 orders of magnitude greater than that predicted solely on the basis of hydrophobic interactions [St. Maurice, M., and Bearne, S. L. (2004) Biochemistry 43, 2524], suggesting that additional specific interactions contribute to binding. To test the hypothesis that cation-π/NH-π interactions between the side chains of Lys 166 and His 297 and the aromatic ring and/or the hydroxamate/hydroximate moiety of BzH contribute to the binding of BzH, site-directed mutagenesis was used to generate the MR variants K166M, K166C, H297N, and K166M/H297N and their binding affinity for various ligands determined using ITC. Comparison of the binding affinities of these MR variants with the intermediate/TS analogues BzH and cyclohexanecarbohydroxamate revealed that cation-π/NH-π interactions between His 297 and the hydroxamate/hydroximate moiety and the phenyl ring of BzH contribute approximately 0.26 and 0.91 kcal/mol to binding, respectively, while interactions with Lys 166 contribute approximately 1.74 and 1.74 kcal/mol, respectively. Similarly, comparison of the binding affinities of these mutants with substrate analogues revealed that Lys 166 contributes >2.93 kcal/mol to the binding of (R)-atrolactate, and His 297 contributes 2.46 kcal/mol to the binding of (S)-atrolactate. These results are consistent with Lys 166 and His 297 playing dual roles in catalysis: they act as Brønsted acid-base catalysts, and they stabilize both the enolate moiety and phenyl ring of the altered substrate in the TS.

Irreversible Processes in Ionized Gases

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

Balescu, R.

1960-01-01

The general theory of irreversible processes, developed by Prigogine and Balescu, is applied to the case of long range interactions in ionized gases. A similar diagram technique permits the systematic selection of all the contributions to the evolution of the distribution function, a an order of approximation equivalent to Debye's equilibrium theory. The infinite series which appear in this way can be summed exactly. The resulting evolution equations have a clear physical significance: they describe interactions of "quasi particles," which are electrons or ions "dressed" by their polarization clouds. These clouds are not a permanent feature, as in equilibrium theory,more » but have a nonequilibrium, changing shape, distorted by the motions of the particles. From the mathematical point of view, these equations exhibit a new type of nonlinearity, which is very directly related to the collective nature of the interactions.« less

Fingering instabilities and pattern formation in a two-component dipolar Bose-Einstein condensate

NASA Astrophysics Data System (ADS)

Xi, Kui-Tian; Byrnes, Tim; Saito, Hiroki

2018-02-01

We study fingering instabilities and pattern formation at the interface of an oppositely polarized two-component Bose-Einstein condensate with strong dipole-dipole interactions in three dimensions. It is shown that the rotational symmetry is spontaneously broken by fingering instability when the dipole-dipole interactions are strengthened. Frog-shaped and mushroom-shaped patterns emerge during the dynamics due to the dipolar interactions. We also demonstrate the spontaneous density modulation and domain growth of a two-component dipolar BEC in the dynamics. Bogoliubov analyses in the two-dimensional approximation are performed, and the characteristic lengths of the domains are estimated analytically. Patterns resembling those in magnetic classical fluids are modulated when the number ratio of atoms, the trap ratio of the external potential, or tilted polarization with respect to the z direction is varied.

The IntAct molecular interaction database in 2012

PubMed Central

Kerrien, Samuel; Aranda, Bruno; Breuza, Lionel; Bridge, Alan; Broackes-Carter, Fiona; Chen, Carol; Duesbury, Margaret; Dumousseau, Marine; Feuermann, Marc; Hinz, Ursula; Jandrasits, Christine; Jimenez, Rafael C.; Khadake, Jyoti; Mahadevan, Usha; Masson, Patrick; Pedruzzi, Ivo; Pfeiffenberger, Eric; Porras, Pablo; Raghunath, Arathi; Roechert, Bernd; Orchard, Sandra; Hermjakob, Henning

2012-01-01

IntAct is an open-source, open data molecular interaction database populated by data either curated from the literature or from direct data depositions. Two levels of curation are now available within the database, with both IMEx-level annotation and less detailed MIMIx-compatible entries currently supported. As from September 2011, IntAct contains approximately 275 000 curated binary interaction evidences from over 5000 publications. The IntAct website has been improved to enhance the search process and in particular the graphical display of the results. New data download formats are also available, which will facilitate the inclusion of IntAct's data in the Semantic Web. IntAct is an active contributor to the IMEx consortium (http://www.imexconsortium.org). IntAct source code and data are freely available at http://www.ebi.ac.uk/intact. PMID:22121220

Adaptive Flight Control for Aircraft Safety Enhancements

NASA Technical Reports Server (NTRS)

Nguyen, Nhan T.; Gregory, Irene M.; Joshi, Suresh M.

2008-01-01

This poster presents the current adaptive control research being conducted at NASA ARC and LaRC in support of the Integrated Resilient Aircraft Control (IRAC) project. The technique "Approximate Stability Margin Analysis of Hybrid Direct-Indirect Adaptive Control" has been developed at NASA ARC to address the needs for stability margin metrics for adaptive control that potentially enables future V&V of adaptive systems. The technique "Direct Adaptive Control With Unknown Actuator Failures" is developed at NASA LaRC to deal with unknown actuator failures. The technique "Adaptive Control with Adaptive Pilot Element" is being researched at NASA LaRC to investigate the effects of pilot interactions with adaptive flight control that can have implications of stability and performance.

Analysis of the thermodynamics of binding of an SH3 domain to proline-rich peptides using a chimeric fusion protein.

PubMed

Candel, Adela M; van Nuland, Nico A J; Martin-Sierra, Francisco M; Martinez, Jose C; Conejero-Lara, Francisco

2008-03-14

A complete understanding of the thermodynamic determinants of binding between SH3 domains and proline-rich peptides is crucial to the development of rational strategies for designing ligands for these important domains. Recently we engineered a single-chain chimeric protein by fusing the alpha-spectrin Src homology region 3 (SH3) domain to the decapeptide APSYSPPPPP (p41). This chimera mimics the structural and energetic features of the interaction between SH3 domains and proline-rich peptides. Here we show that analysing the unfolding thermodynamics of single-point mutants of this chimeric fusion protein constitutes a very useful approach to deciphering the thermodynamics of SH3-ligand interactions. To this end, we investigated the contribution of each proline residue of the ligand sequence to the SH3-peptide interaction by producing six single Pro-Ala mutants of the chimeric protein and analysing their unfolding thermodynamics by differential scanning calorimetry (DSC). Structural analyses of the mutant chimeras by circular dichroism, fluorescence and NMR together with NMR-relaxation measurements indicate conformational flexibility at the binding interface, which is strongly affected by the different Pro-Ala mutations. An analysis of the DSC thermograms on the basis of a three-state unfolding model has allowed us to distinguish and separate the thermodynamic magnitudes of the interaction at the binding interface. The model assumes equilibrium between the "unbound" and "bound" states at the SH3-peptide binding interface. The resulting thermodynamic magnitudes classify the different proline residues according to their importance in the interaction as P2 approximately P7 approximately P10>P9 approximately P6>P8, which agrees well with Lim's model for the interaction between SH3 domains and proline-rich peptides. In addition, the thermodynamic signature of the interaction is the same as that usually found for this type of binding, with a strong enthalpy-entropy compensation for all the mutants. This compensation appears to derive from an increase in conformational flexibility concomitant to the weakening of the interactions at the binding interface. We conclude that our approach, based on DSC and site-directed mutagenesis analysis of chimeric fusion proteins, may serve as a suitable tool to analyse the energetics of weak biomolecular interactions such as those involving SH3 domains.

PharMillenium '99--the second world pharmaceutical congress and exhibition. Accelerating the pipeline: from drug discovery to market. 1-3 February 1999, Washington DC, USA.

PubMed

Fernandes, M

1999-04-01

This highly interactive meeting effectively covered critical issues on every transaction from drug discovery through to development and commercialization. The program included company-specific descriptions of new discovery products, together with seminars by clinical research and site management organizations on the acceleration of development, pharmaco-economics, branding of products, direct-to-consumer advertising, global marketing, management, information technology and business strategy. There were approximately 50 sessions covered by 70 speakers.

Orbital-free bond breaking via machine learning

NASA Astrophysics Data System (ADS)

Snyder, John C.; Rupp, Matthias; Hansen, Katja; Blooston, Leo; Müller, Klaus-Robert; Burke, Kieron

2013-12-01

Using a one-dimensional model, we explore the ability of machine learning to approximate the non-interacting kinetic energy density functional of diatomics. This nonlinear interpolation between Kohn-Sham reference calculations can (i) accurately dissociate a diatomic, (ii) be systematically improved with increased reference data and (iii) generate accurate self-consistent densities via a projection method that avoids directions with no data. With relatively few densities, the error due to the interpolation is smaller than typical errors in standard exchange-correlation functionals.

Blocking the Metastatic Phenotype in Prostate Cancer Through Direct Inhibition of the ETV/PEA3 Transcription Factors

DTIC Science & Technology

2016-11-01

the ortho phenolic aldehyde , a carboxylic acid positioned meta or para to the ring junction, and small hydrophobic groups along the rim of the rings...estimate potential toxicity risks, as outlined in the original proposal and SOW. The phenolic aldehyde present in all three of the first...in the absence of this interaction, however, with an approximately 8-fold shift in IC50. Consistent with this result, reduction of the aldehyde in

Tetragonal Lysozyme Interactions Studied by Site Directed Mutagenesis

NASA Technical Reports Server (NTRS)

Crawford, Lisa; Karr, Laurel J.; Nadarajah, Arunan; Pusey, Marc

1999-01-01

A number of recent experimental and theoretical studies have indicated that tetragonal lysozyme crystal growth proceeds by the addition of aggregates, formed by reversible self association of the solute molecules in the bulk solution. Periodic bond chain and atomic force microscopy studies have indicated that the probable growth unit is at minimum a 43 tetramer, and most likely an octamer composed of two complete turns about the 43 axis. If these results are correct, then there are intermolecular interactions which are only formed in the solution and others only formed at the joining of the growth unit to the crystal surface. We have set out to study these interactions, and the correctness of this hypothesis, using site directed mutagenesis of specific amino acid residues involved in the different bonds. We had initially expressed wild type lysozyme in S. cervasiae with yields of approximately 5 mg/L, which were eventually raised to approximately 40 mg/L. We are now moving the expression to the Pichia system, with anticipated yields of 300 to (3)500 mg/L, comparable to what can be obtained from egg whites. An additional advantage of using recombinant protein is the greater genetic homogeneity of the material obtained and the absence of any other contaminating egg proteins. The first mutation experiments are TYR 23 (Registered) PHE or ALA and ASN 113 (Registered) ALA or ASP. Both TYR 23 and ASN 113 form part of the postulated dimerization intermolecular binding site which lead to the formation of the 43 helix. Tyrosine also participates in an intermolecular hydrogen bond with ARG 114. The results of these and subsequent experiments will be discussed.

Tetragonal Lysozyme Interactions Studied by Site Directed Mutagenesis

NASA Technical Reports Server (NTRS)

Crawford, Lisa; Karr, Laurel; Pusey, Marc

1998-01-01

A number of recent experimental and theoretical studies have indicated that tetragonal lysozyme crystal growth proceeds by the addition of aggregates, formed by reversible self association of the solute molecules in the bulk'solution. Periodic bond chain and atomic force microscopy studies have indicated that the probable growth unit is at minimum a 43 tetramer, and most likely an octamer composed of two complete turns about the 4(sub 3) axis. If these results are correct, then there are intermolecular interactions which are only formed in the solution and others only formed at the joining of the growth unit to the crystal surface. We have set out to study these interactions, and the correctness of this hypothesis, using site directed mutagenesis of specific amino acid residues involved in the different bonds. We had initially expressed wild type lysozyme in S. cervasiae with yields of approximately 5 mg/L, which were eventually raised to approximately 40 mg/L. We are now moving the expression to the Pichia system, with anticipated yields of 300 to greater than 500 mg/L, comparable to what can be obtained from egg whites. An additional advantage of using recombinant protein is the greater genetic homogeneity of the material obtained and the absence of any other contaminating egg proteins. The first mutation experiments are TYR 23 yields PHE or ALA and ASN 113 yields ALA or ASP. Both TYR 23 and ASN 113 form part of the postulated dimerization intermolecular binding site which lead to the formation of the 4(sub 3) helix. Tyrosine also participates in an intermolecular hydrogen bond with ARG 114. The results of these and subsequent experiments will be discussed.

Model of Anisotropic Magnetization of In(1-x)Mn(x)S: Comparison to Experiment

NASA Astrophysics Data System (ADS)

Garner, J.; Franzese, G.; Byrd, Ashlee; Pekarek, T. M.; Miotkowski, I.; Ramdas, A. K.

2004-03-01

Calculations of and experimental results for the anisotropic magnetization of the new III-VI dilute magnetic semiconductor, In(1-x)Mn(x)S, are presented. The model Hamiltonian incorporates the interaction of the incomplete shell of Mn 3d-electrons with the crystal lattice within the point-ion approximation. Other terms in the Hamiltonian include the Zeeman interaction, the spin-orbit and the spin-spin terms. It is assumed the Mn atoms do not interact with each other (this is the singlet model, which is appropriate when x is small, here 2%). The temperature- and field- dependent magnetization is found from the energy eigenvalues of the Hamiltonian matrix, which was expressed in terms of an uncoupled angular momentum basis set. Magnetization versus temperature results are found for several field values, B, pointing along various directions relative to the underlying dilute magnetic semiconductor crystal lattice. In addition, the magnetization versus field is computed for several fixed temperatures and for various B-field directions and magnitudes. Overall, the agreement of this simple model with the experimental data is very good except at low temperatures (< 20 K) and high fields (> a few Tesla). It would be useful for quantitative comparison purposes to have optical absorption data in order to better fix the crystal potential parameters that are input parameters in the theory. In addition, the model could be improved by going beyond the point-ion approximation to better model the covalent bonds in the crystal.* Supported by UNF Research Grants, Research Corporation Award, CC4845, NSF Grant Nos. DMR-03-05653, DMR-01-02699, and ECS-01-29853 and Donors of the American Chemical Society Petroleum Research Fund PRF#40209-B5M, and a Purdue Univ. Academic Reimbursement Grant.

A numerical study of Coulomb interaction effects on 2D hopping transport.

PubMed

Kinkhabwala, Yusuf A; Sverdlov, Viktor A; Likharev, Konstantin K

2006-02-15

We have extended our supercomputer-enabled Monte Carlo simulations of hopping transport in completely disordered 2D conductors to the case of substantial electron-electron Coulomb interaction. Such interaction may not only suppress the average value of hopping current, but also affect its fluctuations rather substantially. In particular, the spectral density S(I)(f) of current fluctuations exhibits, at sufficiently low frequencies, a 1/f-like increase which approximately follows the Hooge scaling, even at vanishing temperature. At higher f, there is a crossover to a broad range of frequencies in which S(I)(f) is nearly constant, hence allowing characterization of the current noise by the effective Fano factor [Formula: see text]. For sufficiently large conductor samples and low temperatures, the Fano factor is suppressed below the Schottky value (F = 1), scaling with the length L of the conductor as F = (L(c)/L)(α). The exponent α is significantly affected by the Coulomb interaction effects, changing from α = 0.76 ± 0.08 when such effects are negligible to virtually unity when they are substantial. The scaling parameter L(c), interpreted as the average percolation cluster length along the electric field direction, scales as [Formula: see text] when Coulomb interaction effects are negligible and [Formula: see text] when such effects are substantial, in good agreement with estimates based on the theory of directed percolation.

Direct application of Padé approximant for solving nonlinear differential equations.

PubMed

Vazquez-Leal, Hector; Benhammouda, Brahim; Filobello-Nino, Uriel; Sarmiento-Reyes, Arturo; Jimenez-Fernandez, Victor Manuel; Garcia-Gervacio, Jose Luis; Huerta-Chua, Jesus; Morales-Mendoza, Luis Javier; Gonzalez-Lee, Mario

2014-01-01

This work presents a direct procedure to apply Padé method to find approximate solutions for nonlinear differential equations. Moreover, we present some cases study showing the strength of the method to generate highly accurate rational approximate solutions compared to other semi-analytical methods. The type of tested nonlinear equations are: a highly nonlinear boundary value problem, a differential-algebraic oscillator problem, and an asymptotic problem. The high accurate handy approximations obtained by the direct application of Padé method shows the high potential if the proposed scheme to approximate a wide variety of problems. What is more, the direct application of the Padé approximant aids to avoid the previous application of an approximative method like Taylor series method, homotopy perturbation method, Adomian Decomposition method, homotopy analysis method, variational iteration method, among others, as tools to obtain a power series solutions to post-treat with the Padé approximant. 34L30.

Spectral Remittance and Transmittance of Visible and Infrared-A Radiation in Human Skin-Comparison Between in vivo Measurements and Model Calculations.

PubMed

Piazena, Helmut; Meffert, Hans; Uebelhack, Ralf

2017-11-01

The aim of the study was to assess the interindividual variability of spectral remittance and spectral transmittance of visible and infrared-A radiations interacting with human skin and subcutaneous tissue, and direct measurements were taken in vivo using healthy persons of different skin color types. Up to wavelengths of about 900 nm, both spectral remittance and spectral transmittance depended significantly on the individual contents of melanin and hemoglobin in the skin, whereas the contents of water and lipids mainly determined spectral slopes of both characteristics of interaction for wavelengths above about 900 nm. In vivo measured data of spectral transmittance showed approximately similar decreases with tissue thickness between about 900 nm and 1100 nm as compared with model data which were calculated using spectral absorption and scattering coefficients of skin samples in vitro published by different authors. In addition, in vivo measured data and in vitro-based model calculations of spectral remittance were approximately comparable in this wavelength range. In contrast, systematic but individually varying differences between both methods were found for both spectral remittance and spectral transmittance at wavelengths below about 900 nm, where interaction of radiation was significantly affected by both melanin and hemoglobin. © 2017 The American Society of Photobiology.

Assessing the performance of the random phase approximation for exchange and superexchange coupling constants in magnetic crystalline solids

NASA Astrophysics Data System (ADS)

Olsen, Thomas

2017-09-01

The random phase approximation (RPA) for total energies has previously been shown to provide a qualitatively correct description of static correlation in molecular systems, where density functional theory (DFT) with local functionals are bound to fail. This immediately poses the question of whether the RPA is also able to capture the correct physics of strongly correlated solids such as Mott insulators. Due to strong electron localization, magnetic interactions in such systems are dominated by superexchange, which in the simplest picture can be regarded as the analog of static correlation for molecules. In this paper, we investigate the performance of the RPA for evaluating both superexchange and direct exchange interactions in the magnetic solids NiO, MnO, Na3Cu2SbO6,Sr2CuO3,Sr2CuTeO6 , and a monolayer of CrI3, which were chosen to represent a broad variety of magnetic interactions. It is found that the RPA can accurately correct the large errors introduced by Hartree-Fock, independent of the input orbitals used for the perturbative expansion. However, in most cases, accuracies similar to RPA can be obtained with DFT+U, which is significantly simpler from a computational point of view.

Minimal-Approximation-Based Distributed Consensus Tracking of a Class of Uncertain Nonlinear Multiagent Systems With Unknown Control Directions.

PubMed

Choi, Yun Ho; Yoo, Sung Jin

2017-03-28

A minimal-approximation-based distributed adaptive consensus tracking approach is presented for strict-feedback multiagent systems with unknown heterogeneous nonlinearities and control directions under a directed network. Existing approximation-based consensus results for uncertain nonlinear multiagent systems in lower-triangular form have used multiple function approximators in each local controller to approximate unmatched nonlinearities of each follower. Thus, as the follower's order increases, the number of the approximators used in its local controller increases. However, the proposed approach employs only one function approximator to construct the local controller of each follower regardless of the order of the follower. The recursive design methodology using a new error transformation is derived for the proposed minimal-approximation-based design. Furthermore, a bounding lemma on parameters of Nussbaum functions is presented to handle the unknown control direction problem in the minimal-approximation-based distributed consensus tracking framework and the stability of the overall closed-loop system is rigorously analyzed in the Lyapunov sense.

A quantum Otto engine with finite heat baths: energy, correlations, and degradation

NASA Astrophysics Data System (ADS)

Pozas-Kerstjens, Alejandro; Brown, Eric G.; Hovhannisyan, Karen V.

2018-04-01

We study a driven harmonic oscillator operating an Otto cycle by strongly interacting with two thermal baths of finite size. Using the tools of Gaussian quantum mechanics, we directly simulate the dynamics of the engine as a whole, without the need to make any approximations. This allows us to understand the non-equilibrium thermodynamics of the engine not only from the perspective of the working medium, but also as it is seen from the thermal baths’ standpoint. For sufficiently large baths, our engine is capable of running a number of perfect cycles, delivering finite power while operating very close to maximal efficiency. Thereafter, having traversed the baths, the perturbations created by the interaction abruptly deteriorate the engine’s performance. We additionally study the correlations generated in the system, and, in particular, we find a direct connection between the build up of bath–bath correlations and the degradation of the engine’s performance over the course of many cycles.

International cometary explorer encounter with giacobini-zinner: magnetic field observations.

PubMed

Smith, E J; Tsurutani, B T; Slvain, J A; Jones, D E; Siscoe, G L; Mendis, D A

1986-04-18

The vector helium magnetometer on the International Cometary Explorer observed the magnetic fields induced by the interaction of comet Giacobini-Zinner with the solar wind. A magnetic tail was penetrated approximately 7800 kilometers downstream from the comet and was found to be 10(4) kilometers wide. It consisted of two lobes, containing oppositely directed fields with strengths up to 60 nanoteslas, separated by a plasma sheet approximately 10(3)kilometers thick containing a thin current sheet. The magnetotail was enclosed in an extended ionosheath characterized by intense hydromagnetic turbulene and interplanetary fields draped around the comet. A distant bow wave, which may or may not have been a bow shock, was observed at both edges of the ionosheath. Weak turbulence was observed well upstream of the bow wave.

Rapid Long-Range Disynaptic Inhibition Explains the Formation of Cortical Orientation Maps

PubMed Central

Antolík, Ján

2017-01-01

Competitive interactions are believed to underlie many types of cortical processing, ranging from memory formation, attention and development of cortical functional organization (e.g., development of orientation maps in primary visual cortex). In the latter case, the competitive interactions happen along the cortical surface, with local populations of neurons reinforcing each other, while competing with those displaced more distally. This specific configuration of lateral interactions is however in stark contrast with the known properties of the anatomical substrate, i.e., excitatory connections (mediating reinforcement) having longer reach than inhibitory ones (mediating competition). No satisfactory biologically plausible resolution of this conflict between anatomical measures, and assumed cortical function has been proposed. Recently a specific pattern of delays between different types of neurons in cat cortex has been discovered, where direct mono-synaptic excitation has approximately the same delay, as the combined delays of the disynaptic inhibitory interactions between excitatory neurons (i.e., the sum of delays from excitatory to inhibitory and from inhibitory to excitatory neurons). Here we show that this specific pattern of delays represents a biologically plausible explanation for how short-range inhibition can support competitive interactions that underlie the development of orientation maps in primary visual cortex. We demonstrate this statement analytically under simplifying conditions, and subsequently show using network simulations that development of orientation maps is preserved when long-range excitation, direct inhibitory to inhibitory interactions, and moderate inequality in the delays between excitatory and inhibitory pathways is added. PMID:28408869

Investigation of head group behaviour of lamellar liquid crystals

NASA Astrophysics Data System (ADS)

Delikatny, E. J.; Burnell, E. E.

A mean field equilibrium statistical mechanical model, based on the Samulski inertial frame model, was developed to simulate experimental dipolar and quadrupolar nmr couplings of isotopically substituted potassium palmitates. An isolated four spin system was synthesized (2,2,3,3,-H4-palmitic acid-d27) and in conjunction with data presented in a previous paper on perdeuterated and carbon 13 labelled soaps, the head group behaviour of the molecule was investigated. Two interactions were considered in the modelling procedure: a mean field steric interaction characterized by a constraining cylinder, and a head group interaction characterized by a mass on the end of a rod of variable length. The rod lies along the first C-C bond direction and accounts for the interaction between polar head group and water via its effect on the moment of inertia of the molecule. In potassium palmitate mean field steric repulsive forces remain constant over the entire temperature range studied. In contrast, electrostatic interactions between polar head group and water, approximately constant at higher temperatures, increase dramatically as the phase transition is approached. This evidence supports a previously proposed model of lipidwater interaction.

You can hide but you have to run: direct detection with vector mediators

NASA Astrophysics Data System (ADS)

D'Eramo, Francesco; Kavanagh, Bradley J.; Panci, Paolo

2016-08-01

We study direct detection in simplified models of Dark Matter (DM) in which interactions with Standard Model (SM) fermions are mediated by a heavy vector boson. We consider fully general, gauge-invariant couplings between the SM, the mediator and both scalar and fermion DM. We account for the evolution of the couplings between the energy scale of the mediator mass and the nuclear energy scale. This running arises from virtual effects of SM particles and its inclusion is not optional. We compare bounds on the mediator mass from direct detection experiments with and without accounting for the running. In some cases the inclusion of these effects changes the bounds by several orders of magnitude, as a consequence of operator mixing which generates new interactions at low energy. We also highlight the importance of these effects when translating LHC limits on the mediator mass into bounds on the direct detection cross section. For an axial-vector mediator, the running can alter the derived bounds on the spin-dependent DM-nucleon cross section by a factor of two or more. Finally, we provide tools to facilitate the inclusion of these effects in future studies: general approximate expressions for the low energy couplings and a public code runDM to evolve the couplings between arbitrary energy scales.

Chemically rich seaweeds poison corals when not controlled by herbivores.

PubMed

Rasher, Douglas B; Hay, Mark E

2010-05-25

Coral reefs are in dramatic global decline, with seaweeds commonly replacing corals. It is unclear, however, whether seaweeds harm corals directly or colonize opportunistically following their decline and then suppress coral recruitment. In the Caribbean and tropical Pacific, we show that, when protected from herbivores, approximately 40 to 70% of common seaweeds cause bleaching and death of coral tissue when in direct contact. For seaweeds that harmed coral tissues, their lipid-soluble extracts also produced rapid bleaching. Coral bleaching and mortality was limited to areas of direct contact with seaweeds or their extracts. These patterns suggest that allelopathic seaweed-coral interactions can be important on reefs lacking herbivore control of seaweeds, and that these interactions involve lipid-soluble metabolites transferred via direct contact. Seaweeds were rapidly consumed when placed on a Pacific reef protected from fishing but were left intact or consumed at slower rates on an adjacent fished reef, indicating that herbivory will suppress seaweeds and lower frequency of allelopathic damage to corals if reefs retain intact food webs. With continued removal of herbivores from coral reefs, seaweeds are becoming more common. This occurrence will lead to increasing frequency of seaweed-coral contacts, increasing allelopathic suppression of remaining corals, and continuing decline of reef corals.

The Kubo-Greenwood formula as a result of the random phase approximation for the electrons of the metal

NASA Astrophysics Data System (ADS)

Ivliev, S. V.

2017-12-01

For calculation of short laser pulse absorption in metal the imaginary part of permittivity, which is simply related to the conductivity, is required. Currently to find the static and dynamic conductivity the Kubo-Greenwood formula is most commonly used. It describes the electromagnetic energy absorption in the one-electron approach. In the present study, this formula is derived directly from the expression for the permittivity expression in the random phase approximation, which in fact is equivalent to the method of the mean field. The detailed analysis of the role of electron-electron interaction in the calculation of the matrix elements of the velocity operator is given. It is shown that in the one-electron random phase approximation the single-particle conductive electron wave functions in the field of fixed ions should be used. The possibility of considering the exchange and correlation effects by means of an amendment to a local function field is discussed.

Direction-specific van der Waals attraction between rutile TiO 2 nanocrystals

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

Zhang, Xin; He, Yang; Sushko, Maria L.

Mutual lattice orientations dictate the types and magnitudes of forces between crystalline particles. When lattice polarizability is anisotropic, the van der Waals dispersion attraction can, in principle, contribute to this direction dependence. Here we report direct measurement of this attraction between rutile nanocrystals, as a function of their mutual orientation and surface hydration extent. At tens of nanometers of separation the attraction is weak and shows no dependence on azimuthal alignment nor surface hydration. At separations of approximately one hydration layer the attraction is strongly dependent on azimuthal alignment, and systematically decreases as intervening water density increases. Measured forces aremore » in close agreement with predictions from Lifshitz theory, and show that dispersion forces are capable of generating a torque between particles interacting in solution and between grains in materials.« less

Newly developed photon-cell interactive Monte Carlo (pciMC) simulation for non-invasive and continuous diagnosis of blood during extracorporeal circulation support

NASA Astrophysics Data System (ADS)

Sakota, Daisuke; Takatani, Setsuo

2011-07-01

We have sought for non-invasive diagnosis of blood during the extracorporeal circulation support. To achieve the goal, we have newly developed a photon-cell interactive Monte Carlo (pciMC) model for optical propagation through blood. The pciMC actually describes the interaction of photons with 3-dimentional biconcave RBCs. The scattering is described by micro-scopical RBC boundary condition based on geometric optics. By using pciMC, we modeled the RBCs inside the extracorporeal circuit will be oriented by the blood flow. The RBCs' orientation was defined as their long axis being directed to the center of the circulation tube. Simultaneously the RBCs were allowed to randomly rotate about the long axis direction. As a result, as flow rate increased, the orientation rate increased and converged to approximately 22% at 0.5 L/min flow rate and above. And finally, by using this model, the pciMC non-invasively and absolutely predicted Hct and hemoglobin with the accuracies of 0.84+/-0.82 [HCT%] and 0.42+/-0.28 [g/dL] respectively against measurements by a blood gas analyzer.

A molecular dynamics study of the binary complexes of APP, JIP1, and the cargo binding domain of KLC.

PubMed

Taylor, Cooper A; Miller, Bill R; Shah, Soleil S; Parish, Carol A

2017-02-01

Mutations in the amyloid precursor protein (APP) are responsible for the formation of amyloid-β peptides. These peptides play a role in Alzheimer's and other dementia-related diseases. The cargo binding domain of the kinesin-1 light chain motor protein (KLC1) may be responsible for transporting APP either directly or via interaction with C-jun N-terminal kinase-interacting protein 1 (JIP1). However, to date there has been no direct experimental or computational assessment of such binding at the atomistic level. We used molecular dynamics and free energy estimations to gauge the affinity for the binary complexes of KLC1, APP, and JIP1. We find that all binary complexes (KLC1:APP, KLC1:JIP1, and APP:JIP1) contain conformations with favorable binding free energies. For KLC1:APP the inclusion of approximate entropies reduces the favorability. This is likely due to the flexibility of the 42-residue APP protein. In all cases we analyze atomistic/residue driving forces for favorable interactions. Proteins 2017; 85:221-234. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Error analysis for fast scintillator-based inertial confinement fusion burn history measurements

NASA Astrophysics Data System (ADS)

Lerche, R. A.; Ognibene, T. J.

1999-01-01

Plastic scintillator material acts as a neutron-to-light converter in instruments that make inertial confinement fusion burn history measurements. Light output for a detected neutron in current instruments has a fast rise time (<20 ps) and a relatively long decay constant (1.2 ns). For a burst of neutrons whose duration is much shorter than the decay constant, instantaneous light output is approximately proportional to the integral of the neutron interaction rate with the scintillator material. Burn history is obtained by deconvolving the exponential decay from the recorded signal. The error in estimating signal amplitude for these integral measurements is calculated and compared with a direct measurement in which light output is linearly proportional to the interaction rate.

On the magnon interaction in haematite. I - Magnon energy of optical mode.

NASA Technical Reports Server (NTRS)

Nagai, O.; Tanaka, T.; Bonavito, N. L.

1972-01-01

The effect of magnon interaction on the magnon energies of haematite was studied by the use of a recently developed random phase approximation. In this study, the spin Hamiltonian and the magnon energy were written in a power series of (1/S), where S denotes the magnitude of spin. It is known that the expression of magnon energy is rigorous up to the second term of this series. It is found that the optic mode energy is small if the free optic mode energy is small, which is contrary to Herbert's (1969) conclusion. This direct proportionality between the optic mode energy and the free optic mode energy was not confirmed in the higher order terms of 1/S.

On Interactions of Oscillation Modes for a Weakly Non-Linear Undamped Elastic Beam with AN External Force

NASA Astrophysics Data System (ADS)

BOERTJENS, G. J.; VAN HORSSEN, W. T.

2000-08-01

In this paper an initial-boundary value problem for the vertical displacement of a weakly non-linear elastic beam with an harmonic excitation in the horizontal direction at the ends of the beam is studied. The initial-boundary value problem can be regarded as a simple model describing oscillations of flexible structures like suspension bridges or iced overhead transmission lines. Using a two-time-scales perturbation method an approximation of the solution of the initial-boundary value problem is constructed. Interactions between different oscillation modes of the beam are studied. It is shown that for certain external excitations, depending on the phase of an oscillation mode, the amplitude of specific oscillation modes changes.

Self diffusion of interacting membrane proteins.

PubMed Central

Abney, J R; Scalettar, B A; Owicki, J C

1989-01-01

A two-dimensional version of the generalized Smoluchowski equation is used to analyze the time (or distance) dependent self diffusion of interacting membrane proteins in concentrated membrane systems. This equation provides a well established starting point for descriptions of the diffusion of particles that interact through both direct and hydrodynamic forces; in this initial work only the effects of direct interactions are explicitly considered. Data describing diffusion in the presence of hard-core repulsions, soft repulsions, and soft repulsions with weak attractions are presented. The effect that interactions have on the self-diffusion coefficient of a real protein molecule from mouse liver gap junctions is also calculated. The results indicate that self diffusion is always inhibited by direct interactions; this observation is interpreted in terms of the caging that will exist at finite protein concentration. It is also noted that, over small distance scales, the diffusion coefficient is determined entirely by the very strong Brownian forces; therefore, as a function of displacement the self-diffusion coefficient decays (rapidly) from its value at infinite dilution to its steady-state interaction-averaged value. The steady-state self-diffusion coefficient describes motion over distance scales that range from approximately 10 nm to cellular dimensions and is the quantity measured in fluorescence recovery after photobleaching experiments. The short-ranged behavior of the diffusion coefficient is important on the interparticle-distance scale and may therefore influence the rate at which nearest-neighbor collisional processes take place. The hard-disk theoretical results presented here are in excellent agreement with lattice Monte-Carlo results obtained by other workers. The concentration dependence of experimentally measured diffusion coefficients of antibody-hapten complexes bound to the membrane surface is consistent with that predicted by the theory. The variation in experimental diffusion coefficients of integral membrane proteins is greater than that predicted by the theory, and may also reflect protein-induced perturbations in membrane viscosity. PMID:2720077

Self-Assembly of Trimer Colloids: Effect of Shape and Interaction Range†

PubMed Central

Hatch, Harold W.; Yang, Seung-Yeob; Mittal, Jeetain; Shen, Vincent K.

2016-01-01

Trimers with one attractive bead and two repulsive beads, similar to recently synthesized trimer patchy colloids, were simulated with flat-histogram Monte Carlo methods to obtain the stable self-assembled structures for different shapes and interaction potentials. Extended corresponding states principle was successfully applied to self-assembling systems in order to approximately collapse the results for models with the same shape, but different interaction range. This helps us directly compare simulation results with previous experiment, and good agreement was found between the two. In addition, a variety of self-assembled structures were observed by varying the trimer geometry, including spherical clusters, elongated clusters, monolayers, and spherical shells. In conclusion, our results help to compare simulations and experiments, via extended corresponding states, and we predict the formation of self-assembled structures for trimer shapes that have not been experimentally synthesized. PMID:27087490

Ionization of Atoms by Slow Heavy Particles, Including Dark Matter.

PubMed

Roberts, B M; Flambaum, V V; Gribakin, G F

2016-01-15

Atoms and molecules can become ionized during the scattering of a slow, heavy particle off a bound electron. Such an interaction involving leptophilic weakly interacting massive particles (WIMPs) is a promising possible explanation for the anomalous 9σ annual modulation in the DAMA dark matter direct detection experiment [R. Bernabei et al., Eur. Phys. J. C 73, 2648 (2013)]. We demonstrate the applicability of the Born approximation for such an interaction by showing its equivalence to the semiclassical adiabatic treatment of atomic ionization by slow-moving WIMPs. Conventional wisdom has it that the ionization probability for such a process should be exponentially small. We show, however, that due to nonanalytic, cusplike behavior of Coulomb functions close to the nucleus this suppression is removed, leading to an effective atomic structure enhancement. We also show that electron relativistic effects actually give the dominant contribution to such a process, enhancing the differential cross section by up to 1000 times.

Probing Sub-GeV Mass Strongly Interacting Dark Matter with a Low-Threshold Surface Experiment.

PubMed

Davis, Jonathan H

2017-11-24

Using data from the ν-cleus detector, based on the surface of Earth, we place constraints on dark matter in the form of strongly interacting massive particles (SIMPs) which interact with nucleons via nuclear-scale cross sections. For large SIMP-nucleon cross sections, the sensitivity of traditional direct dark matter searches using underground experiments is limited by the energy loss experienced by SIMPs, due to scattering with the rock overburden and experimental shielding on their way to the detector apparatus. Hence, a surface-based experiment is ideal for a SIMP search, despite the much larger background resulting from the lack of shielding. We show using data from a recent surface run of a low-threshold cryogenic detector that values of the SIMP-nucleon cross section up to approximately 10^{-27}  cm^{2} can be excluded for SIMPs with masses above 100 MeV.

Older Adults' Internet Use for Health Information: Digital Divide by Race/Ethnicity and Socioeconomic Status.

PubMed

Yoon, Hyunwoo; Jang, Yuri; Vaughan, Phillip W; Garcia, Michael

2018-04-01

Building upon literature suggesting low Internet use among racial/ethnic minorities and socioeconomically disadvantaged groups, this study examined how race/ethnicity and socioeconomic status (SES) influence the Internet use for health information, addressing both independent and interactive effects. Using data from 17,704 older adults in the California Health Interview Survey, logistic regression models were estimated with race/ethnicity (Whites, African Americans, Latinos, and Asians), SES index, and the interaction between race/ethnicity and SES index. Overall, approximately 40% of participants were Internet-users for health information. Direct effects of race/ethnicity and SES-and their interactions-were all found to be significant. Minority status combined with the lowest levels of SES substantially reduced the odds of using Internet for health information. Findings suggest the combination of racial/ethnic minority status and low SES as a source of digital divide, and provide implications for Internet technology training for the target population.

Monte Carlo simulation of a near-continuum shock-shock interaction problem

NASA Technical Reports Server (NTRS)

Carlson, Ann B.; Wilmoth, Richard G.

1992-01-01

A complex shock interaction is calculated with direct simulation Monte Carlo (DSMC). The calculation is performed for the near-continuum flow produced when an incident shock impinges on the bow shock of a 0.1 in. radius cowl lip for freestream conditions of approximately Mach 15 and 35 km altitude. Solutions are presented both for a full finite-rate chemistry calculation and for a case with chemical reactions suppressed. In each case, both the undisturbed flow about the cowl lip and the full shock interaction flowfields are calculated. Good agreement has been obtained between the no-chemistry simulation of the undisturbed flow and a perfect gas solution obtained with the viscous shock-layer method. Large differences in calculated surface properties when different chemical models are used demonstrate the necessity of adequately representing the chemistry when making surface property predictions. Preliminary grid refinement studies make it possible to estimate the accuracy of the solutions.

Spreading of correlations in the Falicov-Kimball model

NASA Astrophysics Data System (ADS)

Herrmann, Andreas J.; Antipov, Andrey E.; Werner, Philipp

2018-04-01

We study dynamical properties of the one- and two-dimensional Falicov-Kimball model using lattice Monte Carlo simulations. In particular, we calculate the spreading of charge correlations in the equilibrium model and after an interaction quench. The results show a reduction of the light-cone velocity with interaction strength at low temperature, while the phase velocity increases. At higher temperature, the initial spreading is determined by the Fermi velocity of the noninteracting system and the maximum range of the correlations decreases with increasing interaction strength. Charge order correlations in the disorder potential enhance the range of the correlations. We also use the numerically exact lattice Monte Carlo results to benchmark the accuracy of equilibrium and nonequilibrium dynamical cluster approximation calculations. It is shown that the bias introduced by the mapping to a periodized cluster is substantial, and that from a numerical point of view, it is more efficient to simulate the lattice model directly.

Lagrangian description of warm plasmas

NASA Technical Reports Server (NTRS)

Kim, H.

1970-01-01

Efforts are described to extend the averaged Lagrangian method of describing small signal wave propagation and nonlinear wave interaction, developed by earlier workers for cold plasmas, to the more general conditions of warm collisionless plasmas, and to demonstrate particularly the effectiveness of the method in analyzing wave-wave interactions. The theory is developed for both the microscopic description and the hydrodynamic approximation to plasma behavior. First, a microscopic Lagrangian is formulated rigorously, and expanded in terms of perturbations about equilibrium. Two methods are then described for deriving a hydrodynamic Lagrangian. In the first of these, the Lagrangian is obtained by velocity integration of the exact microscopic Lagrangian. In the second, the expanded hydrodynamic Lagrangian is obtained directly from the expanded microscopic Lagrangian. As applications of the microscopic Lagrangian, the small-signal dispersion relations and the coupled mode equations are derived for all possible waves in a warm infinite, weakly inhomogeneous magnetoplasma, and their interactions are examined.

Stochastic modeling of mode interactions via linear parabolized stability equations

NASA Astrophysics Data System (ADS)

Ran, Wei; Zare, Armin; Hack, M. J. Philipp; Jovanovic, Mihailo

2017-11-01

Low-complexity approximations of the Navier-Stokes equations have been widely used in the analysis of wall-bounded shear flows. In particular, the parabolized stability equations (PSE) and Floquet theory have been employed to capture the evolution of primary and secondary instabilities in spatially-evolving flows. We augment linear PSE with Floquet analysis to formally treat modal interactions and the evolution of secondary instabilities in the transitional boundary layer via a linear progression. To this end, we leverage Floquet theory by incorporating the primary instability into the base flow and accounting for different harmonics in the flow state. A stochastic forcing is introduced into the resulting linear dynamics to model the effect of nonlinear interactions on the evolution of modes. We examine the H-type transition scenario to demonstrate how our approach can be used to model nonlinear effects and capture the growth of the fundamental and subharmonic modes observed in direct numerical simulations and experiments.

Gauge interaction as periodicity modulation

NASA Astrophysics Data System (ADS)

Dolce, Donatello

2012-06-01

The paper is devoted to a geometrical interpretation of gauge invariance in terms of the formalism of field theory in compact space-time dimensions (Dolce, 2011) [8]. In this formalism, the kinematic information of an interacting elementary particle is encoded on the relativistic geometrodynamics of the boundary of the theory through local transformations of the underlying space-time coordinates. Therefore gauge interactions are described as invariance of the theory under local deformations of the boundary. The resulting local variations of the field solution are interpreted as internal transformations. The internal symmetries of the gauge theory turn out to be related to corresponding space-time local symmetries. In the approximation of local infinitesimal isometric transformations, Maxwell's kinematics and gauge invariance are inferred directly from the variational principle. Furthermore we explicitly impose periodic conditions at the boundary of the theory as semi-classical quantization condition in order to investigate the quantum behavior of gauge interaction. In the abelian case the result is a remarkable formal correspondence with scalar QED.

An Algorithm for the Reconstruction of Neutrino-induced Showers in the ANTARES Neutrino Telescope

NASA Astrophysics Data System (ADS)

Albert, A.; André, M.; Anghinolfi, M.; Anton, G.; Ardid, M.; Aubert, J.-J.; Avgitas, T.; Baret, B.; Barrios-Martí, J.; Basa, S.; Belhorma, B.; Bertin, V.; Biagi, S.; Bormuth, R.; Bourret, S.; Bouwhuis, M. C.; Brânzaş, H.; Bruijn, R.; Brunner, J.; Busto, J.; Capone, A.; Caramete, L.; Carr, J.; Celli, S.; Cherkaoui El Moursli, R.; Chiarusi, T.; Circella, M.; Coelho, J. A. B.; Coleiro, A.; Coniglione, R.; Costantini, H.; Coyle, P.; Creusot, A.; Díaz, A. F.; Deschamps, A.; De Bonis, G.; Distefano, C.; Di Palma, I.; Domi, A.; Donzaud, C.; Dornic, D.; Drouhin, D.; Eberl, T.; El Bojaddaini, I.; El Khayati, N.; Elsässer, D.; Enzenhöfer, A.; Ettahiri, A.; Fassi, F.; Felis, I.; Fusco, L. A.; Gay, P.; Giordano, V.; Glotin, H.; Grégoire, T.; Ruiz, R. Gracia; Graf, K.; Hallmann, S.; van Haren, H.; Heijboer, A. J.; Hello, Y.; Hernández-Rey, J. J.; Hößl, J.; Hofestädt, J.; Hugon, C.; Illuminati, G.; James, C. W.; de Jong, M.; Jongen, M.; Kadler, M.; Kalekin, O.; Katz, U.; Kießling, D.; Kouchner, A.; Kreter, M.; Kreykenbohm, I.; Kulikovskiy, V.; Lachaud, C.; Lahmann, R.; Lefèvre, D.; Leonora, E.; Lotze, M.; Loucatos, S.; Marcelin, M.; Margiotta, A.; Marinelli, A.; Martínez-Mora, J. A.; Mele, R.; Melis, K.; Michael, T.; Migliozzi, P.; Moussa, A.; Navas, S.; Nezri, E.; Organokov, M.; Păvălaş, G. E.; Pellegrino, C.; Perrina, C.; Piattelli, P.; Popa, V.; Pradier, T.; Quinn, L.; Racca, C.; Riccobene, G.; Sánchez-Losa, A.; Saldaña, M.; Salvadori, I.; Samtleben, D. F. E.; Sanguineti, M.; Sapienza, P.; Schüssler, F.; Sieger, C.; Spurio, M.; Stolarczyk, Th.; Taiuti, M.; Tayalati, Y.; Trovato, A.; Turpin, D.; Tönnis, C.; Vallage, B.; Van Elewyck, V.; Versari, F.; Vivolo, D.; Vizzoca, A.; Wilms, J.; Zornoza, J. D.; Zúñiga, J.

2017-12-01

Muons created by {ν }μ charged current (CC) interactions in the water surrounding the ANTARES neutrino telescope have been almost exclusively used so far in searches for cosmic neutrino sources. Due to their long range, highly energetic muons inducing Cherenkov radiation in the water are reconstructed with dedicated algorithms that allow for the determination of the parent neutrino direction with a median angular resolution of about 0.°4 for an {E}-2 neutrino spectrum. In this paper, an algorithm optimized for accurate reconstruction of energy and direction of shower events in the ANTARES detector is presented. Hadronic showers of electrically charged particles are produced by the disintegration of the nucleus both in CC and neutral current interactions of neutrinos in water. In addition, electromagnetic showers result from the CC interactions of electron neutrinos while the decay of a tau lepton produced in {ν }τ CC interactions will, in most cases, lead to either a hadronic or an electromagnetic shower. A shower can be approximated as a point source of photons. With the presented method, the shower position is reconstructed with a precision of about 1 m; the neutrino direction is reconstructed with a median angular resolution between 2° and 3° in the energy range of 1-1000 TeV. In this energy interval, the uncertainty on the reconstructed neutrino energy is about 5%-10%. The increase in the detector sensitivity due to the use of additional information from shower events in the searches for a cosmic neutrino flux is also presented.

Direction-specific van der Waals attraction between rutile TiO2 nanocrystals

NASA Astrophysics Data System (ADS)

Zhang, Xin; He, Yang; Sushko, Maria L.; Liu, Jia; Luo, Langli; De Yoreo, James J.; Mao, Scott X.; Wang, Chongmin; Rosso, Kevin M.

2017-04-01

Mutual lattice orientations dictate the types and magnitudes of forces between crystalline particles. When lattice polarizability is anisotropic, the van der Waals dispersion attraction can, in principle, contribute to this direction dependence. We report measurement of this attraction between rutile nanocrystals, as a function of their mutual orientation and surface hydration extent. At tens of nanometers of separation, the attraction is weak and shows no dependence on azimuthal alignment or surface hydration. At separations of approximately one hydration layer, the attraction is strongly dependent on azimuthal alignment and systematically decreases as intervening water density increases. Measured forces closely agree with predictions from Lifshitz theory and show that dispersion forces can generate a torque between particles interacting in solution and between grains in materials.

Ambient occlusion effects for combined volumes and tubular geometry.

PubMed

Schott, Mathias; Martin, Tobias; Grosset, A V Pascal; Smith, Sean T; Hansen, Charles D

2013-06-01

This paper details a method for interactive direct volume rendering that computes ambient occlusion effects for visualizations that combine both volumetric and geometric primitives, specifically tube-shaped geometric objects representing streamlines, magnetic field lines or DTI fiber tracts. The algorithm extends the recently presented the directional occlusion shading model to allow the rendering of those geometric shapes in combination with a context providing 3D volume, considering mutual occlusion between structures represented by a volume or geometry. Stream tube geometries are computed using an effective spline-based interpolation and approximation scheme that avoids self-intersection and maintains coherent orientation of the stream tube segments to avoid surface deforming twists. Furthermore, strategies to reduce the geometric and specular aliasing of the stream tubes are discussed.

Ambient Occlusion Effects for Combined Volumes and Tubular Geometry

PubMed Central

Schott, Mathias; Martin, Tobias; Grosset, A.V. Pascal; Smith, Sean T.; Hansen, Charles D.

2013-01-01

This paper details a method for interactive direct volume rendering that computes ambient occlusion effects for visualizations that combine both volumetric and geometric primitives, specifically tube-shaped geometric objects representing streamlines, magnetic field lines or DTI fiber tracts. The algorithm extends the recently presented the directional occlusion shading model to allow the rendering of those geometric shapes in combination with a context providing 3D volume, considering mutual occlusion between structures represented by a volume or geometry. Stream tube geometries are computed using an effective spline-based interpolation and approximation scheme that avoids self-intersection and maintains coherent orientation of the stream tube segments to avoid surface deforming twists. Furthermore, strategies to reduce the geometric and specular aliasing of the stream tubes are discussed. PMID:23559506

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

NASA Astrophysics Data System (ADS)

Noah, Joyce E.

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

Anisotropic surface-state-mediated RKKY interaction between adatoms on a hexagonal lattice

NASA Astrophysics Data System (ADS)

Patrone, Paul N.; Einstein, T. L.

2012-01-01

Motivated by recent numerical studies of Ag on Pt(111), we derive an expression for the RKKY interaction mediated by surface states, considering the effect of anisotropy in the Fermi edge. Our analysis is based on a stationary phase approximation. The main contribution to the interaction comes from electrons whose Fermi velocity vF is parallel to the vector R connecting the interacting adatoms; we show that, in general, the corresponding Fermi wave vector kF is not parallel to R. The interaction is oscillatory; the amplitude and wavelength of oscillations have angular dependence arising from the anisotropy of the surface-state band structure. The wavelength, in particular, is determined by the projection of this kF (corresponding to vF) onto the direction of R. Our analysis is easily generalized to other systems. For Ag on Pt(111), our results indicate that the RKKY interaction between pairs of adatoms should be nearly isotropic and so cannot account for the anisotropy found in the studies motivating our work. However, for metals with surface-state dispersions similar to Be(101¯0), we show that the RKKY interaction should have considerable anisotropy.

Wedge sampling for computing clustering coefficients and triangle counts on large graphs

DOE PAGES

Seshadhri, C.; Pinar, Ali; Kolda, Tamara G.

2014-05-08

Graphs are used to model interactions in a variety of contexts, and there is a growing need to quickly assess the structure of such graphs. Some of the most useful graph metrics are based on triangles, such as those measuring social cohesion. Despite the importance of these triadic measures, algorithms to compute them can be extremely expensive. We discuss the method of wedge sampling. This versatile technique allows for the fast and accurate approximation of various types of clustering coefficients and triangle counts. Furthermore, these techniques are extensible to counting directed triangles in digraphs. Our methods come with provable andmore » practical time-approximation tradeoffs for all computations. We provide extensive results that show our methods are orders of magnitude faster than the state of the art, while providing nearly the accuracy of full enumeration.« less

Neutron Imaging Camera

NASA Technical Reports Server (NTRS)

Hunter, Stanley; deNolfo, G. A.; Barbier, L. M.; Link, J. T.; Son, S.; Floyd, S. R.; Guardala, N.; Skopec, M.; Stark, B.

2008-01-01

The Neutron Imaging Camera (NIC) is based on the Three-dimensional Track Imager (3DTI) technology developed at GSFC for gamma-ray astrophysics applications. The 3-DTI, a large volume time-projection chamber, provides accurate, approximately 0.4 mm resolution, 3-D tracking of charged particles. The incident direction of fast neutrons, En > 0.5 MeV, are reconstructed from the momenta and energies of the proton and triton fragments resulting from (sup 3)He(n,p) (sup 3)H interactions in the 3-DTI volume. The performance of the NIC from laboratory and accelerator tests is presented.

Structural Response Prediction: Full-field, Dynamic Pressure and Displacement Measurements of a Panel Excited by Shock Boundary-layer Interaction

DTIC Science & Technology

2015-02-01

research cell14. The RC-19 facility is a continuous flow wind tunnel designed to study the mechanisms that govern the mixing and combustion process... angle of 39° from the tunnel bottom wall. The shock generator can translate 170 mm in the flow direction to allow for the shock wave to impinge from...approximate absolute pressure of 20.5 kPa. A series of “ wind -off” images for PSP were collected at that time. The tunnel was then started by setting the

Antisymmetrization effects and the form factor of the real part of the. cap alpha. -nucleus potential

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

Majka, Z.; Budzanowski, A.; Grotowski, K.

1978-07-01

Antisymmetrization effects in the ..cap alpha..-nucleus interaction are investigated on the basis of a microscopic model in an one nucleon exchange approximation. It influences the form factor, increasing the halfway radius and decreasing the diffuseness as compared with the direct term of the potential only. Antisymmetrization preserves the shape of the potential which can be parametrized by a Woods-Saxon squared form. The phenomenological potential with the energy independent form factor of the above shape fits experimental data in a wide energy region.

Implementation of a finite-amplitude method in a relativistic meson-exchange model

NASA Astrophysics Data System (ADS)

Sun, Xuwei; Lu, Dinghui

2017-08-01

The finite-amplitude method is a feasible numerical approach to large scale random phase approximation calculations. It avoids the storage and calculation of residual interaction elements as well as the diagonalization of the RPA matrix, which will be prohibitive when the configuration space is huge. In this work we finished the implementation of a finite-amplitude method in a relativistic meson exchange mean field model with axial symmetry. The direct variation approach makes our FAM scheme capable of being extended to the multipole excitation case.

Influence of the quantum dot geometry on p -shell transitions in differently charged quantum dots

NASA Astrophysics Data System (ADS)

Holtkemper, M.; Reiter, D. E.; Kuhn, T.

2018-02-01

Absorption spectra of neutral, negatively, and positively charged semiconductor quantum dots are studied theoretically. We provide an overview of the main energetic structure around the p -shell transitions, including the influence of nearby nominally dark states. Based on the envelope function approximation, we treat the four-band Luttinger theory as well as the direct and short-range exchange Coulomb interactions within a configuration interaction approach. The quantum dot confinement is approximated by an anisotropic harmonic potential. We present a detailed investigation of state mixing and correlations mediated by the individual interactions. Differences and similarities between the differently charged quantum dots are highlighted. Especially large differences between negatively and positively charged quantum dots become evident. We present a visualization of energetic shifts and state mixtures due to changes in size, in-plane asymmetry, and aspect ratio. Thereby we provide a better understanding of the experimentally hard to access question of quantum dot geometry effects. Our findings show a method to determine the in-plane asymmetry from photoluminescence excitation spectra. Furthermore, we supply basic knowledge for tailoring the strength of certain state mixtures or the energetic order of particular excited states via changes of the shape of the quantum dot. Such knowledge builds the basis to find the optimal QD geometry for possible applications and experiments using excited states.

Approximate symmetries in atomic nuclei from a large-scale shell-model perspective

NASA Astrophysics Data System (ADS)

Launey, K. D.; Draayer, J. P.; Dytrych, T.; Sun, G.-H.; Dong, S.-H.

2015-05-01

In this paper, we review recent developments that aim to achieve further understanding of the structure of atomic nuclei, by capitalizing on exact symmetries as well as approximate symmetries found to dominate low-lying nuclear states. The findings confirm the essential role played by the Sp(3, ℝ) symplectic symmetry to inform the interaction and the relevant model spaces in nuclear modeling. The significance of the Sp(3, ℝ) symmetry for a description of a quantum system of strongly interacting particles naturally emerges from the physical relevance of its generators, which directly relate to particle momentum and position coordinates, and represent important observables, such as, the many-particle kinetic energy, the monopole operator, the quadrupole moment and the angular momentum. We show that it is imperative that shell-model spaces be expanded well beyond the current limits to accommodate particle excitations that appear critical to enhanced collectivity in heavier systems and to highly-deformed spatial structures, exemplified by the second 0+ state in 12C (the challenging Hoyle state) and 8Be. While such states are presently inaccessible by large-scale no-core shell models, symmetry-based considerations are found to be essential.

Diffusiophoretic self-propulsion for partially catalytic spherical colloids.

PubMed

de Graaf, Joost; Rempfer, Georg; Holm, Christian

2015-04-01

Colloidal spheres with a partial platinum surface coating perform autophoretic motion when suspended in hydrogen peroxide solution. We present a theoretical analysis of the self-propulsion velocity of these particles using a continuum multi-component, self-diffusiophoretic model. With this model as a basis, we show how the slip-layer approximation can be derived and in which limits it holds. First, we consider the differences between the full multi-component model and the slip-layer approximation. Then the slip model is used to demonstrate and explore the sensitive nature of the particle's velocity on the details of the molecule-surface interaction. We find a strong asymmetry in the dependence of the colloid's velocity as a function of the level of catalytic coating, when there is a different interaction between the solute and solvent molecules and the inert and catalytic part of the colloid, respectively. The direction of motion can even be reversed by varying the level of the catalytic coating. Finally, we investigate the robustness of these results with respect to variations in the reaction rate near the edge between the catalytic and inert parts of the particle. Our results are of significant interest to the interpretation of experimental results on the motion of self-propelled particles.

Identifying traction-separation behavior of self-adhesive polymeric films from in situ digital images under T-peeling

NASA Astrophysics Data System (ADS)

Nase, Michael; Rennert, Mirko; Naumenko, Konstantin; Eremeyev, Victor A.

2016-06-01

In this paper procedures are developed to identify traction-separation curves from digital images of the deformed flexible films during peeling. T-peel tests were performed for self-adhesive polymeric films. High quality photographs of the deformed shape within and outside the zone of adhesive interaction were made in situ by the digital light microscope. The deformed line is approximated by a power series with coefficients computed by minimizing a least squares functional. Two approaches to identify the traction-separation curve for the given deformation line are proposed. The first one is based on the energy integral of the non-linear theory of rods and allows the direct evaluation of the adhesion force potential. The second one utilizes the complementary energy type variational equation and the Ritz method to compute the adhesion force. The accuracy of both approaches is analyzed with respect to different approximations for the deformed line and the force of interaction. The obtained traction vs. axial coordinate and the traction-separation curves provide several properties of the adhesive system including the maximum adhesion force, the length of the adhesive zone and the equilibrium position, where the adhesive force is zero while the separation is positive.

Nonlocal Symmetries, Conservation Laws and Interaction Solutions of the Generalised Dispersive Modified Benjamin-Bona-Mahony Equation

NASA Astrophysics Data System (ADS)

Yan, Xue-Wei; Tian, Shou-Fu; Dong, Min-Jie; Wang, Xiu-Bin; Zhang, Tian-Tian

2018-05-01

We consider the generalised dispersive modified Benjamin-Bona-Mahony equation, which describes an approximation status for long surface wave existed in the non-linear dispersive media. By employing the truncated Painlevé expansion method, we derive its non-local symmetry and Bäcklund transformation. The non-local symmetry is localised by a new variable, which provides the corresponding non-local symmetry group and similarity reductions. Moreover, a direct method can be provided to construct a kind of finite symmetry transformation via the classic Lie point symmetry of the normal prolonged system. Finally, we find that the equation is a consistent Riccati expansion solvable system. With the help of the Jacobi elliptic function, we get its interaction solutions between solitary waves and cnoidal periodic waves.

Limits on spin-dependent WIMP-nucleon cross sections from the XENON10 experiment.

PubMed

Angle, J; Aprile, E; Arneodo, F; Baudis, L; Bernstein, A; Bolozdynya, A; Coelho, L C C; Dahl, C E; DeViveiros, L; Ferella, A D; Fernandes, L M P; Fiorucci, S; Gaitskell, R J; Giboni, K L; Gomez, R; Hasty, R; Kastens, L; Kwong, J; Lopes, J A M; Madden, N; Manalaysay, A; Manzur, A; McKinsey, D N; Monzani, M E; Ni, K; Oberlack, U; Orboeck, J; Plante, G; Santorelli, R; dos Santos, J M F; Shagin, P; Shutt, T; Sorensen, P; Schulte, S; Winant, C; Yamashita, M

2008-08-29

XENON10 is an experiment to directly detect weakly interacting massive particles (WIMPs), which may comprise the bulk of the nonbaryonic dark matter in our Universe. We report new results for spin-dependent WIMP-nucleon interactions with 129Xe and 131Xe from 58.6 live days of operation at the Laboratori Nazionali del Gran Sasso. Based on the nonobservation of a WIMP signal in 5.4 kg of fiducial liquid xenon mass, we exclude previously unexplored regions in the theoretically allowed parameter space for neutralinos. We also exclude a heavy Majorana neutrino with a mass in the range of approximately 10 GeV/c2-2 TeV/c2 as a dark matter candidate under standard assumptions for its density and distribution in the galactic halo.

Fast Electron Correlation Methods for Molecular Clusters without Basis Set Superposition Errors

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

Kamiya, Muneaki; Hirata, So; Valiev, Marat

2008-02-19

Two critical extensions to our fast, accurate, and easy-to-implement binary or ternary interaction method for weakly-interacting molecular clusters [Hirata et al. Mol. Phys. 103, 2255 (2005)] have been proposed, implemented, and applied to water hexamers, hydrogen fluoride chains and rings, and neutral and zwitterionic glycine–water clusters with an excellent result for an initial performance assessment. Our original method included up to two- or three-body Coulomb, exchange, and correlation energies exactly and higher-order Coulomb energies in the dipole–dipole approximation. In this work, the dipole moments are replaced by atom-centered point charges determined so that they reproduce the electrostatic potentials of themore » cluster subunits as closely as possible and also self-consistently with one another in the cluster environment. They have been shown to lead to dramatic improvement in the description of short-range electrostatic potentials not only of large, charge-separated subunits like zwitterionic glycine but also of small subunits. Furthermore, basis set superposition errors (BSSE) known to plague direct evaluation of weak interactions have been eliminated by com-bining the Valiron–Mayer function counterpoise (VMFC) correction with our binary or ternary interaction method in an economical fashion (quadratic scaling n2 with respect to the number of subunits n when n is small and linear scaling when n is large). A new variant of VMFC has also been proposed in which three-body and all higher-order Coulomb effects on BSSE are estimated approximately. The BSSE-corrected ternary interaction method with atom-centered point charges reproduces the VMFC-corrected results of conventional electron correlation calculations within 0.1 kcal/mol. The proposed method is significantly more accurate and also efficient than conventional correlation methods uncorrected of BSSE.« less

Capacitive charge storage at an electrified interface investigated via direct first-principles simulations [Direct Simulation of Capacitive Charging of Graphene and Implications for Supercapacitor Design

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

Radin, Maxwell D.; Ogitsu, Tadashi; Biener, Juergen

Understanding the impact of interfacial electric fields on electronic structure is crucial to improving the performance of materials in applications based on charged interfaces. Supercapacitors store energy directly in the strong interfacial field between a solid electrode and a liquid electrolyte; however, the complex interplay between the two is often poorly understood, particularly for emerging low-dimensional electrode materials that possess unconventional electronic structure. Typical descriptions tend to neglect the specific electrode-electrolyte interaction, approximating the intrinsic “quantum capacitance” of the electrode in terms of a fixed electronic density of states. Instead, we introduce a more accurate first-principles approach for directly simulatingmore » charge storage in model capacitors using the effective screening medium method, which implicitly accounts for the presence of the interfacial electric field. Applying this approach to graphene supercapacitor electrodes, we find that results differ significantly from the predictions of fixed-band models, leading to improved consistency with experimentally reported capacitive behavior. The differences are traced to two key factors: the inhomogeneous distribution of stored charge due to poor electronic screening and interfacial contributions from the specific interaction with the electrolyte. Lastly, our results are used to revise the conventional definition of quantum capacitance and to provide general strategies for improving electrochemical charge storage, particularly in graphene and similar low-dimensional materials.« less

Capacitive charge storage at an electrified interface investigated via direct first-principles simulations [Direct Simulation of Capacitive Charging of Graphene and Implications for Supercapacitor Design

DOE PAGES

Radin, Maxwell D.; Ogitsu, Tadashi; Biener, Juergen; ...

2015-03-11

Understanding the impact of interfacial electric fields on electronic structure is crucial to improving the performance of materials in applications based on charged interfaces. Supercapacitors store energy directly in the strong interfacial field between a solid electrode and a liquid electrolyte; however, the complex interplay between the two is often poorly understood, particularly for emerging low-dimensional electrode materials that possess unconventional electronic structure. Typical descriptions tend to neglect the specific electrode-electrolyte interaction, approximating the intrinsic “quantum capacitance” of the electrode in terms of a fixed electronic density of states. Instead, we introduce a more accurate first-principles approach for directly simulatingmore » charge storage in model capacitors using the effective screening medium method, which implicitly accounts for the presence of the interfacial electric field. Applying this approach to graphene supercapacitor electrodes, we find that results differ significantly from the predictions of fixed-band models, leading to improved consistency with experimentally reported capacitive behavior. The differences are traced to two key factors: the inhomogeneous distribution of stored charge due to poor electronic screening and interfacial contributions from the specific interaction with the electrolyte. Lastly, our results are used to revise the conventional definition of quantum capacitance and to provide general strategies for improving electrochemical charge storage, particularly in graphene and similar low-dimensional materials.« less

You can hide but you have to run: Direct detection with vector mediators

DOE PAGES

D’Eramo, Francesco; Kavanagh, Bradley J.; Panci, Paolo

2016-08-18

We study direct detection in simplified models of Dark Matter (DM) in which interactions with Standard Model (SM) fermions are mediated by a heavy vector boson. We consider fully general, gauge-invariant couplings between the SM, the mediator and both scalar and fermion DM. We account for the evolution of the couplings between the energy scale of the mediator mass and the nuclear energy scale. This running arises from virtual effects of SM particles and its inclusion is not optional. We compare bounds on the mediator mass from direct detection experiments with and without accounting for the running. In some casesmore » the inclusion of these effects changes the bounds by several orders of magnitude, as a consequence of operator mixing which generates new interactions at low energy. We also highlight the importance of these effects when translating LHC limits on the mediator mass into bounds on the direct detection cross section. For an axial-vector mediator, the running can alter the derived bounds on the spin-dependent DM-nucleon cross section by a factor of two or more. Lastly, we provide tools to facilitate the inclusion of these effects in future studies: general approximate expressions for the low energy couplings and a public code runDM to evolve the couplings between arbitrary energy scales.« less

You can hide but you have to run: Direct detection with vector mediators

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

D’Eramo, Francesco; Kavanagh, Bradley J.; Panci, Paolo

We study direct detection in simplified models of Dark Matter (DM) in which interactions with Standard Model (SM) fermions are mediated by a heavy vector boson. We consider fully general, gauge-invariant couplings between the SM, the mediator and both scalar and fermion DM. We account for the evolution of the couplings between the energy scale of the mediator mass and the nuclear energy scale. This running arises from virtual effects of SM particles and its inclusion is not optional. We compare bounds on the mediator mass from direct detection experiments with and without accounting for the running. In some casesmore » the inclusion of these effects changes the bounds by several orders of magnitude, as a consequence of operator mixing which generates new interactions at low energy. We also highlight the importance of these effects when translating LHC limits on the mediator mass into bounds on the direct detection cross section. For an axial-vector mediator, the running can alter the derived bounds on the spin-dependent DM-nucleon cross section by a factor of two or more. Lastly, we provide tools to facilitate the inclusion of these effects in future studies: general approximate expressions for the low energy couplings and a public code runDM to evolve the couplings between arbitrary energy scales.« less

Application of viscous-inviscid interaction methods to transonic turbulent flows

NASA Technical Reports Server (NTRS)

Lee, D.; Pletcher, R. H.

1986-01-01

Two different viscous-inviscid interaction schemes were developed for the analysis of steady, turbulent, transonic, separated flows over axisymmetric bodies. The viscous and inviscid solutions are coupled through the displacement concept using a transpiration velocity approach. In the semi-inverse interaction scheme, the viscous and inviscid equations are solved in an explicitly separate manner and the displacement thickness distribution is iteratively updated by a simple coupling algorithm. In the simultaneous interaction method, local solutions of viscous and inviscid equations are treated simultaneously, and the displacement thickness is treated as an unknown and is obtained as a part of the solution through a global iteration procedure. The inviscid flow region is described by a direct finite-difference solution of a velocity potential equation in conservative form. The potential equation is solved on a numerically generated mesh by an approximate factorization (AF2) scheme in the semi-inverse interaction method and by a successive line overrelaxation (SLOR) scheme in the simultaneous interaction method. The boundary-layer equations are used for the viscous flow region. The continuity and momentum equations are solved inversely in a coupled manner using a fully implicit finite-difference scheme.

Evidence signaling the start of enhanced counterjet flow in the symbiotic system R AquarII

NASA Technical Reports Server (NTRS)

Michalitsianos, A. G.; Perez, M.; Kafatos, M.

1994-01-01

The velocity struture of strong far-UV emission lines observed in the symbiotic variable R Aqr suggests the start of new jet activity which will probably culminate in the appearance of a series of intense nebular emission knots within a decade. This is indicated by a systematic redward wavelength drift of emission lines, which we have followed with the International Ultraviolet Explorer (IUE) since the discovery of the brilliant northeast jet emission knots more than 10 years ago. The C IV wavelengths 1548, 1550 resonance lines, which previously showed a prominent blue asymmetric wing that extended to velocities in excess -200 km/s, exhibit red wing asymmetry that extends to speeds of approximately +200 km/s in late 1992. The C IV line profile structure is consistent with the model proposed by Solf (1993), who explains the appearance of the northeast jet knots in terms of a approximately 300-500 km/s collimated wind that collides with slower moving material expelled earlier in a nova outburst that occurred approximately 190 yr ago. Based upon these high-resolution UV spectra, similar emission structues should appear southwest of the central star when the counterwind (or stream) interacts with material in the southwest inner nebula. The apparent change in direction of flow could result from a precessing accretion disk that alters the projection angle of collimated flow from the disk poles. The direction of the collimated wind may be related to the binary orbit, because the velocity shifts associated with emission lines formed in the flow change direction on a timescale which is comparable to the binary period.

A theoretical formulation of wave-vortex interactions

NASA Technical Reports Server (NTRS)

Wu, J. Z.; Wu, J. M.

1989-01-01

A unified theoretical formulation for wave-vortex interaction, designated the '(omega, Pi) framework,' is presented. Based on the orthogonal decomposition of fluid dynamic interactions, the formulation can be used to study a variety of problems, including the interaction of a longitudinal (acoustic) wave and/or transverse (vortical) wave with a main vortex flow. Moreover, the formulation permits a unified treatment of wave-vortex interaction at various approximate levels, where the normal 'piston' process and tangential 'rubbing' process can be approximated dfferently.

Direct differentiation of the quasi-incompressible fluid formulation of fluid-structure interaction using the PFEM

NASA Astrophysics Data System (ADS)

Zhu, Minjie; Scott, Michael H.

2017-07-01

Accurate and efficient response sensitivities for fluid-structure interaction (FSI) simulations are important for assessing the uncertain response of coastal and off-shore structures to hydrodynamic loading. To compute gradients efficiently via the direct differentiation method (DDM) for the fully incompressible fluid formulation, approximations of the sensitivity equations are necessary, leading to inaccuracies of the computed gradients when the geometry of the fluid mesh changes rapidly between successive time steps or the fluid viscosity is nonzero. To maintain accuracy of the sensitivity computations, a quasi-incompressible fluid is assumed for the response analysis of FSI using the particle finite element method and DDM is applied to this formulation, resulting in linearized equations for the response sensitivity that are consistent with those used to compute the response. Both the response and the response sensitivity can be solved using the same unified fractional step method. FSI simulations show that although the response using the quasi-incompressible and incompressible fluid formulations is similar, only the quasi-incompressible approach gives accurate response sensitivity for viscous, turbulent flows regardless of time step size.

Kinetic structures of quasi-perpendicular shocks in global particle-in-cell simulations

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

Peng, Ivy Bo, E-mail: bopeng@kth.se; Markidis, Stefano; Laure, Erwin

2015-09-15

We carried out global Particle-in-Cell simulations of the interaction between the solar wind and a magnetosphere to study the kinetic collisionless physics in super-critical quasi-perpendicular shocks. After an initial simulation transient, a collisionless bow shock forms as a result of the interaction of the solar wind and a planet magnetic dipole. The shock ramp has a thickness of approximately one ion skin depth and is followed by a trailing wave train in the shock downstream. At the downstream edge of the bow shock, whistler waves propagate along the magnetic field lines and the presence of electron cyclotron waves has beenmore » identified. A small part of the solar wind ion population is specularly reflected by the shock while a larger part is deflected and heated by the shock. Solar wind ions and electrons are heated in the perpendicular directions. Ions are accelerated in the perpendicular direction in the trailing wave train region. This work is an initial effort to study the electron and ion kinetic effects developed near the bow shock in a realistic magnetic field configuration.« less

Mode-coupling and wave-particle interactions for unstable ion-acoustic waves.

NASA Technical Reports Server (NTRS)

Martin, P.; Fried, B. D.

1972-01-01

A theory for the spatial development of linearly unstable, coupled waves is presented in which both quasilinear and mode-coupling effects are treated in a self-consistent manner. Steady-state excitation of two waves is assumed at the boundary x = 0, the plasma being homogeneous in the y and z directions. Coupled equations are derived for the x dependence of the amplitudes of the primary waves and the secondary waves, correct through terms of second order in the wave amplitude, but without the usual approximation of small growth rates. This general formalism is then applied to the case of coupled ion-acoustic waves driven unstable by an ion beam streaming in the direction of the x axis. If the modifications of the ion beam by the waves (quasilinear effects) are ignored, explosive instabilities (singularities in all of the amplitudes at finite x) are found even when all of the waves have positive energy. If these wave-particle interactions are included, the solutions are no longer singular, and all of the amplitudes have finite maxima.

Mode coupling and wave particle interactions for unstable ion acoustic waves

NASA Technical Reports Server (NTRS)

Martin, P.; Fried, B. D.

1972-01-01

A theory for the spatial development of linearly unstable, coupled waves is presented in which both quasi-linear and mode coupling effects are treated in a self-consistent manner. Steady state excitation of two waves is assumed at the boundary x = 0, the plasma being homogeneous in the y and z directions. Coupled equations are derived for the x dependence of the amplitudes of the primary waves and the secondary waves, correct through second order terms in the wave amplitude, but without usual approximation of small growth rates. This general formalism is then applied to the case of coupled ion acoustic waves driven unstable by an ion beam streaming in the direction of the x axis. If the modifications of the ion beam by the waves (quasi-linear effects) are ignored, explosive instabilities (singularities in all of the amplitudes at finite x) are found, even when all of the waves have positive energy. If these wave-particle interactions are included, the solutions are no longer singular, and all of the amplitudes have finite maxima.

Flow-field Survey of an Empennage Wake Interacting with a Pusher Propeller

NASA Technical Reports Server (NTRS)

Horne, W. Clifton; Soderman, Paul T.

1988-01-01

The flow field between a model empennage and a 591-mm-diameter pusher propeller was studied in the Ames 7- by 10-Foot Wind Tunnel with directional pressure probes and hot-wire anemometers. The region probed was bounded by the empennage trailing edge and downstream propeller. The wake properties, including effects of propeller operation on the empennage wake, were investigated for two empennage geometries: one, a vertical tail fin, the other, a Y-tail with a 34 deg dihedral. Results showed that the effect of the propeller on the empennage wake upstream of the propeller was not strong. The flow upstream of the propeller was accelerated in the streamwise direction by the propeller, but the empennage wake width and velocity defect were relatively unaffected by the presence of the propeller. The peak turbulence in the wake near the propeller tip station, 0.66 diameter behind the vertical tail fin, was approximately 3 percent of the free-stream velocity. The velocity field data can be used in predictions of the acoustic field due to propeller-wake interaction.

Phospholipase D2 Mediates Survival Signaling through Direct Regulation of Akt in Glioblastoma Cells*♦

PubMed Central

Bruntz, Ronald C.; Taylor, Harry E.; Lindsley, Craig W.; Brown, H. Alex

2014-01-01

The lack of innovative drug targets for glioblastoma multiforme (GBM) limits patient survival to approximately 1 year following diagnosis. The pro-survival kinase Akt provides an ideal target for the treatment of GBM as Akt signaling is frequently activated in this cancer type. However, the central role of Akt in physiological processes limits its potential as a therapeutic target. In this report, we show that the lipid-metabolizing enzyme phospholipase D (PLD) is a novel regulator of Akt in GBM. Studies using a combination of small molecule PLD inhibitors and siRNA knockdowns establish phosphatidic acid, the product of the PLD reaction, as an essential component for the membrane recruitment and activation of Akt. Inhibition of PLD enzymatic activity and subsequent Akt activation decreases GBM cell viability by specifically inhibiting autophagic flux. We propose a mechanism whereby phosphorylation of beclin1 by Akt prevents binding of Rubicon (RUN domain cysteine-rich domain containing beclin1-interacting protein), an interaction known to inhibit autophagic flux. These findings provide a novel framework through which Akt inhibition can be achieved without directly targeting the kinase. PMID:24257753

Interactive Near-Field Illumination for Photorealistic Augmented Reality with Varying Materials on Mobile Devices.

PubMed

Rohmer, Kai; Buschel, Wolfgang; Dachselt, Raimund; Grosch, Thorsten

2015-12-01

At present, photorealistic augmentation is not yet possible since the computational power of mobile devices is insufficient. Even streaming solutions from stationary PCs cause a latency that affects user interactions considerably. Therefore, we introduce a differential rendering method that allows for a consistent illumination of the inserted virtual objects on mobile devices, avoiding delays. The computation effort is shared between a stationary PC and the mobile devices to make use of the capacities available on both sides. The method is designed such that only a minimum amount of data has to be transferred asynchronously between the participants. This allows for an interactive illumination of virtual objects with a consistent appearance under both temporally and spatially varying real illumination conditions. To describe the complex near-field illumination in an indoor scenario, HDR video cameras are used to capture the illumination from multiple directions. In this way, sources of illumination can be considered that are not directly visible to the mobile device because of occlusions and the limited field of view. While our method focuses on Lambertian materials, we also provide some initial approaches to approximate non-diffuse virtual objects and thereby allow for a wider field of application at nearly the same cost.

Robust Nonlinear Causality Analysis of Nonstationary Multivariate Physiological Time Series.

PubMed

Schack, Tim; Muma, Michael; Feng, Mengling; Guan, Cuntai; Zoubir, Abdelhak M

2018-06-01

An important research area in biomedical signal processing is that of quantifying the relationship between simultaneously observed time series and to reveal interactions between the signals. Since biomedical signals are potentially nonstationary and the measurements may contain outliers and artifacts, we introduce a robust time-varying generalized partial directed coherence (rTV-gPDC) function. The proposed method, which is based on a robust estimator of the time-varying autoregressive (TVAR) parameters, is capable of revealing directed interactions between signals. By definition, the rTV-gPDC only displays the linear relationships between the signals. We therefore suggest to approximate the residuals of the TVAR process, which potentially carry information about the nonlinear causality by a piece-wise linear time-varying moving-average model. The performance of the proposed method is assessed via extensive simulations. To illustrate the method's applicability to real-world problems, it is applied to a neurophysiological study that involves intracranial pressure, arterial blood pressure, and brain tissue oxygenation level (PtiO2) measurements. The rTV-gPDC reveals causal patterns that are in accordance with expected cardiosudoral meachanisms and potentially provides new insights regarding traumatic brain injuries. The rTV-gPDC is not restricted to the above problem but can be useful in revealing interactions in a broad range of applications.

Hyper-Rayleigh scattering in centrosymmetric systems

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

Williams, Mathew D.; Ford, Jack S.; Andrews, David L., E-mail: david.andrews@physics.org

Hyper-Rayleigh scattering (HRS) is an incoherent mechanism for optical second harmonic generation. The frequency-doubled light that emerges from this mechanism is not emitted in a laser-like manner, in the forward direction; it is scattered in all directions. The underlying theory for this effect involves terms that are quadratic in the incident field and involves an even-order optical susceptibility (for a molecule, its associated hyperpolarizability). In consequence, HRS is often regarded as formally forbidden in centrosymmetric media. However, for the fundamental three-photon interaction, theory based on the standard electric dipole approximation, representable as E1{sup 3}, does not account for all experimentalmore » observations. The relevant results emerge upon extending the theory to include E1{sup 2}M1 and E1{sup 2}E2 contributions, incorporating one magnetic dipolar or electric quadrupolar interaction, respectively, to a consistent level of multipolar expansion. Both additional interactions require the deployment of higher orders in the multipole expansion, with the E1{sup 2}E2 interaction analogous in rank and parity to a four-wave susceptibility. To elicit the correct form of response from fluid or disordered media invites a tensor representation which does not oversimplify the molecular components, yet which can produce results to facilitate the interpretation of experimental observations. The detailed derivation in this work leads to results which are summarized for the following: perpendicular detection of polarization components both parallel and perpendicular to the pump radiation, leading to distinct polarization ratio results, as well as a reversal ratio for forward scattered circular polarizations. The results provide a route to handling data with direct physical interpretation, to enable the more sophisticated design of molecules with sought nonlinear optical properties.« less

Theory of Mind Experience Sampling in Typical Adults

PubMed Central

Coffey, Anna; Povinelli, Daniel J.; Pruett, John R.

2013-01-01

We explored the frequency with which typical adults make Theory of Mind (ToM) attributions, and under what circumstances these attributions occur. We used an experience sampling method to query 30 typical adults about their everyday thoughts. Participants carried a Personal Data Assistant (PDA) that prompted them to categorize their thoughts as Action, Mental State, or Miscellaneous at approximately 30 pseudo-random times during a continuous 10-hr period. Additionally, participants noted the direction of their thought (self vs. other) and degree of socializing (with people vs. alone) at the time of inquiry. We were interested in the relative frequency of ToM (mental state attributions) and how prominent they were in immediate social exchanges. Analyses of multiple choice answers suggest that typical adults: 1) spend more time thinking about actions than mental states and miscellaneous things, 2) exhibit a higher degree of own- versus other-directed thought when alone, and 3) make mental state attributions more frequently when not interacting (offline) than while interacting with others (online). A significant 3-way interaction between thought type, direction of thought, and socializing emerged because action but not mental state thoughts about others occurred more frequently when participants were interacting with people versus when alone; whereas there was an increase in the frequency of both action and mental state attributions about the self when participants were alone as opposed to socializing. A secondary analysis of coded free text responses supports findings 1–3. The results of this study help to create a more naturalistic picture of ToM use in everyday life and the method shows promise for future study of typical and atypical thought processes. PMID:23685620

Theory of Mind experience sampling in typical adults.

PubMed

Bryant, Lauren; Coffey, Anna; Povinelli, Daniel J; Pruett, John R

2013-09-01

We explored the frequency with which typical adults make Theory of Mind (ToM) attributions, and under what circumstances these attributions occur. We used an experience sampling method to query 30 typical adults about their everyday thoughts. Participants carried a Personal Data Assistant (PDA) that prompted them to categorize their thoughts as Action, Mental State, or Miscellaneous at approximately 30 pseudo-random times during a continuous 10-h period. Additionally, participants noted the direction of their thought (self versus other) and degree of socializing (with people versus alone) at the time of inquiry. We were interested in the relative frequency of ToM (mental state attributions) and how prominent they were in immediate social exchanges. Analyses of multiple choice answers suggest that typical adults: (1) spend more time thinking about actions than mental states and miscellaneous things, (2) exhibit a higher degree of own- versus other-directed thought when alone, and (3) make mental state attributions more frequently when not interacting (offline) than while interacting with others (online). A significant 3-way interaction between thought type, direction of thought, and socializing emerged because action but not mental state thoughts about others occurred more frequently when participants were interacting with people versus when alone; whereas there was an increase in the frequency of both action and mental state attributions about the self when participants were alone as opposed to socializing. A secondary analysis of coded free text responses supports findings 1-3. The results of this study help to create a more naturalistic picture of ToM use in everyday life and the method shows promise for future study of typical and atypical thought processes. Copyright © 2013 Elsevier Inc. All rights reserved.

Hyper-Rayleigh scattering in centrosymmetric systems

NASA Astrophysics Data System (ADS)

Williams, Mathew D.; Ford, Jack S.; Andrews, David L.

2015-09-01

Hyper-Rayleigh scattering (HRS) is an incoherent mechanism for optical second harmonic generation. The frequency-doubled light that emerges from this mechanism is not emitted in a laser-like manner, in the forward direction; it is scattered in all directions. The underlying theory for this effect involves terms that are quadratic in the incident field and involves an even-order optical susceptibility (for a molecule, its associated hyperpolarizability). In consequence, HRS is often regarded as formally forbidden in centrosymmetric media. However, for the fundamental three-photon interaction, theory based on the standard electric dipole approximation, representable as E13, does not account for all experimental observations. The relevant results emerge upon extending the theory to include E12M1 and E12E2 contributions, incorporating one magnetic dipolar or electric quadrupolar interaction, respectively, to a consistent level of multipolar expansion. Both additional interactions require the deployment of higher orders in the multipole expansion, with the E12E2 interaction analogous in rank and parity to a four-wave susceptibility. To elicit the correct form of response from fluid or disordered media invites a tensor representation which does not oversimplify the molecular components, yet which can produce results to facilitate the interpretation of experimental observations. The detailed derivation in this work leads to results which are summarized for the following: perpendicular detection of polarization components both parallel and perpendicular to the pump radiation, leading to distinct polarization ratio results, as well as a reversal ratio for forward scattered circular polarizations. The results provide a route to handling data with direct physical interpretation, to enable the more sophisticated design of molecules with sought nonlinear optical properties.

Application of a Phase-resolving, Directional Nonlinear Spectral Wave Model

NASA Astrophysics Data System (ADS)

Davis, J. R.; Sheremet, A.; Tian, M.; Hanson, J. L.

2014-12-01

We describe several applications of a phase-resolving, directional nonlinear spectral wave model. The model describes a 2D surface gravity wave field approaching a mildly sloping beach with parallel depth contours at an arbitrary angle accounting for nonlinear, quadratic triad interactions. The model is hyperbolic, with the initial wave spectrum specified in deep water. Complex amplitudes are generated based on the random phase approximation. The numerical implementation includes unidirectional propagation as a special case. In directional mode, it solves the system of equations in the frequency-alongshore wave number space. Recent enhancements of the model include the incorporation of dissipation caused by breaking and propagation over a viscous mud layer and the calculation of wave induced setup. Applications presented include: a JONSWAP spectrum with a cos2s directional distribution, for shore-perpendicular and oblique propagation, a study of the evolution of a single directional triad, and several preliminary comparisons to wave spectra collected at the USACE-FRF in Duck, NC which show encouraging results although further validation with a wider range of beach slopes and wave conditions is needed.

Overview: Parity Violation and Fundamental Symmetries

NASA Astrophysics Data System (ADS)

Carlini, Roger

2017-09-01

The fields of nuclear and particle physics have undertaken extensive programs of research to search for evidence of new phenomena via the precision measurement of observables that are well predicted within the standard model of electroweak interaction. It is already known that the standard model is incomplete as it does not include gravity and dark matter/energy and therefore likely the low energy approximation of a more complex theory. This talk will be an overview of the motivation, experimental methods and status of some of these efforts (past and future) related to precision in-direct searches that are complementary to the direct searches underway at the Large Hadron Collider. This abstract is for the invited talk associated with the Mini-symposium titled ``Electro-weak Physics and Fundamental Symmetries'' organized by Julie Roche.

Comparative DMFT study of the eg-orbital Hubbard model in thin films

NASA Astrophysics Data System (ADS)

Rüegg, Andreas; Hung, Hsiang-Hsuan; Gull, Emanuel; Fiete, Gregory A.

2014-02-01

Heterostructures of transition-metal oxides have emerged as a new route to engineer electronic systems with desired functionalities. Motivated by these developments, we study a two-orbital Hubbard model in a thin-film geometry confined along the cubic [001] direction using the dynamical mean-field theory. We contrast the results of two approximate impurity solvers (exact diagonalization and one-crossing approximation) to the results of the numerically exact continuous-time quantum Monte Carlo solver. Consistent with earlier studies, we find that the one-crossing approximation performs well in the insulating regime, while the advantage of the exact-diagonalization-based solver is more pronounced in the metallic regime. We then investigate various aspects of strongly correlated eg-orbital systems in thin-film geometries. In particular, we show how the interfacial orbital polarization dies off quickly a few layers from the interface and how the film thickness affects the location of the interaction-driven Mott transition. In addition, we explore the changes in the electronic structure with varying carrier concentration and identify large variations of the orbital polarization in the strongly correlated regime.

Excitation energy migration processes in various multi-porphyrin assemblies.

PubMed

Yang, Jaesung; Kim, Dongho

2012-08-13

The electronic interactions and excitation energy transfer (EET) processes of a variety of multi-porphyrin arrays with linear, cyclic and box architectures have been explored. Directly meso-meso linked linear arrays (Z(N)) exhibit strong excitonic coupling with an exciton coherence length of approximately 6 porphyrin units, while fused linear arrays (T(N)) exhibit extensive π-conjugation over the whole array. The excitonic coherence length in directly linked cyclic porphyrin rings (CZ(N)) was determined to be approximately 2.7 porphyrin units by simultaneous analysis of fluorescence intensities and lifetimes at the single-molecule level. By performing transient absorption (TA) and TA anisotropy decay measurements, the EET rates in m-phenylene linked cyclic porphyrin wheels C12ZA and C24ZB were determined to be 4 and 36 ps(-1), respectively. With increasing the size of C(N)ZA, the EET efficiencies decrease owing to the structural distortions that produce considerable non-radiative decay pathways. Finally, the EET rates of self-assembled porphyrin boxes consisting of directly linked diporphyrins, B1A, B2A and B3A, are 48, 98 and 361 ps(-1), respectively. The EET rates of porphyrin boxes consisting of alkynylene-bridged diporphyrins, B2B and B4B, depend on the conformation of building blocks (planar or orthogonal) rather than the length of alkynylene linkers.

The optimized effective potential and the self-interaction correction in density functional theory: Application to molecules

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

Garza, Jorge; Nichols, Jeffrey A.; Dixon, David A.

2000-05-08

The Krieger, Li, and Iafrate approximation to the optimized effective potential including the self-interaction correction for density functional theory has been implemented in a molecular code, NWChem, that uses Gaussian functions to represent the Kohn and Sham spin-orbitals. The differences between the implementation of the self-interaction correction in codes where planewaves are used with an optimized effective potential are discussed. The importance of the localization of the spin-orbitals to maximize the exchange-correlation of the self-interaction correction is discussed. We carried out exchange-only calculations to compare the results obtained with these approximations, and those obtained with the local spin density approximation,more » the generalized gradient approximation and Hartree-Fock theory. Interesting results for the energy difference (GAP) between the highest occupied molecular orbital, HOMO, and the lowest unoccupied molecular orbital, LUMO, (spin-orbital energies of closed shell atoms and molecules) using the optimized effective potential and the self-interaction correction have been obtained. The effect of the diffuse character of the basis set on the HOMO and LUMO eigenvalues at the various levels is discussed. Total energies obtained with the optimized effective potential and the self-interaction correction show that the exchange energy with these approximations is overestimated and this will be an important topic for future work. (c) 2000 American Institute of Physics.« less

Direct Investigation of Slow Correlated Dynamics in Proteins via Dipolar Interactions

PubMed Central

Fenwick, R. Bryn; Schwieters, Charles D.; Vögeli, Beat

2016-01-01

The synchronization of native state motions as they transition between microstates influences catalysis kinetics, mediates allosteric interactions and reduces the conformational entropy of proteins. However, it has proven difficult to describe native microstates because they are usually minimally frustrated and may interconvert on the μs-ms time scale. Direct observation of concerted equilibrium fluctuations would therefore be an important tool for describing protein native states. Here we propose a strategy that relates NMR cross-correlated relaxation (CCR) rates between dipolar interactions to residual dipolar couplings (RDCs) of individual consecutive HN–N and Hα–Cα bonds, which act as a proxy for the peptide planes and the side chains respectively. Using Xplor-NIH ensemble structure calculations restrained with the RDC and CCR data we observe collective motions on time scales slower than nanoseconds in the backbone for GB3. To directly access the correlations from CCR we develop a structure-free data analysis. The resulting dynamic correlation map is consistent with the ensemble-restrained simulations and reveals a complex network. In general we find that the bond motions are on average slightly correlated, and that the local environment dominates many observations. Despite this, some patterns are typical over entire secondary structure elements. In the β-sheet, nearly all bonds are weakly correlated and there is an approximately binary alternation in correlation intensity corresponding to the solvent exposure/shielding alternation of the side chains. For α-helices there is also a weak correlation in the HN-N bonds and the degree of correlation involving Hα-Cα bonds is directly affected by side-chain fluctuations, while loops show complex and non-uniform behavior. PMID:27331619

Capacitive charge storage at an electrified interface investigated via direct first-principles simulations

NASA Astrophysics Data System (ADS)

Radin, Maxwell D.; Ogitsu, Tadashi; Biener, Juergen; Otani, Minoru; Wood, Brandon C.

2015-03-01

Understanding the impact of interfacial electric fields on electronic structure is crucial to improving the performance of materials in applications based on charged interfaces. Supercapacitors store energy directly in the strong interfacial field between a solid electrode and a liquid electrolyte; however, the complex interplay between the two is often poorly understood, particularly for emerging low-dimensional electrode materials that possess unconventional electronic structure. Typical descriptions tend to neglect the specific electrode-electrolyte interaction, approximating the intrinsic "quantum capacitance" of the electrode in terms of a fixed electronic density of states. Instead, we introduce a more accurate first-principles approach for directly simulating charge storage in model capacitors using the effective screening medium method, which implicitly accounts for the presence of the interfacial electric field. Applying this approach to graphene supercapacitor electrodes, we find that results differ significantly from the predictions of fixed-band models, leading to improved consistency with experimentally reported capacitive behavior. The differences are traced to two key factors: the inhomogeneous distribution of stored charge due to poor electronic screening and interfacial contributions from the specific interaction with the electrolyte. Our results are used to revise the conventional definition of quantum capacitance and to provide general strategies for improving electrochemical charge storage, particularly in graphene and similar low-dimensional materials.

Comparative study of substrate and product binding to the human ABO(H) blood group glycosyltransferases.

PubMed

Soya, Naoto; Shoemaker, Glen K; Palcic, Monica M; Klassen, John S

2009-11-01

The first comparative thermodynamic study of the human blood group glycosyltransferases, alpha-(1-->3)-N-acetylgalactosaminyltransferase (GTA) and alpha-(1-->3)-galactosyltransferase (GTB), interacting with donor substrates, donor and acceptor analogs, and trisaccharide products in vitro is reported. The binding constants, measured at 24 degrees C with the direct electrospray ionization mass spectrometry (ES-MS) assay, provide new insights into these model GTs and their interactions with substrate and product. Notably, the recombinant forms of GTA and GTB used in this study are shown to exist as homodimers, stabilized by noncovalent interactions at neutral pH. In the absence of divalent metal ion, neither GTA nor GTB exhibits any appreciable affinity for its native donors (UDP-GalNAc, UDP-Gal). Upon introduction of Mn(2+), both donors undergo enzyme-catalyzed hydrolysis in the presence of either GTA or GTB. Hydrolysis of UDP-GalNAc in the presence of GTA proceeds very rapidly under the solution conditions investigated and a binding constant could not be directly measured. In contrast, the rate of hydrolysis of UDP-Gal in the presence of GTB is significantly slower and, utilizing a modified approach to analyze the ES-MS data, a binding constant of 2 x 10(4) M(-1) was established. GTA and GTB bind the donor analogs UDP-GlcNAc, UDP-Glc with affinities similar to those measured for UDP-Gal and UDP-GalNAc (GTB only), suggesting that the native donors and donor analogs bind to the GTA and GTB through similar interactions. The binding constant determined for GTA and UDP-GlcNAc (approximately 1 x 10(4) M(-1)), therefore, provides an estimate for the binding constant for GTA and UDP-GalNAc. Binding of GTA and GTB with the A and B trisaccharide products was also investigated for the first time. In the absence of UDP and Mn(2+), both GTA and GTB recognize their respective trisaccharide products but with a low affinity approximately 10(3) M(-1); the presence of UDP and Mn(2+) has no effect on A trisaccharide binding but precludes B-trisaccharide binding.

Unified TeV scale picture of baryogenesis and dark matter.

PubMed

Babu, K S; Mohapatra, R N; Nasri, Salah

2007-04-20

We present a simple extension of the minimal supersymmetric standard model which provides a unified picture of cosmological baryon asymmetry and dark matter. Our model introduces a gauge singlet field N and a color triplet field X which couple to the right-handed quark fields. The out-of-equilibrium decay of the Majorana fermion N mediated by the exchange of the scalar field X generates adequate baryon asymmetry for MN approximately 100 GeV and MX approximately TeV. The scalar partner of N (denoted N1) is naturally the lightest SUSY particle as it has no gauge interactions and plays the role of dark matter. The model is experimentally testable in (i) neutron-antineutron oscillations with a transition time estimated to be around 10(10)sec, (ii) discovery of colored particles X at LHC with mass of order TeV, and (iii) direct dark matter detection with a predicted cross section in the observable range.

Model of chiral spin liquids with Abelian and non-Abelian topological phases

NASA Astrophysics Data System (ADS)

Chen, Jyong-Hao; Mudry, Christopher; Chamon, Claudio; Tsvelik, A. M.

2017-12-01

We present a two-dimensional lattice model for quantum spin-1/2 for which the low-energy limit is governed by four flavors of strongly interacting Majorana fermions. We study this low-energy effective theory using two alternative approaches. The first consists of a mean-field approximation. The second consists of a random phase approximation (RPA) for the single-particle Green's functions of the Majorana fermions built from their exact forms in a certain one-dimensional limit. The resulting phase diagram consists of two competing chiral phases, one with Abelian and the other with non-Abelian topological order, separated by a continuous phase transition. Remarkably, the Majorana fermions propagate in the two-dimensional bulk, as in the Kitaev model for a spin liquid on the honeycomb lattice. We identify the vison fields, which are mobile (they are static in the Kitaev model) domain walls propagating along only one of the two space directions.

Comparative study of Nd:YAG laser-induced breakdown spectroscopy and transversely excited atmospheric CO2 laser-induced gas plasma spectroscopy on chromated copper arsenate preservative-treated wood.

PubMed

Khumaeni, Ali; Lie, Zener Sukra; Niki, Hideaki; Lee, Yong Inn; Kurihara, Kazuyoshi; Wakasugi, Motoomi; Takahashi, Touru; Kagawa, Kiichiro

2012-03-01

Taking advantage of the specific characteristics of a transversely excited atmospheric (TEA) CO(2) laser, a sophisticated technique for the analysis of chromated copper arsenate (CCA) in wood samples has been developed. In this study, a CCA-treated wood sample with a dimension of 20 mm × 20 mm and a thickness of 2 mm was attached in contact to a nickel plate (20 mm × 20 mm × 0.15 mm), which functions as a subtarget. When the TEA CO(2) laser was successively irradiated onto the wood surface, a hole with a diameter of approximately 2.5 mm was produced inside the sample and the laser beam was directly impinged onto the metal subtarget. Strong and stable gas plasma with a very large diameter of approximately 10 mm was induced once the laser beam had directly struck the metal subtarget. This gas plasma then interacted with the fine particles of the sample inside the hole and finally the particles were effectively dissociated and excited in the gas plasma region. By using this technique, high precision and sensitive analysis of CCA-treated wood sample was realized. A linear calibration curve of Cr was successfully made using the CCA-treated wood sample. The detection limits of Cr, Cu, and As were estimated to be approximately 1, 2, and 15 mg/kg, respectively. In the case of standard LIBS using the Nd:YAG laser, the analytical intensities fluctuate and the detection limit was much lower at approximately one-tenth that of TEA CO(2) laser. © 2012 Optical Society of America

Microscopic description of elastic and direct inelastic nucleon scattering off spherical nuclei

NASA Astrophysics Data System (ADS)

Dupuis, M.

2017-05-01

The purpose of this study is to improve the modeling of nucleon direct inelastic scattering to the continuum using a microscopic and parameter-free approach. For the first time, direct elastic scattering, inelastic scattering to discrete excitations and to the continuum are described within a microscopic approach without adjustable parameters. Proton scattering off 90Zr and 208Pb are the reactions used as test case examples of the calculations. The model uses the Melbourne g-matrix and the Random Phase Approximation description of nuclear states, implemented with the Gogny D1S interaction. The relevant optical and transition potentials in a finite nucleus are calculated within a local density approximation. As we use the nuclear matter approach we limit our study to incident energies above 40 MeV. We first checked that this model provides an accurate account of measured cross sections for elastic scattering and inelastic scattering to discrete states. It is then applied to the direct inelastic scattering to the continuum considering all one-phonon excitations predicted within the RPA approach. This accounts for a part of the direct pre-equilibrium emission, often labeled as the one-step direct process in quantum-based approaches. Our approach provides a very accurate description of angular distributions where the one-step process dominates. The impact of collective excitations is shown to be non negligible for energy transfer to the target up to 20 MeV, decreasing as the incident energy increases. For incident energies above 80 MeV, our modeling provides a good account of direct proton emission for an energy transfer to the target up to 30 MeV. However, the proton emission we predict underestimates the measured cross sections for incident energies below 80 MeV. We compare our prediction to those of the phenomenological exciton model to help interpret this result. Directions that may improve our modeling are discussed.

Construction of exchange-correlation functionals through interpolation between the non-interacting and the strong-correlation limit

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

Zhou, Yongxi; Ernzerhof, Matthias, E-mail: Matthias.Ernzerhof@UMontreal.ca; Bahmann, Hilke

Drawing on the adiabatic connection of density functional theory, exchange-correlation functionals of Kohn-Sham density functional theory are constructed which interpolate between the extreme limits of the electron-electron interaction strength. The first limit is the non-interacting one, where there is only exchange. The second limit is the strong correlated one, characterized as the minimum of the electron-electron repulsion energy. The exchange-correlation energy in the strong-correlation limit is approximated through a model for the exchange-correlation hole that is referred to as nonlocal-radius model [L. O. Wagner and P. Gori-Giorgi, Phys. Rev. A 90, 052512 (2014)]. Using the non-interacting and strong-correlated extremes, variousmore » interpolation schemes are presented that yield new approximations to the adiabatic connection and thus to the exchange-correlation energy. Some of them rely on empiricism while others do not. Several of the proposed approximations yield the exact exchange-correlation energy for one-electron systems where local and semi-local approximations often fail badly. Other proposed approximations generalize existing global hybrids by using a fraction of the exchange-correlation energy in the strong-correlation limit to replace an equal fraction of the semi-local approximation to the exchange-correlation energy in the strong-correlation limit. The performance of the proposed approximations is evaluated for molecular atomization energies, total atomic energies, and ionization potentials.« less

Integral representation of channel flow with interacting particles

NASA Astrophysics Data System (ADS)

Fouxon, Itzhak; Ge, Zhouyang; Brandt, Luca; Leshansky, Alexander

2017-12-01

We construct a boundary integral representation for the low-Reynolds-number flow in a channel in the presence of freely suspended particles (or droplets) of arbitrary size and shape. We demonstrate that lubrication theory holds away from the particles at horizontal distances exceeding the channel height and derive a multipole expansion of the flow which is dipolar to the leading approximation. We show that the dipole moment of an arbitrary particle is a weighted integral of the stress and the flow at the particle surface, which can be determined numerically. We introduce the equation of motion that describes hydrodynamic interactions between arbitrary, possibly different, distant particles, with interactions determined by the product of the mobility matrix and the dipole moment. Further, the problem of three identical interacting spheres initially aligned in the streamwise direction is considered and the experimentally observed "pair exchange" phenomenon is derived analytically and confirmed numerically. For nonaligned particles, we demonstrate the formation of a configuration with one particle separating from a stable pair. Our results suggest that in a dilute initially homogenous particulate suspension flowing in a channel the particles will eventually separate into singlets and pairs.

How staff pursue questions to adults with intellectual disabilities.

PubMed

Finlay, W M L; Antaki, C

2012-04-01

When support staff use questions to instruct, advise or guide adults with intellectual disabilities (ID), or to solicit information from them, the interaction does not always proceed smoothly, particularly when replies are ambiguous, absent or not obviously relevant. That can lead to interactional trouble and dissatisfaction, or worse. We report on the ways in which staff members transform their questions over a series of conversational turns in order to solicit an adequate reply, and thereby to fulfil the interactional goal of the question. Our data come from approximately 30 h of recordings of natural conversation between staff members and adults with ID in two residential and one outdoor activities settings. We identify seven practices by which staff attempt to resolve the dilemma between undue direction and premature closure. These include: expansion of the original question, simplifying its format, changing its content in various ways and realising its alternatives in physical form. We highlight strategies which produce answers satisfactory to both parties, and improve the quality of interaction between staff and people with ID. © 2011 The Authors. Journal of Intellectual Disability Research © 2011 Blackwell Publishing Ltd.

A test of the social cohesion hypothesis: interactive female marmots remain at home.

PubMed

Blumstein, Daniel T; Wey, Tina W; Tang, Karisa

2009-08-22

Individuals frequently leave home before reaching reproductive age, but the proximate causes of natal dispersal remain relatively unknown. The social cohesion hypothesis predicts that individuals who engage in more (affiliative) interactions are less likely to disperse. Despite the intuitive nature of this hypothesis, support is both limited and equivocal. We used formal social network analyses to quantify precisely both direct and indirect measures of social cohesion in yellow-bellied marmots. Because approximately 50 per cent of female yearlings disperse, we expected that social relationships and network measures of cohesion would predict dispersal. By contrast, because most male yearlings disperse, we expected that social relationships and cohesion would play a less important role. We found that female yearlings that interacted with more individuals, and those that were more socially embedded in their groups, were less likely to disperse. For males, social interactions were relatively unimportant determinants of dispersal. This is the first strong support for the social cohesion hypothesis and suggests that the specific nature of social relationships, not simply the number of affiliative relationships, may influence the propensity to disperse.

A test of the social cohesion hypothesis: interactive female marmots remain at home

PubMed Central

Blumstein, Daniel T.; Wey, Tina W.; Tang, Karisa

2009-01-01

Individuals frequently leave home before reaching reproductive age, but the proximate causes of natal dispersal remain relatively unknown. The social cohesion hypothesis predicts that individuals who engage in more (affiliative) interactions are less likely to disperse. Despite the intuitive nature of this hypothesis, support is both limited and equivocal. We used formal social network analyses to quantify precisely both direct and indirect measures of social cohesion in yellow-bellied marmots. Because approximately 50 per cent of female yearlings disperse, we expected that social relationships and network measures of cohesion would predict dispersal. By contrast, because most male yearlings disperse, we expected that social relationships and cohesion would play a less important role. We found that female yearlings that interacted with more individuals, and those that were more socially embedded in their groups, were less likely to disperse. For males, social interactions were relatively unimportant determinants of dispersal. This is the first strong support for the social cohesion hypothesis and suggests that the specific nature of social relationships, not simply the number of affiliative relationships, may influence the propensity to disperse. PMID:19493901

27 CFR 9.141 - Escondido Valley.

Code of Federal Regulations, 2012 CFR

2012-04-01

... westerly direction approximately 17 miles; (5) The boundary continues to follow the 3000 foot contour line... intermittent stream approximately 18 miles east of the city of Fort Stockton (standard reference GE3317 on the... easterly direction approximately 9 miles until a southbound trail diverges from I-10 just past the point...

27 CFR 9.141 - Escondido Valley.

Code of Federal Regulations, 2010 CFR

2010-04-01

... westerly direction approximately 17 miles; (5) The boundary continues to follow the 3000 foot contour line... intermittent stream approximately 18 miles east of the city of Fort Stockton (standard reference GE3317 on the... easterly direction approximately 9 miles until a southbound trail diverges from I-10 just past the point...

27 CFR 9.141 - Escondido Valley.

Code of Federal Regulations, 2014 CFR

2014-04-01

... westerly direction approximately 17 miles; (5) The boundary continues to follow the 3000 foot contour line... intermittent stream approximately 18 miles east of the city of Fort Stockton (standard reference GE3317 on the... easterly direction approximately 9 miles until a southbound trail diverges from I-10 just past the point...

27 CFR 9.141 - Escondido Valley.

Code of Federal Regulations, 2013 CFR

2013-04-01

... westerly direction approximately 17 miles; (5) The boundary continues to follow the 3000 foot contour line... intermittent stream approximately 18 miles east of the city of Fort Stockton (standard reference GE3317 on the... easterly direction approximately 9 miles until a southbound trail diverges from I-10 just past the point...

27 CFR 9.141 - Escondido Valley.

Code of Federal Regulations, 2011 CFR

2011-04-01

... westerly direction approximately 17 miles; (5) The boundary continues to follow the 3000 foot contour line... intermittent stream approximately 18 miles east of the city of Fort Stockton (standard reference GE3317 on the... easterly direction approximately 9 miles until a southbound trail diverges from I-10 just past the point...

Bounded-Degree Approximations of Stochastic Networks

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

Quinn, Christopher J.; Pinar, Ali; Kiyavash, Negar

2017-06-01

We propose algorithms to approximate directed information graphs. Directed information graphs are probabilistic graphical models that depict causal dependencies between stochastic processes in a network. The proposed algorithms identify optimal and near-optimal approximations in terms of Kullback-Leibler divergence. The user-chosen sparsity trades off the quality of the approximation against visual conciseness and computational tractability. One class of approximations contains graphs with speci ed in-degrees. Another class additionally requires that the graph is connected. For both classes, we propose algorithms to identify the optimal approximations and also near-optimal approximations, using a novel relaxation of submodularity. We also propose algorithms to identifymore » the r-best approximations among these classes, enabling robust decision making.« less

Remarks on turbulent constitutive relations

NASA Technical Reports Server (NTRS)

Shih, Tsan-Hsing; Lumley, John L.

1993-01-01

The paper demonstrates that the concept of turbulent constitutive relations can be used to construct general models for various turbulent correlations. Some of the Generalized Cayley-Hamilton formulas for relating tensor products of higher extension to tensor products of lower extension are introduced. The combination of dimensional analysis and invariant theory can lead to 'turbulent constitutive relations' (or general turbulence models) for, in principle, any turbulent correlations. As examples, the constitutive relations for Reynolds stresses and scalar fluxes are derived. The results are consistent with ones from Renormalization Group (RNG) theory and two-scale Direct-Interaction Approximation (DIA) method, but with a more general form.

Inertial Range Dynamics in Boussinesq Turbulence

NASA Technical Reports Server (NTRS)

Rubinstein, Robert

1996-01-01

L'vov and Falkovich have shown that the dimensionally possible inertial range scaling laws for Boussinesq turbulence, Kolmogorov and Bolgiano scaling, describe steady states with constant flux of kinetic energy and of entropy respectively. These scaling laws are treated as similarity solutions of the direct interaction approximation for Boussinesq turbulence. The Kolmogorov scaling solution corresponds to a weak perturbation by gravity of a state in which the temperature is a passive scalar but in which a source of temperature fluctuations exists. Using standard inertial range balances, the renormalized viscosity and conductivity, turbulent Prandtl number, and spectral scaling law constants are computed for Bolgiano scaling.

Phenomenology of ELDER dark matter

NASA Astrophysics Data System (ADS)

Kuflik, Eric; Perelstein, Maxim; Lorier, Nicolas Rey-Le; Tsai, Yu-Dai

2017-08-01

We explore the phenomenology of Elastically Decoupling Relic (ELDER) dark matter. ELDER is a thermal relic whose present density is determined primarily by the cross-section of its elastic scattering off Standard Model (SM) particles. Assuming that this scattering is mediated by a kinetically mixed dark photon, we argue that the ELDER scenario makes robust predictions for electron-recoil direct-detection experiments, as well as for dark photon searches. These predictions are independent of the details of interactions within the dark sector. Together with the closely related Strongly-Interacting Massive Particle (SIMP) scenario, the ELDER predictions provide a physically motivated, well-defined target region, which will be almost entirely accessible to the next generation of searches for sub-GeV dark matter and dark photons. We provide useful analytic approximations for various quantities of interest in the ELDER scenario, and discuss two simple renormalizable toy models which incorporate the required strong number-changing interactions among the ELDERs, as well as explicitly implement the coupling to electrons via the dark photon portal.

Gauge invariance of excitonic linear and nonlinear optical response

NASA Astrophysics Data System (ADS)

Taghizadeh, Alireza; Pedersen, T. G.

2018-05-01

We study the equivalence of four different approaches to calculate the excitonic linear and nonlinear optical response of multiband semiconductors. These four methods derive from two choices of gauge, i.e., length and velocity gauges, and two ways of computing the current density, i.e., direct evaluation and evaluation via the time-derivative of the polarization density. The linear and quadratic response functions are obtained for all methods by employing a perturbative density-matrix approach within the mean-field approximation. The equivalence of all four methods is shown rigorously, when a correct interaction Hamiltonian is employed for the velocity gauge approaches. The correct interaction is written as a series of commutators containing the unperturbed Hamiltonian and position operators, which becomes equivalent to the conventional velocity gauge interaction in the limit of infinite Coulomb screening and infinitely many bands. As a case study, the theory is applied to hexagonal boron nitride monolayers, and the linear and nonlinear optical response found in different approaches are compared.

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

NASA Astrophysics Data System (ADS)

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

2016-05-01

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

Effect of cosolvent on protein stability: A theoretical investigation

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

Chalikian, Tigran V., E-mail: chalikan@phm.utoronto.ca

2014-12-14

We developed a statistical thermodynamic algorithm for analyzing solvent-induced folding/unfolding transitions of proteins. The energetics of protein transitions is governed by the interplay between the cavity formation contribution and the term reflecting direct solute-cosolvent interactions. The latter is viewed as an exchange reaction in which the binding of a cosolvent to a solute is accompanied by release of waters of hydration to the bulk. Our model clearly differentiates between the stoichiometric and non-stoichiometric interactions of solvent or co-solvent molecules with a solute. We analyzed the urea- and glycine betaine (GB)-induced conformational transitions of model proteins of varying size which aremore » geometrically approximated by a sphere in their native state and a spherocylinder in their unfolded state. The free energy of cavity formation and its changes accompanying protein transitions were computed based on the concepts of scaled particle theory. The free energy of direct solute-cosolvent interactions were analyzed using empirical parameters previously determined for urea and GB interactions with low molecular weight model compounds. Our computations correctly capture the mode of action of urea and GB and yield realistic numbers for (∂ΔG°/∂a{sub 3}){sub T,P} which are related to the m-values of protein denaturation. Urea is characterized by negative values of (∂ΔG°/∂a{sub 3}){sub T,P} within the entire range of urea concentrations analyzed. At concentrations below ∼1 M, GB exhibits positive values of (∂ΔG°/∂a{sub 3}){sub T,P} which turn positive at higher GB concentrations. The balance between the thermodynamic contributions of cavity formation and direct solute-cosolvent interactions that, ultimately, defines the mode of cosolvent action is extremely subtle. A 20% increase or decrease in the equilibrium constant for solute-cosolvent binding may change the sign of (∂ΔG°/∂a{sub 3}){sub T,P} thereby altering the mode of cosolvent action (stabilizing to destabilizing or vice versa)« less

Effect of cosolvent on protein stability: A theoretical investigation

NASA Astrophysics Data System (ADS)

Chalikian, Tigran V.

2014-12-01

We developed a statistical thermodynamic algorithm for analyzing solvent-induced folding/unfolding transitions of proteins. The energetics of protein transitions is governed by the interplay between the cavity formation contribution and the term reflecting direct solute-cosolvent interactions. The latter is viewed as an exchange reaction in which the binding of a cosolvent to a solute is accompanied by release of waters of hydration to the bulk. Our model clearly differentiates between the stoichiometric and non-stoichiometric interactions of solvent or co-solvent molecules with a solute. We analyzed the urea- and glycine betaine (GB)-induced conformational transitions of model proteins of varying size which are geometrically approximated by a sphere in their native state and a spherocylinder in their unfolded state. The free energy of cavity formation and its changes accompanying protein transitions were computed based on the concepts of scaled particle theory. The free energy of direct solute-cosolvent interactions were analyzed using empirical parameters previously determined for urea and GB interactions with low molecular weight model compounds. Our computations correctly capture the mode of action of urea and GB and yield realistic numbers for (∂ΔG°/∂a3)T,P which are related to the m-values of protein denaturation. Urea is characterized by negative values of (∂ΔG°/∂a3)T,P within the entire range of urea concentrations analyzed. At concentrations below ˜1 M, GB exhibits positive values of (∂ΔG°/∂a3)T,P which turn positive at higher GB concentrations. The balance between the thermodynamic contributions of cavity formation and direct solute-cosolvent interactions that, ultimately, defines the mode of cosolvent action is extremely subtle. A 20% increase or decrease in the equilibrium constant for solute-cosolvent binding may change the sign of (∂ΔG°/∂a3)T,P thereby altering the mode of cosolvent action (stabilizing to destabilizing or vice versa).

Cobalt adatoms on graphene: Effects of anisotropies on the correlated electronic structure

NASA Astrophysics Data System (ADS)

Mozara, R.; Valentyuk, M.; Krivenko, I.; Şaşıoǧlu, E.; Kolorenč, J.; Lichtenstein, A. I.

2018-02-01

Impurities on surfaces experience a geometric symmetry breaking induced not only by the on-site crystal-field splitting and the orbital-dependent hybridization, but also by different screening of the Coulomb interaction in different directions. We present a many-body study of the Anderson impurity model representing a Co adatom on graphene, taking into account all anisotropies of the effective Coulomb interaction, which we obtained by the constrained random-phase approximation. The most pronounced differences are naturally displayed by the many-body self-energy projected onto the single-particle states. For the solution of the Anderson impurity model and analytical continuation of the Matsubara data, we employed new implementations of the continuous-time hybridization expansion quantum Monte Carlo and the stochastic optimization method, and we verified the results in parallel with the exact diagonalization method.

The impact of supernova fragments on the evolution of multisupernova remnants

NASA Technical Reports Server (NTRS)

Franco, J.; Ferrara, A.; Rozyczka, M.; Tenorio-Tgale, G.; Cox, D. P.

1993-01-01

Analytical approximations and 2D hydrodynamical simulations are used to examine the interaction of supernova fragments with the internal structure of large multisupernova remnants (MSRs). The fragments are thermalized by reverse shocks generated in the interaction with the MSR interior, which is assumed to be hot and rarefied. The evolution is divided into two stages: before and after reaching a reference distance, R(E), from the explosion site. As the density of the expanding fragment drops, the reverse shock accelerates, and, when the distance R(E) is reached, it begins to effectively erode the fragment. At some selected evolutionary times, the X-ray emission from the shocked fragment is also calculated. The direct bombardment of the MRS shell by the shocked fragment has a series of important consequences: it excites, punctures, and deforms the expanding shell.

Solar wind/local interstellar medium interaction including charge exchange with neural hydrogen

NASA Technical Reports Server (NTRS)

Pauls, H. Louis; Zank, Gary P.

1995-01-01

We present results from a hydrodynamic model of the interaction of the solar wind with the local interstellar medium (LISM), self-consistently taking into account the effects of charge exchange between the plasma component and the interstellar neutrals. The simulation is fully time dependent, and is carried out in two or three dimensions, depending on whether the helio-latitudinal dependence of the solar wind speed and number density (both giving rise to three dimensional effects) are included. As a first approximation it is assumed that the neutral component of the flow can be described by a single, isotropic fluid. Clearly, this is not the actual situation, since charge exchange with the supersonic solar wind plasma in the region of the nose results in a 'second' neutral fluid propagating in the opposite direction as that of the LISM neutrals.

``Glue" approximation for the pairing interaction in the Hubbard model with next nearest neighbor hopping

NASA Astrophysics Data System (ADS)

Khatami, Ehsan; Macridin, Alexandru; Jarrell, Mark

2008-03-01

Recently, several authors have employed the ``glue" approximation for the Cuprates in which the full pairing vertex is approximated by the spin susceptibility. We study this approximation using Quantum Monte Carlo Dynamical Cluster Approximation methods on a 2D Hubbard model. By considering a reasonable finite value for the next nearest neighbor hopping, we find that this ``glue" approximation, in the current form, does not capture the correct pairing symmetry. Here, d-wave is not the leading pairing symmetry while it is the dominant symmetry using the ``exact" QMC results. We argue that the sensitivity of this approximation to the band structure changes leads to this inconsistency and that this form of interaction may not be the appropriate description of the pairing mechanism in Cuprates. We suggest improvements to this approximation which help to capture the the essential features of the QMC data.

Molecular-Scale Structural Controls on Nanoscale Growth Processes: Step-Specific Regulation of Biomineral Morphology

NASA Astrophysics Data System (ADS)

Dove, P. M.; Davis, K. J.; De Yoreo, J. J.; Orme, C. A.

2001-12-01

Deciphering the complex strategies by which organisms produce nanocrystalline materials with exquisite morphologies is central to understanding biomineralizing systems. One control on the morphology of biogenic nanoparticles is the specific interactions of their surfaces with the organic functional groups provided by the organism and the various inorganic species present in the ambient environment. It is now possible to directly probe the microscopic structural controls on crystal morphology by making quantitative measurements of the dynamic processes occurring at the mineral-water interface. These observations can provide crucial information concerning the actual mechanisms of growth that is otherwise unobtainable through macroscopic techniques. Here we use in situ molecular-scale observations of step dynamics and growth hillock morphology to directly resolve roles of principal impurities in regulating calcite surface morphologies. We show that the interactions of certain inorganic as well as organic impurities with the calcite surface are dependent upon the molecular-scale structures of step-edges. These interactions can assume a primary role in directing crystal morphology. In calcite growth experiments containing magnesium, we show that growth hillock structures become modified owing to the preferential inhibition of step motion along directions approximately parallel to the [010]. Compositional analyses have shown that Mg incorporates at different levels into the two types of nonequivalent steps, which meet at the hillock corner parallel to [010]. A simple calculation of the strain caused by this difference indicates that we should expect a significant retardation at this corner, in agreement with the observed development of [010] steps. If the low-energy step-risers produced by these [010] steps is perpendicular to the c-axis as seems likely from crystallographic considerations, this effect provides a plausible mechanism for the elongated calcite crystal habits found in natural environments that contain magnesium. In a separate study, step-specific interactions are also found between chiral aspartate molecules and the calcite surface. The L and D- aspartate enantiomers exhibit structure preferences for the different types of step-risers on the calcite surface. These site-specific interactions result in the transfer of asymmetry from the organic molecule to the crystal surface through the formation of chiral growth hillocks and surface morphologies. These studies yield direct experimental insight into the molecular-scale structural controls on nanocrystal morphology in biomineralizing systems.

Nightside electron precipitation at Mars: Geographic variability and dependence on solar wind conditions

NASA Astrophysics Data System (ADS)

Lillis, Robert J.; Brain, David A.

2013-06-01

Electron precipitation is usually the dominant source of energy input to the nightside Martian atmosphere, with consequences for ionospheric densities, chemistry, electrodynamics, communications, and navigation. We examine downward-traveling superthermal electron flux on the Martian nightside from May 1999 to November 2006 at 400 km altitude and 2 A.M. local time. Electron precipitation is geographically organized by crustal magnetic field strength and elevation angle, with higher fluxes occurring in regions of weak and/or primarily vertical crustal fields, while stronger and more horizontal fields retard electron access to the atmosphere. We investigate how these crustal field-organized precipitation patterns vary with proxies for solar wind (SW) pressure and interplanetary magnetic field (IMF) direction. Generally, higher precipitating fluxes accompany higher SW pressures. Specifically, we identify four characteristic spectral behaviors: (1) "stable" regions where fluxes increase mildly with SW pressure, (2) "high-flux" regions where accelerated (peaked) spectra are more common and where fluxes below ~500 eV are largely independent of SW pressure, (3) permanent plasma voids, and (4) intermittent plasma voids where fluxes depend strongly on SW pressure. The locations, sizes, shapes, and absence/existence of these plasma voids vary significantly with solar wind pressure proxy and moderately with IMF proxy direction; average precipitating fluxes are 40% lower in strong crustal field regions and 15% lower globally for approximately southwest proxy directions compared with approximately northeast directions. This variation of the strength and geographic pattern of the shielding effect of Mars' crustal fields exemplifies the complex interaction between those fields and the solar wind.

Continuous depth-of-interaction encoding using phosphor-coated scintillators.

PubMed

Du, Huini; Yang, Yongfeng; Glodo, Jarek; Wu, Yibao; Shah, Kanai; Cherry, Simon R

2009-03-21

We investigate a novel detector using a lutetium oxyorthosilicate (LSO) scintillator and YGG (yttrium-aluminum-gallium oxide:cerium, Y(3)(Al,Ga)(5)O(12):Ce) phosphor to construct a detector with continuous depth-of-interaction (DOI) information. The far end of the LSO scintillator is coated with a thin layer of YGG phosphor powder which absorbs some fraction of the LSO scintillation light and emits wavelength-shifted photons with a characteristic decay time of approximately 50 ns. The near end of the LSO scintillator is directly coupled to a photodetector. The photodetector detects a mixture of the LSO light and the light emitted by YGG. With appropriate placement of the coating, the ratio of the light converted from the YGG coating with respect to the unconverted LSO light can be made to depend on the interaction depth. DOI information can then be estimated by inspecting the overall light pulse decay time. Experiments were conducted to optimize the coating method. 19 ns decay time differences across the length of the detector were achieved experimentally when reading out a 1.5 x 1.5 x 20 mm(3) LSO crystal with unpolished surfaces and half-coated with YGG phosphor. The same coating scheme was applied to a 4 x 4 LSO array. Pulse shape discrimination (PSD) methods were studied to extract DOI information from the pulse shape changes. The DOI full-width-half-maximum (FWHM) resolution was found to be approximately 8 mm for this 2 cm thick array.

Second order nonlinear QED processes in ultra-strong laser fields

NASA Astrophysics Data System (ADS)

Mackenroth, Felix

2017-10-01

In the interaction of ultra-intense laser fields with matter the ever increasing peak laser intensities render nonlinear QED effects ever more important. For long, ultra-intense laser pulses scattering large systems, like a macroscopic plasma, the interaction time can be longer than the scattering time, leading to multiple scatterings. These are usually approximated as incoherent cascades of single-vertex processes. Under certain conditions, however, this common cascade approximation may be insufficient, as it disregards several effects such as coherent processes, quantum interferences or pulse shape effects. Quantifying deviations of the full amplitude of multiple scatterings from the commonly employed cascade approximations is a formidable, yet unaccomplished task. In this talk we are going to discuss how to compute second order nonlinear QED amplitudes and relate them to the conventional cascade approximation. We present examples for typical second order processes and benchmark the full result against common approximations. We demonstrate that the approximation of multiple nonlinear QED scatterings as a cascade of single interactions has certain limitations and discuss these limits in light of upcoming experimental tests.

Quantified Energy Dissipation Rates in the Terrestrial Bow Shock. 2; Waves and Dissipation

NASA Technical Reports Server (NTRS)

Wilson, L. B., III; Sibeck, D. G.; Breneman, A. W.; Le Contel, O.; Cully, C.; Turner, D. L.; Angelopoulos, V.; Malaspina, D. M.

2014-01-01

We present the first quantified measure of the energy dissipation rates, due to wave-particle interactions, in the transition region of the Earth's collision-less bow shock using data from the Time History of Events and Macro-Scale Interactions during Sub-Storms spacecraft. Our results show that wave-particle interactions can regulate the global structure and dominate the energy dissipation of collision-less shocks. In every bow shock crossing examined, we observed both low-frequency (less than 10 hertz) and high-frequency (approximately or greater than10 hertz) electromagnetic waves throughout the entire transition region and into the magnetosheath. The low-frequency waves were consistent with magnetosonic-whistler waves. The high-frequency waves were combinations of ion-acoustic waves, electron cyclotron drift instability driven waves, electrostatic solitary waves, and whistler mode waves. The high-frequency waves had the following: (1) peak amplitudes exceeding delta B approximately equal to 10 nanoteslas and delta E approximately equal to 300 millivolts per meter, though more typical values were delta B approximately equal to 0.1-1.0 nanoteslas and delta E approximately equal to 10-50 millivolts per meter (2) Poynting fluxes in excess of 2000 microWm(sup -2) (micro-waves per square meter) (typical values were approximately 1-10 microWm(sup -2) (micro-waves per square meter); (3) resistivities greater than 9000 omega meters; and (4) associated energy dissipation rates greater than 10 microWm(sup -3) (micro-waves per cubic meter). The dissipation rates due to wave-particle interactions exceeded rates necessary to explain the increase in entropy across the shock ramps for approximately 90 percent of the wave burst durations. For approximately 22 percent of these times, the wave-particle interactions needed to only be less than or equal to 0.1 percent efficient to balance the nonlinear wave steepening that produced the shock waves. These results show that wave-particle interactions have the capacity to regulate the global structure and dominate the energy dissipation of collision-less shocks.

Approximation for discrete Fourier transform and application in study of three-dimensional interacting electron gas.

PubMed

Yan, Xin-Zhong

2011-07-01

The discrete Fourier transform is approximated by summing over part of the terms with corresponding weights. The approximation reduces significantly the requirement for computer memory storage and enhances the numerical computation efficiency with several orders without losing accuracy. As an example, we apply the algorithm to study the three-dimensional interacting electron gas under the renormalized-ring-diagram approximation where the Green's function needs to be self-consistently solved. We present the results for the chemical potential, compressibility, free energy, entropy, and specific heat of the system. The ground-state energy obtained by the present calculation is compared with the existing results of Monte Carlo simulation and random-phase approximation.

Calculation of the Coulomb Fission Cross Sections for Pb-Pb and Bi-Pb Interactions at 158 A GeV

NASA Technical Reports Server (NTRS)

Poyser, William J.; Ahern, Sean C.; Norbury, John W.; Tripathi, R. K.

2002-01-01

The Weizsacker-Williams (WW) method of virtual quanta is used to make approximate cross section calculations for peripheral relativistic heavy-ion collisions. We calculated the Coulomb fission cross sections for projectile ions of Pb-208 and Bi-209 with energies of 158 A GeV interacting with a Pb-208 target. We also calculated the electromagnetic absorption cross section for Pb-208 ion interacting as described. For comparison we use both the full WW method and a standard approximate WW method. The approximate WW method in larger cross sections compared to the more accurate full WW method.

Dynamic simulation of concentrated macromolecular solutions with screened long-range hydrodynamic interactions: Algorithm and limitations

PubMed Central

Ando, Tadashi; Chow, Edmond; Skolnick, Jeffrey

2013-01-01

Hydrodynamic interactions exert a critical effect on the dynamics of macromolecules. As the concentration of macromolecules increases, by analogy to the behavior of semidilute polymer solutions or the flow in porous media, one might expect hydrodynamic screening to occur. Hydrodynamic screening would have implications both for the understanding of macromolecular dynamics as well as practical implications for the simulation of concentrated macromolecular solutions, e.g., in cells. Stokesian dynamics (SD) is one of the most accurate methods for simulating the motions of N particles suspended in a viscous fluid at low Reynolds number, in that it considers both far-field and near-field hydrodynamic interactions. This algorithm traditionally involves an O(N3) operation to compute Brownian forces at each time step, although asymptotically faster but more complex SD methods are now available. Motivated by the idea of hydrodynamic screening, the far-field part of the hydrodynamic matrix in SD may be approximated by a diagonal matrix, which is equivalent to assuming that long range hydrodynamic interactions are completely screened. This approximation allows sparse matrix methods to be used, which can reduce the apparent computational scaling to O(N). Previously there were several simulation studies using this approximation for monodisperse suspensions. Here, we employ newly designed preconditioned iterative methods for both the computation of Brownian forces and the solution of linear systems, and consider the validity of this approximation in polydisperse suspensions. We evaluate the accuracy of the diagonal approximation method using an intracellular-like suspension. The diffusivities of particles obtained with this approximation are close to those with the original method. However, this approximation underestimates intermolecular correlated motions, which is a trade-off between accuracy and computing efficiency. The new method makes it possible to perform large-scale and long-time simulation with an approximate accounting of hydrodynamic interactions. PMID:24089734

Direction-specific van der Waals attraction between rutile TiO2 nanocrystals.

PubMed

Zhang, Xin; He, Yang; Sushko, Maria L; Liu, Jia; Luo, Langli; De Yoreo, James J; Mao, Scott X; Wang, Chongmin; Rosso, Kevin M

2017-04-28

Mutual lattice orientations dictate the types and magnitudes of forces between crystalline particles. When lattice polarizability is anisotropic, the van der Waals dispersion attraction can, in principle, contribute to this direction dependence. We report measurement of this attraction between rutile nanocrystals, as a function of their mutual orientation and surface hydration extent. At tens of nanometers of separation, the attraction is weak and shows no dependence on azimuthal alignment or surface hydration. At separations of approximately one hydration layer, the attraction is strongly dependent on azimuthal alignment and systematically decreases as intervening water density increases. Measured forces closely agree with predictions from Lifshitz theory and show that dispersion forces can generate a torque between particles interacting in solution and between grains in materials. Copyright © 2017, American Association for the Advancement of Science.

Combination of the pair density approximation and the Takahashi–Imada approximation for path integral Monte Carlo simulations

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

Zillich, Robert E., E-mail: robert.zillich@jku.at

2015-11-15

We construct an accurate imaginary time propagator for path integral Monte Carlo simulations for heterogeneous systems consisting of a mixture of atoms and molecules. We combine the pair density approximation, which is highly accurate but feasible only for the isotropic interactions between atoms, with the Takahashi–Imada approximation for general interactions. We present finite temperature simulations results for energy and structure of molecules–helium clusters X{sup 4}He{sub 20} (X=HCCH and LiH) which show a marked improvement over the Trotter approximation which has a 2nd-order time step bias. We show that the 4th-order corrections of the Takahashi–Imada approximation can also be applied perturbativelymore » to a 2nd-order simulation.« less

Pathogenic Leptospira Species Acquire Factor H and Vitronectin via the Surface Protein LcpA

PubMed Central

da Silva, Ludmila Bezerra; Miragaia, Lidia dos Santos; Breda, Leandro Carvalho Dantas; Abe, Cecilia Mari; Schmidt, Mariana Costa Braga; Moro, Ana Maria; Monaris, Denize; Conde, Jonas Nascimento; Józsi, Mihály; Isaac, Lourdes; Abreu, Patrícia Antônia Estima

2014-01-01

Upon infection, pathogenic Leptospira species bind several complement regulators in order to overcome host innate immunity. We previously characterized a 20-kDa leptospiral surface protein which interacts with C4b binding protein (C4BP): leptospiral complement regulator-acquiring protein A (LcpA). Here we show that LcpA also interacts with human factor H (FH), which remains functionally active once bound to the protein. Antibodies directed against short consensus repeat 20 (SCR20) inhibited binding of FH to LcpA by approximately 90%, thus confirming that this particular domain is involved in the interaction. We have also shown for the first time that leptospires bind human vitronectin and that the interaction is mediated by LcpA. Coincubation with heparin blocked LcpA-vitronectin interaction in a dose-dependent manner, strongly suggesting that binding may occur through the heparin binding domains of vitronectin. LcpA also bound to the terminal pathway component C9 and inhibited Zn2+-induced polymerization and membrane attack complex (MAC) formation. Competitive binding assays indicated that LcpA interacts with C4BP, FH, and vitronectin through distinct sites. Taken together, our findings indicate that LcpA may play a role in leptospiral immune evasion. PMID:25534939

Pathogenic Leptospira species acquire factor H and vitronectin via the surface protein LcpA.

PubMed

da Silva, Ludmila Bezerra; Miragaia, Lidia Dos Santos; Breda, Leandro Carvalho Dantas; Abe, Cecilia Mari; Schmidt, Mariana Costa Braga; Moro, Ana Maria; Monaris, Denize; Conde, Jonas Nascimento; Józsi, Mihály; Isaac, Lourdes; Abreu, Patrícia Antônia Estima; Barbosa, Angela Silva

2015-03-01

Upon infection, pathogenic Leptospira species bind several complement regulators in order to overcome host innate immunity. We previously characterized a 20-kDa leptospiral surface protein which interacts with C4b binding protein (C4BP): leptospiral complement regulator-acquiring protein A (LcpA). Here we show that LcpA also interacts with human factor H (FH), which remains functionally active once bound to the protein. Antibodies directed against short consensus repeat 20 (SCR20) inhibited binding of FH to LcpA by approximately 90%, thus confirming that this particular domain is involved in the interaction. We have also shown for the first time that leptospires bind human vitronectin and that the interaction is mediated by LcpA. Coincubation with heparin blocked LcpA-vitronectin interaction in a dose-dependent manner, strongly suggesting that binding may occur through the heparin binding domains of vitronectin. LcpA also bound to the terminal pathway component C9 and inhibited Zn(2+)-induced polymerization and membrane attack complex (MAC) formation. Competitive binding assays indicated that LcpA interacts with C4BP, FH, and vitronectin through distinct sites. Taken together, our findings indicate that LcpA may play a role in leptospiral immune evasion. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Jahn-Teller transition in TiF3 investigated using density-functional theory

NASA Astrophysics Data System (ADS)

Perebeinos, Vasili; Vogt, Tom

2004-03-01

We use first-principles density-functional theory to calculate the electronic and magnetic properties of TiF3 using the full-potential-linearized augmented-plane-wave method. The local density approximation (LDA) predicts a fully saturated ferromagnetic metal and finds degenerate energy minima for high- and low-symmetry structures. The experimentally observed Jahn-Teller phase transition at Tc=370 K cannot be driven by the electron-phonon interaction alone, which is usually described accurately by the LDA. Electron correlations beyond the LDA are essential to lift the degeneracy of the singly occupied Ti t2g orbital. Although the on-site Coulomb correlations are important, the direction of the t2g-level splitting is determined by dipole-dipole interactions. The LDA+U functional predicts an aniferromagnetic insulator with an orbitally ordered ground state. The input parameters U=8.1 eV and J=0.9 eV for the Ti 3d orbital were found by varying the total charge on the TiF2-6 ion using the molecular NRLMOL code. We estimate the Heisenberg exchange constant for spin 1/2 on a cubic lattice to be approximately 24 K. The symmetry lowering energy in LDA+U is about 900 K per TiF3 formula unit.

Candidates for direct laser cooling of diatomic molecules with the simplest 1Σ -1Σ electronic system

NASA Astrophysics Data System (ADS)

Li, Chuanliang; Li, Yachao; Ji, Zhonghua; Qiu, Xuanbing; Lai, Yunzhong; Wei, Jilin; Zhao, Yanting; Deng, Lunhua; Chen, Yangqin; Liu, Jinjun

2018-06-01

We propose to utilize the 1Σ-1Σ electronic transition system for direct laser cooling of heteronuclear diatomic molecules. AgH, as well as its deuterium isotopolog AgD, is used as an example to illustrate the cooling schemes. Potential-energy curves and relevant molecular parameters of both AgH and AgD, including the spin-orbit constants and the electronic transition dipole moments, are determined in internally contracted multiconfiguration-reference configuration interaction calculations. The highly diagonal Franck-Condon matrices of the A 1Σ+-X 1Σ+ transitions predicted by the calculations suggest the existence of quasi-closed-cycle transitions, which renders these molecules suitable for direct laser cooling. By solving rate equations numerically, we demonstrated that both AgH and AgD molecules can be cooled from 25 K to 2 mK temperature in approximately 20 ms. Our investigation elucidates and supports the hypothesis that molecules in the simplest 1Σ-1Σ system can serve as favorable candidates for direct laser cooling.

Contrasting guest binding interaction of cucurbit[7-8]urils with neutral red dye: controlled exchange of multiple guests.

PubMed

Shaikh, Mhejabeen; Choudhury, Sharmistha Dutta; Mohanty, Jyotirmayee; Bhasikuttan, Achikanath C; Pal, Haridas

2010-07-14

Interactions among macrocyclic hosts and dyes/drugs have been explored extensively for their direct usage in controlled uptake and release of large number of potential drug molecules. In this paper we report the non-covalent interaction of cucurbit[8]uril macrocycle (CB8) with a biologically important dye, neutral red, by absorption and fluorescence spectroscopy. A comparative analysis with the complexation behaviour of the dye with CB7, the lower homologue of CB8, indicates contrasting guest binding behaviour with significant changes in the photophysical characteristics of the dye. While CB7 interaction leads to a 1 ratio 1 stoichiometry resulting in approximately 6 fold enhancement in the fluorescence emission of the dye, CB8 displays signatures for a 1 ratio 2 host-guest stoichiometry with drastic reduction in the fluorescence emission. Apart from the evaluation of approximately 2 unit shift in the protolytic equilibrium on complexation (pK(a) shift), the measurements with tryptophan established a selective guest exchange to favour a co-localized dimer inside the CB8 cavity. In a protein medium (BSA), the 1 ratio 2 complex was converted to a 1 ratio 1 ratio 1 CB8-NRH(+)-BSA complex. The finding that NRH(+) can be transferred from CB8 to BSA, even though the binding constant for NRH(+)-CB8 is much higher than NRH(+)-BSA, is projected for a controlled slow release of NRH(+) towards BSA. Since the release and activity of drugs can be controlled by regulating the protolytic equilibrium, the macromolecular encapsulation and release of NRH(+) demonstrated here provide information relevant to host-guest based drug delivery systems and its applications.

An iterative method for hydrodynamic interactions in Brownian dynamics simulations of polymer dynamics

NASA Astrophysics Data System (ADS)

Miao, Linling; Young, Charles D.; Sing, Charles E.

2017-07-01

Brownian Dynamics (BD) simulations are a standard tool for understanding the dynamics of polymers in and out of equilibrium. Quantitative comparison can be made to rheological measurements of dilute polymer solutions, as well as direct visual observations of fluorescently labeled DNA. The primary computational challenge with BD is the expensive calculation of hydrodynamic interactions (HI), which are necessary to capture physically realistic dynamics. The full HI calculation, performed via a Cholesky decomposition every time step, scales with the length of the polymer as O(N3). This limits the calculation to a few hundred simulated particles. A number of approximations in the literature can lower this scaling to O(N2 - N2.25), and explicit solvent methods scale as O(N); however both incur a significant constant per-time step computational cost. Despite this progress, there remains a need for new or alternative methods of calculating hydrodynamic interactions; large polymer chains or semidilute polymer solutions remain computationally expensive. In this paper, we introduce an alternative method for calculating approximate hydrodynamic interactions. Our method relies on an iterative scheme to establish self-consistency between a hydrodynamic matrix that is averaged over simulation and the hydrodynamic matrix used to run the simulation. Comparison to standard BD simulation and polymer theory results demonstrates that this method quantitatively captures both equilibrium and steady-state dynamics after only a few iterations. The use of an averaged hydrodynamic matrix allows the computationally expensive Brownian noise calculation to be performed infrequently, so that it is no longer the bottleneck of the simulation calculations. We also investigate limitations of this conformational averaging approach in ring polymers.

Laser-Matter Interaction in Dielectrics: Insight from Picosecond-Pulsed Second-Harmonic Generation in Periodically Poled LiTaO3

NASA Astrophysics Data System (ADS)

Louchev, Oleg A.; Wada, Satoshi; Panchenko, Vladislav Ya.

2017-08-01

We develop a modified two-temperature (2T) model of laser-matter interaction in dielectrics based on experimental insight from picosecond-pulsed high-frequency temperature-controlled second-harmonic (515 nm) generation in periodically poled stoichiometric LiTaO3 crystal and required for computational treatment of short-pulsed nonlinear optics and materials processing applications. We show that the incorporation of an extended set of recombination-kinetics-related energy-release and heat-exchange processes following short-pulsed photoionization by two-photon absorption of the second harmonic allows accurate simulation of the electron-lattice relaxation dynamics and electron-lattice temperature evolution in LiTaO3 crystal in nonlinear laser-frequency conversion. Our experimentally confirmed model and detailed simulation study show that two-photon ionization with the recombination mechanism via ion-electron-lattice interaction followed by a direct transfer of the recombination energy to the lattice is the main laser-matter energy-transfer pathway responsible for the majority of the crystal lattice heating (approximately 90%) continuing for approximately 50 ps after laser-pulse termination and competing with effect of electron-phonon energy transfer from the free electrons. This time delay is due to a recombination bottleneck which hinders faster relaxation to thermal equilibrium in photoionized dielectric crystal. Generally, our study suggests that in dielectrics photoionized by short-pulsed radiation with intensity range used in nonlinear laser-frequency conversion, the electron-lattice relaxation period is defined by the recombination-stage bottleneck of a few tens of picoseconds and not by the time of the electron-phonon energy transfer. This modification of the 2T model can be applied to a broad range of processes involving laser-matter interactions in dielectrics and semiconductors for charge density reaching the range of 1021- 1022 cm-3 .

Neutrino flavor instabilities in a time-dependent supernova model

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

Abbar, Sajad; Duan, Huaiyu

2015-10-19

In this study, a dense neutrino medium such as that inside a core-collapse supernova can experience collective flavor conversion or oscillations because of the neutral-current weak interaction among the neutrinos. This phenomenon has been studied in a restricted, stationary supernova model which possesses the (spatial) spherical symmetry about the center of the supernova and the (directional) axial symmetry around the radial direction. Recently it has been shown that these spatial and directional symmetries can be broken spontaneously by collective neutrino oscillations. In this letter we analyze the neutrino flavor instabilities in a time-dependent supernova model. Our results show that collectivemore » neutrino oscillations start at approximately the same radius in both the stationary and time-dependent supernova models unless there exist very rapid variations in local physical conditions on timescales of a few microseconds or shorter. Our results also suggest that collective neutrino oscillations can vary rapidly with time in the regimes where they do occur which need to be studied in time-dependent supernova models.« less

Spatially Complete Surface Albedo Data Sets: Value-Added Products Derived from Terra MODIS Land Products

NASA Technical Reports Server (NTRS)

Moody, Eric G.; King, Michael D.; Platnick, Steven; Schaaf, Crystal B.; Gao, Feng

2004-01-01

Spectral land surface albedo is an important parameter for describing the radiative properties of the Earth. Accordingly it reflects the consequences of natural and human interactions, such as anthropogenic, meteorological, and phenological effects, on global and local climatological trends. Consequently, albedos are integral parts in a variety of research areas, such as general circulation models (GCMs), energy balance studies, modeling of land use and land use change, and biophysical, oceanographic, and meteorological studies. Recent observations of diffuse bihemispherical (white-sky) and direct beam directional hemispherical (black-sky ) land surface albedo included in the MOD43B3 product from MODIS instruments aboard NASA's Terra and Aqua satellite platforms have provided researchers with unprecedented spatial, spectral, and temporal characteristics. Cloud and seasonal snow cover, however, curtail retrievals to approximately half the global land surfaces on an annual equal-angle basis, precluding MOD43B3 albedo products from direct inclusion in some research projects and production environments.

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

Trevisanutto, Paolo E.; Vignale, Giovanni, E-mail: vignaleg@missouri.edu

Ab initio electronic structure calculations of two-dimensional layered structures are typically performed using codes that were developed for three-dimensional structures, which are periodic in all three directions. The introduction of a periodicity in the third direction (perpendicular to the layer) is completely artificial and may lead in some cases to spurious results and to difficulties in treating the action of external fields. In this paper we develop a new approach, which is “native” to quasi-2D materials, making use of basis function that are periodic in the plane, but atomic-like in the perpendicular direction. We show how some of the basicmore » tools of ab initio electronic structure theory — density functional theory, GW approximation and Bethe-Salpeter equation — are implemented in the new basis. We argue that the new approach will be preferable to the conventional one in treating the peculiarities of layered materials, including the long range of the unscreened Coulomb interaction in insulators, and the effects of strain, corrugations, and external fields.« less

Dimensionality of consumer search space drives trophic interaction strengths.

PubMed

Pawar, Samraat; Dell, Anthony I; Savage, Van M

2012-06-28

Trophic interactions govern biomass fluxes in ecosystems, and stability in food webs. Knowledge of how trophic interaction strengths are affected by differences among habitats is crucial for understanding variation in ecological systems. Here we show how substantial variation in consumption-rate data, and hence trophic interaction strengths, arises because consumers tend to encounter resources more frequently in three dimensions (3D) (for example, arboreal and pelagic zones) than two dimensions (2D) (for example, terrestrial and benthic zones). By combining new theory with extensive data (376 species, with body masses ranging from 5.24 × 10(-14) kg to 800 kg), we find that consumption rates scale sublinearly with consumer body mass (exponent of approximately 0.85) for 2D interactions, but superlinearly (exponent of approximately 1.06) for 3D interactions. These results contradict the currently widespread assumption of a single exponent (of approximately 0.75) in consumer-resource and food-web research. Further analysis of 2,929 consumer-resource interactions shows that dimensionality of consumer search space is probably a major driver of species coexistence, and the stability and abundance of populations.

Reducing orbital eccentricity of precessing black-hole binaries

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

Buonanno, Alessandra; Taracchini, Andrea; Kidder, Lawrence E.

2011-05-15

Building initial conditions for generic binary black-hole evolutions which are not affected by initial spurious eccentricity remains a challenge for numerical-relativity simulations. This problem can be overcome by applying an eccentricity-removal procedure which consists of evolving the binary black hole for a couple of orbits, estimating the resulting eccentricity, and then restarting the simulation with corrected initial conditions. The presence of spins can complicate this procedure. As predicted by post-Newtonian theory, spin-spin interactions and precession prevent the binary from moving along an adiabatic sequence of spherical orbits, inducing oscillations in the radial separation and in the orbital frequency. For single-spinmore » binary black holes these oscillations are a direct consequence of monopole-quadrupole interactions. However, spin-induced oscillations occur at approximately twice the orbital frequency, and therefore can be distinguished and disentangled from the initial spurious eccentricity which occurs at approximately the orbital frequency. Taking this into account, we develop a new eccentricity-removal procedure based on the derivative of the orbital frequency and find that it is rather successful in reducing the eccentricity measured in the orbital frequency to values less than 10{sup -4} when moderate spins are present. We test this new procedure using numerical-relativity simulations of binary black holes with mass ratios 1.5 and 3, spin magnitude 0.5, and various spin orientations. The numerical simulations exhibit spin-induced oscillations in the dynamics at approximately twice the orbital frequency. Oscillations of similar frequency are also visible in the gravitational-wave phase and frequency of the dominant l=2, m=2 mode.« less

Titan Submarine: Exploring The Depths of Kraken Mare

NASA Technical Reports Server (NTRS)

Oleson, Steven R.; Lorenz, Ralph D.; Paul, Michael V.

2015-01-01

The conceptual design of a submarine for Saturn's moon Titan was a funded NASA Innovative Advanced Concepts (NIAC) Phase I for 2014. The effort investigated what science a submarine for Titan's liquid hydrocarbon approximately 93 Kelvin (-180 degrees Centigrade) seas might accomplish and what that submarine might look like. Focusing on a flagship class science system (approximately100 kilograms) it was found that a submersible platform can accomplish extensive and exciting science both above and below the surface of the Kraken Mare The submerged science includes mapping using side looking sonar, imaging and spectroscopy of the sea at all depths, as well as sampling of the sea's bottom and shallow shoreline. While surfaced the submarine will not only sense weather conditions (including the interaction between the liquid and atmosphere) but also image the shoreline, as much as 2 kilometers inland. This imaging requirement pushed the landing date to Titan's next summer period (approximately 2047) to allow for continuous lighted conditions, as well as direct-to-Earth (DTE) communication, avoiding the need for a separate relay orbiter spacecraft. Submerged and surfaced investigation are key to understanding both the hydrological cycle of Titan as well as gather hints to how life may have begun on Earth using liquid/sediment/chemical interactions. An estimated 25 megabits of data per day would be generated by the various science packages. Most of the science packages (electronics at least) can be safely kept inside the submarine pressure vessel and warmed by the isotope power system. This paper discusses the results of Phase I as well as the plans for Phase II.

Space Radiation Transport Code Development: 3DHZETRN

NASA Technical Reports Server (NTRS)

Wilson, John W.; Slaba, Tony C.; Badavi, Francis F.; Reddell, Brandon D.; Bahadori, Amir A.

2015-01-01

The space radiation transport code, HZETRN, has been used extensively for research, vehicle design optimization, risk analysis, and related applications. One of the simplifying features of the HZETRN transport formalism is the straight-ahead approximation, wherein all particles are assumed to travel along a common axis. This reduces the governing equation to one spatial dimension allowing enormous simplification and highly efficient computational procedures to be implemented. Despite the physical simplifications, the HZETRN code is widely used for space applications and has been found to agree well with fully 3D Monte Carlo simulations in many circumstances. Recent work has focused on the development of 3D transport corrections for neutrons and light ions (Z < 2) for which the straight-ahead approximation is known to be less accurate. Within the development of 3D corrections, well-defined convergence criteria have been considered, allowing approximation errors at each stage in model development to be quantified. The present level of development assumes the neutron cross sections have an isotropic component treated within N explicit angular directions and a forward component represented by the straight-ahead approximation. The N = 1 solution refers to the straight-ahead treatment, while N = 2 represents the bi-directional model in current use for engineering design. The figure below shows neutrons, protons, and alphas for various values of N at locations in an aluminum sphere exposed to a solar particle event (SPE) spectrum. The neutron fluence converges quickly in simple geometry with N > 14 directions. The improved code, 3DHZETRN, transports neutrons, light ions, and heavy ions under space-like boundary conditions through general geometry while maintaining a high degree of computational efficiency. A brief overview of the 3D transport formalism for neutrons and light ions is given, and extensive benchmarking results with the Monte Carlo codes Geant4, FLUKA, and PHITS are provided for a variety of boundary conditions and geometries. Improvements provided by the 3D corrections are made clear in the comparisons. Developments needed to connect 3DHZETRN to vehicle design and optimization studies will be discussed. Future theoretical development will relax the forward plus isotropic interaction assumption to more general angular dependence.

Observations of SKS splitting beneath the Central and Southern External Dinarides in the Adria-Eurasia convergence zone

NASA Astrophysics Data System (ADS)

Subašić, Senad; Prevolnik, Snježan; Herak, Davorka; Herak, Marijan

2017-05-01

Seismic anisotropy beneath the greater region of the Central and Southern External Dinarides is estimated from observations of SKS splitting. The area is located in the broad and complex Africa-Eurasia convergent plate boundary zone, where the Adriatic microplate interacts with the Dinarides. We analyzed recordings of 12 broadband seismic stations located in the Croatian coastal region. Evidence of seismic anisotropy was found beneath all stations. Fast axis directions are oriented approximately in the NE-SW to NNE-SSW direction, perpendicularly to the strike of the Dinarides. Average delay times range between 0.6 and 1.0 s. A counter-clockwise rotation in average fast axis directions was observed for the stations in the northern part with respect to the stations in the southern part of the studied area. Fast axis directions coincide with the assumed direction of asthenospheric flow through a slab-gap below the Northern and Central External Dinarides, with the maximum tectonic stress orientation in the crust, and with fast directions of Pg and Sg-waves in the crust. These observations suggest that the detected SKS birefringence is primarily caused by the preferred lattice orientation of mantle minerals generated by the asthenospheric flow directed SW-NE to SSW-NNE, with a possible contribution from the crust.

The nematode homologue of Mediator complex subunit 28, F28F8.5, is a critical regulator of C. elegans development

PubMed Central

Kostrouchová, Markéta; Kostrouch, David; Kaššák, Filip; Kostrouchová, Veronika; Benda, Aleš; Krause, Michael W.; Saudek, Vladimír; Kostrouchová, Marta

2017-01-01

The evolutionarily conserved Mediator complex is a critical player in regulating transcription. Comprised of approximately two dozen proteins, the Mediator integrates diverse regulatory signals through direct protein-protein interactions that, in turn, modulate the influence of Mediator on RNA Polymerase II activity. One Mediator subunit, MED28, is known to interact with cytoplasmic structural proteins, providing a potential direct link between cytoplasmic dynamics and the control of gene transcription. Although identified in many animals and plants, MED28 is not present in yeast; no bona fide MED28 has been described previously in Caenorhabditis elegans. Here, we identify bioinformatically F28F8.5, an uncharacterized predicted protein, as the nematode homologue of MED28. As in other Metazoa, F28F8.5 has dual nuclear and cytoplasmic localization and plays critical roles in the regulation of development. F28F8.5 is a vital gene and its null mutants have severely malformed gonads and do not reproduce. F28F8.5 interacts on the protein level with the Mediator subunits MDT-6 and MDT-30. Our results indicate that F28F8.5 is an orthologue of MED28 and suggest that the potential to link cytoplasmic and nuclear events is conserved between MED28 vertebrate and nematode orthologues. PMID:28603670

The nematode homologue of Mediator complex subunit 28, F28F8.5, is a critical regulator of C. elegans development.

PubMed

Kostrouchová, Markéta; Kostrouch, David; Chughtai, Ahmed A; Kaššák, Filip; Novotný, Jan P; Kostrouchová, Veronika; Benda, Aleš; Krause, Michael W; Saudek, Vladimír; Kostrouchová, Marta; Kostrouch, Zdeněk

2017-01-01

The evolutionarily conserved Mediator complex is a critical player in regulating transcription. Comprised of approximately two dozen proteins, the Mediator integrates diverse regulatory signals through direct protein-protein interactions that, in turn, modulate the influence of Mediator on RNA Polymerase II activity. One Mediator subunit, MED28, is known to interact with cytoplasmic structural proteins, providing a potential direct link between cytoplasmic dynamics and the control of gene transcription. Although identified in many animals and plants, MED28 is not present in yeast; no bona fide MED28 has been described previously in Caenorhabditis elegans. Here, we identify bioinformatically F28F8.5, an uncharacterized predicted protein, as the nematode homologue of MED28. As in other Metazoa, F28F8.5 has dual nuclear and cytoplasmic localization and plays critical roles in the regulation of development. F28F8.5 is a vital gene and its null mutants have severely malformed gonads and do not reproduce. F28F8.5 interacts on the protein level with the Mediator subunits MDT-6 and MDT-30. Our results indicate that F28F8.5 is an orthologue of MED28 and suggest that the potential to link cytoplasmic and nuclear events is conserved between MED28 vertebrate and nematode orthologues.

WDR36 and P53 Gene Variants and Susceptibility to Primary Open-Angle Glaucoma: Analysis of Gene-Gene Interactions

PubMed Central

Blanco-Marchite, Cristina; Sánchez-Sánchez, Francisco; López-Garrido, María-Pilar; Iñigez-de-Onzoño, Mercedes; López-Martínez, Francisco; López-Sánchez, Enrique; Alvarez, Lydia; Rodríguez-Calvo, Pedro-Pablo; Méndez-Hernández, Carmen; Fernández-Vega, Luis; García-Sánchez, Julián; Coca-Prados, Miguel; García-Feijoo, Julián

2011-01-01

Purpose. To investigate the role of WDR36 and P53 sequence variations in POAG susceptibility. Methods. The authors performed a case-control genetic association study in 268 unrelated Spanish patients (POAG1) and 380 control subjects matched for sex, age, and ethnicity. WDR36 sequence variations were screened by either direct DNA sequencing or denaturing high-performance liquid chromatography. P53 polymorphisms p.R72P and c.97–147ins16bp were analyzed by single-nucleotide polymorphism (SNP) genotyping and PCR, respectively. Positive SNP and haplotype associations were reanalyzed in a second sample of 211 patients and in combined cases (n = 479). Results. The authors identified almost 50 WDR36 sequence variations, of which approximately two-thirds were rare and one-third were polymorphisms. Approximately half the variants were novel. Eight patients (2.9%) carried rare mutations that were not identified in the control group (P = 0.001). Six Tag SNPs were expected to be structured in three common haplotypes. Haplotype H2 was consistently associated with the disease (P = 0.0024 in combined cases). According to a dominant model, genotypes containing allele P of the P53 p.R72P SNP slightly increased glaucoma risk. Glaucoma susceptibility associated with different WDR36 genotypes also increased significantly in combination with the P53 RP risk genotype, indicating the existence of a genetic interaction. For instance, the OR of the H2 diplotype estimated for POAG1 and combined cases rose approximately 1.6 times in the two-locus genotype H2/RP. Conclusions. Rare WDR36 variants and the P53 p.R72P polymorphism behaved as moderate glaucoma risk factors in Spanish patients. The authors provide evidence for a genetic interaction between WDR36 and P53 variants in POAG susceptibility, although this finding must be confirmed in other populations. PMID:21931130

Linking North Atlantic Teleconnections to Latitudinal Variability of Wave Climate Along the North American Atlantic Coast

NASA Astrophysics Data System (ADS)

Provancha, C.; Adams, P. N.; Hegermiller, C.; Storlazzi, C. D.

2015-12-01

Shoreline change via coastal erosion and accretion is largely influenced by variations in ocean wave climate. Identifying the sources of these variations is challenging because the timing of wave energy delivery varies over multiple timescales within ocean basins. We present the results of an investigation of USACE Wave Information Studies hindcast hourly wave heights, periods, and directions along the North American Atlantic coast from 1980-2012, designed to explore links between wave climate and teleconnection patterns. Trends in median and extreme significant wave heights (SWHs) demonstrate that mean monthly SWHs increased from 1 to 5 cm/yr along the roughly 3000 km reach of study area, with changes in hurricane season waves appearing to be most influential in producing the overall trends. Distributions of SWHs categorized by North Atlantic Oscillation (NAO) phase, show that positive-period NAO SWHs are greater than negative-period NAO SWHs along the entire eastern seaboard (25°N to 45°N). The most prominent wave direction off Cape Cod, MA during positive-period NAO is approximately 105°, as compared to approximately 75° during negative-period NAO. Prominent wave directions between Cape Canaveral, FL, and Savannah, GA exhibit a similar shift but during opposite phases of the NAO. The results of this analysis suggest that the atmosphere-ocean interactions associated with contrasting NAO phases can significantly change the wave climate observed offshore along the North American Atlantic coast, altering alongshore wave energy fluxes and sediment transport patterns along the coast.

Electron density determination and bonding in tetragonal binary intermetallics by convergent beam electron diffraction

NASA Astrophysics Data System (ADS)

Sang, Xiahan

Intermetallics offer unique property combinations often superior to those of more conventional solid solution alloys of identical composition. Understanding of bonding in intermetallics would greatly accelerate development of intermetallics for advanced and high performance engineering applications. Tetragonal intermetallics L10 ordered TiAl, FePd and FePt are used as model systems to experimentally measure their electron densities using quantitative convergent beam electron diffraction (QCBED) method and then compare details of the 3d-4d (FePd) and 3d-5d (FePt) electron interactions to elucidate their role on properties of the respective ferromagnetic L10-ordered intermetallics FePd and FePt. A new multi-beam off-zone axis condition QCBED method has been developed to increase sensitivity of CBED patterns to change of structure factors and the anisotropic Debye-Waller (DW) factors. Unprecedented accuracy and precision in structure and DW factor measurements has been achieved by acquiring CBED patterns using beam-sample geometry that ensures strong dynamical interaction between the fast electrons and the periodic potential in the crystalline samples. This experimental method has been successfully applied to diamond cubic Si, and chemically ordered B2 cubic NiAl, tetragonal L10 ordered TiAl and FePd. The accurate and precise experimental DW and structure factors for L10 TiAl and FePd allow direct evaluation of computer calculations using the current state of the art density functional theory (DFT) based electron structure modeling. The experimental electron density difference map of L1 0 TiAl shows that the DFT calculations describe bonding to a sufficient accuracy for s- and p- electrons interaction, e. g., the Al-layer. However, it indicate significant quantitative differences to the experimental measurements for the 3d-3d interactions of the Ti atoms, e.g. in the Ti layers. The DFT calculations for L10 FePd also show that the current DFT approximations insufficiently describe the interaction between Fe-Fe (3d-3d), Fe-Pd (3d-4d) and Pd-Pd (4d-4d) electrons, which indicates the necessity to evaluate applicability of different DFT approximations, and also provides experimental data for the development of new DFT approximation that better describes transition metal based intermetallic systems.

Kindlin-2 directly binds actin and regulates integrin outside-in signaling

PubMed Central

Bledzka, Kamila; Bialkowska, Katarzyna; Sossey-Alaoui, Khalid; Vaynberg, Julia; Pluskota, Elzbieta

2016-01-01

Reduced levels of kindlin-2 (K2) in endothelial cells derived from K2+/− mice or C2C12 myoblastoid cells treated with K2 siRNA showed disorganization of their actin cytoskeleton and decreased spreading. These marked changes led us to examine direct binding between K2 and actin. Purified K2 interacts with F-actin in cosedimentation and surface plasmon resonance analyses and induces actin aggregation. We further find that the F0 domain of K2 binds actin. A mutation, LK47/AA, within a predicted actin binding site (ABS) of F0 diminishes its interaction with actin by approximately fivefold. Wild-type K2 and K2 bearing the LK47/AA mutation were equivalent in their ability to coactivate integrin αIIbβ3 in a CHO cell system when coexpressed with talin. However, K2-LK47/AA exhibited a diminished ability to support cell spreading and actin organization compared with wild-type K2. The presence of an ABS in F0 of K2 that influences outside-in signaling across integrins establishes a new foundation for considering how kindlins might regulate cellular responses. PMID:27044892

Modeling direct band-to-band tunneling: From bulk to quantum-confined semiconductor devices

NASA Astrophysics Data System (ADS)

Carrillo-Nuñez, H.; Ziegler, A.; Luisier, M.; Schenk, A.

2015-06-01

A rigorous framework to study direct band-to-band tunneling (BTBT) in homo- and hetero-junction semiconductor nanodevices is introduced. An interaction Hamiltonian coupling conduction and valence bands (CVBs) is derived using a multiband envelope method. A general form of the BTBT probability is then obtained from the linear response to the "CVBs interaction" that drives the system out of equilibrium. Simple expressions in terms of the one-electron spectral function are developed to compute the BTBT current in two- and three-dimensional semiconductor structures. Additionally, a two-band envelope equation based on the Flietner model of imaginary dispersion is proposed for the same purpose. In order to characterize their accuracy and differences, both approaches are compared with full-band, atomistic quantum transport simulations of Ge, InAs, and InAs-Si Esaki diodes. As another numerical application, the BTBT current in InAs-Si nanowire tunnel field-effect transistors is computed. It is found that both approaches agree with high accuracy. The first one is considerably easier to conceive and could be implemented straightforwardly in existing quantum transport tools based on the effective mass approximation to account for BTBT in nanodevices.

A diffusion approximation for ocean wave scatterings by randomly distributed ice floes

NASA Astrophysics Data System (ADS)

Zhao, Xin; Shen, Hayley

2016-11-01

This study presents a continuum approach using a diffusion approximation method to solve the scattering of ocean waves by randomly distributed ice floes. In order to model both strong and weak scattering, the proposed method decomposes the wave action density function into two parts: the transmitted part and the scattered part. For a given wave direction, the transmitted part of the wave action density is defined as the part of wave action density in the same direction before the scattering; and the scattered part is a first order Fourier series approximation for the directional spreading caused by scattering. An additional approximation is also adopted for simplification, in which the net directional redistribution of wave action by a single scatterer is assumed to be the reflected wave action of a normally incident wave into a semi-infinite ice cover. Other required input includes the mean shear modulus, diameter and thickness of ice floes, and the ice concentration. The directional spreading of wave energy from the diffusion approximation is found to be in reasonable agreement with the previous solution using the Boltzmann equation. The diffusion model provides an alternative method to implement wave scattering into an operational wave model.

Modification of Surface Energy via Direct Laser Ablative Surface Patterning

NASA Technical Reports Server (NTRS)

Wohl, Christopher J., Jr. (Inventor); Belcher, Marcus A. (Inventor); Connell, John W. (Inventor); Hopkins, John W. (Inventor)

2015-01-01

Surface energy of a substrate is changed without the need for any template, mask, or additional coating medium applied to the substrate. At least one beam of energy directly ablates a substrate surface to form a predefined topographical pattern at the surface. Each beam of energy has a width of approximately 25 micrometers and an energy of approximately 1-500 microJoules. Features in the topographical pattern have a width of approximately 1-500 micrometers and a height of approximately 1.4-100 micrometers.

Uni-directional optical pulses, temporal propagation, and spatial and temporal dispersion

NASA Astrophysics Data System (ADS)

Kinsler, P.

2018-02-01

I derive a temporally propagated uni-directional optical pulse equation valid in the few cycle limit. Temporal propagation is advantageous because it naturally preserves causality, unlike the competing spatially propagated models. The exact coupled bi-directional equations that this approach generates can be efficiently approximated down to a uni-directional form in cases where an optical pulse changes little over one optical cycle. They also permit a direct term-to-term comparison of the exact bi-directional theory with its corresponding approximate uni-directional theory. Notably, temporal propagation handles dispersion in a different way, and this difference serves to highlight existing approximations inherent in spatially propagated treatments of dispersion. Accordingly, I emphasise the need for future work in clarifying the limitations of the dispersion conversion required by these types of approaches; since the only alternative in the few cycle limit may be to resort to the much more computationally intensive full Maxwell equation solvers.

Femtosecond studies of protein-ligand hydrophobic binding and dynamics: human serum albumin.

PubMed

Zhong, D; Douhal, A; Zewail, A H

2000-12-19

In this contribution, we report studies of the nature of the dynamics and hydrophobic binding in protein-ligand complexes of human serum albumin with 2-(2'-hydroxyphenyl)-4-methyloxazole. With femtosecond time resolution, we examined the orientational motion of the ligand, its intrinsic nuclear motions, and the lifetime changes in the hydrophobic phase. For comparisons, with similar but chemical nanocavities, we also studied the same ligand in micelles and cyclodextrins. The hydrophobic interactions in the binding crevice are much stronger than those observed in cyclodextrins and micelles. The confined geometry restrains the nonradiative decay and significantly lengthens the excited-state lifetime. The observed dynamics over the femtosecond-to-nanosecond time scale indicate that the binding structure is rigid and the local motions of the ligand are nearly "frozen" in the protein. Another major finding is the elucidation of the directed dynamics by the protein. Proton transfer and intramolecular twisting of 2-(2'-hydroxyphenyl)-4-methyloxazole were observed to evolve along two routes: one involves the direct stretching motion in the molecular plane (approximately 200 fs) and is not sensitive to the environment; the second, less dominant, is related to the twisting motion (approximately 3 ps) of the two heterocyclic rings and drastically slows down in the protein hydrophobic pocket.

A Reduced-Order Model For Zero-Mass Synthetic Jet Actuators

NASA Technical Reports Server (NTRS)

Yamaleev, Nail K.; Carpenter, Mark H.; Vatsa, Veer S.

2007-01-01

Accurate details of the general performance of fluid actuators is desirable over a range of flow conditions, within some predetermined error tolerance. Designers typically model actuators with different levels of fidelity depending on the acceptable level of error in each circumstance. Crude properties of the actuator (e.g., peak mass rate and frequency) may be sufficient for some designs, while detailed information is needed for other applications (e.g., multiple actuator interactions). This work attempts to address two primary objectives. The first objective is to develop a systematic methodology for approximating realistic 3-D fluid actuators, using quasi-1-D reduced-order models. Near full fidelity can be achieved with this approach at a fraction of the cost of full simulation and only a modest increase in cost relative to most actuator models used today. The second objective, which is a direct consequence of the first, is to determine the approximate magnitude of errors committed by actuator model approximations of various fidelities. This objective attempts to identify which model (ranging from simple orifice exit boundary conditions to full numerical simulations of the actuator) is appropriate for a given error tolerance.

Exact and approximate many-body dynamics with stochastic one-body density matrix evolution

NASA Astrophysics Data System (ADS)

Lacroix, Denis

2005-06-01

We show that the dynamics of interacting fermions can be exactly replaced by a quantum jump theory in the many-body density matrix space. In this theory, jumps occur between densities formed of pairs of Slater determinants, Dab=|Φa><Φb|, where each state evolves according to the stochastic Schrödinger equation given by O. Juillet and Ph. Chomaz [Phys. Rev. Lett. 88, 142503 (2002)]. A stochastic Liouville-von Neumann equation is derived as well as the associated. Bogolyubov-Born-Green-Kirwood-Yvon hierarchy. Due to the specific form of the many-body density along the path, the presented theory is equivalent to a stochastic theory in one-body density matrix space, in which each density matrix evolves according to its own mean-field augmented by a one-body noise. Guided by the exact reformulation, a stochastic mean-field dynamics valid in the weak coupling approximation is proposed. This theory leads to an approximate treatment of two-body effects similar to the extended time-dependent Hartree-Fock scheme. In this stochastic mean-field dynamics, statistical mixing can be directly considered and jumps occur on a coarse-grained time scale. Accordingly, numerical effort is expected to be significantly reduced for applications.

Antibody-mediated fluorescence enhancement based on shifting the intramolecular dimer<-->monomer equilibrium of fluorescent dyes.

PubMed

Wei, A P; Blumenthal, D K; Herron, J N

1994-05-01

A novel concept is described for directly coupling fluorescence emission to protein-ligand binding. It is based on shifting the intramolecular monomer<-->dimer equilibrium of two fluorescent dyes linked by a short spacer. A 13-residue peptide, recognized by a monoclonal antibody against human chorionic gonadotrophin (hCG), was labeled with fluorescein (F) and tetramethylrhodamine (T) at its N- and C-terminus, respectively. Spectral evidence suggests that when the conjugate is free in solution, F and T exist as an intramolecular dimer. Fluorescence quenching of fluorescein and rhodamine is approximately 98% and approximately 90%, respectively, due to dimerization. When the double-labeled peptide is bound to anti-hCG, however, the rhodamine fluorescence increases by up to 7.8-fold, depending upon the excitation wavelength. This is attributed to the dissociation of intramolecular dimers brought about by conformational changes of the conjugate upon binding. Fluorescein fluorescence, on the other hand, was still quenched because of excited-state energy transfer and residual ground-state interactions. Antibody binding also resulted in a approximately 3.4-fold increase in fluorescence anisotropy of the peptide. These changes in intensity and anisotropy allow direct measurement of antigen-antibody binding with a fluorescence plate reader or a polarization analyzer, without the need for separation steps and labeling antibodies. Because recent advances in peptide technology have allowed rapid and economical identification of antigen-mimicking peptides, the double-labeled peptide approach offers many opportunities for developing new diagnostic assays and screening new therapeutic drugs. It also has many potential applications to techniques involving recombinant antibodies, biosensors, cell sorting, and DNA probes.

Dam break problem for the focusing nonlinear Schrödinger equation and the generation of rogue waves

NASA Astrophysics Data System (ADS)

El, G. A.; Khamis, E. G.; Tovbis, A.

2016-09-01

We propose a novel, analytically tractable, scenario of the rogue wave formation in the framework of the small-dispersion focusing nonlinear Schrödinger (NLS) equation with the initial condition in the form of a rectangular barrier (a ‘box’). We use the Whitham modulation theory combined with the nonlinear steepest descent for the semi-classical inverse scattering transform, to describe the evolution and interaction of two counter-propagating nonlinear wave trains—the dispersive dam break flows—generated in the NLS box problem. We show that the interaction dynamics results in the emergence of modulated large-amplitude quasi-periodic breather lattices whose amplitude profiles are closely approximated by the Akhmediev and Peregrine breathers within certain space-time domain. Our semi-classical analytical results are shown to be in excellent agreement with the results of direct numerical simulations of the small-dispersion focusing NLS equation.

Symplectic no-core configuration interaction framework for ab initio nuclear structure. II. Structure of rotational states

NASA Astrophysics Data System (ADS)

Caprio, Mark A.; McCoy, Anna E.; Dytrych, Tomas

2017-09-01

Rotational band structure is readily apparent as an emergent phenomenon in ab initio nuclear many-body calculations of light nuclei, despite the incompletely converged nature of most such calculations at present. Nuclear rotation in light nuclei can be analyzed in terms of approximate dynamical symmetries of the nuclear many-body problem: in particular, Elliott's SU (3) symmetry of the three-dimensional harmonic oscillator and the symplectic Sp (3 , R) symmetry of three-dimensional phase space. Calculations for rotational band members in the ab initio symplectic no-core configuration interaction (SpNCCI) framework allow us to directly examine the SU (3) and Sp (3 , R) nature of rotational states. We present results for rotational bands in p-shell nuclei. Supported by the US DOE under Award No. DE-FG02-95ER-40934 and the Czech Science Foundation under Grant No. 16-16772S.

Simulation of Orientation in Injection Molding of High Aspect Ratio Particle Thermoplastic Composites

NASA Astrophysics Data System (ADS)

Vélez-García, Gregorio M.; Ortman, Kevin C.; Eberle, Aaron P. R.; Wapperom, Peter; Baird, Donald G.

2008-07-01

A 2D coupled Hele-Shaw flow approximation for predicting the flow-induced orientation of high aspect ratio particles in injection molded composite parts is presented. For a highly concentrated short glass fiber PBT suspension, the impact of inter-particle interactions and the orientation at the gate is investigated for a center-gated disk using material parameters determined from rheometry. Experimental orientation is determined from confocal laser micrographs using the methods of ellipses. The constitutive equations are discretized using discontinuous Galerkin Finite Elements. Model predictions are significantly improved by using a localized orientation measured experimentally at the gate region instead of random or averaged gapwise measured orientation assumed in previous studies. The predicted profile in different radial positions can be related to the layered structure along the gapwise direction. Model modifications including interactions have lower impact than the initial conditions.

Real-time "x-ray vision" for healthcare simulation: an interactive projective overlay system to enhance intubation training and other procedural training.

PubMed

Samosky, Joseph T; Baillargeon, Emma; Bregman, Russell; Brown, Andrew; Chaya, Amy; Enders, Leah; Nelson, Douglas A; Robinson, Evan; Sukits, Alison L; Weaver, Robert A

2011-01-01

We have developed a prototype of a real-time, interactive projective overlay (IPO) system that creates augmented reality display of a medical procedure directly on the surface of a full-body mannequin human simulator. These images approximate the appearance of both anatomic structures and instrument activity occurring within the body. The key innovation of the current work is sensing the position and motion of an actual device (such as an endotracheal tube) inserted into the mannequin and using the sensed position to control projected video images portraying the internal appearance of the same devices and relevant anatomic structures. The images are projected in correct registration onto the surface of the simulated body. As an initial practical prototype to test this technique we have developed a system permitting real-time visualization of the intra-airway position of an endotracheal tube during simulated intubation training.

One-dimensional magnetic fluctuations in the spin-2 triangular lattice alpha-NaMnO2.

PubMed

Stock, C; Chapon, L C; Adamopoulos, O; Lappas, A; Giot, M; Taylor, J W; Green, M A; Brown, C M; Radaelli, P G

2009-08-14

The S=2 anisotropic triangular lattice alpha-NaMnO2 is studied by neutron inelastic scattering. Antiferromagnetic order occurs at T< or =45 K with opening of a spin gap. The spectral weight of the magnetic dynamics above the gap (Delta approximately equal to 7.5 meV) has been analyzed by the single-mode approximation. Excellent agreement with the experiment is achieved when a dominant exchange interaction (|J|/k(B) approximately 73 K), along the monoclinic b axis and a sizable easy-axis magnetic anisotropy (|D|/k(B) approximately 3 K) are considered. Despite earlier suggestions for two-dimensional spin interactions, the dynamics illustrate strongly coupled antiferromagnetic S=2 chains and cancellation of the interchain exchange due to the lattice topology. alpha-NaMnO2 therefore represents a model system where the geometric frustration is resolved through the lowering of the dimensionality of the spin interactions.

[Cost accounting for gastrectomy under critical path--the usefulness of direct accounting of personnel expenses and a guide to shortening hospital stay].

PubMed

Nozue, M; Maruyama, T; Imamura, F; Fukue, M

2000-08-01

In this study, cost accounting was made for a surgical case of gastrectomy according to critical path (path) and the economic contribution of the path was determined. In addition, changes in the cost percentage with changes in number of hospital days were simulated. Basically, cost accounting was done by means of cost accounting by departments, which meets the concept of direct cost accounting of administered accounts. Personnel expenses were calculated by means of both direct and indirect calculations. In the direct method, the total hours personnel participated were recorded for calculation. In the indirect method, personnel expenses were calculated from the ratio of the income of the surgical department to that of other departments. Purchase prices for all materials and drugs used were recorded to check buying costs. According to the direct calculating method, the personnel expenses came to approximately 300,000 yen, total cost was approximately 700,000 yen, and the cost percentage was 59%. According to the indirect method, the personnel expenses were approximately 540,000 yen and the total cost was approximately 940,000 yen, the cost percentage being 80%. A simulation study of changes in the cost with changes in hospital days revealed that the cost percentages were assessed to be approximately 53% in 19 hospital days and approximately 45% in 12 hospital days.

Momentum and particle transport in a nonhomogenous canopy

NASA Astrophysics Data System (ADS)

Gould, Andrew W.

Turbulent particle transport through the air plays an important role in the life cycle of many plant pathogens. In this study, data from a field experiment was analyzed to explore momentum and particle transport within a grape vineyard. The overall goal of these experiments was to understand how the architecture of a sparse agricultural canopy interacts with turbulent flow and ultimately determines the dispersion of airborne fungal plant pathogens. Turbulence in the vineyard canopy was measured using an array of four sonic anemometers deployed at heights z/H 0.4, 0.9, 1.45, and 1.95 where z is the height of the each sonic and H is the canopy height. In addition to turbulence measurements from the sonic anemometers, particle dispersion was measured using inert particles with the approximate size and density of powdery mildew spores and a roto-rod impaction trap array. Measurements from the sonic anemometers demonstrate that first and second order statistics of the wind field are dependent on wind direction orientation with respect to vineyard row direction. This dependence is a result of wind channeling which transfers energy between the velocity components when the wind direction is not aligned with the rows. Although the winds have a strong directional dependence, spectra analysis indicates that the structure of the turbulent flow is not fundamentally altered by the interaction between wind direction and row direction. Examination of a limited number of particle release events indicates that the wind turning and channeling observed in the momentum field impacts particle dispersion. For row-aligned flow, particle dispersion in the direction normal to the flow is decreased relative to the plume spread predicted by a standard Gaussian plume model. For flow that is not aligned with the row direction, the plume is found to rotate in the same manner as the momentum field.

Constraint on the second functional derivative of the exchange-correlation energy

NASA Astrophysics Data System (ADS)

Joubert, D. P.

2012-09-01

Using the density functional adiabatic connection approach for an N-electron system it is shown that ? γ is the coupling constant that scales the electron-electron interaction strength. For the non-interacting Kohn-Sham Hamiltonian γ = 0 and for the fully interacting system γ = 1. ? is the Hartree plus exchange-correlation energy while f 0(r) and fγ(r) are the Fukui functions of the non-interacting and interacting systems, respectively. This identity can serve to test the internal self-consistency or quality of approximate functionals. The quality of some popular approximate exchange and correlation functionals are tested for a simple model system.

Sculpting proteins interactively: continual energy minimization embedded in a graphical modeling system.

PubMed

Surles, M C; Richardson, J S; Richardson, D C; Brooks, F P

1994-02-01

We describe a new paradigm for modeling proteins in interactive computer graphics systems--continual maintenance of a physically valid representation, combined with direct user control and visualization. This is achieved by a fast algorithm for energy minimization, capable of real-time performance on all atoms of a small protein, plus graphically specified user tugs. The modeling system, called Sculpt, rigidly constrains bond lengths, bond angles, and planar groups (similar to existing interactive modeling programs), while it applies elastic restraints to minimize the potential energy due to torsions, hydrogen bonds, and van der Waals and electrostatic interactions (similar to existing batch minimization programs), and user-specified springs. The graphical interface can show bad and/or favorable contacts, and individual energy terms can be turned on or off to determine their effects and interactions. Sculpt finds a local minimum of the total energy that satisfies all the constraints using an augmented Lagrange-multiplier method; calculation time increases only linearly with the number of atoms because the matrix of constraint gradients is sparse and banded. On a 100-MHz MIPS R4000 processor (Silicon Graphics Indigo), Sculpt achieves 11 updates per second on a 20-residue fragment and 2 updates per second on an 80-residue protein, using all atoms except non-H-bonding hydrogens, and without electrostatic interactions. Applications of Sculpt are described: to reverse the direction of bundle packing in a designed 4-helix bundle protein, to fold up a 2-stranded beta-ribbon into an approximate beta-barrel, and to design the sequence and conformation of a 30-residue peptide that mimics one partner of a protein subunit interaction. Computer models that are both interactive and physically realistic (within the limitations of a given force field) have 2 significant advantages: (1) they make feasible the modeling of very large changes (such as needed for de novo design), and (2) they help the user understand how different energy terms interact to stabilize a given conformation. The Sculpt paradigm combines many of the best features of interactive graphical modeling, energy minimization, and actual physical models, and we propose it as an especially productive way to use current and future increases in computer speed.

Spherical solid model system: Exact evaluation of the van der Waals interaction between a microscopic or submacroscopic spherical solid and a deformable fluid interface

NASA Astrophysics Data System (ADS)

Wang, Y. Z.; Wang, B.; Xiong, X. M.; Zhang, J. X.

2011-03-01

In many previous research work associated with studying the deformation of the fluid interface interacting with a solid, the theoretical calculation of the surface energy density on the deformed fluid interface (or its interaction surface pressure) is often approximately obtained by using the expression for the interaction energy per unit area (or pressure) between two parallel macroscopic plates, e.g. σ(D) = - A / 12 πD2or π(D) = - A / 6 πD3for the van der Waals (vdW) interaction, through invoking the Derjaguin approximation (DA). This approximation however would result in over- or even inaccurate-prediction of the interaction force and the corresponding deformation of the fluid interface due to the invalidation of Derjaguin approximation in cases of microscopic or submacroscopic solids. To circumvent the above limitations existing in the previous DA-based theoretical work, a more accurate and quantitative theoretical model, available for exactly calculating the vdW-induced deformation of a planar fluid interface interacting with a sphere, and the interaction forces taking into account its change, is presented in this paper. The validity and advantage of the new mathematical and physical technique is rigorously verified by comparison with the numerical results on basis of the previous Paraboloid solid (PS) model and the Hamaker's sphere-flat expression (viz. F = - 2 Aa3 / (3 D2( D + 2 a) 2)), as well as its well-known DA-based general form of F / a = - A / 6z p02.

Multidimensional directional flux weighted upwind scheme for multiphase flow modeling in heterogeneous porous media

NASA Astrophysics Data System (ADS)

Jin, G.

2012-12-01

Multiphase flow modeling is an important numerical tool for a better understanding of transport processes in the fields including, but not limited to, petroleum reservoir engineering, remedy of ground water contamination, and risk evaluation of greenhouse gases such as CO2 injected into deep saline reservoirs. However, accurate numerical modeling for multiphase flow remains many challenges that arise from the inherent tight coupling and strong non-linear nature of the governing equations and the highly heterogeneous media. The existence of counter current flow which is caused by the effect of adverse relative mobility contrast and gravitational and capillary forces will introduce additional numerical instability. Recently multipoint flux approximation (MPFA) has become a subject of extensive research and has been demonstrated with great success in reducing considerable grid orientation effects compared to the conventional single point upstream (SPU) weighting scheme, especially in higher dimensions. However, the present available MPFA schemes are mathematically targeted to certain types of grids in two dimensions, a more general form of MPFA scheme is needed for both 2-D and 3-D problems. In this work a new upstream weighting scheme based on multipoint directional incoming fluxes is proposed which incorporates full permeability tensor to account for the heterogeneity of the porous media. First, the multiphase governing equations are decoupled into an elliptic pressure equation and a hyperbolic or parabolic saturation depends on whether the gravitational and capillary pressures are presented or not. Next, a dual secondary grid (called finite volume grid) is formulated from a primary grid (called finite element grid) to create interaction regions for each grid cell over the entire simulation domain. Such a discretization must ensure the conservation of mass and maintain the continuity of the Darcy velocity across the boundaries between neighboring interaction regions. The pressure field is then implicitly calculated from the pressure equation, which in turn results in the derived velocity field for directional flux calculation at each grid node. Directional flux at the center of each interaction surface is also calculated by interpolation from the element nodal fluxes using shape functions. The MPFA scheme is performed by a specific linear combination of all incoming fluxes into the upstream cell represented by either nodal fluxes or interpolated surface boundary fluxes to produce an upwind directional fluxed weighted relative mobility at the center of the interaction region boundary. Such an upwind weighted relative mobility is then used for calculating the saturations of each fluid phase explicitly. The proposed upwind weighting scheme has been implemented into a mixed finite element-finite volume (FE-FV) method, which allows for handling complex reservoir geometry with second-order accuracies in approximating primary variables. The numerical solver has been tested with several bench mark test problems. The application of the proposed scheme to migration path analysis of CO2 injected into deep saline reservoirs in 3-D has demonstrated its ability and robustness in handling multiphase flow with adverse mobility contrast in highly heterogeneous porous media.

A mean spherical model for soft potentials: The hard core revealed as a perturbation

NASA Technical Reports Server (NTRS)

Rosenfeld, Y.; Ashcroft, N. W.

1978-01-01

The mean spherical approximation for fluids is extended to treat the case of dense systems interacting via soft-potentials. The extension takes the form of a generalized statement concerning the behavior of the direct correlation function c(r) and radial distribution g(r). From a detailed analysis that views the hard core portion of a potential as a perturbation on the whole, a specific model is proposed which possesses analytic solutions for both Coulomb and Yukawa potentials, in addition to certain other remarkable properties. A variational principle for the model leads to a relatively simple method for obtaining numerical solutions.

Studies of electron-polyatomic-molecule collisions Applications to e-CH4

NASA Technical Reports Server (NTRS)

Lima, M. A. P.; Gibson, T. L.; Mckoy, V.; Huo, W. M.

1985-01-01

The first application of the Schwinger multichannel formulation to low-energy electron collisions with a nonlinear polyatomic target is reported. Integral and differential cross sections are obtained for e-CH4 collisions from 3 to 20 eV at the static-plus-exchange interaction level. In these studies, the exchange potential is directly evaluated and not approximated by local models. An interesting feature of the small-angle differential cross section is ascribed to polarization effects and not reproduced at the static-plus-exchange level. These differential cross sections are found to be in reasonable agreement with existing measurements at 7.5 eV and higher energies.

A grid spacing control technique for algebraic grid generation methods

NASA Technical Reports Server (NTRS)

Smith, R. E.; Kudlinski, R. A.; Everton, E. L.

1982-01-01

A technique which controls the spacing of grid points in algebraically defined coordinate transformations is described. The technique is based on the generation of control functions which map a uniformly distributed computational grid onto parametric variables defining the physical grid. The control functions are smoothed cubic splines. Sets of control points are input for each coordinate directions to outline the control functions. Smoothed cubic spline functions are then generated to approximate the input data. The technique works best in an interactive graphics environment where control inputs and grid displays are nearly instantaneous. The technique is illustrated with the two-boundary grid generation algorithm.

Active and hibernating turbulence in drag-reducing plane Couette flows

NASA Astrophysics Data System (ADS)

Pereira, Anselmo S.; Mompean, Gilmar; Thais, Laurent; Soares, Edson J.; Thompson, Roney L.

2017-08-01

In this paper we analyze the active and hibernating turbulence in drag-reducing plane Couette flows using direct numerical simulations of the viscoelastic finitely extensible nonlinear elastic model with the Peterlin approximation fluids. The polymer-turbulence interactions are studied from an energetic standpoint for a range of Weissenberg numbers (from 2 up to 30), fixing the Reynolds number based on the plate velocities at 4000, the viscosity ratio at 0.9, and the maximum polymer molecule extensibility at 100. The qualitative picture that emerges from this investigation is a cyclic mechanism of energy exchange between the polymers and turbulence that drives the flow through an oscillatory behavior.

Nonlinear cascades in two-dimensional turbulent magnetoconvection.

PubMed

Skandera, Dan; Müller, Wolf-Christian

2009-06-05

The dynamics of spectral transport in two-dimensional turbulent convection of electrically conducting fluids is studied by means of direct numerical simulations in the frame of the magnetohydrodynamic Boussinesq approximation. The system performs quasioscillations between two different regimes of small-scale turbulence: one dominated by nonlinear magnetohydrodynamic interactions; the other governed by buoyancy forces. The self-excited change of turbulent states is reported here for the first time. The process is controlled by the ideal invariant cross helicity, H;{C}=integral_{S}dSv.b. The observations are explained by the interplay of convective driving with the nonlinear spectral transfer of total magnetohydrodynamic energy and cross helicity.

Ternary metal-rich sulfide with a layered structure

DOEpatents

Franzen, Hugo F.; Yao, Xiaoqiang

1993-08-17

A ternary Nb-Ta-S compound is provided having the atomic formula, Nb.sub.1.72 Ta.sub.3.28 S.sub.2, and exhibiting a layered structure in the sequence S-M3-M2-M1-M2-M3-S wherein S represents sulfur layers and M1, M2, and M3 represent Nb/Ta mixed metal layers. This sequence generates seven sheets stacked along the [001] direction of an approximate body centered cubic crystal structure with relatively weak sulfur-to-sulfur van der Waals type interactions between adjacent sulfur sheets and metal-to-metal bonding within and between adjacent mixed metal sheets.

Center for Modeling of Turbulence and Transition (CMOTT). Research briefs: 1990

NASA Technical Reports Server (NTRS)

Povinelli, Louis A. (Compiler); Liou, Meng-Sing (Compiler); Shih, Tsan-Hsing (Compiler)

1991-01-01

Brief progress reports of the Center for Modeling of Turbulence and Transition (CMOTT) research staff from May 1990 to May 1991 are given. The objectives of the CMOTT are to develop, validate, and implement the models for turbulence and boundary layer transition in the practical engineering flows. The flows of interest are three dimensional, incompressible, and compressible flows with chemistry. The schemes being studied include the two-equation and algebraic Reynolds stress models, the full Reynolds stress (or second moment closure) models, the probability density function models, the Renormalization Group Theory (RNG) and Interaction Approximation (DIA), the Large Eddy Simulation (LES) and Direct Numerical Simulation (DNS).

A molecular theory of liquid interfaces.

PubMed

Kovalenko, Andriy; Hirata, Fumio

2005-04-21

We propose a site site generalization of the Lovett-Mow-Buff-Wertheim integro-differential equation for the one-particle density distributions to polyatomic fluids. The method provides microscopic description of liquid interfaces of molecular fluids and solutions. It uses the inhomogeneous site-site direct correlation function of molecular fluid consistently constructed by nonlinear interpolation between the homogeneous ones. The site site correlations of the coexisting bulk phases are obtained from the reference interaction site model (RISM) integral equation with our closure approximation. For illustration, we calculated the structure of the planar liquid-vapor as well as liquid-liquid interfaces of n-hexane and methanol at ambient conditions.

Reconciling phase diffusion and Hartree-Fock approximation in condensate systems

NASA Astrophysics Data System (ADS)

Giorgi, Gian Luca; de Pasquale, Ferdinando

2012-01-01

Despite the weakly interacting regime, the physics of Bose-Einstein condensates is widely affected by particle-particle interactions. They determine quantum phase diffusion, which is known to be the main cause of loss of coherence. Studying a simple model of two interacting Bose systems, we show how to predict the appearance of phase diffusion beyond the Bogoliubov approximation, providing a self-consistent treatment in the framework of a generalized Hartree-Fock-Bogoliubov perturbation theory.

Human apolipoprotein B mRNA-editing enzyme-catalytic polypeptide-like 3G (APOBEC3G) is incorporated into HIV-1 virions through interactions with viral and nonviral RNAs.

PubMed

Svarovskaia, Evguenia S; Xu, Hongzhan; Mbisa, Jean L; Barr, Rebekah; Gorelick, Robert J; Ono, Akira; Freed, Eric O; Hu, Wei-Shau; Pathak, Vinay K

2004-08-20

Apolipoprotein B mRNA-editing enzyme-catalytic polypeptide-like 3G (APOBEC3G) is a host cytidine deaminase that is packaged into virions and confers resistance to retroviral infection. APOBEC3G deaminates deoxycytidines in minus strand DNA to deoxyuridines, resulting in G to A hypermutation and viral inactivation. Human immunodeficiency virus type 1 (HIV-1) virion infectivity factor counteracts the antiviral activity of APOBEC3G by inducing its proteosomal degradation and preventing virion incorporation. To elucidate the mechanism of viral suppression by APOBEC3G, we developed a sensitive cytidine deamination assay and analyzed APOBEC3G virion incorporation in a series of HIV-1 deletion mutants. Virus-like particles derived from constructs in which pol, env, and most of gag were deleted still contained high levels of cytidine deaminase activity; in addition, coimmunoprecipitation of APOBEC3G and HIV-1 Gag in the presence and absence of RNase A indicated that the two proteins do not interact directly but form an RNase-sensitive complex. Viral particles lacking HIV-1 genomic RNA which were generated from the gag-pol expression constructs pC-Help and pSYNGP packaged APOBEC3G at 30-40% of the wild-type level, indicating that interactions with viral RNA are not necessary for incorporation. In addition, viral particles produced from an nucleocapsid zinc finger mutant contained approximately 1% of the viral genomic RNA but approximately 30% of the cytidine deaminase activity. The reduction in APOBEC3G incorporation was equivalent to the reduction in the total RNA present in the nucleocapsid mutant virions. These results indicate that interactions with viral proteins or viral genomic RNA are not essential for APOBEC3G incorporation and suggest that APOBEC3G interactions with viral and nonviral RNAs that are packaged into viral particles are sufficient for APOBEC3G virion incorporation.

Investigating the nature of co-occurring depression and anxiety: Comparing diagnostic and dimensional research approaches.

PubMed

Kircanski, Katharina; LeMoult, Joelle; Ordaz, Sarah; Gotlib, Ian H

2017-07-01

Although approximately half of adults diagnosed with a depressive or anxiety disorder exhibit their simultaneous co-occurrence, traditional research has centered on single-target diagnoses, overlooking comorbidities within samples. In this article, we review and extend the literature that directly investigates co-occurring depression and anxiety, with the goal of shifting the focus from co-occurring diagnoses to symptom dimensions. First, we review studies that have directly compared psychobiological features (neural, neuroendocrine, autonomic) across depression, anxiety, and their co-occurrence, defined either categorically or dimensionally. Second, we analyze adults' diurnal cortisol secretion to examine the independent and interactive relations of continuously-assessed depressive and anxiety symptoms to neuroendocrine function. Previous findings on the psychobiology of diagnostic co-occurrence are mixed. While nascent, evidence from dimensionally focused studies suggests that co-occurring levels of depressive and anxiety symptoms can interact with one another, as reflected in a distinct psychobiological profile for individuals with high levels of both symptom dimensions. Results of our analyses support this formulation: we found that depressive and anxiety symptom dimensions interacted consistently in their relation to the measures of diurnal cortisol. The illustrative sample was relatively small and included only women; future research should examine generalizability of these findings. A dimensional approach to investigating the psychobiology of co-occurring depression and anxiety affords both conceptual and practical advantages. Simultaneously assessing depressive and anxiety symptom dimensions can efficiently capture their unique, shared, and interactive features, thereby identifying targets for intervention across a wide range of symptom presentations. Published by Elsevier B.V.

Vespertilionid bats control the width of their biosonar sound beam dynamically during prey pursuit

PubMed Central

Jakobsen, Lasse; Surlykke, Annemarie

2010-01-01

Animals using sound for communication emit directional signals, focusing most acoustic energy in one direction. Echolocating bats are listening for soft echoes from insects. Therefore, a directional biosonar sound beam greatly increases detection probability in the forward direction and decreases off-axis echoes. However, high directionality has context-specific disadvantages: at close range the detection space will be vastly reduced, making a broad beam favorable. Hence, a flexible system would be very advantageous. We investigated whether bats can dynamically change directionality of their biosonar during aerial pursuit of insects. We trained five Myotis daubentonii and one Eptesicus serotinus to capture tethered mealworms and recorded their echolocation signals with a multimicrophone array. The results show that the bats broaden the echolocation beam drastically in the terminal phase of prey pursuit. M. daubentonii increased the half-amplitude angle from approximately 40° to approximately 90° horizontally and from approximately 45° to more than 90° vertically. The increase in beam width is achieved by lowering the frequency by roughly one octave from approximately 55 kHz to approximately 27.5 kHz. The E. serotinus showed beam broadening remarkably similar to that of M. daubentonii. Our results demonstrate dynamic control of beam width in both species. Hence, we propose directionality as an explanation for the frequency decrease observed in the buzz of aerial hawking vespertilionid bats. We predict that future studies will reveal dynamic control of beam width in a broad range of acoustically communicating animals. PMID:20643943

Vespertilionid bats control the width of their biosonar sound beam dynamically during prey pursuit.

PubMed

Jakobsen, Lasse; Surlykke, Annemarie

2010-08-03

Animals using sound for communication emit directional signals, focusing most acoustic energy in one direction. Echolocating bats are listening for soft echoes from insects. Therefore, a directional biosonar sound beam greatly increases detection probability in the forward direction and decreases off-axis echoes. However, high directionality has context-specific disadvantages: at close range the detection space will be vastly reduced, making a broad beam favorable. Hence, a flexible system would be very advantageous. We investigated whether bats can dynamically change directionality of their biosonar during aerial pursuit of insects. We trained five Myotis daubentonii and one Eptesicus serotinus to capture tethered mealworms and recorded their echolocation signals with a multimicrophone array. The results show that the bats broaden the echolocation beam drastically in the terminal phase of prey pursuit. M. daubentonii increased the half-amplitude angle from approximately 40 degrees to approximately 90 degrees horizontally and from approximately 45 degrees to more than 90 degrees vertically. The increase in beam width is achieved by lowering the frequency by roughly one octave from approximately 55 kHz to approximately 27.5 kHz. The E. serotinus showed beam broadening remarkably similar to that of M. daubentonii. Our results demonstrate dynamic control of beam width in both species. Hence, we propose directionality as an explanation for the frequency decrease observed in the buzz of aerial hawking vespertilionid bats. We predict that future studies will reveal dynamic control of beam width in a broad range of acoustically communicating animals.

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

Subramaniam, S.; Marti, T.; Khorana, H.G.

Previous studies with site-specific mutants of bacteriorhodopsin have demonstrated that replacement of Asp-85 or Arg-82 affects the absorption spectrum. Between pH 5.5 and 7, the Asp-85----Glu and Arg-82----Ala mutants exist in a pH-dependent equilibrium between purple (lambda max approximately 550/540 nm) and blue (lambda max approximately 600/590 nm) forms of the pigment. Measurement of proton transport as a function of wavelength in reconstituted vesicles shows that proton-pumping activities for the above mutants reside exclusively in their respective purple species. For both mutants, formation of the blue form with decreasing pH is accompanied by loss of proton transport activity. The Asp-85----Asnmore » mutant displays a blue chromophore (lambda max approximately 588 nm), is inactive in proton translocation from pH 5 to 7.5, and shows no transition to the purple form. In contrast, the Asp-212----Asn mutant is purple (lambda max approximately 555 nm) and shows no transition to a blue chromophore with decreasing pH. The experiments suggest that (i) the pKa of the purple-to-blue transition is directly influenced by the pKa of the carboxylate at residue 85 and (ii) the relative strengths of interaction between the protonated Schiff base, Asp-85, Asp-212, and Arg-82 make a major contribution to the regulation of color and function of bacteriorhodopsin.« less

Long-range interactions in magnetic bilayer above the critical temperature

NASA Astrophysics Data System (ADS)

de Souza, R. M. V.; Pereira, T. A. S.; Godoy, M.; de Arruda, A. S.

2018-01-01

In this paper we have studied the stabilization of the long-range order in (z ; x) -plane of two isotropic Heisenberg ferromagnetic monolayers coupled by a short-range exchange interaction (J⊥), by a long range dipole-dipole interactions and a magnetic field. We have applied a magnetic field along of the z-direction to study the thermodynamic properties above the critical temperature. The dispersion relation ω and the magnetization are given as function of dipolar anisotropy parameter defined as Ed =(gμ) 2 S /a3J∥ and for other Hamiltonian parameters, and they are calculated by the double-time Zubarev-Tyablikov Green's functions in the random-phase approximation (RPA). The results show that the system is unstable for values of Ed ≥ 0.012 with external magnetic field ranging between H /J∥ = 0 and 10-3. The instability appears for Ed larger then Edc = 0.0158 with H /J∥ = 10-5, Edc = 0.02885 with H /J∥ = 10-4, and Edc = 0.115 with H /J∥ = 10-3, i.e., a small magnetic field is sufficient to maintain the magnetic order in a greater range of the dipolar interaction.

Physical Forces between Humans and How Humans Attract and Repel Each Other Based on Their Social Interactions in an Online World

PubMed Central

Thurner, Stefan; Fuchs, Benedikt

2015-01-01

Physical interactions between particles are the result of the exchange of gauge bosons. Human interactions are mediated by the exchange of messages, goods, money, promises, hostilities, etc. While in the physical world interactions and their associated forces have immediate dynamical consequences (Newton’s laws) the situation is not clear for human interactions. Here we quantify the relative acceleration between humans who interact through the exchange of messages, goods and hostilities in a massive multiplayer online game. For this game we have complete information about all interactions (exchange events) between about 430,000 players, and about their trajectories (movements) in the metric space of the game universe at any point in time. We use this information to derive “interaction potentials" for communication, trade and attacks and show that they are harmonic in nature. Individuals who exchange messages and trade goods generally attract each other and start to separate immediately after exchange events end. The form of the interaction potential for attacks mirrors the usual “hit-and-run" tactics of aggressive players. By measuring interaction intensities as a function of distance, velocity and acceleration, we show that “forces" between players are directly related to the number of exchange events. We find an approximate power-law decay of the likelihood for interactions as a function of distance, which is in accordance with previous real world empirical work. We show that the obtained potentials can be understood with a simple model assuming an exchange-driven force in combination with a distance-dependent exchange rate. PMID:26196505

Physical Forces between Humans and How Humans Attract and Repel Each Other Based on Their Social Interactions in an Online World.

PubMed

Thurner, Stefan; Fuchs, Benedikt

2015-01-01

Physical interactions between particles are the result of the exchange of gauge bosons. Human interactions are mediated by the exchange of messages, goods, money, promises, hostilities, etc. While in the physical world interactions and their associated forces have immediate dynamical consequences (Newton's laws) the situation is not clear for human interactions. Here we quantify the relative acceleration between humans who interact through the exchange of messages, goods and hostilities in a massive multiplayer online game. For this game we have complete information about all interactions (exchange events) between about 430,000 players, and about their trajectories (movements) in the metric space of the game universe at any point in time. We use this information to derive "interaction potentials" for communication, trade and attacks and show that they are harmonic in nature. Individuals who exchange messages and trade goods generally attract each other and start to separate immediately after exchange events end. The form of the interaction potential for attacks mirrors the usual "hit-and-run" tactics of aggressive players. By measuring interaction intensities as a function of distance, velocity and acceleration, we show that "forces" between players are directly related to the number of exchange events. We find an approximate power-law decay of the likelihood for interactions as a function of distance, which is in accordance with previous real world empirical work. We show that the obtained potentials can be understood with a simple model assuming an exchange-driven force in combination with a distance-dependent exchange rate.

Numerical Simulations of Light Bullets, Using The Full Vector, Time Dependent, Nonlinear Maxwell Equations

NASA Technical Reports Server (NTRS)

Goorjian, Peter M.; Silberberg, Yaron; Kwak, Dochan (Technical Monitor)

1994-01-01

This paper will present results in computational nonlinear optics. An algorithm will be described that solves the full vector nonlinear Maxwell's equations exactly without the approximations that are currently made. Present methods solve a reduced scalar wave equation, namely the nonlinear Schrodinger equation, and neglect the optical carrier. Also, results will be shown of calculations of 2-D electromagnetic nonlinear waves computed by directly integrating in time the nonlinear vector Maxwell's equations. The results will include simulations of 'light bullet' like pulses. Here diffraction and dispersion will be counteracted by nonlinear effects. The time integration efficiently implements linear and nonlinear convolutions for the electric polarization, and can take into account such quantum effects as Kerr and Raman interactions. The present approach is robust and should permit modeling 2-D and 3-D optical soliton propagation, scattering, and switching directly from the full-vector Maxwell's equations.

Structural disorder and elementary magnetic properties of triangular lattice ErMgGaO 4 single crystals

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

Cevallos, F. Alex; Stolze, Karoline; Cava, Robert J.

The single crystal growth, structure, and basic magnetic properties of ErMgGaO 4 are reported. The structure consists of triangular layers of magnetic ErO 6 octahedra separated by a double layer of randomly occupied non-magnetic (Ga,Mg)O 5 bipyramids. The Er atoms are positionally disordered. Magnetic measurements parallel and perpendicular to the c axis of a single crystal reveal dominantly antiferromagnetic interactions, with a small degree of magnetic anisotropy. A weighted average of the directional data suggests an antiferromagnetic Curie Weiss temperature of approximately -30 K. Below 10 K the temperature dependences of the inverse susceptibilities in the in-plane and perpendicular-to planemore » directions are parallel, indicative of an isotropic magnetic moment at low temperatures. In conclusion, no sign of magnetic ordering is observed above 1.8 K, suggesting that ErMgGaO 4 is a geometrically frustrated magnet.« less

Effects of Different Polarization Strategies on Laser Cutting with Direct Diode Lasers

NASA Astrophysics Data System (ADS)

Rodrigues, G. Costa; Duflou, J. R.

As Direct Diode Lasers are introduced as an emerging technology for laser cutting of metal sheets, new challenges arise. The relatively low beam quality remains a limitation to the maximum cutting speed. One way to balance this may be a strategic use of laser polarization in order to influence laser material interaction in the cutting kerf. In this paper the effects of cross-, linear-, radial- and azimuthal- laser beam polarization arrangements are studied with both Fusion and Flame cutting at an output power of approximately 750W. Different combinations of materials and thicknesses were cut and the maximum cutting speed and edge quality analyzed. It is found that at similar cutting edge quality, improvements in cutting speed can go up to 40% with an inert gas, such as Nitrogen, and up to 20% with a reactive gas, such as Oxygen, in agreement with analytical models for absorption previously developed by the authors.

EPR study of copper(II) ions in zinc 1-malate trihydrate

NASA Astrophysics Data System (ADS)

Bonomo, Raffaele P.; Di Bilio, Angel J.; Riggi, Francesco

1988-10-01

The EPR spectrum of Cu 2+ ions in zinc 1-malate trihydrate has been measured at 150 K for a large number of orientations of the applied magnetic field. Analysis yields the following spin Hamiltonian parameters: g x=2.0894±0.0009, A x=-12.0±1.5, g y=2.0879±0.0005, A y=-8.7±1.0, R=-0.7±1.5, g z=2.4249±0.0005, A z=-120.1±0.9, P=9.9±0.5, where the units of A and P are 10 4 cm -1. The Zeeman and hyperfine coupling tensors are coincident within 2°. The spectrum shows forbidden transitions with abnormal intensity due to a large quadrupolar interaction. The direction of g z points towards the hydroxyl oxygen while the g x and g y directions lie approximately along the metal-carboxylate oxygen bond.

Numerical Simulations of Light Bullets, Using The Full Vector, Time Dependent, Nonlinear Maxwell Equations

NASA Technical Reports Server (NTRS)

Goorjian, Peter M.; Silberberg, Yaron; Kwak, Dochan (Technical Monitor)

1995-01-01

This paper will present results in computational nonlinear optics. An algorithm will be described that solves the full vector nonlinear Maxwell's equations exactly without the approximations that we currently made. Present methods solve a reduced scalar wave equation, namely the nonlinear Schrodinger equation, and neglect the optical carrier. Also, results will be shown of calculations of 2-D electromagnetic nonlinear waves computed by directly integrating in time the nonlinear vector Maxwell's equations. The results will include simulations of 'light bullet' like pulses. Here diffraction and dispersion will be counteracted by nonlinear effects. The time integration efficiently implements linear and nonlinear convolutions for the electric polarization, and can take into account such quantum effects as Karr and Raman interactions. The present approach is robust and should permit modeling 2-D and 3-D optical soliton propagation, scattering, and switching directly from the full-vector Maxwell's equations.

Structural disorder and elementary magnetic properties of triangular lattice ErMgGaO 4 single crystals

DOE PAGES

Cevallos, F. Alex; Stolze, Karoline; Cava, Robert J.

2018-03-23

The single crystal growth, structure, and basic magnetic properties of ErMgGaO 4 are reported. The structure consists of triangular layers of magnetic ErO 6 octahedra separated by a double layer of randomly occupied non-magnetic (Ga,Mg)O 5 bipyramids. The Er atoms are positionally disordered. Magnetic measurements parallel and perpendicular to the c axis of a single crystal reveal dominantly antiferromagnetic interactions, with a small degree of magnetic anisotropy. A weighted average of the directional data suggests an antiferromagnetic Curie Weiss temperature of approximately -30 K. Below 10 K the temperature dependences of the inverse susceptibilities in the in-plane and perpendicular-to planemore » directions are parallel, indicative of an isotropic magnetic moment at low temperatures. In conclusion, no sign of magnetic ordering is observed above 1.8 K, suggesting that ErMgGaO 4 is a geometrically frustrated magnet.« less

Model of chiral spin liquids with Abelian and non-Abelian topological phases

DOE PAGES

Chen, Jyong-Hao; Mudry, Christopher; Chamon, Claudio; ...

2017-12-15

In this article, we present a two-dimensional lattice model for quantum spin-1/2 for which the low-energy limit is governed by four flavors of strongly interacting Majorana fermions. We study this low-energy effective theory using two alternative approaches. The first consists of a mean-field approximation. The second consists of a random phase approximation (RPA) for the single-particle Green's functions of the Majorana fermions built from their exact forms in a certain one-dimensional limit. The resulting phase diagram consists of two competing chiral phases, one with Abelian and the other with non-Abelian topological order, separated by a continuous phase transition. Remarkably, themore » Majorana fermions propagate in the two-dimensional bulk, as in the Kitaev model for a spin liquid on the honeycomb lattice. We identify the vison fields, which are mobile (they are static in the Kitaev model) domain walls propagating along only one of the two space directions.« less

High baryon and energy densities achievable in heavy-ion collisions at √{sN N}=39 GeV

NASA Astrophysics Data System (ADS)

Ivanov, Yu. B.; Soldatov, A. A.

2018-02-01

Baryon and energy densities, which are reached in central Au+Au collisions at collision energy of √{sN N}= 39 GeV, are estimated within the model of three-fluid dynamics. It is shown that the initial thermalized mean proper baryon and energy densities in a sizable central region approximately are nB/n0≈ 10 and ɛ ≈ 40 GeV/fm3, respectively. The study indicates that the deconfinement transition at the stage of interpenetration of colliding nuclei makes the system quite opaque. The final fragmentation regions in these collisions are formed not only by primordial fragmentation fireballs, i.e., the baryon-rich matter passed through the interaction region (containing approximately 30% of the total baryon charge), but also by the baryon-rich regions of the central fireball pushed out to peripheral rapidities by the subsequent almost one-dimensional expansion of the central fireball along the beam direction.

Universal single level implicit algorithm for gasdynamics

NASA Technical Reports Server (NTRS)

Lombard, C. K.; Venkatapthy, E.

1984-01-01

A single level effectively explicit implicit algorithm for gasdynamics is presented. The method meets all the requirements for unconditionally stable global iteration over flows with mixed supersonic and supersonic zones including blunt body flow and boundary layer flows with strong interaction and streamwise separation. For hyperbolic (supersonic flow) regions the method is automatically equivalent to contemporary space marching methods. For elliptic (subsonic flow) regions, rapid convergence is facilitated by alternating direction solution sweeps which bring both sets of eigenvectors and the influence of both boundaries of a coordinate line equally into play. Point by point updating of the data with local iteration on the solution procedure at each spatial step as the sweeps progress not only renders the method single level in storage but, also, improves nonlinear accuracy to accelerate convergence by an order of magnitude over related two level linearized implicit methods. The method derives robust stability from the combination of an eigenvector split upwind difference method (CSCM) with diagonally dominant ADI(DDADI) approximate factorization and computed characteristic boundary approximations.

Theoretical approach to the ground state of spherically confined Yukawa plasmas

NASA Astrophysics Data System (ADS)

Henning, Christian; Bonitz, Michael; Piel, Alexander; Ludwig, Patrick; Baumgartner, Henning

2007-11-01

Recently spherical 3D dust crystals (aka Yukawa balls) were discovered [1], which allow direct observation of strong correlation phenomena and the structure of which is well explained by computer simulations of charged Yukawa interacting particles within an external parabolic confinement [2]. Here we present an analytical approach to the ground state of these systems using the minimization of the system's energy. Applying the non-local mean-field approximation we show that screening has a dramatic effect on the density profile, which can be derived explicitly [3]. In addition the local density approximation allows for the inclusion of correlations, which further improves the results in the regime of large screening [4]. Comparisons with MD simulations of Yukawa balls show excellent agreement.[1] O. Arp et al. Phys. Rev. Lett. 93, 165004 (2004)[2] M. Bonitz et al., Phys. Rev. Lett. 96, 075001 (2006)[3] C. Henning et al., Phys. Rev. E 74, 056403 (2006)[4] C. Henning at al., Phys. Rev. E (2007)

Optical properties of electrohydrodynamic convection patterns: rigorous and approximate methods.

PubMed

Bohley, Christian; Heuer, Jana; Stannarius, Ralf

2005-12-01

We analyze the optical behavior of two-dimensionally periodic structures that occur in electrohydrodynamic convection (EHC) patterns in nematic sandwich cells. These structures are anisotropic, locally uniaxial, and periodic on the scale of micrometers. For the first time, the optics of these structures is investigated with a rigorous method. The method used for the description of the electromagnetic waves interacting with EHC director patterns is a numerical approach that discretizes directly the Maxwell equations. It works as a space-grid-time-domain method and computes electric and magnetic fields in time steps. This so-called finite-difference-time-domain (FDTD) method is able to generate the fields with arbitrary accuracy. We compare this rigorous method with earlier attempts based on ray-tracing and analytical approximations. Results of optical studies of EHC structures made earlier based on ray-tracing methods are confirmed for thin cells, when the spatial periods of the pattern are sufficiently large. For the treatment of small-scale convection structures, the FDTD method is without alternatives.

Model of chiral spin liquids with Abelian and non-Abelian topological phases

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

Chen, Jyong-Hao; Mudry, Christopher; Chamon, Claudio

In this article, we present a two-dimensional lattice model for quantum spin-1/2 for which the low-energy limit is governed by four flavors of strongly interacting Majorana fermions. We study this low-energy effective theory using two alternative approaches. The first consists of a mean-field approximation. The second consists of a random phase approximation (RPA) for the single-particle Green's functions of the Majorana fermions built from their exact forms in a certain one-dimensional limit. The resulting phase diagram consists of two competing chiral phases, one with Abelian and the other with non-Abelian topological order, separated by a continuous phase transition. Remarkably, themore » Majorana fermions propagate in the two-dimensional bulk, as in the Kitaev model for a spin liquid on the honeycomb lattice. We identify the vison fields, which are mobile (they are static in the Kitaev model) domain walls propagating along only one of the two space directions.« less

Role of Direct and Indirect Violence Exposure on Externalizing Behavior in Children.

PubMed

Fleckman, Julia M; Drury, Stacy S; Taylor, Catherine A; Theall, Katherine P

2016-06-01

The objective of this study was to examine the association between externalizing behaviors and indirect violence exposure, assessed both within the household and at the community level, as well as the interaction effect of indirect and direct violence exposure. A sample of parents of children ages 4-15 who have not been referred or enrolled in child welfare (n = 82) were recruited from the greater New Orleans community. Externalizing behavior was assessed with the Child Behavior Checklist (CBCL). The child's indirect exposure to violence included witnessing community violence, witnessing physical assault, and witnessing fighting or domestic violence at home. Direct exposure to violence included the child experiencing physical aggression from a caregiver. All assessments were based on caregiver reports. To decrease potential for confounding, children were matched for analysis based on age, Hurricane Katrina exposure, and their propensity to be exposed to high indirect violence. Cumulative indirect exposure to violence was significantly positively correlated with CBCL scores. After controlling for key covariates, CBCL externalizing T score increased significantly by approximately 1.25 points for each level increase in indirect violence exposure (β = 1.25, SE = 0.57, p = 0.027). There also was a significant interaction between indirect and direct exposure to violence in the association with CBCL score (β = -0.08, SE = 0.03, p = 0.002). These findings extend previous research by demonstrating that exposure to both direct and cross-contextual indirect violence influences externalizing behaviors in children. Additionally, the findings suggest that community and household social environments are both important targets for interventions designed to decrease externalizing behaviors and improve long-term outcomes for youth at risk of exposure to violence.

Laboratory Study of Water Surface Roughness Generation by Wave-Current Interaction

NASA Technical Reports Server (NTRS)

Klinke, Jochen

2000-01-01

Within the framework of this project, the blocking of waves by inhomogeneous currents was studied. A laboratory experiment was conducted in collaboration with Steven R. Long at the linear wave tank of the NASA Air-Sea Interaction Facility, Wallops Island, VA during May 1999. Mechanically-generated waves were blocked approximately 3m upstream from the wave paddle by an opposing current. A false bottom was used to obtain a spatially varying flow field in the measurement section of the wave tank. We used an imaging slope gauge, which was mounted directly underneath the sloping section of the false tank bottom to observe the wave field. For a given current speed, the amplitude and the frequency of the waves was adjusted so that the blocking occurred within the observed footprint. Image sequences of up to 600 images at up 100 Hz sampling rate were recorded for an area of approximately 25cm x 25cm. Unlike previous measurements with wave wire gauges, the captured image sequences show the generation of the capillary waves at the blocking point and give detailed insight into the spatial and temporal evolution of the blocking process. The image data were used to study the wave-current interaction for currents from 5 to 25 cm/s and waves with frequencies between 1 and 3 Hz. First the images were calibrated with regard to size and slope. Then standard Fourier techniques as well the empirical mode decomposition method developed by Dr. Norden Huang and Dr. Steven R. Long were employed to quantify the wave number downshift from the gravity to the capillary regime.

Improved Modeling of Side-Chain–Base Interactions and Plasticity in Protein–DNA Interface Design

PubMed Central

Thyme, Summer B.; Baker, David; Bradley, Philip

2012-01-01

Combinatorial sequence optimization for protein design requires libraries of discrete side-chain conformations. The discreteness of these libraries is problematic, particularly for long, polar side chains, since favorable interactions can be missed. Previously, an approach to loop remodeling where protein backbone movement is directed by side-chain rotamers predicted to form interactions previously observed in native complexes (termed “motifs”) was described. Here, we show how such motif libraries can be incorporated into combinatorial sequence optimization protocols and improve native complex recapitulation. Guided by the motif rotamer searches, we made improvements to the underlying energy function, increasing recapitulation of native interactions. To further test the methods, we carried out a comprehensive experimental scan of amino acid preferences in the I-AniI protein–DNA interface and found that many positions tolerated multiple amino acids. This sequence plasticity is not observed in the computational results because of the fixed-backbone approximation of the model. We improved modeling of this diversity by introducing DNA flexibility and reducing the convergence of the simulated annealing algorithm that drives the design process. In addition to serving as a benchmark, this extensive experimental data set provides insight into the types of interactions essential to maintain the function of this potential gene therapy reagent. PMID:22426128

Improved modeling of side-chain--base interactions and plasticity in protein--DNA interface design.

PubMed

Thyme, Summer B; Baker, David; Bradley, Philip

2012-06-08

Combinatorial sequence optimization for protein design requires libraries of discrete side-chain conformations. The discreteness of these libraries is problematic, particularly for long, polar side chains, since favorable interactions can be missed. Previously, an approach to loop remodeling where protein backbone movement is directed by side-chain rotamers predicted to form interactions previously observed in native complexes (termed "motifs") was described. Here, we show how such motif libraries can be incorporated into combinatorial sequence optimization protocols and improve native complex recapitulation. Guided by the motif rotamer searches, we made improvements to the underlying energy function, increasing recapitulation of native interactions. To further test the methods, we carried out a comprehensive experimental scan of amino acid preferences in the I-AniI protein-DNA interface and found that many positions tolerated multiple amino acids. This sequence plasticity is not observed in the computational results because of the fixed-backbone approximation of the model. We improved modeling of this diversity by introducing DNA flexibility and reducing the convergence of the simulated annealing algorithm that drives the design process. In addition to serving as a benchmark, this extensive experimental data set provides insight into the types of interactions essential to maintain the function of this potential gene therapy reagent. Published by Elsevier Ltd.

Conditions where random phase approximation becomes exact in the high-density limit

NASA Astrophysics Data System (ADS)

Morawetz, Klaus; Ashokan, Vinod; Bala, Renu; Pathak, Kare Narain

2018-04-01

It is shown that, in d -dimensional systems, the vertex corrections beyond the random phase approximation (RPA) or G W approximation scales with the power d -β -α of the Fermi momentum if the relation between Fermi energy and Fermi momentum is ɛf˜pfβ and the interacting potential possesses a momentum power law of ˜p-α . The condition d -β -α <0 specifies systems where RPA is exact in the high-density limit. The one-dimensional structure factor is found to be the interaction-free one in the high-density limit for contact interaction. A cancellation of RPA and vertex corrections render this result valid up to second order in contact interaction. For finite-range potentials of cylindrical wires a large-scale cancellation appears and is found to be independent of the width parameter of the wire. The proposed high-density expansion agrees with the quantum Monte Carlo simulations.

LAMMPS framework for dynamic bonding and an application modeling DNA

NASA Astrophysics Data System (ADS)

Svaneborg, Carsten

2012-08-01

We have extended the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) to support directional bonds and dynamic bonding. The framework supports stochastic formation of new bonds, breakage of existing bonds, and conversion between bond types. Bond formation can be controlled to limit the maximal functionality of a bead with respect to various bond types. Concomitant with the bond dynamics, angular and dihedral interactions are dynamically introduced between newly connected triplets and quartets of beads, where the interaction type is determined from the local pattern of bead and bond types. When breaking bonds, all angular and dihedral interactions involving broken bonds are removed. The framework allows chemical reactions to be modeled, and use it to simulate a simplistic, coarse-grained DNA model. The resulting DNA dynamics illustrates the power of the present framework. Catalogue identifier: AEME_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEME_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public Licence No. of lines in distributed program, including test data, etc.: 2 243 491 No. of bytes in distributed program, including test data, etc.: 771 Distribution format: tar.gz Programming language: C++ Computer: Single and multiple core servers Operating system: Linux/Unix/Windows Has the code been vectorized or parallelized?: Yes. The code has been parallelized by the use of MPI directives. RAM: 1 Gb Classification: 16.11, 16.12 Nature of problem: Simulating coarse-grain models capable of chemistry e.g. DNA hybridization dynamics. Solution method: Extending LAMMPS to handle dynamic bonding and directional bonds. Unusual features: Allows bonds to be created and broken while angular and dihedral interactions are kept consistent. Additional comments: The distribution file for this program is approximately 36 Mbytes and therefore is not delivered directly when download or E-mail is requested. Instead an html file giving details of how the program can be obtained is sent. Running time: Hours to days. The examples provided in the distribution take just seconds to run.

Ions interacting in solution: Moving from intrinsic to collective properties

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

Duignan, Timothy T.; Baer, Marcel D.; Mundy, Christopher J.

A crucial determinant of Hofmeister effects is the direct interaction of ions in solution with the charged groups on the surface of larger particles. Understanding ion–ion interactions in solution is therefore a necessary first step to explaining Hofmeister effects. Here, we advocate an approach to modeling these types of properties where state of the art Ab Initio Molecular Dynamics (AIMD) simulation of ions in solution is used to establish benchmark values for the intrinsic properties of ions in solution such as solvation structures and ion–ion Potentials of Mean Force (PMFs). This information can then be combined with or used to parametrize and improve reduced models, which use approximations such as the continuum solvent model.(CSM) These reduced models can then be used to calculate collective and concentration dependent properties of electrolyte solution and so make accurate predictions about complex systems of relevance for direct applications. We provide an example of this approach using AIMD calculations of the sodium chloride dimer to calculate osmotic coefficients of all 20 alkali halide electrolytes. This research used resources of the National Energy Research Scientific Computing Center, a DOE Office of Science User Facility supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. TD and CJM were supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. MDB was supported by MSmore » $$^{3}$$ (Materials Synthesis and Simulation Across Scales) Initiative, a Laboratory Directed Research and Development Program at Pacific Northwest National Laboratory (PNNL). PNNL is a multiprogram national laboratory operated by Battelle for the U.S. Department of Energy.« less

The kinetochore proteins CENP-E and CENP-F directly and specifically interact with distinct BUB mitotic checkpoint Ser/Thr kinases.

PubMed

Ciossani, Giuseppe; Overlack, Katharina; Petrovic, Arsen; Huis In 't Veld, Pim J; Koerner, Carolin; Wohlgemuth, Sabine; Maffini, Stefano; Musacchio, Andrea

2018-05-10

The segregation of chromosomes during cell division relies on the function of the kinetochores, protein complexes that physically connect chromosomes with microtubules of the spindle. The metazoan proteins, centromere protein E (CENP-E) and CENP-F, are components of a fibrous layer of mitotic kinetochores named the corona. Several of their features suggest that CENP-E and CENP-F are paralogs: they are very large (comprising approximately 2700 and 3200 residues, respectively), contain abundant predicted coiled-coil structures, are C-terminally prenylated, and are endowed with microtubule-binding sites at their termini. Moreover, CENP-E contains an ATP-hydrolyzing motor domain that promotes microtubule plus end-directed motion. Here, we show that both CENP-E and CENP-F are recruited to mitotic kinetochores independently of the main corona constituent, the Rod-Zwilch-ZW10 (RZZ) complex. We identified specific interactions of CENP-F and CENP-E with budding uninhibited by benzimidazole 1 (BUB1) and BUB1-related (BUBR1) mitotic checkpoint Ser/Thr kinases, respectively, paralogous proteins involved in mitotic checkpoint control and chromosome alignment. Whereas BUBR1 was dispensable for kinetochore localization of CENP-E, BUB1 was stringently required for CENP-F localization. Through biochemical reconstitution, we demonstrated that the CENP-E-BUBR1 and CENP-F-BUB1 interactions are direct and require similar determinants, a dimeric coiled-coil in CENP-E or CENP-F and a kinase domain in BUBR1 or BUB1. Our findings are consistent with the existence of structurally similar BUB1-CENP-F and BUBR1-CENP-E complexes, supporting the notion that CENP-E and CENP-F are evolutionarily related. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

Temperature dependences of the time of electron-electron interactions in two-dimensional heterojunction

NASA Astrophysics Data System (ADS)

Bukhenskyy, K. V.; Dubois, A. B.; Kucheryavyy, S. I.; Mashnina, S. N.; Safoshkin, A. S.; Baukov, A. A.; Shchigorev, E. Yu

2017-12-01

The article discusses the joint solution of the Schrödinger and Poisson equations for two-dimensional semiconductor heterojunction. The application of a triangular potential of well approximation for the calculation of the electron-electron interaction is offered in the paper. The influence of the parameters of the selected approximation was analyzed.

Approximate bound-state solutions of the Dirac equation for the generalized yukawa potential plus the generalized tensor interaction

NASA Astrophysics Data System (ADS)

Ikot, Akpan N.; Maghsoodi, Elham; Hassanabadi, Hassan; Obu, Joseph A.

2014-05-01

In this paper, we obtain the approximate analytical bound-state solutions of the Dirac particle with the generalized Yukawa potential within the framework of spin and pseudospin symmetries for the arbitrary к state with a generalized tensor interaction. The generalized parametric Nikiforov-Uvarov method is used to obtain the energy eigenvalues and the corresponding wave functions in closed form. We also report some numerical results and present figures to show the effect of the tensor interaction.

Coupled multipolar interactions in small-particle metallic clusters.

PubMed

Pustovit, Vitaly N; Sotelo, Juan A; Niklasson, Gunnar A

2002-03-01

We propose a new formalism for computing the optical properties of small clusters of particles. It is a generalization of the coupled dipole-dipole particle-interaction model and allows one in principle to take into account all multipolar interactions in the long-wavelength limit. The method is illustrated by computations of the optical properties of N = 6 particle clusters for different multipolar approximations. We examine the effect of separation between particles and compare the optical spectra with the discrete-dipole approximation and the generalized Mie theory.

Solutions of the Dirac Equation with the Shifted DENG-FAN Potential Including Yukawa-Like Tensor Interaction

NASA Astrophysics Data System (ADS)

Yahya, W. A.; Falaye, B. J.; Oluwadare, O. J.; Oyewumi, K. J.

2013-08-01

By using the Nikiforov-Uvarov method, we give the approximate analytical solutions of the Dirac equation with the shifted Deng-Fan potential including the Yukawa-like tensor interaction under the spin and pseudospin symmetry conditions. After using an improved approximation scheme, we solved the resulting schr\\"{o}dinger-like equation analytically. Numerical results of the energy eigenvalues are also obtained, as expected, the tensor interaction removes degeneracies between spin and pseudospin doublets.

On direct theorems for best polynomial approximation

NASA Astrophysics Data System (ADS)

Auad, A. A.; AbdulJabbar, R. S.

2018-05-01

This paper is to obtain similarity for the best approximation degree of functions, which are unbounded in L p,α (A = [0,1]), which called weighted space by algebraic polynomials. {E}nH{(f)}p,α and the best approximation degree in the same space on the interval [0,2π] by trigonometric polynomials {E}nT{(f)}p,α of direct wellknown theorems in forms the average modules.

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

PubMed

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

2016-05-13

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

Verification of Anderson superexchange in MnO via magnetic pair distribution function analysis and ab initio theory

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

Benjamin A. Frandsen; Brunelli, Michela; Page, Katharine

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

Verification of Anderson superexchange in MnO via magnetic pair distribution function analysis and ab initio theory

DOE PAGES

Benjamin A. Frandsen; Brunelli, Michela; Page, Katharine; ...

2016-05-11

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

Volumetric flow around a swimming lamprey

NASA Astrophysics Data System (ADS)

Lehn, Andrea M.; Colin, Sean P.; Costello, John H.; Leftwich, Megan C.; Tytell, Eric D.

2015-11-01

A primary experimental technique for studying fluid-structure interactions around swimming fish has been planar dimensional particle image velocimetry (PIV). Typically, two components of the velocity vector are measured in a plane, in the case of swimming studies, directly behind the animal. While useful, this approach provides little to no insight about fluid structure interactions above and below the fish. For fish with a small height relative to body length, such as the long and approximately cylindrical lamprey, 3D information is essential to characterize how these fish interact with their fluid environment. This study presents 3D flow structures along the body and in the wake of larval lamprey, P etromyzon m arinus , which are 10-15 cm long. Lamprey swim through a 1000 cm3 field of view in a standard 10 gallon tank illuminated by a green laser. Data are collected using the three component velocimeter V3V system by TSI, Inc. and processed using Insight 4G software. This study expands on previous works that show two pairs of vortices each tail beat in the mid-plane of the lamprey wake. NSF DMS 1062052.

76 FR 76162 - Federal Open Market Committee; Domestic Policy Directive of November 1-2, 2011

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-06

... approximately 6 years to 30 years with a total face value of $400 billion, and to sell Treasury securities with remaining maturities of 3 years or less with a total face value of $400 billion. The Committee also directs... face value of domestic securities at approximately $2.6 trillion. The Committee directs the Desk to...

A Generalized Weizsacker-Williams Method Applied to Pion Production in Proton-Proton Collisions

NASA Technical Reports Server (NTRS)

Ahern, Sean C.; Poyser, William J.; Norbury, John W.; Tripathi, R. K.

2002-01-01

A new "Generalized" Weizsacker-Williams method (GWWM) is used to calculate approximate cross sections for relativistic peripheral proton-proton collisions. Instead of a mass less photon mediator, the method allows for the mediator to have mass for short range interactions. This method generalizes the Weizsacker-Williams method (WWM) from Coulomb interactions to GWWM for strong interactions. An elastic proton-proton cross section is calculated using GWWM with experimental data for the elastic p+p interaction, where the mass p+ is now the mediator. The resulting calculated cross sections is compared to existing data for the elastic proton-proton interaction. A good approximate fit is found between the data and the calculation.

A diagrammatic formulation of the kinetic theory of fluctuations in equilibrium classical fluids. VI. Binary collision approximations for the memory function for self-correlation functions

NASA Astrophysics Data System (ADS)

Noah-Vanhoucke, Joyce E.; Andersen, Hans C.

2007-08-01

We use computer simulation results for a dense Lennard-Jones fluid for a range of temperatures to test the accuracy of various binary collision approximations for the memory function for density fluctuations in liquids. The approximations tested include the moderate density approximation of the generalized Boltzmann-Enskog memory function (MGBE) of Mazenko and Yip [Statistical Mechanics. Part B. Time-Dependent Processes, edited by B. J. Berne (Plenum, New York, 1977)], the binary collision approximation (BCA) and the short time approximation (STA) of Ranganathan and Andersen [J. Chem. Phys. 121, 1243 (2004); J. Phys. Chem. 109, 21437 (2005)] and various other approximations we derived by using diagrammatic methods. The tests are of two types. The first is a comparison of the correlation functions predicted by each approximate memory function with the simulation results, especially for the self-longitudinal current correlation (SLCC) function. The second is a direct comparison of each approximate memory function with a memory function numerically extracted from the correlation function data. The MGBE memory function is accurate at short times but decays to zero too slowly and gives a poor description of the correlation function at intermediate times. The BCA is exact at zero time, but it predicts a correlation function that diverges at long times. The STA gives a reasonable description of the SLCC but does not predict the correct temperature dependence of the negative dip in the function that is associated with caging at low temperatures. None of the other binary collision approximations is a systematic improvement on the STA. The extracted memory functions have a rapidly decaying short time part, much like the STA, and a much smaller, more slowly decaying part of the type predicted by a mode coupling theory. Theories that use mode coupling commonly include a binary collision term in the memory function but do not discuss in detail the nature of that term. It is clear from the present work that the short time part of the memory function has a behavior associated with brief binary repulsive collisions, such as those described by the STA. Collisions that include attractive as well as repulsive interactions, such as those of the MGBE, have a much longer duration, and theories that include them have memory functions that decay to zero much too slowly to provide a good first approximation of the correlation function. This leads us to speculate that the memory function for density fluctuations can be usefully regarded as a sum of at least three parts: a contribution from repulsive binary collisions (the STA or something similar to it), another short time part that is related to all the other interactions (but whose nature is not understood), and a longer time slowly decaying part that describes caging (of the type predicted by the mode coupling theory).

Quantitative vs. subjective portal verification using digital portal images.

PubMed

Bissett, R; Leszczynski, K; Loose, S; Boyko, S; Dunscombe, P

1996-01-15

Off-line, computer-aided prescription (simulator) and treatment (portal) image registration using chamfer matching has been implemented on PC based viewing station. The purposes of this study were (a) to evaluate the performance of interactive anatomy and field edge extraction and subsequent registration, and (b) to compare observer's perceptions of field accuracy with measured discrepancies following anatomical registration. Prescription-treatment image pairs for 48 different patients were examined in this study. Digital prescription images were produced with the aid of a television camera and a digital frame grabber, while the treatment images were obtained directly from an on-line portal imaging system. To facilitate perception of low contrast anatomical detail, on-line portal images were enhanced with selective adaptive histogram equalization prior to extraction of anatomical edges. Following interactive extraction of anatomical and field border information by an experienced observer, the identified anatomy was registered using chamfer matching. The degree of conformity between the prescription and treatment fields was quantified using several parameters, which included relative prescription field coverage and overcoverage, as well as the translational and rotational displacements as measured by chamfer matching applied to the boundaries of the two fields. These quantitative measures were compared with subjective evaluations made by four radiation oncologists. All the images in this series that included a range of the most commonly seen treatment sites were registered and the conformity parameters were found. The mean treatment/prescription field coverage and overcoverage were approximately 95 and 7%, respectively before registration. The mean translational displacement in the transverse and cranio-caudal directions were 2.9 and 3.4 mm, respectively. The mean rotational displacement was approximately 2 degrees. For all four oncologists, the portals classified as unacceptable, in terms of the field placement, exhibited significantly higher (p < 0.03) translational errors in the transverse direction. The field coverages were significantly lower (p < 0.05) and the translational errors in the cranio-caudal direction were significantly higher (p < 0.05) for the portals rated as unacceptable by two of the oncologists. From the parameters that were used to quantify the degree of conformity between the prescription and treatment fields, the translational error in the transverse direction correlated best with the oncologists' assessments on the field placement. Field coverage and translational error in the cranio-caudal direction correlated well with assessments of only two out of the four participating oncologists. This can be explained by the fact that for the majority of treatment sites included in the study the positioning of field borders was more critical for the transverse direction. A conclusion for the design of future quantitative and automated on-line portal verification systems is that they will have to model different perceived significances of different types of localization errors intrinsic to oncologist evaluation of portal images.

Fundamental Statistical Descriptions of Plasma Turbulence in Magnetic Fields

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

John A. Krommes

2001-02-16

A pedagogical review of the historical development and current status (as of early 2000) of systematic statistical theories of plasma turbulence is undertaken. Emphasis is on conceptual foundations and methodology, not practical applications. Particular attention is paid to equations and formalism appropriate to strongly magnetized, fully ionized plasmas. Extensive reference to the literature on neutral-fluid turbulence is made, but the unique properties and problems of plasmas are emphasized throughout. Discussions are given of quasilinear theory, weak-turbulence theory, resonance-broadening theory, and the clump algorithm. Those are developed independently, then shown to be special cases of the direct-interaction approximation (DIA), which providesmore » a central focus for the article. Various methods of renormalized perturbation theory are described, then unified with the aid of the generating-functional formalism of Martin, Siggia, and Rose. A general expression for the renormalized dielectric function is deduced and discussed in detail. Modern approaches such as decimation and PDF methods are described. Derivations of DIA-based Markovian closures are discussed. The eddy-damped quasinormal Markovian closure is shown to be nonrealizable in the presence of waves, and a new realizable Markovian closure is presented. The test-field model and a realizable modification thereof are also summarized. Numerical solutions of various closures for some plasma-physics paradigms are reviewed. The variational approach to bounds on transport is developed. Miscellaneous topics include Onsager symmetries for turbulence, the interpretation of entropy balances for both kinetic and fluid descriptions, self-organized criticality, statistical interactions between disparate scales, and the roles of both mean and random shear. Appendices are provided on Fourier transform conventions, dimensional and scaling analysis, the derivations of nonlinear gyrokinetic and gyrofluid equations, stochasticity criteria for quasilinear theory, formal aspects of resonance-broadening theory, Novikov's theorem, the treatment of weak inhomogeneity, the derivation of the Vlasov weak-turbulence wave kinetic equation from a fully renormalized description, some features of a code for solving the direct-interaction approximation and related Markovian closures, the details of the solution of the EDQNM closure for a solvable three-wave model, and the notation used in the article.« less

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

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

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

2014-05-14

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

Physical foundation of the fluid particle dynamics method for colloid dynamics simulation.

PubMed

Furukawa, Akira; Tateno, Michio; Tanaka, Hajime

2018-05-16

Colloid dynamics is significantly influenced by many-body hydrodynamic interactions mediated by a suspending fluid. However, theoretical and numerical treatments of such interactions are extremely difficult. To overcome this situation, we developed a fluid particle dynamics (FPD) method [H. Tanaka and T. Araki, Phys. Rev. Lett., 2000, 35, 3523], which is based on two key approximations: (i) a colloidal particle is treated as a highly viscous particle and (ii) the viscosity profile is described by a smooth interfacial profile function. Approximation (i) makes our method free from the solid-fluid boundary condition, significantly simplifying the treatment of many-body hydrodynamic interactions while satisfying the incompressible condition without the Stokes approximation. Approximation (ii) allows us to incorporate an extra degree of freedom in a fluid, e.g., orientational order and concentration, as an additional field variable. Here, we consider two fundamental problems associated with these approximations. One is the introduction of thermal noise and the other is the incorporation of coupling of the colloid surface with an order parameter introduced into a fluid component, which is crucial when considering colloidal particles suspended in a complex fluid. Here, we show that our FPD method makes it possible to simulate colloid dynamics properly while including full hydrodynamic interactions, inertia effects, incompressibility, thermal noise, and additional degrees of freedom of a fluid, which may be relevant for wide applications in colloidal and soft matter science.

Application of the Boundary Element Method to Elastic Wave Scattering Problems in Ultrasonic Nondestructive Evaluation.

NASA Astrophysics Data System (ADS)

Schafbuch, Paul Jay

The boundary element method (BEM) is used to numerically simulate the interaction of ultrasonic waves with material defects such as voids, inclusions, and open cracks. The time harmonic formulation is in 3D and therefore allows flaws of arbitrary shape to be modeled. The BEM makes such problems feasible because the underlying boundary integral equation only requires a surface (2D) integration and difficulties associated with the seemingly infinite extent of the host domain are not encountered. The computer code utilized in this work is built upon recent advances in elastodynamic boundary element theory such as a scheme for self adjusting integration order and singular integration regularization. Incident fields may be taken as compressional or shear plane waves or predicted by an approximate Gauss -Hermite beam model. The code is highly optimized for voids and has been coupled with computer aided engineering packages for automated flaw shape definition and mesh generation. Subsequent graphical display of intermediate results supports model refinement and physical interpretation. Final results are typically cast in a nondestructive evaluation (NDE) context as either scattering amplitudes or flaw signals (via a measurement model based on a reciprocity integral). The near field is also predicted which allows for improved physical insight into the scattering process and the evaluation of certain modeling approximations. The accuracy of the BEM approach is first examined by comparing its predictions to those of other models for single, isolated scatterers. The comparisons are with the predictions of analytical solutions for spherical defects and with MOOT and T-matrix calculations for axisymmetric flaws. Experimental comparisons are also made for volumetric shapes with different characteristic dimensions in all three directions, since no other numerical approach has yet produced results of this type. Theoretical findings regarding the fictitious eigenfrequency difficulty are substantiated through the analytical solution of a fundamental elastodynamics problem and corresponding BEM studies. Given the confidence in the BEM technique engendered by these comparisons, it is then used to investigate the modeling of "open", cracklike defects amenable to a volumetric formulation. The limits of applicability of approximate theories (e.g., quasistatic, Kirchhoff, and geometric theory of diffraction) are explored for elliptical cracks, from this basis. The problem of two interacting scatterers is then considered. Results from a fully implicit approach and from a more efficient hybrid scheme are compared with generalized Born and farfield approximate interaction theories.

Application of the boundary element method to elastic wave scattering problems in ultrasonic nondestructive evaluation

NASA Astrophysics Data System (ADS)

Schafbuch, Paul Jay

1991-02-01

The boundary element method (BEM) is used to numerically simulate the interaction of ultrasonic waves with material defects such as voids, inclusions, and open cracks. The time harmonic formulation is in 3D and therefore allows flaws of arbitrary shape to be modeled. The BEM makes such problems feasible because the underlying boundary integral equation only requires a surface (2D) integration and difficulties associated with the seemingly infinite extent of the host domain are not encountered. The computer code utilized in this work is built upon recent advances in elastodynamic boundary element theory such as a scheme for self adjusting integration order and singular integration regularization. Incident fields may be taken as compressional or shear plane waves or predicted by an approximate Gauss-Hermite beam model. The code is highly optimized for voids and has been coupled with computer aided engineering packages for automated flaw shape definition and mesh generation. Subsequent graphical display of intermediate results supports model refinement and physical interpretation. Final results are typically cast in a nondestructive evaluation (NDE) context as either scattering amplitudes or flaw signals (via a measurement model based on a reciprocity integral). The near field is also predicted which allows for improved physical insight into the scattering process and the evaluation of certain modeling approximations. The accuracy of the BEM approach is first examined by comparing its predictions to those of other models for single, isolated scatters. The comparisons are with the predictions of analytical solutions for spherical defects and with MOOT and T-matrix calculations for axisymmetric flaws. Experimental comparisons are also made for volumetric shapes with different characteristic dimensions in all three directions, since no other numerical approach has yet produced results of this type. Theoretical findings regarding the fictitious eigenfrequency difficulty are substantiated through the analytical solution of a fundamental elastodynamics problem and corresponding BEM studies. Given the confidence in the BEM technique engendered by these comparisons, it is then used to investigate the modeling of 'open', cracklike defects amenable to a volumetric formulation. The limits of applicability of approximate theories (e.g., quasistatic, Kirchhoff, and geometric theory of diffraction) are explored for elliptical cracks, from this basis. The problem of two interacting scatterers is then considered. Results from a fully implicit approach and from a more efficient hybrid scheme are compared with generalized Born and farfield approximate interaction theories.

Testing co-evolutionary hypotheses over geological timescales: interactions between Mesozoic non-avian dinosaurs and cycads.

PubMed

Butler, Richard J; Barrett, Paul M; Kenrick, Paul; Penn, Malcolm G

2009-02-01

The significance of co-evolution over ecological timescales is well established, yet it remains unclear to what extent co-evolutionary processes contribute to driving large-scale evolutionary and ecological changes over geological timescales. Some of the most intriguing and pervasive long-term co-evolutionary hypotheses relate to proposed interactions between herbivorous non-avian dinosaurs and Mesozoic plants, including cycads. Dinosaurs have been proposed as key dispersers of cycad seeds during the Mesozoic, and temporal variation in cycad diversity and abundance has been linked to dinosaur faunal changes. Here we assess the evidence for proposed hypotheses of trophic and evolutionary interactions between these two groups using diversity analyses, a new database of Cretaceous dinosaur and plant co-occurrence data, and a geographical information system (GIS) as a visualisation tool. Phylogenetic evidence suggests that the origins of several key biological properties of cycads (e.g. toxins, bright-coloured seeds) likely predated the origin of dinosaurs. Direct evidence of dinosaur-cycad interactions is lacking, but evidence from extant ecosystems suggests that dinosaurs may plausibly have acted as seed dispersers for cycads, although it is likely that other vertebrate groups (e.g. birds, early mammals) also played a role. Although the Late Triassic radiations of dinosaurs and cycads appear to have been approximately contemporaneous, few significant changes in dinosaur faunas coincide with the late Early Cretaceous cycad decline. No significant spatiotemporal associations between particular dinosaur groups and cycads can be identified - GIS visualisation reveals disparities between the spatiotemporal distributions of some dinosaur groups (e.g. sauropodomorphs) and cycads that are inconsistent with co-evolutionary hypotheses. The available data provide no unequivocal support for any of the proposed co-evolutionary interactions between cycads and herbivorous dinosaurs - diffuse co-evolutionary scenarios that are proposed to operate over geological timescales are plausible, but such hypotheses need to be firmly grounded on direct evidence of interaction and may be difficult to support given the patchiness of the fossil record.

Electron plasma environment at comet Grigg-Skjellerup: General observations and comparison with the environment at comet Halley

NASA Technical Reports Server (NTRS)

Reme, H.; Mazelle, C.; Sauvaud, J. A.; D'Uston, C.; Froment, F.; Lin, R. P.; Anderson, K. A.; Carlson, C. W.; Larson, D. E.; Korth, A.

1993-01-01

The three-dimensional electron spectrometer of the Reme plasma analyzer-complete positive ion, electron and ram negative ion measurements near comet Halley (RPA-COPERNIC) experiment aboard the Giotto spacecraft, although damaged during the comet Halley encounter in March 1986, has provided very new results during the encounter on July 10, 1992, with the weakly active comet Grigg-Skjellerup (G-S). The main characteristic features of the highly structured interaction region extending from approximately 26,500 km inbound to approximately 37,200 km outbound are presented. These results are compared to the results obtained by the same instrument during the Giotto comet Halley fly-by. Despite the large difference in the size of the interaction regions (approximately 60,000 km for G-S, approximately 2000,000 km for Halley) due to 2 orders of magnitude difference in cometary neutral gas production rate, there are striking similarities in the solar wind interactions with the two comets.

Design and isolation of ribozyme-substrate pairs using RNase P-based ribozymes containing altered substrate binding sites.

PubMed Central

Mobley, E M; Pan, T

1999-01-01

Substrate recognition and cleavage by the bacterial RNase P RNA requires two domains, a specificity domain, or S-domain, and a catalytic domain, or C-domain. The S-domain binds the T stem-loop region in a pre-tRNA substrate to confer specificity for tRNA substrates. In this work, the entire S-domain of the Bacillus subtilis RNase P RNA is replaced with an artificial substrate binding module. New RNA substrates are isolated by in vitro selection using two libraries containing random regions of 60 nt. At the end of the selection, the cleavage rates of the substrate library are approximately 0.7 min(-1)in 10 mM MgCl(2)at 37 degrees C, approximately 4-fold better than the cleavage of a pre-tRNA substrate by the wild-type RNase P RNA under the same conditions. The contribution of the S-domain replacement to the catalytic efficiency is from 6- to 22 000-fold. Chemical and nuclease mapping of two ribozyme-product complexes shows that this contribution correlates with direct interactions between the S-domain replacement and the selected substrate. These results demonstrate the feasibility of design and isolation of RNase P-based, matching ribozyme-substrate pairs without prior knowledge of the sequence or structure of the interactive modules in the ribozyme or substrate. PMID:10518624

Resonating group method as applied to the spectroscopy of α-transfer reactions

NASA Astrophysics Data System (ADS)

Subbotin, V. B.; Semjonov, V. M.; Gridnev, K. A.; Hefter, E. F.

1983-10-01

In the conventional approach to α-transfer reactions the finite- and/or zero-range distorted-wave Born approximation is used in liaison with a macroscopic description of the captured α particle in the residual nucleus. Here the specific example of 16O(6Li,d)20Ne reactions at different projectile energies is taken to present a microscopic resonating group method analysis of the α particle in the final nucleus (for the reaction part the simple zero-range distorted-wave Born approximation is employed). In the discussion of suitable nucleon-nucleon interactions, force number one of the effective interactions presented by Volkov is shown to be most appropriate for the system considered. Application of the continuous analog of Newton's method to the evaluation of the resonating group method equations yields an increased accuracy with respect to traditional methods. The resonating group method description induces only minor changes in the structures of the angular distributions, but it does serve its purpose in yielding reliable and consistent spectroscopic information. NUCLEAR STRUCTURE 16O(6Li,d)20Ne; E=20 to 32 MeV; calculated B(E2); reduced widths, dσdΩ extracted α-spectroscopic factors. ZRDWBA with microscope RGM description of residual α particle in 20Ne; application of continuous analog of Newton's method; tested and applied Volkov force No. 1; direct mechanism.

Testing the Perey effect

DOE PAGES

Titus, L. J.; Nunes, Filomena M.

2014-03-12

Here, the effects of non-local potentials have historically been approximately included by applying a correction factor to the solution of the corresponding equation for the local equivalent interaction. This is usually referred to as the Perey correction factor. In this work we investigate the validity of the Perey correction factor for single-channel bound and scattering states, as well as in transfer (p, d) cross sections. Method: We solve the scattering and bound state equations for non-local interactions of the Perey-Buck type, through an iterative method. Using the distorted wave Born approximation, we construct the T-matrix for (p,d) on 17O, 41Ca,more » 49Ca, 127Sn, 133Sn, and 209Pb at 20 and 50 MeV. As a result, we found that for bound states, the Perey corrected wave function resulting from the local equation agreed well with that from the non-local equation in the interior region, but discrepancies were found in the surface and peripheral regions. Overall, the Perey correction factor was adequate for scattering states, with the exception of a few partial waves corresponding to the grazing impact parameters. These differences proved to be important for transfer reactions. In conclusion, the Perey correction factor does offer an improvement over taking a direct local equivalent solution. However, if the desired accuracy is to be better than 10%, the exact solution of the non-local equation should be pursued.« less

Direct measurements of multiple adhesive alignments and unbinding trajectories between cadherin extracellular domains.

PubMed Central

Sivasankar, S; Gumbiner, B; Leckband, D

2001-01-01

Direct measurements of the interactions between antiparallel, oriented monolayers of the complete extracellular region of C-cadherin demonstrate that, rather than binding in a single unique orientation, the cadherins adhere in three distinct alignments. The strongest adhesion is observed when the opposing extracellular fragments are completely interdigitated. A second adhesive alignment forms when the interdigitated proteins separate by 70 +/- 10 A. A third complex forms at a bilayer separation commensurate with the approximate overlap of cadherin extracellular domains 1 and 2 (CEC1-2). The locations of the energy minima are independent of both the surface density of bound cadherin and the stiffness of the force transducer. Using surface element integration, we show that two flat surfaces that interact through an oscillatory potential will exhibit discrete minima at the same locations in the force profile measured between hemicylinders covered with identical materials. The measured interaction profiles, therefore, reflect the relative separations at which the antiparallel proteins adhere, and are unaffected by the curvature of the underlying substrate. The successive formation and rupture of multiple protein contacts during detachment can explain the observed sluggish unbinding of cadherin monolayers. Velocity-distance profiles, obtained by quantitative video analysis of the unbinding trajectory, exhibit three velocity regimes, the transitions between which coincide with the positions of the adhesive minima. These findings suggest that cadherins undergo multiple stage unbinding, which may function to impede adhesive failure under force. PMID:11259289

Impact of Transpacific Aerosol on Air Quality over the United States: A Perspective from Aerosol-Cloud-Radiation Interactions

NASA Technical Reports Server (NTRS)

Tao, Zhining; Yu, Hongbin; Chin, Mian

2015-01-01

Observations have well established that aerosols from various sources in Asia, Europe, and Africa can travel across the Pacific and reach the contiguous United States (U.S.) at least on episodic bases throughout a year, with a maximum import in spring. The imported aerosol not only can serve as an additional source to regional air pollution (e.g., direct input), but also can influence regional air quality through the aerosol-cloud-radiation (ACR) interactions that change local and regional meteorology. This study assessed impacts of the transpacific aerosol on air quality, focusing on surface ozone and PM2.5, over the U.S. using the NASA Unified Weather Research Forecast model. Based on the results of 3- month (April to June of 2010) simulations, the impact of direct input (as an additional source) of transpacific aerosol caused an increase of surface PM2.5 concentration by approximately 1.5 micro-g/cu m over the west coast and about 0.5 micro-g/cu m over the east coast of the U.S. By influencing key meteorological processes through the ACR interactions, the transpacific aerosol exerted a significant effect on both surface PM2.5 (+/-6 micro-g/cu m3) and ozone (+/-12 ppbv) over the central and eastern U.S. This suggests that the transpacific transport of aerosol could either improve or deteriorate local air quality and complicate local effort toward the compliance with the U.S. National Ambient Air Quality Standards.

γ-decay of {}_{8}^{16}{{\\rm{O}}}_{8}\\,{and}\\,{}_{7}^{16}{{\\rm{N}}}_{9} in proton-neutron Tamm-Dancoff and random phase approximations with optimized surface δ interaction

NASA Astrophysics Data System (ADS)

Pahlavani, M. R.; Firoozi, B.

2016-09-01

γ-ray transitions from excited states of {}16{{N}} and {}16{{O}} isomers that appear in the γ spectrum of the {}616{{{C}}}10\\to {}716{{{N}}}9\\to {}816{{{O}}}8 beta decay chain are investigated. The theoretical approach used in this research starts with a mean-field potential consisting of a phenomenological Woods-Saxon potential including spin-orbit and Coulomb terms (for protons) in order to obtain single-particle energies and wave functions for nucleons in a nucleus. A schematic residual surface delta interaction is then employed on the top of the mean field and is treated within the proton-neutron Tamm-Dancoff approximation (pnTDA) and the proton-neutron random phase approximation. The goal is to use an optimized surface delta interaction interaction, as a residual interaction, to improve the results. We have used artificial intelligence algorithms to establish a good agreement between theoretical and experimental energy spectra. The final results of the ‘optimized’ calculations are reasonable via this approach.

The stress intensity factors for a periodic array of interacting coplanar penny-shaped cracks

PubMed Central

Lekesiz, Huseyin; Katsube, Noriko; Rokhlin, Stanislav I.; Seghi, Robert R.

2013-01-01

The effect of crack interactions on stress intensity factors is examined for a periodic array of coplanar penny-shaped cracks. Kachanov’s approximate method for crack interactions (Int. J. Solid. Struct. 1987; 23(1):23–43) is employed to analyze both hexagonal and square crack configurations. In approximating crack interactions, the solution converges when the total truncation number of the cracks is 109. As expected, due to high density packing crack interaction in the hexagonal configuration is stronger than that in the square configuration. Based on the numerical results, convenient fitting equations for quick evaluation of the mode I stress intensity factors are obtained as a function of crack density and angle around the crack edge for both crack configurations. Numerical results for the mode II and III stress intensity factors are presented in the form of contour lines for the case of Poisson’s ratio ν =0.3. Possible errors for these problems due to Kachanov’s approximate method are estimated. Good agreement is observed with the limited number of results available in the literature and obtained by different methods. PMID:27175035

Many-body Green’s function theory for electron-phonon interactions: Ground state properties of the Holstein dimer

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

Säkkinen, Niko; Leeuwen, Robert van; Peng, Yang

2015-12-21

We study ground-state properties of a two-site, two-electron Holstein model describing two molecules coupled indirectly via electron-phonon interaction by using both exact diagonalization and self-consistent diagrammatic many-body perturbation theory. The Hartree and self-consistent Born approximations used in the present work are studied at different levels of self-consistency. The governing equations are shown to exhibit multiple solutions when the electron-phonon interaction is sufficiently strong, whereas at smaller interactions, only a single solution is found. The additional solutions at larger electron-phonon couplings correspond to symmetry-broken states with inhomogeneous electron densities. A comparison to exact results indicates that this symmetry breaking is stronglymore » correlated with the formation of a bipolaron state in which the two electrons prefer to reside on the same molecule. The results further show that the Hartree and partially self-consistent Born solutions obtained by enforcing symmetry do not compare well with exact energetics, while the fully self-consistent Born approximation improves the qualitative and quantitative agreement with exact results in the same symmetric case. This together with a presented natural occupation number analysis supports the conclusion that the fully self-consistent approximation describes partially the bipolaron crossover. These results contribute to better understanding how these approximations cope with the strong localizing effect of the electron-phonon interaction.« less

Selective Sampling with Direct Ion Mobility Spectrometric Detection for Explosives Analysis

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

Harvey, Scott D; Ewing, Robert G; Waltman, Melanie J

2009-06-29

This study investigates the potential and limitations of a streamlined, field-deployable analytical approach that involves selective capture of explosive materials with direct analysis by ion mobility spectrometry (IMS). Selective capture of explosives was performed on deactivated quartz fiber filters impregnated with metal β-diketonate polymers. These Lewis acidic polymers selectively interact with Lewis base analytes such as explosives. The filter coupons could be directly inserted into an IMS instrument for analysis. The uptake kinetics of 2,4,6-trinitrotoluene (TNT) from a saturated atmosphere were characterized, and based on these studies, passive equilibrium sampling was applied to estimate the TNT concentration within an ammunitionmore » magazine that contained bulk TNT. Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) uptake from a saturated environment also was examined over a one-month period. Each incremental sampling period showed increasing quantities of RDX culminating with collection of approximately 5 ng of RDX on the coupon at the end of one month. This is the first time that gas-phase uptake of RDX has been demonstrated.« less

Chirally directed formation of nanometer-scale proline clusters.

PubMed

Myung, Sunnie; Fioroni, Marco; Julian, Ryan R; Koeniger, Stormy L; Baik, Mu-Hyun; Clemmer, David E

2006-08-23

Ion mobility measurements, combined with molecular mechanics simulations, are used to study enantiopure and racemic proline clusters formed by electrospray ionization. Broad distributions of cluster sizes and charge states are observed, ranging from clusters containing only a few proline units to clusters that contain more than 100 proline units (i.e., protonated clusters of the form [xPro + nH](n+) with x = 1 to >100 and n = 1-7). As the sizes of clusters increase, there is direct evidence for nanometer scale, chirally induced organization into specific structures. For n = 4 and 5, enantiopure clusters of approximately 50 to 100 prolines assemble into structures that are more elongated than the most compact structure that is observed from the racemic proline clusters. A molecular analogue, cis-4-hydroxy-proline, displays significantly different behavior, indicating that in addition to the rigidity of the side chain ring, intermolecular interactions are important in the formation of chirally directed clusters. This is the first case in which assemblies of chirally selective elongated structures are observed in this size range of amino acid clusters. Relationships between enantiopurity, cluster shape, and overall energetics are discussed.

Efficient visibility encoding for dynamic illumination in direct volume rendering.

PubMed

Kronander, Joel; Jönsson, Daniel; Löw, Joakim; Ljung, Patric; Ynnerman, Anders; Unger, Jonas

2012-03-01

We present an algorithm that enables real-time dynamic shading in direct volume rendering using general lighting, including directional lights, point lights, and environment maps. Real-time performance is achieved by encoding local and global volumetric visibility using spherical harmonic (SH) basis functions stored in an efficient multiresolution grid over the extent of the volume. Our method enables high-frequency shadows in the spatial domain, but is limited to a low-frequency approximation of visibility and illumination in the angular domain. In a first pass, level of detail (LOD) selection in the grid is based on the current transfer function setting. This enables rapid online computation and SH projection of the local spherical distribution of visibility information. Using a piecewise integration of the SH coefficients over the local regions, the global visibility within the volume is then computed. By representing the light sources using their SH projections, the integral over lighting, visibility, and isotropic phase functions can be efficiently computed during rendering. The utility of our method is demonstrated in several examples showing the generality and interactive performance of the approach.

Synthesis and Analysis of Custom Bi-directional Reflectivity Distribution Functions in DIRSIG

NASA Astrophysics Data System (ADS)

Dank, J.; Allen, D.

2016-09-01

The bi-directional reflectivity distribution (BRDF) function is a fundamental optical property of materials, characterizing important properties of light scattered by a surface. For accurate radiance calculations using synthetic targets and numerical simulations such as the Digital Imaging and Remote Sensing Image Generation (DIRSIG) model, fidelity of the target BRDFs is critical. While fits to measured BRDF data can be used in DIRSIG, obtaining high-quality data over a large spectral continuum can be time-consuming and expensive, requiring significant investment in illumination sources, sensors, and other specialized hardware. As a consequence, numerous parametric BRDF models are available to approximate actual behavior; but these all have shortcomings. Further, DIRSIG doesn't allow direct visualization of BRDFs, making it difficult for the user to understand the numerical impact of various models. Here, we discuss the innovative use of "mixture maps" to synthesize custom BRDFs as linear combinations of parametric models and measured data. We also show how DIRSIG's interactive mode can be used to visualize and analyze both available parametric models currently used in DIRSIG and custom BRDFs developed using our methods.

Interaction function of oscillating coupled neurons

PubMed Central

Dodla, Ramana; Wilson, Charles J.

2013-01-01

Large scale simulations of electrically coupled neuronal oscillators often employ the phase coupled oscillator paradigm to understand and predict network behavior. We study the nature of the interaction between such coupled oscillators using weakly coupled oscillator theory. By employing piecewise linear approximations for phase response curves and voltage time courses, and parameterizing their shapes, we compute the interaction function for all such possible shapes and express it in terms of discrete Fourier modes. We find that reasonably good approximation is achieved with four Fourier modes that comprise of both sine and cosine terms. PMID:24229210

Approximation of reliability of direct genomic breeding values

USDA-ARS?s Scientific Manuscript database

Two methods to efficiently approximate theoretical genomic reliabilities are presented. The first method is based on the direct inverse of the left hand side (LHS) of mixed model equations. It uses the genomic relationship matrix for a small subset of individuals with the highest genomic relationshi...

First-order approximation error analysis of Risley-prism-based beam directing system.

PubMed

Zhao, Yanyan; Yuan, Yan

2014-12-01

To improve the performance of a Risley-prism system for optical detection and measuring applications, it is necessary to be able to determine the direction of the outgoing beam with high accuracy. In previous works, error sources and their impact on the performance of the Risley-prism system have been analyzed, but their numerical approximation accuracy was not high. Besides, pointing error analysis of the Risley-prism system has provided results for the case when the component errors, prism orientation errors, and assembly errors are certain. In this work, the prototype of a Risley-prism system was designed. The first-order approximations of the error analysis were derived and compared with the exact results. The directing errors of a Risley-prism system associated with wedge-angle errors, prism mounting errors, and bearing assembly errors were analyzed based on the exact formula and the first-order approximation. The comparisons indicated that our first-order approximation is accurate. In addition, the combined errors produced by the wedge-angle errors and mounting errors of the two prisms together were derived and in both cases were proved to be the sum of errors caused by the first and the second prism separately. Based on these results, the system error of our prototype was estimated. The derived formulas can be implemented to evaluate beam directing errors of any Risley-prism beam directing system with a similar configuration.

Statistical mechanics of the mixed majority minority game with random external information

NASA Astrophysics Data System (ADS)

DeMartino, A.; Giardina, I.; Mosetti, G.

2003-08-01

We study the asymptotic macroscopic properties of the mixed majority-minority game, modelling a population in which two types of heterogeneous adaptive agents, namely 'fundamentalists' driven by differentiation and 'trend-followers' driven by imitation, interact. The presence of a fraction f of trend-followers is shown to induce (a) a significant loss of informational efficiency with respect to a pure minority game (in particular, an efficient, unpredictable phase exists only for f < 1/2), and (b) a catastrophic increase of global fluctuations for f > 1/2. We solve the model by means of an approximate static (replica) theory and by a direct dynamical (generating functional) technique. The two approaches coincide and match numerical results convincingly.

Isotopic response with small scintillator based gamma-ray spectrometers

DOEpatents

Madden, Norman W [Sparks, NV; Goulding, Frederick S [Lafayette, CA; Asztalos, Stephen J [Oakland, CA

2012-01-24

The intrinsic background of a gamma ray spectrometer is significantly reduced by surrounding the scintillator with a second scintillator. This second (external) scintillator surrounds the first scintillator and has an opening of approximately the same diameter as the smaller central scintillator in the forward direction. The second scintillator is selected to have a higher atomic number, and thus has a larger probability for a Compton scattering interaction than within the inner region. Scattering events that are essentially simultaneous in coincidence to the first and second scintillators, from an electronics perspective, are precluded electronically from the data stream. Thus, only gamma-rays that are wholly contained in the smaller central scintillator are used for analytic purposes.

Parametric resonant triad interactions in a free shear layer

NASA Technical Reports Server (NTRS)

Mallier, R.; Maslowe, S. A.

1993-01-01

We investigate the weakly nonlinear evolution of a triad of nearly-neutral modes superimposed on a mixing layer with velocity profile u bar equals Um + tanh y. The perturbation consists of a plane wave and a pair of oblique waves each inclined at approximately 60 degrees to the mean flow direction. Because the evolution occurs on a relatively fast time scale, the critical layer dynamics dominate the process and the amplitude evolution of the oblique waves is governed by an integro-differential equation. The long-time solution of this equation predicts very rapid (exponential of an exponential) amplification and we discuss the pertinence of this result to vortex pairing phenomena in mixing layers.

Direct Estimation of Local pH Change at Infection Sites of Fungi in Potato Tubers.

PubMed

Tardi-Ovadia, R; Linker, R; Tsror Lahkim, L

2017-01-01

Fungi can modify the pH in or around the infected site via alkalization or acidification, and pH monitoring may provide valuable information on host-fungus interactions. The objective of the present study was to examine the ability of two fungi, Colletotrichum coccodes and Helminthosporium solani, to modify the pH of potato tubers during artificial inoculation in situ. Both fungi cause blemishes on potato tubers, which downgrades tuber quality and yield. Direct visualization and estimation of pH changes near the inoculation area were achieved using pH indicators and image analysis. The results showed that the pH of the area infected by either fungus increased from potato native pH of approximately 6.0 to 7.4 to 8.0. By performing simple analysis of the images, it was also possible to derive the growth curve of each fungus and estimate the lag phase of the radial growth: 10 days for C. coccodes and 17 days H. solani. In addition, a distinctive halo (an edge area with increased pH) was observed only during the lag phase of H. solani infection. pH modulation is a major factor in pathogen-host interaction and the proposed method offers a simple and rapid way to monitor these changes.

Anisotropic bulk and planar Heisenberg ferromagnets in uniform, arbitrarily oriented magnetic fields

NASA Astrophysics Data System (ADS)

Vanherck, Joren; Sorée, Bart; Magnus, Wim

2018-07-01

Today, further downscaling of mobile electronic devices poses serious problems, such as energy consumption and local heat dissipation. In this context, spin wave majority gates made of very thin ferromagnetic films may offer a viable alternative. However, similar downscaling of magnetic thin films eventually enforces the latter to operate as quasi-2D magnets, the magnetic properties of which are not yet fully understood, especially those related to anisotropies and external magnetic fields in arbitrary directions. To this end, we have investigated the behaviour of an easy-plane and easy-axis anisotropic ferromagnet—both in two and three dimensions—subjected to a uniform magnetic field, applied along an arbitrary direction. In this paper, a spin- Heisenberg Hamiltonian with anisotropic exchange interactions is solved using double-time temperature-dependent Green’s functions and the Tyablikov decoupling approximation. We determine various magnetic properties such as the Curie temperature and the magnetization as a function of temperature and the applied magnetic field, discussing the impact of the system’s dimensionality and the type of anisotropy. The magnetic reorientation transition taking place in anisotropic Heisenberg ferromagnets is studied in detail. Importantly, spontaneous magnetization is found to be absent for easy-plane 2D spin systems with short range interactions.

Turbulent flame-wall interaction: a DNS study

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

Chen, Jackie; Hawkes, Evatt R; Sankaran, Ramanan

2010-01-01

A turbulent flame-wall interaction (FWI) configuration is studied using three-dimensional direct numerical simulation (DNS) and detailed chemical kinetics. The simulations are used to investigate the effects of the wall turbulent boundary layer (i) on the structure of a hydrogen-air premixed flame, (ii) on its near-wall propagation characteristics and (iii) on the spatial and temporal patterns of the convective wall heat flux. Results show that the local flame thickness and propagation speed vary between the core flow and the boundary layer, resulting in a regime change from flamelet near the channel centreline to a thickened flame at the wall. This findingmore » has strong implications for the modelling of turbulent combustion using Reynolds-averaged Navier-Stokes or large-eddy simulation techniques. Moreover, the DNS results suggest that the near-wall coherent turbulent structures play an important role on the convective wall heat transfer by pushing the hot reactive zone towards the cold solid surface. At the wall, exothermic radical recombination reactions become important, and are responsible for approximately 70% of the overall heat release rate at the wall. Spectral analysis of the convective wall heat flux provides an unambiguous picture of its spatial and temporal patterns, previously unobserved, that is directly related to the spatial and temporal characteristic scalings of the coherent near-wall turbulent structures.« less

Adolescent over-general memory, life events and mental health outcomes: Findings from a UK cohort study

PubMed Central

Crane, Catherine; Heron, Jon; Gunnell, David; Lewis, Glyn; Evans, Jonathan; Williams, J. Mark G.

2016-01-01

Previous research suggesting that over-general memory (OGM) may moderate the effect of life events on depressive symptoms and suicidality has sampled older adolescents or adults, or younger adolescents in high-risk populations, and has been conducted over relatively short follow-up periods. The authors examined the relationship between OGM at age 13 and life events and mental health outcomes (depression, self-harm, suicidal ideation and planning) at age 16 years within a sample of 5792 adolescents participating in the Avon Longitudinal Study of Parents and Children (ALSPAC), approximately 3800 of whom had also provided data on depression and self-harm. There was no clear evidence of either direct or interactive effects of OGM at age 13 on levels of depression at age 16. Similarly there was no clear evidence of either direct or interactive effects of OGM on suicidal ideation and self-harm. Although there was some evidence that over-general autobiographical memory was associated with reduced risk of suicidal planning and increased risk of self-harm, these associations were absent when confounding variables were taken into account. The findings imply that although OGM is a marker of vulnerability to depression and related psychopathology in high-risk groups, this cannot be assumed to generalise to whole populations. PMID:25716137

Adolescent over-general memory, life events and mental health outcomes: Findings from a UK cohort study.

PubMed

Crane, Catherine; Heron, Jon; Gunnell, David; Lewis, Glyn; Evans, Jonathan; Williams, J Mark G

2016-01-01

Previous research suggesting that over-general memory (OGM) may moderate the effect of life events on depressive symptoms and suicidality has sampled older adolescents or adults, or younger adolescents in high-risk populations, and has been conducted over relatively short follow-up periods. The authors examined the relationship between OGM at age 13 and life events and mental health outcomes (depression, self-harm, suicidal ideation and planning) at age 16 years within a sample of 5792 adolescents participating in the Avon Longitudinal Study of Parents and Children (ALSPAC), approximately 3800 of whom had also provided data on depression and self-harm. There was no clear evidence of either direct or interactive effects of OGM at age 13 on levels of depression at age 16. Similarly there was no clear evidence of either direct or interactive effects of OGM on suicidal ideation and self-harm. Although there was some evidence that over-general autobiographical memory was associated with reduced risk of suicidal planning and increased risk of self-harm, these associations were absent when confounding variables were taken into account. The findings imply that although OGM is a marker of vulnerability to depression and related psychopathology in high-risk groups, this cannot be assumed to generalise to whole populations.

Niflumic acid alters gating of HCN2 pacemaker channels by interaction with the outer region of S4 voltage sensing domains.

PubMed

Cheng, Lan; Sanguinetti, Michael C

2009-05-01

Niflumic acid, 2-[[3-(trifluoromethyl)phenyl]amino]pyridine-3-carboxylic acid (NFA), is a nonsteroidal anti-inflammatory drug that also blocks or modifies the gating of many ion channels. Here, we investigated the effects of NFA on hyperpolarization-activated cyclic nucleotide-gated cation (HCN) pacemaker channels expressed in X. laevis oocytes using site-directed mutagenesis and the two-electrode voltage-clamp technique. Extracellular NFA acted rapidly and caused a slowing of activation and deactivation and a hyperpolarizing shift in the voltage dependence of HCN2 channel activation (-24.5 +/- 1.2 mV at 1 mM). Slowed channel gating and reduction of current magnitude was marked in oocytes treated with NFA, while clamped at 0 mV but minimal in oocytes clamped at -100 mV, indicating the drug preferentially interacts with channels in the closed state. NFA at 0.1 to 3 mM shifted the half-point for channel activation in a concentration-dependent manner, with an EC(50) of 0.54 +/- 0.068 mM and a predicted maximum shift of -38 mV. NFA at 1 mM also reduced maximum HCN2 conductance by approximately 20%, presumably by direct block of the pore. The rapid onset and state-dependence of NFA-induced changes in channel gating suggests an interaction with the extracellular region of the S4 transmembrane helix, the primary voltage-sensing domain of HCN2. Neutralization (by mutation to Gln) of any three of the outer four basic charged residues in S4, but not single mutations, abrogated the NFA-induced shift in channel activation. We conclude that NFA alters HCN2 gating by interacting with the extracellular end of the S4 voltage sensor domains.

Streptococcus mutans dextransucrase: stimulation by phospholipids from human sera and oral fluids.

PubMed Central

Schachtele, C F; Harlander, S K; Bracke, J W; Ostrum, L C; Maltais, J A; Billings, R J

1978-01-01

Serum, gingival crevicular fluid, and parotid, submandibular, and labial minor gland saliva from four individuals stimulated glucan formation from sucrose by the Streptococcus mutans strain 6715 dextransucrase (EC 2.4.1.5). At final dilutions of 1:10 all of the fluids stimulated crude enzyme preparations approximately 1.8-fold. The fluids stimulated the purified water-insoluble glucan-synthesizing form of the dextransucrase approximately 3.2-fold and the water-soluble glucan-producing form of the enzyme approximately 2.4-fold. The fluids all contained concentrations of stimulatory material that could be reduced to undetectable levels only after dilutions of greater than 1:1,000. The increased rates of glucan formation caused by the fluids and dextran were additive, indicating that stimulation by the fluids was primarily due to interactions with entities other than glucan primer molecules. In contrast, the elevated levels of glucan formation in the presence of the fluids was not further enhanced by the addition of lysophosphatidylcholine. Lysophosphatidylcholine purified from parotid and submandibular saliva by solvent extraction and thin-layer chromatography stimulated the dextransucrase as effectively as egg yolk lysophosphatidylcholine. Thus, phospholipids normally found in human oral fluids can enhance the activity of an enzyme believed to be directly associated with the cariogenic potential of S. mutans. PMID:365766

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

Rebolini, Elisa, E-mail: rebolini@lct.jussieu.fr; Toulouse, Julien, E-mail: julien.toulouse@upmc.fr; Savin, Andreas, E-mail: savin@lct.jussieu.fr

We present a study of the variation of total energies and excitation energies along a range-separated adiabatic connection. This connection links the non-interacting Kohn–Sham electronic system to the physical interacting system by progressively switching on the electron–electron interactions whilst simultaneously adjusting a one-electron effective potential so as to keep the ground-state density constant. The interactions are introduced in a range-dependent manner, first introducing predominantly long-range, and then all-range, interactions as the physical system is approached, as opposed to the conventional adiabatic connection where the interactions are introduced by globally scaling the standard Coulomb interaction. Reference data are reported for themore » He and Be atoms and the H{sub 2} molecule, obtained by calculating the short-range effective potential at the full configuration-interaction level using Lieb's Legendre-transform approach. As the strength of the electron–electron interactions increases, the excitation energies, calculated for the partially interacting systems along the adiabatic connection, offer increasingly accurate approximations to the exact excitation energies. Importantly, the excitation energies calculated at an intermediate point of the adiabatic connection are much better approximations to the exact excitation energies than are the corresponding Kohn–Sham excitation energies. This is particularly evident in situations involving strong static correlation effects and states with multiple excitation character, such as the dissociating H{sub 2} molecule. These results highlight the utility of long-range interacting reference systems as a starting point for the calculation of excitation energies and are of interest for developing and analyzing practical approximate range-separated density-functional methodologies.« less

Approximate error conjugation gradient minimization methods

DOEpatents

Kallman, Jeffrey S

2013-05-21

In one embodiment, a method includes selecting a subset of rays from a set of all rays to use in an error calculation for a constrained conjugate gradient minimization problem, calculating an approximate error using the subset of rays, and calculating a minimum in a conjugate gradient direction based on the approximate error. In another embodiment, a system includes a processor for executing logic, logic for selecting a subset of rays from a set of all rays to use in an error calculation for a constrained conjugate gradient minimization problem, logic for calculating an approximate error using the subset of rays, and logic for calculating a minimum in a conjugate gradient direction based on the approximate error. In other embodiments, computer program products, methods, and systems are described capable of using approximate error in constrained conjugate gradient minimization problems.

Perturbation Theory versus Thermodynamic Integration. Beyond a Mean-Field Treatment of Pair Correlations in a Nematic Model Liquid Crystal.

PubMed

Schoen, Martin; Haslam, Andrew J; Jackson, George

2017-10-24

The phase behavior and structure of a simple square-well bulk fluid with anisotropic interactions is described in detail. The orientation dependence of the intermolecular interactions allows for the formation of a nematic liquid-crystalline phase in addition to the more conventional isotropic gas and liquid phases. A version of classical density functional theory (DFT) is employed to determine the properties of the model, and comparisons are made with the corresponding data from Monte Carlo (MC) computer simulations in both the grand canonical and canonical ensembles, providing a benchmark to assess the adequacy of the DFT results. A novel element of the DFT approach is the assumption that the structure of the fluid is dominated by intermolecular interactions in the isotropic fluid. A so-called augmented modified mean-field (AMMF) approximation is employed accounting for the influence of anisotropic interactions. The AMMF approximation becomes exact in the limit of vanishing density. We discuss advantages and disadvantages of the AMMF approximation with respect to an accurate description of isotropic and nematic branches of the phase diagram, the degree of orientational order, and orientation-dependent pair correlations. The performance of the AMMF approximations is found to be good in comparison with the MC data; the AMMF approximation has clear advantages with respect to an accurate and more detailed description of the fluid structure. Possible strategies to improve the DFT are discussed.

Directional Radio-Frequency Identification Tag Reader

NASA Technical Reports Server (NTRS)

Medelius, Pedro J.; Taylor, John D.; Henderson, John J.

2004-01-01

A directional radio-frequency identification (RFID) tag reader has been designed to facilitate finding a specific object among many objects in a crowded room. The device could be an adjunct to an electronic inventory system that tracks RFID-tagged objects as they move through reader-equipped doorways. Whereas commercial RFID-tag readers do not measure directions to tagged objects, the device is equipped with a phased-array antenna and a received signal-strength indicator (RSSI) circuit for measuring direction. At the beginning of operation, it is set to address only the RFID tag of interest. It then continuously transmits a signal to interrogate that tag while varying the radiation pattern of the antenna. It identifies the direction to the tag as the radiation pattern direction of peak strength of the signal returned by the tag. An approximate distance to the tag is calculated from the peak signal strength. The direction and distance can be displayed on a screen. A prototype containing a Yagi antenna was found to be capable of detecting a 915.5-MHz tag at a distance of approximately equal to 15 ft (approximately equal to 4.6 m).

Quasi-planar elemental clusters in pair interactions approximation

NASA Astrophysics Data System (ADS)

Chkhartishvili, Levan

2016-01-01

The pair-interactions approximation, when applied to describe elemental clusters, only takes into account bonding between neighboring atoms. According to this approach, isomers of wrapped forms of 2D clusters - nanotubular and fullerene-like structures - and truly 3D clusters, are generally expected to be more stable than their quasi-planar counterparts. This is because quasi-planar clusters contain more peripheral atoms with dangling bonds and, correspondingly, fewer atoms with saturated bonds. However, the differences in coordination numbers between central and peripheral atoms lead to the polarization of bonds. The related corrections to the molar binding energy can make small, quasi-planar clusters more stable than their 2D wrapped allotropes and 3D isomers. The present work provides a general theoretical frame for studying the relative stability of small elemental clusters within the pair interactions approximation.

A statistical state dynamics approach to wall turbulence.

PubMed

Farrell, B F; Gayme, D F; Ioannou, P J

2017-03-13

This paper reviews results obtained using statistical state dynamics (SSD) that demonstrate the benefits of adopting this perspective for understanding turbulence in wall-bounded shear flows. The SSD approach used in this work employs a second-order closure that retains only the interaction between the streamwise mean flow and the streamwise mean perturbation covariance. This closure restricts nonlinearity in the SSD to that explicitly retained in the streamwise constant mean flow together with nonlinear interactions between the mean flow and the perturbation covariance. This dynamical restriction, in which explicit perturbation-perturbation nonlinearity is removed from the perturbation equation, results in a simplified dynamics referred to as the restricted nonlinear (RNL) dynamics. RNL systems, in which a finite ensemble of realizations of the perturbation equation share the same mean flow, provide tractable approximations to the SSD, which is equivalent to an infinite ensemble RNL system. This infinite ensemble system, referred to as the stochastic structural stability theory system, introduces new analysis tools for studying turbulence. RNL systems provide computationally efficient means to approximate the SSD and produce self-sustaining turbulence exhibiting qualitative features similar to those observed in direct numerical simulations despite greatly simplified dynamics. The results presented show that RNL turbulence can be supported by as few as a single streamwise varying component interacting with the streamwise constant mean flow and that judicious selection of this truncated support or 'band-limiting' can be used to improve quantitative accuracy of RNL turbulence. These results suggest that the SSD approach provides new analytical and computational tools that allow new insights into wall turbulence.This article is part of the themed issue 'Toward the development of high-fidelity models of wall turbulence at large Reynolds number'. © 2017 The Author(s).

A statistical state dynamics approach to wall turbulence

PubMed Central

Gayme, D. F.; Ioannou, P. J.

2017-01-01

This paper reviews results obtained using statistical state dynamics (SSD) that demonstrate the benefits of adopting this perspective for understanding turbulence in wall-bounded shear flows. The SSD approach used in this work employs a second-order closure that retains only the interaction between the streamwise mean flow and the streamwise mean perturbation covariance. This closure restricts nonlinearity in the SSD to that explicitly retained in the streamwise constant mean flow together with nonlinear interactions between the mean flow and the perturbation covariance. This dynamical restriction, in which explicit perturbation–perturbation nonlinearity is removed from the perturbation equation, results in a simplified dynamics referred to as the restricted nonlinear (RNL) dynamics. RNL systems, in which a finite ensemble of realizations of the perturbation equation share the same mean flow, provide tractable approximations to the SSD, which is equivalent to an infinite ensemble RNL system. This infinite ensemble system, referred to as the stochastic structural stability theory system, introduces new analysis tools for studying turbulence. RNL systems provide computationally efficient means to approximate the SSD and produce self-sustaining turbulence exhibiting qualitative features similar to those observed in direct numerical simulations despite greatly simplified dynamics. The results presented show that RNL turbulence can be supported by as few as a single streamwise varying component interacting with the streamwise constant mean flow and that judicious selection of this truncated support or ‘band-limiting’ can be used to improve quantitative accuracy of RNL turbulence. These results suggest that the SSD approach provides new analytical and computational tools that allow new insights into wall turbulence. This article is part of the themed issue ‘Toward the development of high-fidelity models of wall turbulence at large Reynolds number’. PMID:28167577

Direct pair production in heavy-ion--atom collisions

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

Anholt, R.; Jakubassa-Amundsen, D.H.; Amundsen, P.A.

1983-02-01

Direct pair production in approx.5-MeV/amu heavy-ion--atom collisions with uranium target atoms is calculated with the plane-wave Born approximation and the semiclassical approximation. Briggs's approximation is used to obtain the electron and positron wave functions. Since pair production involves high momentum transfer q from the moving projectile to the vacuum, use is made of a high-q approximation to greatly simplify the numerical computations. Coulomb deflection of the projectile, the effect of finite nuclear size on the elec- tronic wave functions, and the energy loss by the projectile exciting the pair are all taken into account in these calculations.

Approximation of reliabilities for multiple-trait model with maternal effects.

PubMed

Strabel, T; Misztal, I; Bertrand, J K

2001-04-01

Reliabilities for a multiple-trait maternal model were obtained by combining reliabilities obtained from single-trait models. Single-trait reliabilities were obtained using an approximation that supported models with additive and permanent environmental effects. For the direct effect, the maternal and permanent environmental variances were assigned to the residual. For the maternal effect, variance of the direct effect was assigned to the residual. Data included 10,550 birth weight, 11,819 weaning weight, and 3,617 postweaning gain records of Senepol cattle. Reliabilities were obtained by generalized inversion and by using single-trait and multiple-trait approximation methods. Some reliabilities obtained by inversion were negative because inbreeding was ignored in calculating the inverse of the relationship matrix. The multiple-trait approximation method reduced the bias of approximation when compared with the single-trait method. The correlations between reliabilities obtained by inversion and by multiple-trait procedures for the direct effect were 0.85 for birth weight, 0.94 for weaning weight, and 0.96 for postweaning gain. Correlations for maternal effects for birth weight and weaning weight were 0.96 to 0.98 for both approximations. Further improvements can be achieved by refining the single-trait procedures.

Target mediated drug disposition with drug–drug interaction, Part II: competitive and uncompetitive cases

PubMed Central

Jusko, William J.; Schropp, Johannes

2017-01-01

We present competitive and uncompetitive drug–drug interaction (DDI) with target mediated drug disposition (TMDD) equations and investigate their pharmacokinetic DDI properties. For application of TMDD models, quasi-equilibrium (QE) or quasi-steady state (QSS) approximations are necessary to reduce the number of parameters. To realize those approximations of DDI TMDD models, we derive an ordinary differential equation (ODE) representation formulated in free concentration and free receptor variables. This ODE formulation can be straightforward implemented in typical PKPD software without solving any non-linear equation system arising from the QE or QSS approximation of the rapid binding assumptions. This manuscript is the second in a series to introduce and investigate DDI TMDD models and to apply the QE or QSS approximation. PMID:28074396

The walking behaviour of pedestrian social groups and its impact on crowd dynamics.

PubMed

Moussaïd, Mehdi; Perozo, Niriaska; Garnier, Simon; Helbing, Dirk; Theraulaz, Guy

2010-04-07

Human crowd motion is mainly driven by self-organized processes based on local interactions among pedestrians. While most studies of crowd behaviour consider only interactions among isolated individuals, it turns out that up to 70% of people in a crowd are actually moving in groups, such as friends, couples, or families walking together. These groups constitute medium-scale aggregated structures and their impact on crowd dynamics is still largely unknown. In this work, we analyze the motion of approximately 1500 pedestrian groups under natural condition, and show that social interactions among group members generate typical group walking patterns that influence crowd dynamics. At low density, group members tend to walk side by side, forming a line perpendicular to the walking direction. As the density increases, however, the linear walking formation is bent forward, turning it into a V-like pattern. These spatial patterns can be well described by a model based on social communication between group members. We show that the V-like walking pattern facilitates social interactions within the group, but reduces the flow because of its "non-aerodynamic" shape. Therefore, when crowd density increases, the group organization results from a trade-off between walking faster and facilitating social exchange. These insights demonstrate that crowd dynamics is not only determined by physical constraints induced by other pedestrians and the environment, but also significantly by communicative, social interactions among individuals.

Experimental study of vorticity-strain rate interaction in turbulent partially-premixed jet flames using tomographic particle image velocimetry

DOE PAGES

Coriton, Bruno; Frank, Jonathan H.

2016-02-16

In turbulent flows, the interaction between vorticity, ω, and strain rate, s, is considered a primary mechanism for the transfer of energy from large to small scales through vortex stretching. The ω-s coupling in turbulent jet flames is investigated using tomographic particle image velocimetry (TPIV). TPIV provides a direct measurement of the three-dimensional velocity field from which ω and s are determined. The effects of combustion and mean shear on the ω-s interaction are investigated in turbulent partially premixed methane/air jet flames with high and low probabilities of localized extinction as well as in a non-reacting isothermal air jet withmore » Reynolds number of approximately 13,000. Results show that combustion causes structures of high vorticity and strain rate to agglomerate in highly correlated, elongated layers that span the height of the probe volume. In the non-reacting jet, these structures have a more varied morphology, greater fragmentation, and are not as well correlated. The enhanced spatiotemporal correlation of vorticity and strain rate in the stable flame results in stronger ω-s interaction characterized by increased enstrophy and strain-rate production rates via vortex stretching and straining, respectively. The probability of preferential local alignment between ω and the eigenvector of the intermediate principal strain rate, s 2, which is intrinsic to the ω-s coupling in turbulent flows, is larger in the flames and increases with the flame stability. The larger mean shear in the flame imposes a preferential orientation of ω and s 2 tangential to the shear layer. The extensive and compressive principal strain rates, s 1 and s 3, respectively, are preferentially oriented at approximately 45° with respect to the jet axis. As a result, the production rates of strain and vorticity tend to be dominated by instances in which ω is parallel to the s 1¯-s 2¯ plane and orthogonal to s 3¯.« less

Pseudouridine and N6-methyladenosine modifications weaken PUF protein/RNA interactions

PubMed Central

AlSadhan, Ishraq; Merriman, Dawn K.; Al-Hashimi, Hashim M.; Herschlag, Daniel

2017-01-01

RNA modifications are ubiquitous in biology, with over 100 distinct modifications. While the vast majority were identified and characterized on abundant noncoding RNA such as tRNA and rRNA, the advent of sensitive sequencing-based approaches has led to the discovery of extensive and regulated modification of eukaryotic messenger RNAs as well. The two most abundant mRNA modifications—pseudouridine (Ψ) and N6-methyladenosine (m6A)—affect diverse cellular processes including mRNA splicing, localization, translation, and decay and modulate RNA structure. Here, we test the hypothesis that RNA modifications directly affect interactions between RNA-binding proteins and target RNA. We show that Ψ and m6A weaken the binding of the human single-stranded RNA binding protein Pumilio 2 (hPUM2) to its consensus motif, with individual modifications having effects up to approximately threefold and multiple modifications giving larger effects. While there are likely to be some cases where RNA modifications essentially fully ablate protein binding, here we see modest responses that may be more common. Such modest effects could nevertheless profoundly alter the complex landscape of RNA:protein interactions, and the quantitative rather than qualitative nature of these effects underscores the need for quantitative, systems-level accounting of RNA:protein interactions to understand post-transcriptional regulation. PMID:28138061

A complete multifluid model for bipolar semiconductors, with interacting carriers, phonons, and photons

NASA Astrophysics Data System (ADS)

Rossani, A.

2017-12-01

If electrons (e) and holes (h) in metals or semiconductors are heated to the temperatures T_e and T_h greater than the lattice temperature, the electron-phonon interaction causes energy relaxation. In the non-uniform case a momentum relaxation occurs as well. In view of such an application, a new model, based on an asymptotic procedure for solving the kinetic equations of carriers, phonons, and photons, is proposed, which gives naturally the displaced Maxwellian at the leading order. Several generation-recombination (GR) events occur in bipolar semiconductors. In the presence of photons the most important ones are the radiative GR events, direct, indirect, and exciton-catalyzed. Phonons and photons are treated here as a participating species, with their own equation. All the phonon-photon interactions are accounted for. Moreover, carrier-photon (Compton) interactions are introduced, which make complete the model. After that, balance equations for the electron number, hole number, energy densities, and momentum densities are constructed, which constitute now a system of macroscopic equations for the chemical potentials (carriers), the temperatures (carriers and bosons), and the drift velocities (carriers and bosons). In the drift-diffusion approximation the constitutive laws are derived and the Onsager relations recovered, even in the presence of an external magnetic field.

Alternative method of quantum state tomography toward a typical target via a weak-value measurement

NASA Astrophysics Data System (ADS)

Chen, Xi; Dai, Hong-Yi; Yang, Le; Zhang, Ming

2018-03-01

There is usually a limitation of weak interaction on the application of weak-value measurement. This limitation dominates the performance of the quantum state tomography toward a typical target in the finite and high-dimensional complex-valued superposition of its basis states, especially when the compressive sensing technique is also employed. Here we propose an alternative method of quantum state tomography, presented as a general model, toward such typical target via weak-value measurement to overcome such limitation. In this model the pointer for the weak-value measurement is a qubit, and the target-pointer coupling interaction is no longer needed within the weak interaction limitation, meanwhile this interaction under the compressive sensing can be described with the Taylor series of the unitary evolution operator. The postselection state at the target is the equal superposition of all basis states, and the pointer readouts are gathered under multiple Pauli operator measurements. The reconstructed quantum state is generated from an optimization algorithm of total variation augmented Lagrangian alternating direction algorithm. Furthermore, we demonstrate an example of this general model for the quantum state tomography toward the planar laser-energy distribution and discuss the relations among some parameters at both our general model and the original first-order approximate model for this tomography.

Solvation effects on chemical shifts by embedded cluster integral equation theory.

PubMed

Frach, Roland; Kast, Stefan M

2014-12-11

The accurate computational prediction of nuclear magnetic resonance (NMR) parameters like chemical shifts represents a challenge if the species studied is immersed in strongly polarizing environments such as water. Common approaches to treating a solvent in the form of, e.g., the polarizable continuum model (PCM) ignore strong directional interactions such as H-bonds to the solvent which can have substantial impact on magnetic shieldings. We here present a computational methodology that accounts for atomic-level solvent effects on NMR parameters by extending the embedded cluster reference interaction site model (EC-RISM) integral equation theory to the prediction of chemical shifts of N-methylacetamide (NMA) in aqueous solution. We examine the influence of various so-called closure approximations of the underlying three-dimensional RISM theory as well as the impact of basis set size and different treatment of electrostatic solute-solvent interactions. We find considerable and systematic improvement over reference PCM and gas phase calculations. A smaller basis set in combination with a simple point charge model already yields good performance which can be further improved by employing exact electrostatic quantum-mechanical solute-solvent interaction energies. A larger basis set benefits more significantly from exact over point charge electrostatics, which can be related to differences of the solvent's charge distribution.

Transfer of sulfur from IscS to IscU during Fe/S cluster assembly.

PubMed

Urbina, H D; Silberg, J J; Hoff, K G; Vickery, L E

2001-11-30

The cysteine desulfurase enzymes NifS and IscS provide sulfur for the biosynthesis of Fe/S proteins. NifU and IscU have been proposed to serve as template or scaffold proteins in the initial Fe/S cluster assembly events, but the mechanism of sulfur transfer from NifS or IscS to NifU or IscU has not been elucidated. We have employed [(35)S]cysteine radiotracer studies to monitor sulfur transfer between IscS and IscU from Escherichia coli and have used direct binding measurements to investigate interactions between the proteins. IscS catalyzed transfer of (35)S from [(35)S]cysteine to IscU in the absence of additional thiol reagents, suggesting that transfer can occur directly and without involvement of an intermediate carrier. Surface plasmon resonance studies and isothermal titration calorimetry measurements further revealed that IscU binds to IscS with high affinity (K(d) approximately 2 microm) in support of a direct transfer mechanism. Transfer was inhibited by treatment of IscU with iodoacetamide, and (35)S was released by reducing reagents, suggesting that transfer of persulfide sulfur occurs to cysteinyl groups of IscU. A deletion mutant of IscS lacking C-terminal residues 376-413 (IscSDelta376-413) displayed cysteine desulfurase activity similar to the full-length protein but exhibited lower binding affinity for IscU, decreased ability to transfer (35)S to IscU, and reduced activity in assays of Fe/S cluster assembly on IscU. The findings with IscSDelta376-413 provide additional support for a mechanism of sulfur transfer involving a direct interaction between IscS and IscU and suggest that the C-terminal region of IscS may be important for binding IscU.

The Brownian mean field model

NASA Astrophysics Data System (ADS)

Chavanis, Pierre-Henri

2014-05-01

We discuss the dynamics and thermodynamics of the Brownian mean field (BMF) model which is a system of N Brownian particles moving on a circle and interacting via a cosine potential. It can be viewed as the canonical version of the Hamiltonian mean field (HMF) model. The BMF model displays a second order phase transition from a homogeneous phase to an inhomogeneous phase below a critical temperature T c = 1 / 2. We first complete the description of this model in the mean field approximation valid for N → +∞. In the strong friction limit, the evolution of the density towards the mean field Boltzmann distribution is governed by the mean field Smoluchowski equation. For T < T c , this equation describes a process of self-organization from a non-magnetized (homogeneous) phase to a magnetized (inhomogeneous) phase. We obtain an analytical expression for the temporal evolution of the magnetization close to T c . Then, we take fluctuations (finite N effects) into account. The evolution of the density is governed by the stochastic Smoluchowski equation. From this equation, we derive a stochastic equation for the magnetization and study its properties both in the homogenous and inhomogeneous phase. We show that the fluctuations diverge at the critical point so that the mean field approximation ceases to be valid. Actually, the limits N → +∞ and T → T c do not commute. The validity of the mean field approximation requires N( T - T c ) → +∞ so that N must be larger and larger as T approaches T c . We show that the direction of the magnetization changes rapidly close to T c while its amplitude takes a long time to relax. We also indicate that, for systems with long-range interactions, the lifetime of metastable states scales as e N except close to a critical point. The BMF model shares many analogies with other systems of Brownian particles with long-range interactions such as self-gravitating Brownian particles, the Keller-Segel model describing the chemotaxis of bacterial populations, the Kuramoto model describing the collective synchronization of coupled oscillators, the Desai-Zwanzig model, and the models describing the collective motion of social organisms such as bird flocks or fish schools.

Spontaneous Symmetry Breaking in Interdependent Networked Game

PubMed Central

Jin, Qing; Wang, Lin; Xia, Cheng-Yi; Wang, Zhen

2014-01-01

Spatial evolution game has traditionally assumed that players interact with direct neighbors on a single network, which is isolated and not influenced by other systems. However, this is not fully consistent with recent research identification that interactions between networks play a crucial rule for the outcome of evolutionary games taking place on them. In this work, we introduce the simple game model into the interdependent networks composed of two networks. By means of imitation dynamics, we display that when the interdependent factor α is smaller than a threshold value αC, the symmetry of cooperation can be guaranteed. Interestingly, as interdependent factor exceeds αC, spontaneous symmetry breaking of fraction of cooperators presents itself between different networks. With respect to the breakage of symmetry, it is induced by asynchronous expansion between heterogeneous strategy couples of both networks, which further enriches the content of spatial reciprocity. Moreover, our results can be well predicted by the strategy-couple pair approximation method. PMID:24526076

Keratinocyte-melanocyte interactions during melanosome transfer.

PubMed

Seiberg, M

2001-08-01

The epidermal-melanin unit is composed of one melanocyte and approximately 36 neighboring keratinocytes, working in synchrony to produce and distribute melanin. Melanin is synthesized in melanosomes, transferred to the dendrite tips, and translocated into keratinocytes, forming caps over the keratinocyte nuclei. The molecular and cellular mechanisms involved in melanosome transfer and the keratinocyte-melanocyte interactions required for this process are not yet completely understood. Suggested mechanisms of melanosome transfer include melanosome release and endocytosis, direct inoculation ('injection'), keratinocyte-melanocyte membrane fusion, and phagocytosis. Studies of the keratinocyte receptor protease-activated receptor-2 (PAR-2) support the phagocytosis theory. PAR-2 controls melanosome ingestion and phagocytosis by keratinocytes and exerts a regulatory role in skin pigmentation. Modulation of PAR-2 activity can enhance or decrease melanosome transfer and affects pigmentation only when there is keratinocyte-melanocyte contact. Moreover, PAR-2 is induced by UV irradiation and inhibition of PAR-2 activation results in the prevention of UVB-induced tanning. The role of PAR-2 in mediating UV-induced responses remains to be elucidated.

Development of automated high throughput single molecular microfluidic detection platform for signal transduction analysis

NASA Astrophysics Data System (ADS)

Huang, Po-Jung; Baghbani Kordmahale, Sina; Chou, Chao-Kai; Yamaguchi, Hirohito; Hung, Mien-Chie; Kameoka, Jun

2016-03-01

Signal transductions including multiple protein post-translational modifications (PTM), protein-protein interactions (PPI), and protein-nucleic acid interaction (PNI) play critical roles for cell proliferation and differentiation that are directly related to the cancer biology. Traditional methods, like mass spectrometry, immunoprecipitation, fluorescence resonance energy transfer, and fluorescence correlation spectroscopy require a large amount of sample and long processing time. "microchannel for multiple-parameter analysis of proteins in single-complex (mMAPS)"we proposed can reduce the process time and sample volume because this system is composed by microfluidic channels, fluorescence microscopy, and computerized data analysis. In this paper, we will present an automated mMAPS including integrated microfluidic device, automated stage and electrical relay for high-throughput clinical screening. Based on this result, we estimated that this automated detection system will be able to screen approximately 150 patient samples in a 24-hour period, providing a practical application to analyze tissue samples in a clinical setting.

Behavioral interactions of penned red and arctic foxes

USGS Publications Warehouse

Rudzinski, D.R.; Graves, H.B.; Sargeant, A.B.; Storm, G.L.

1982-01-01

Expansion of the geographical distribution of red foxes (Vulpes vulpes) into the far north tundra region may lead to competition between arctic (Alopex lagopus) and red foxes for space and resources. Behavioral interactions between red and arctic foxes were evaluated during 9 trials conducted in a 4.05-ha enclosure near Woodworth, North Dakota. Each trial consisted of introducing a male-female pair of arctic foxes into the enclosure and allowing them to acclimate for approximately a week before releasing a female red fox into the enclosure, followed by her mate a few days later. In 8 of 9 trials, red foxes were dominant over arctic foxes during encounters. Activity of the arctic foxes decreased upon addition of red foxes. Arctic foxes tried unsuccessfully to defend preferred den, resting, and feeding areas. Even though the outcome of competition between red and arctic foxes in the Arctic is uncertain, the more aggressive red fox can dominate arctic foxes in direct competition for den sites and other limited resources.

Direct measurement of interaction forces between a single bacterium and a flat plate.

PubMed

Klein, Jonah D; Clapp, Aaron R; Dickinson, Richard B

2003-05-15

A technique for precisely measuring the equilibrium and viscous interaction forces between a single bacterium and a flat surface as functions of separation distance is described. A single-beam gradient optical trap was used to micromanipulate the bacterium against a flat surface while evanescent wave light scattering was used to measure separation distances. Calibrating the optical trap far from the surface allowed the trapped bacterium to be used as a force probe. Equilibrium force-distance profiles were determined by measuring the deflection of the cell from the center of the optical trap at various trap positions. Simultaneously, viscous forces were determined by measuring the relaxation time for the fluctuating bacterium. Absolute distances were determined using a best-fit approximation to the theoretical prediction for the hindered mobility of a diffusing sphere near a wall. Using this approach, forces in the range from 0.01 to 4 pN were measured at near-nanometer resolution between Staphylococcus aureus and glass that was bare or coated with adsorbed protein.

Large-eddy simulation of the passage of a shock wave through homogeneous turbulence

NASA Astrophysics Data System (ADS)

Braun, N. O.; Pullin, D. I.; Meiron, D. I.

2017-11-01

The passage of a nominally plane shockwave through homogeneous, compressible turbulence is a canonical problem representative of flows seen in supernovae, supersonic combustion engines, and inertial confinement fusion. The interaction of isotropic turbulence with a stationary normal shockwave is considered at inertial range Taylor Reynolds numbers, Reλ = 100 - 2500 , using Large Eddy Simulation (LES). The unresolved, subgrid terms are approximated by the stretched-vortex model (Kosovic et al., 2002), which allows self-consistent reconstruction of the subgrid contributions to the turbulent statistics of interest. The mesh is adaptively refined in the vicinity of the shock to resolve small amplitude shock oscillations, and the implications of mesh refinement on the subgrid modeling are considered. Simulations are performed at a range of shock Mach numbers, Ms = 1.2 - 3.0 , and turbulent Mach numbers, Mt = 0.06 - 0.18 , to explore the parameter space of the interaction at high Reynolds number. The LES shows reasonable agreement with linear analysis and lower Reynolds number direct numerical simulations. LANL Subcontract 305963.

A variation-perturbation method for atomic and molecular interactions. I - Theory. II - The interaction potential and van der Waals molecule for Ne-HF

NASA Astrophysics Data System (ADS)

Gallup, G. A.; Gerratt, J.

1985-09-01

The van der Waals energy between the two parts of a system is a very small fraction of the total electronic energy. In such cases, calculations have been based on perturbation theory. However, such an approach involves certain difficulties. For this reason, van der Waals energies have also been directly calculated from total energies. But such a method has definite limitations as to the size of systems which can be treated, and recently ab initio calculations have been combined with damped semiempirical long-range dispersion potentials to treat larger systems. In this procedure, large basis set superposition errors occur, which must be removed by the counterpoise method. The present investigation is concerned with an approach which is intermediate between the previously considered procedures. The first step in the new approach involves a variational calculation based upon valence bond functions. The procedure includes also the optimization of excited orbitals, and an approximation of atomic integrals and Hamiltonian matrix elements.

A recipe for free-energy functionals of polarizable molecular fluids

NASA Astrophysics Data System (ADS)

Sundararaman, Ravishankar; Letchworth-Weaver, Kendra; Arias, T. A.

2014-04-01

Classical density-functional theory is the most direct approach to equilibrium structures and free energies of inhomogeneous liquids, but requires the construction of an approximate free-energy functional for each liquid of interest. We present a general recipe for constructing functionals for small-molecular liquids based only on bulk experimental properties and ab initio calculations of a single solvent molecule. This recipe combines the exact free energy of the non-interacting system with fundamental measure theory for the repulsive contribution and a weighted density functional for the short-ranged attractive interactions. We add to these ingredients a weighted polarization functional for the long-range correlations in both the rotational and molecular-polarizability contributions to the dielectric response. We also perform molecular dynamics calculations for the free energy of cavity formation and the high-field dielectric response, and show that our free-energy functional adequately describes these properties (which are key for accurate solvation calculations) for all three solvents in our study: water, chloroform, and carbon tetrachloride.

Linear arrangements of nano-scale ferromagnetic particles spontaneously formed in a copper-base Cu-Ni-Co alloy

NASA Astrophysics Data System (ADS)

Sakakura, Hibiki; Kim, Jun-Seop; Takeda, Mahoto

2018-03-01

We have investigated the influence of magnetic interactions on the microstructural evolution of nano-scale granular precipitates formed spontaneously in an annealed Cu-20at%Ni-5at%Co alloy and the associated changes of magnetic properties. The techniques used included transmission electron microscopy, superconducting quantum interference device (SQUID) magnetometry, magneto-thermogravimetry (MTG), and first-principles calculations based on the method of Koster-Korringa-Rostker with the coherent potential approximation. Our work has revealed that the nano-scale spherical and cubic precipitates which formed on annealing at 873 K and 973 K comprise mainly cobalt and nickel with a small amount of copper, and are arranged in the 〈1 0 0〉 direction of the copper matrix. The SQUID and MTG measurements suggest that magnetic properties such as coercivity and Curie temperature are closely correlated with the microstructure. The combination of results suggests that magnetic interactions between precipitates during annealing can explain consistently the observed precipitation phenomena.

Characterization of nanoscale spatial distribution of small molecules in amorphous polymer matrices

NASA Astrophysics Data System (ADS)

Ricarte, Ralm; Hillmyer, Marc; Lodge, Timothy

Hydroxypropyl methylcellulose acetate succinate (HPMCAS) can significantly enhance the efficacy of active pharmaceutical ingredients (APIs). Yet, the interactions between species in HPMCAS-API blends are not understood. Elucidating these interactions is difficult because the spatial distributions of HPMCAS and API in the blends are ambiguous; the polymer and drug may be molecularly mixed or the species may form phase separated domains. As these phase separated domains may be less than 100 nm in size, traditional characterization techniques may not accurately evaluate the spatial distribution. To address this challenge, we explore the use of electron energy-loss spectroscopy (EELS) for detecting the model API phenytoin in an HPMCAS-phenytoin blend. Using EELS, we directly measured with high accuracy and precision the phenytoin concentrations in several blends. We present evidence that suggests phase separation occurs in blends that have a phenytoin loading of approximately 50 wt percent. Finally, we demonstrate that this technique achieves a sub-100 nm spatial resolution and can detect several other APIs.

Trapped one-dimensional ideal Fermi gas with a single impurity

NASA Astrophysics Data System (ADS)

Astrakharchik, G. E.; Brouzos, I.

2013-08-01

Ground-state properties of a single impurity in a one-dimensional Fermi gas are investigated in uniform and trapped geometries. The energy of a trapped system is obtained (i) by generalizing the McGuire expression from a uniform to trapped system (ii) within the local density approximation (iii) using the perturbative approach in the case of a weakly interacting impurity and (iv) diffusion Monte Carlo method. We demonstrate that there is a closed formula based on the exact solution of the homogeneous case which provides a precise estimation for the energy of a trapped system even for a small number of fermions and arbitrary coupling constant of the impurity. Using this expression, we analyze energy contributions from kinetic, interaction, and potential components, as well as spatial properties such as the system size and the pair-correlation function. Finally, we calculate the frequency of the breathing mode. Our analysis is directly connected and applicable to the recent experiments in microtraps.

Helminths and intestinal barrier function

PubMed Central

McKay, Derek M.; Shute, Adam; Lopes, Fernando

2017-01-01

ABSTRACT Approximately one-sixth of the worlds' population is infected with helminths and this class of parasite takes a major toll on domestic livestock. The majority of species of parasitic helminth that infect mammals live in the gut (the only niche for tapeworms) where they contact the hosts' epithelial cells. Here, the helminth-intestinal epithelial interface is reviewed in terms of the impact on, and regulation of epithelial barrier function, both intrinsic (epithelial permeability) and extrinsic (mucin, bacterial peptides, commensal bacteria) elements of the barrier. The data available on direct effects of helminths on epithelial permeability are scant, fragmentary and pales in comparison with knowledge of mobilization of immune reactions and effector cells in response to helminth parasites and how these impact intestinal barrier function. The interaction of helminth-host and helminth-host-bacteria is an important determinant of gut form and function and precisely defining these interactions will radically alter our understanding of normal gut physiology and pathophysiological reactions, revealing new approaches to infection with parasitic helminths, bacterial pathogens and idiopathic auto-inflammatory disease. PMID:28452686

Direct evidence for high affinity blockade of NaV1.6 channel subtype by huwentoxin-IV spider peptide, using multiscale functional approaches.

PubMed

Gonçalves, Tânia C; Boukaiba, Rachid; Molgó, Jordi; Amar, Muriel; Partiseti, Michel; Servent, Denis; Benoit, Evelyne

2018-05-01

The Chinese bird spider huwentoxin-IV (HwTx-IV) is well-known to be a highly potent blocker of Na V 1.7 subtype of voltage-gated sodium (Na V ) channels, a genetically validated analgesic target, and thus promising as a potential lead molecule for the development of novel pain therapeutics. In the present study, the interaction between HwTx-IV and Na V 1.6 channel subtype was investigated using multiscale (from in vivo to individual cell) functional approaches. HwTx-IV was approximatively 2 times more efficient than tetrodotoxin (TTX) to inhibit the compound muscle action potential recorded from the mouse skeletal neuromuscular system in vivo, and 30 times more effective to inhibit nerve-evoked than directly-elicited muscle contractile force of isolated mouse hemidiaphragms. These results strongly suggest that the inhibition of nerve-evoked skeletal muscle functioning, produced by HwTx-IV, resulted from a toxin-induced preferential blockade of Na V 1.6, compared to Na V 1.4, channel subtype. This was confirmed by whole-cell automated patch-clamp experiments performed on human embryonic kidney (HEK)-293 cells overexpressing hNa V 1.1-1.8 channel subtypes. HwTx-IV was also approximatively 850 times more efficient to inhibit TTX-sensitive than TTX-resistant sodium currents recorded from mouse dorsal root ganglia neurons. Finally, based on our data, we predict that blockade of the Na V 1.6 channel subtype was involved in the in vivo toxicity of HwTx-IV, although this toxicity was more than 2 times lower than that of TTX. In conclusion, our results provide detailed information regarding the effects of HwTx-IV and allow a better understanding of the side-effect mechanisms involved in vivo and of channel subtype interactions resulting from the toxin activity. Copyright © 2018 Elsevier Ltd. All rights reserved.

Dynamic nuclear polarization enhanced nuclear magnetic resonance and electron spin resonance studies of hydration and local water dynamics in micelle and vesicle assemblies.

PubMed

McCarney, Evan R; Armstrong, Brandon D; Kausik, Ravinath; Han, Songi

2008-09-16

We present a unique analysis tool for the selective detection of local water inside soft molecular assemblies (hydrophobic cores, vesicular bilayers, and micellar structures) suspended in bulk water. Through the use of dynamic nuclear polarization (DNP), the (1)H NMR signal of water is amplified, as it interacts with stable radicals that possess approximately 658 times higher spin polarization. We utilized stable nitroxide radicals covalently attached along the hydrophobic tail of stearic acid molecules that incorporate themselves into surfactant-based micelle or vesicle structures. Here, we present a study of local water content and fluid viscosity inside oleate micelles and vesicles and Triton X-100 micelles to serve as model systems for soft molecular assemblies. This approach is unique because the amplification of the NMR signal is performed in bulk solution and under ambient conditions with site-specific spin labels that only detect the water that is directly interacting with the localized spin labels. Continuous wave (cw) electron spin resonance (ESR) analysis provides rotational dynamics of the spin-labeled molecular chain segments and local polarity parameters that can be related to hydration properties, whereas we show that DNP-enhanced (1)H NMR analysis of fluid samples directly provides translational water dynamics and permeability of the local environment probed by the spin label. Our technique therefore has the potential to become a powerful analysis tool, complementary to cw ESR, to study hydration characteristics of surfactant assemblies, lipid bilayers, or protein aggregates, where water dynamics is a key parameter of their structure and function. In this study, we find that there is significant penetration of water inside the oleate micelles with a higher average local water viscosity (approximately 1.8 cP) than in bulk water, and Triton X-100 micelles and oleate vesicle bilayers mostly exclude water while allowing for considerable surfactant chain motion and measurable water permeation through the soft structure.

Approximate arbitrary κ-state solutions of Dirac equation with Schiöberg and Manning-Rosen potentials within the coulomb-like Yukawa-like and generalized tensor interactions

NASA Astrophysics Data System (ADS)

Ikot, Akpan N.; Hassanabadi, Hassan; Obong, Hillary Patrick; Mehraban, H.; Yazarloo, Bentol Hoda

2015-07-01

The effects of Coulomb-like tensor (CLT), Yukawa-like tensor (YLT) and generalized tensor (GLT) interactions are investigated in the Dirac theory with Schiöberg and Manning-Rosen potentials within the framework of spin and pseudospin symmetries using the Nikiforov-Uvarov method. The bound state energy spectra and the radial wave functions have been approximately obtained in the case of spin and pseudospin symmetries. We have also reported some numerical results and figures to show the effects these tensor interactions.

Phenomenological Study of Interaction between Solar Acoustic Waves and Sunspots from Measured Scattered Wavefunctions

NASA Astrophysics Data System (ADS)

Yang, Ming-Hsu; Chou, Dean-Yi; Zhao, Hui; Liang, Zhi-Chao

2012-08-01

The solar acoustic waves around a sunspot are modified because of the interaction with the sunspot. The interaction can be viewed as that the sunspot, excited by the incident wave, generates the scattered wave, and the scattered wave is added to the incident wave to form the total wave around the sunspot. We define an interaction parameter, which could be complex, describing the interaction between the acoustic waves and the sunspot. The scattered wavefunction on the surface can be expressed as a two-dimensional integral of the product of the Green's function, the wavefunction, and the two-dimensional interaction parameter over the sunspot area for the Born approximation of different orders. We assume a simple model for the two-dimensional interaction parameter distribution: its absolute value is axisymmetric with a Gaussian distribution and its phase is a constant. The measured scattered wavefunctions of various modes for NOAAs 11084 and 11092 are fitted to the theoretical scattered wavefunctions to determine the three model parameters, magnitude, Gaussian radius, and phase, for the Born approximation of different orders. The three model parameters converge to some values at high-order Born approximations. The result of the first-order Born approximation is significantly different from the convergent value in some cases. The rate of convergence depends on the sunspot size and wavelength. It converges more rapidly for the smaller sunspot and longer wavelength. The magnitude increases with mode frequency and degree for each radial order. The Gaussian radius is insensitive to frequency and degree. The spatial range of the interaction parameter is greater than that of the continuum intensity deficit, but smaller than that of the acoustic power deficit of the sunspot. The phase versus phase speed falls into a small range. This suggests that the phase could be a function phase speed. NOAAs 11084 and 11092 have a similar magnitude and phase, although the ratio of their sizes is 0.75.

An equation-free probabilistic steady-state approximation: dynamic application to the stochastic simulation of biochemical reaction networks.

PubMed

Salis, Howard; Kaznessis, Yiannis N

2005-12-01

Stochastic chemical kinetics more accurately describes the dynamics of "small" chemical systems, such as biological cells. Many real systems contain dynamical stiffness, which causes the exact stochastic simulation algorithm or other kinetic Monte Carlo methods to spend the majority of their time executing frequently occurring reaction events. Previous methods have successfully applied a type of probabilistic steady-state approximation by deriving an evolution equation, such as the chemical master equation, for the relaxed fast dynamics and using the solution of that equation to determine the slow dynamics. However, because the solution of the chemical master equation is limited to small, carefully selected, or linear reaction networks, an alternate equation-free method would be highly useful. We present a probabilistic steady-state approximation that separates the time scales of an arbitrary reaction network, detects the convergence of a marginal distribution to a quasi-steady-state, directly samples the underlying distribution, and uses those samples to accurately predict the state of the system, including the effects of the slow dynamics, at future times. The numerical method produces an accurate solution of both the fast and slow reaction dynamics while, for stiff systems, reducing the computational time by orders of magnitude. The developed theory makes no approximations on the shape or form of the underlying steady-state distribution and only assumes that it is ergodic. We demonstrate the accuracy and efficiency of the method using multiple interesting examples, including a highly nonlinear protein-protein interaction network. The developed theory may be applied to any type of kinetic Monte Carlo simulation to more efficiently simulate dynamically stiff systems, including existing exact, approximate, or hybrid stochastic simulation techniques.

Transition state theory for activated systems with driven anharmonic barriers.

PubMed

Revuelta, F; Craven, Galen T; Bartsch, Thomas; Borondo, F; Benito, R M; Hernandez, Rigoberto

2017-08-21

Classical transition state theory has been extended to address chemical reactions across barriers that are driven and anharmonic. This resolves a challenge to the naive theory that necessarily leads to recrossings and approximate rates because it relies on a fixed dividing surface. We develop both perturbative and numerical methods for the computation of a time-dependent recrossing-free dividing surface for a model anharmonic system in a solvated environment that interacts strongly with an oscillatory external field. We extend our previous work, which relied either on a harmonic approximation or on periodic force driving. We demonstrate that the reaction rate, expressed as the long-time flux of reactive trajectories, can be extracted directly from the stability exponents, namely, Lyapunov exponents, of the moving dividing surface. Comparison to numerical results demonstrates the accuracy and robustness of this approach for the computation of optimal (recrossing-free) dividing surfaces and reaction rates in systems with Markovian solvation forces. The resulting reaction rates are in strong agreement with those determined from the long-time flux of reactive trajectories.

A Comparison of Peak Electric Fields and GICs in the Pacific Northwest Using 1-D and 3-D Conductivity

NASA Astrophysics Data System (ADS)

Gannon, J. L.; Birchfield, A. B.; Shetye, K. S.; Overbye, T. J.

2017-11-01

Geomagnetically induced currents (GICs) are a result of the changing magnetic fields during a geomagnetic disturbance interacting with the deep conductivity structures of the Earth. When assessing GIC hazard, it is a common practice to use layer-cake or one-dimensional conductivity models to approximate deep Earth conductivity. In this paper, we calculate the electric field and estimate GICs induced in the long lines of a realistic system model of the Pacific Northwest, using the traditional 1-D models, as well as 3-D models represented by Earthscope's Electromagnetic transfer functions. The results show that the peak electric field during a given event has considerable variation across the analysis region in the Pacific Northwest, but the 1-D physiographic approximations may accurately represent the average response of an area, although corrections are needed. Rotations caused by real deep Earth conductivity structures greatly affect the direction of the induced electric field. This effect may be just as, or more, important than peak intensity when estimating GICs induced in long bulk power system lines.

Thrust and torque vector characteristics of axially-symmetric E-sail

NASA Astrophysics Data System (ADS)

Bassetto, Marco; Mengali, Giovanni; Quarta, Alessandro A.

2018-05-01

The Electric Solar Wind Sail is an innovative propulsion system concept that gains propulsive acceleration from the interaction with charged particles released by the Sun. The aim of this paper is to obtain analytical expressions for the thrust and torque vectors of a spinning sail of given shape. Under the only assumption that each tether belongs to a plane containing the spacecraft spin axis, a general analytical relation is found for the thrust and torque vectors as a function of the spacecraft attitude relative to an orbital reference frame. The results are then applied to the noteworthy situation of a Sun-facing sail, that is, when the spacecraft spin axis is aligned with the Sun-spacecraft line, which approximatively coincides with the solar wind direction. In that case, the paper discusses the equilibrium shape of the generic conducting tether as a function of the sail geometry and the spin rate, using both a numerical and an analytical (approximate) approach. As a result, the structural characteristics of the conducting tether are related to the spacecraft geometric parameters.

Counterflow diffusion flames: effects of thermal expansion and non-unity Lewis numbers

NASA Astrophysics Data System (ADS)

Koundinyan, Sushilkumar P.; Matalon, Moshe; Stewart, D. Scott

2018-05-01

In this work we re-examine the counterflow diffusion flame problem focusing in particular on the flame-flow interactions due to thermal expansion and its influence on various flame properties such as flame location, flame temperature, reactant leakage and extinction conditions. The analysis follows two different procedures: an asymptotic approximation for large activation energy chemical reactions, and a direct numerical approach. The asymptotic treatment follows the general theory of Cheatham and Matalon, which consists of a free-boundary problem with jump conditions across the surface representing the reaction sheet, and is well suited for variable-density flows and for mixtures with non-unity and distinct Lewis numbers for the fuel and oxidiser. Due to density variations, the species and energy transport equations are coupled to the Navier-Stokes equations and the problem does not possess an analytical solution. We thus propose and implement a methodology for solving the free-boundary problem numerically. Results based on the asymptotic approximation are then verified against those obtained from the 'exact' numerical integration of the governing equations, comparing predictions of the various flame properties.

A Robust and Fast Method to Compute Shallow States without Adjustable Parameters: Simulations for a Silicon-Based Qubit

NASA Astrophysics Data System (ADS)

Debernardi, Alberto; Fanciulli, Marco

Within the framework of the envelope function approximation we have computed - without adjustable parameters and with a reduced computational effort due to analytical expression of relevant Hamiltonian terms - the energy levels of the shallow P impurity in silicon and the hyperfine and superhyperfine splitting of the ground state. We have studied the dependence of these quantities on the applied external electric field along the [001] direction. Our results reproduce correctly the experimental splitting of the impurity ground states detected at zero electric field and provide reliable predictions for values of the field where experimental data are lacking. Further, we have studied the effect of confinement of a shallow state of a P atom at the center of a spherical Si-nanocrystal embedded in a SiO2 matrix. In our simulations the valley-orbit interaction of a realistically screened Coulomb potential and of the core potential are included exactly, within the numerical accuracy due to the use of a finite basis set, while band-anisotropy effects are taken into account within the effective-mass approximation.

Falls: Epidemiology, Pathophysiology, and Relationship to Fracture

PubMed Central

Berry, Sarah D.; Miller, Ram

2009-01-01

Falls are common in the elderly, and frequently result in injury, disability, and institutionalization. Although the causes of falls are complex, most falls result from an interaction between individual characteristics that increase an individual's propensity to fall and acute mediating risk factors that provide the opportunity to fall. Predisposing risk factors include age-associated changes in strength and balance, age-associated comorbidities such as osteoarthritis, visual impairment and dementia, psychotropic medications, and certain footwear. Fewer studies have focused on acute precipitating factors, but environmental and situational factors are clearly important to the risk of falls. Approximately 30% of falls result in an injury that requires medical attention and with fractures occurring in approximately 10% of falls. Fractures associated with falls are multi-factorial in origin. In addition to the traditional risk factors for falls, the fall descent, fall impact, and bone strength are all important determinants of whether a fracture will occur as a result of an event. In recent years, numerous studies have been directed toward the development of effective fall and fall-related fracture prevention interventions. PMID:19032925

Temperature scaling in a dense vibrofluidized granular material.

PubMed

Sunthar, P; Kumaran, V

1999-08-01

The leading order "temperature" of a dense two-dimensional granular material fluidized by external vibrations is determined. The grain interactions are characterized by inelastic collisions, but the coefficient of restitution is considered to be close to 1, so that the dissipation of energy during a collision is small compared to the average energy of a particle. An asymptotic solution is obtained where the particles are considered to be elastic in the leading approximation. The velocity distribution is a Maxwell-Boltzmann distribution in the leading approximation. The density profile is determined by solving the momentum balance equation in the vertical direction, where the relation between the pressure and density is provided by the virial equation of state. The temperature is determined by relating the source of energy due to the vibrating surface and the energy dissipation due to inelastic collisions. The predictions of the present analysis show good agreement with simulation results at higher densities where theories for a dilute vibrated granular material, with the pressure-density relation provided by the ideal gas law, are in error.

Exploration of dynamical regimes of irradiated small protonated water clusters

NASA Astrophysics Data System (ADS)

Ndongmouo Taffoti, U. F.; Dinh, P. M.; Reinhard, P.-G.; Suraud, E.; Wang, Z. P.

2010-05-01

We explore from a theoretical perspective the dynamical response of small water clusters, (H2O)nH3O+ with n=1,2,3, to a short laser pulse for various frequencies, from infrared (IR) to ultra-violet (UV) and intensities (from 6×10^{13} W/cm^2 to 5×10^{14} W/cm^2). To that end, we use time-dependent local-density approximation for the electrons, coupled to molecular dynamics for the atomic cores (TDLDA-MD). The local-density approximation is augmented by a self-interaction correction (SIC) to allow for a correct description of electron emission. For IR frequencies, we see a direct coupling of the laser field to the very light H+ ions in the clusters. Resonant coupling (in the UV) and/or higher intensities lead to fast ionization with subsequent Coulomb explosion. The stability against Coulomb pressure increases with system size. Excitation to lower ionization stages induced strong ionic vibrations. The latter maintain a rather harmonic pattern in spite of the sizeable amplitudes (often 10% of the bond length).

Poly(amidoamine) dendrimers on lipid bilayers II: Effects of bilayer phase and dendrimer termination.

PubMed

Kelly, Christopher V; Leroueil, Pascale R; Orr, Bradford G; Banaszak Holl, Mark M; Andricioaei, Ioan

2008-08-07

The molecular structures and enthalpy release of poly(amidoamine) (PAMAM) dendrimers binding to 1,2-dimyristoyl- sn-glycero-3-phosphocholine (DMPC) bilayers were explored through atomistic molecular dynamics. Three PAMAM dendrimer terminations were examined: protonated primary amine, neutral acetamide, and deprotonated carboxylic acid. Fluid and gel lipid phases were examined to extract the effects of lipid tail mobility on the binding of generation-3 dendrimers, which are directly relevant to the nanoparticle interactions involving lipid rafts, endocytosis, lipid removal, and/or membrane pores. Upon binding to gel phase lipids, dendrimers remained spherical, had a constant radius of gyration, and approximately one-quarter of the terminal groups were in close proximity to the lipids. In contrast, upon binding to fluid phase bilayers, dendrimers flattened out with a large increase in their asphericity and radii of gyration. Although over twice as many dendrimer-lipid contacts were formed on fluid versus gel phase lipids, the dendrimer-lipid interaction energy was only 20% stronger. The greatest enthalpy release upon binding was between the charged dendrimers and the lipid bilayer. However, the stronger binding to fluid versus gel phase lipids was driven by the hydrophobic interactions between the inner dendrimer and lipid tails.

Ultrafast dynamics induced by the interaction of molecules with electromagnetic fields: Several quantum, semiclassical, and classical approaches.

PubMed

Antipov, Sergey V; Bhattacharyya, Swarnendu; El Hage, Krystel; Xu, Zhen-Hao; Meuwly, Markus; Rothlisberger, Ursula; Vaníček, Jiří

2017-11-01

Several strategies for simulating the ultrafast dynamics of molecules induced by interactions with electromagnetic fields are presented. After a brief overview of the theory of molecule-field interaction, we present several representative examples of quantum, semiclassical, and classical approaches to describe the ultrafast molecular dynamics, including the multiconfiguration time-dependent Hartree method, Bohmian dynamics, local control theory, semiclassical thawed Gaussian approximation, phase averaging, dephasing representation, molecular mechanics with proton transfer, and multipolar force fields. In addition to the general overview, some focus is given to the description of nuclear quantum effects and to the direct dynamics, in which the ab initio energies and forces acting on the nuclei are evaluated on the fly. Several practical applications, performed within the framework of the Swiss National Center of Competence in Research "Molecular Ultrafast Science and Technology," are presented: These include Bohmian dynamics description of the collision of H with H 2 , local control theory applied to the photoinduced ultrafast intramolecular proton transfer, semiclassical evaluation of vibrationally resolved electronic absorption, emission, photoelectron, and time-resolved stimulated emission spectra, infrared spectroscopy of H-bonding systems, and multipolar force fields applications in the condensed phase.

Orbital order and effective mass enhancement in t2 g two-dimensional electron gases

NASA Astrophysics Data System (ADS)

Tolsma, John; Principi, Alessandro; Polini, Marco; MacDonald, Allan

2015-03-01

It is now possible to prepare d-electron two-dimensional electron gas systems that are confined near oxide heterojunctions and contain t2 g electrons with a density much smaller than one electron per metal atom. I will discuss a generic model that captures all qualitative features of electron-electron interaction physics in t2 g two-dimensional electron gas systems, and the use of a GW approximation to explore t2 g quasiparticle properties in this new context. t2 g electron gases contain a high density isotropic light mass xy component and low-density xz and yz anisotropic components with light and heavy masses in orthogonal directions. The high density light mass band screens interactions within the heavy bands. As a result the wave vector dependence of the self-energy is reduced and the effective mass is increased. When the density in the heavy bands is low, the difference in anisotropy between the two heavy bands favors orbital order. When orbital order does not occur, interactions still reshape the heavy-band Fermi surfaces. I will discuss these results in the context of recently reported magnetotransport experiments.

Adaptive vibrational configuration interaction (A-VCI): A posteriori error estimation to efficiently compute anharmonic IR spectra

NASA Astrophysics Data System (ADS)

Garnier, Romain; Odunlami, Marc; Le Bris, Vincent; Bégué, Didier; Baraille, Isabelle; Coulaud, Olivier

2016-05-01

A new variational algorithm called adaptive vibrational configuration interaction (A-VCI) intended for the resolution of the vibrational Schrödinger equation was developed. The main advantage of this approach is to efficiently reduce the dimension of the active space generated into the configuration interaction (CI) process. Here, we assume that the Hamiltonian writes as a sum of products of operators. This adaptive algorithm was developed with the use of three correlated conditions, i.e., a suitable starting space, a criterion for convergence, and a procedure to expand the approximate space. The velocity of the algorithm was increased with the use of a posteriori error estimator (residue) to select the most relevant direction to increase the space. Two examples have been selected for benchmark. In the case of H2CO, we mainly study the performance of A-VCI algorithm: comparison with the variation-perturbation method, choice of the initial space, and residual contributions. For CH3CN, we compare the A-VCI results with a computed reference spectrum using the same potential energy surface and for an active space reduced by about 90%.

Ultrafast dynamics induced by the interaction of molecules with electromagnetic fields: Several quantum, semiclassical, and classical approaches

PubMed Central

Antipov, Sergey V.; Bhattacharyya, Swarnendu; El Hage, Krystel; Xu, Zhen-Hao; Meuwly, Markus; Rothlisberger, Ursula; Vaníček, Jiří

2018-01-01

Several strategies for simulating the ultrafast dynamics of molecules induced by interactions with electromagnetic fields are presented. After a brief overview of the theory of molecule-field interaction, we present several representative examples of quantum, semiclassical, and classical approaches to describe the ultrafast molecular dynamics, including the multiconfiguration time-dependent Hartree method, Bohmian dynamics, local control theory, semiclassical thawed Gaussian approximation, phase averaging, dephasing representation, molecular mechanics with proton transfer, and multipolar force fields. In addition to the general overview, some focus is given to the description of nuclear quantum effects and to the direct dynamics, in which the ab initio energies and forces acting on the nuclei are evaluated on the fly. Several practical applications, performed within the framework of the Swiss National Center of Competence in Research “Molecular Ultrafast Science and Technology,” are presented: These include Bohmian dynamics description of the collision of H with H2, local control theory applied to the photoinduced ultrafast intramolecular proton transfer, semiclassical evaluation of vibrationally resolved electronic absorption, emission, photoelectron, and time-resolved stimulated emission spectra, infrared spectroscopy of H-bonding systems, and multipolar force fields applications in the condensed phase. PMID:29376107

Adaptive vibrational configuration interaction (A-VCI): A posteriori error estimation to efficiently compute anharmonic IR spectra.

PubMed

Garnier, Romain; Odunlami, Marc; Le Bris, Vincent; Bégué, Didier; Baraille, Isabelle; Coulaud, Olivier

2016-05-28

A new variational algorithm called adaptive vibrational configuration interaction (A-VCI) intended for the resolution of the vibrational Schrödinger equation was developed. The main advantage of this approach is to efficiently reduce the dimension of the active space generated into the configuration interaction (CI) process. Here, we assume that the Hamiltonian writes as a sum of products of operators. This adaptive algorithm was developed with the use of three correlated conditions, i.e., a suitable starting space, a criterion for convergence, and a procedure to expand the approximate space. The velocity of the algorithm was increased with the use of a posteriori error estimator (residue) to select the most relevant direction to increase the space. Two examples have been selected for benchmark. In the case of H2CO, we mainly study the performance of A-VCI algorithm: comparison with the variation-perturbation method, choice of the initial space, and residual contributions. For CH3CN, we compare the A-VCI results with a computed reference spectrum using the same potential energy surface and for an active space reduced by about 90%.

EEG correlates of social interaction at distance

PubMed Central

Giroldini, William; Pederzoli, Luciano; Bilucaglia, Marco; Caini, Patrizio; Ferrini, Alessandro; Melloni, Simone; Prati, Elena; Tressoldi, Patrizio

2016-01-01

This study investigated EEG correlates of social interaction at distance between twenty-five pairs of participants who were not connected by any traditional channels of communication. Each session involved the application of 128 stimulations separated by intervals of random duration ranging from 4 to 6 seconds. One of the pair received a one-second stimulation from a light signal produced by an arrangement of red LEDs, and a simultaneous 500 Hz sinusoidal audio signal of the same length. The other member of the pair sat in an isolated sound-proof room, such that any sensory interaction between the pair was impossible. An analysis of the Event-Related Potentials associated with sensory stimulation using traditional averaging methods showed a distinct peak at approximately 300 ms, but only in the EEG activity of subjects who were directly stimulated. However, when a new algorithm was applied to the EEG activity based on the correlation between signals from all active electrodes, a weak but robust response was also detected in the EEG activity of the passive member of the pair, particularly within 9 – 10 Hz in the Alpha range. Using the Bootstrap method and the Monte Carlo emulation, this signal was found to be statistically significant. PMID:26966513

Multi-hump bright solitons in a Schrödinger-mKdV system

NASA Astrophysics Data System (ADS)

Cisneros-Ake, Luis A.; Parra Prado, Hugo; López Villatoro, Diego Joselito; Carretero-González, R.

2018-03-01

We consider the problem of energy transport in a Davydov model along an anharmonic crystal medium obeying quartic longitudinal interactions corresponding to rigid interacting particles. The Zabusky and Kruskal unidirectional continuum limit of the original discrete equations reduces, in the long wave approximation, to a coupled system between the linear Schrödinger (LS) equation and the modified Korteweg-de Vries (mKdV) equation. Single- and two-hump bright soliton solutions for this LS-mKdV system are predicted to exist by variational means and numerically confirmed. The one-hump bright solitons are found to be the anharmonic supersonic analogue of the Davydov's solitons while the two-hump (in both components) bright solitons are found to be a novel type of soliton consisting of a two-soliton solution of mKdV trapped by the wave function associated to the LS equation. This two-hump soliton solution, as a two component solution, represents a new class of polaron solution to be contrasted with the two-soliton interaction phenomena from soliton theory, as revealed by a variational approach and direct numerical results for the two-soliton solution.

Binding of copper to lysozyme: Spectroscopic, isothermal titration calorimetry and molecular docking studies

NASA Astrophysics Data System (ADS)

Jing, Mingyang; Song, Wei; Liu, Rutao

2016-07-01

Although copper is essential to all living organisms, its potential toxicity to human health have aroused wide concerns. Previous studies have reported copper could alter physical properties of lysozyme. The direct binding of copper with lysozyme might induce the conformational and functional changes of lysozyme and then influence the body's resistance to bacterial attack. To better understand the potential toxicity and toxic mechanisms of copper, the interaction of copper with lysozyme was investigated by biophysical methods including multi-spectroscopic measurements, isothermal titration calorimetry (ITC), molecular docking study and enzyme activity assay. Multi-spectroscopic measurements proved that copper quenched the intrinsic fluorescence of lysozyme in a static process accompanied by complex formation and conformational changes. The ITC results indicated that the binding interaction was a spontaneous process with approximately three thermodynamical binding sites at 298 K and the hydrophobic force is the predominant driven force. The enzyme activity was obviously inhibited by the addition of copper with catalytic residues Glu 35 and Asp 52 locating at the binding sites. This study helps to elucidate the molecular mechanism of the interaction between copper and lysozyme and provides reference for toxicological studies of copper.

Anharmonicity Rise the Thermal Conductivity in Amorphous Silicon

NASA Astrophysics Data System (ADS)

Lv, Wei; Henry, Asegun

We recently proposed a new method called Direct Green-Kubo Modal Analysis (GKMA) method, which has been shown to calculate the thermal conductivity (TC) of several amorphous materials accurately. A-F method has been widely used for amorphous materials. However, researchers have found out that it failed on several different materials. The missing component of A-F method is the harmonic approximation and considering only the interactions of modes with similar frequencies, which neglect interactions of modes with large frequency difference. On the contrary, GKMA method, which is based on molecular dynamics, intrinsically includes all types of phonon interactions. In GKMA method, each mode's TC comes from both mode self-correlations (autocorrelations) and mode-mode correlations (crosscorrelations). We have demonstrated that the GKMA predicted TC of a-Si from Tersoff potential is in excellent agreement with one of experimental results. In this work, we will present the GKMA applications on a-Si using multiple potentials and gives us more insight of the effect of anharmonicity on the TC of amorphous silicon. This research was supported Intel grant AGMT DTD 1-15-13 and computational resources by NSF supported XSEDE resources under allocations DMR130105 and TG- PHY130049.

New constraints and discovery potential of sub-GeV dark matter with xenon detectors

NASA Astrophysics Data System (ADS)

McCabe, Christopher

2017-08-01

Existing xenon dark matter (DM) direct detection experiments can probe the DM-nucleon interaction of DM with a sub-GeV mass through a search for photon emission from the recoiling xenon atom. We show that LUX's constraints on sub-GeV DM, which utilize the scintillation (S1) and ionization (S2) signals, are approximately 3 orders of magnitude more stringent than previous xenon constraints in this mass range, derived from the XENON10 and XENON100 S2-only searches. The new LUX constraints provide the most stringent direct detection constraints for DM particles with a mass below 0.5 GeV. In addition, the photon emission signal in LUX and its successor LZ maintain the discrimination between background and signal events so that an unambiguous discovery of sub-GeV DM is possible. We show that LZ has the potential to reconstruct the DM mass with ≃20 % accuracy for particles lighter than 0.5 GeV.

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

Park, Jaehong; Reid, Obadiah G.; Blackburn, Jeffrey L.

The strong quantum confinement and low dielectric screening impart single-walled carbon nanotubes with exciton-binding energies substantially exceeding kBT at room temperature. Despite these large binding energies, reported photoluminescence quantum yields are typically low and some studies suggest that photoexcitation of carbon nanotube excitonic transitions can produce free charge carriers. Here we report the direct measurement of long-lived free-carrier generation in chirality-pure, single-walled carbon nanotubes in a low dielectric solvent. Time-resolved microwave conductivity enables contactless and quantitative measurement of the real and imaginary photoconductance of individually suspended nanotubes. We found that the conditions of the microwave conductivity measurement allow us tomore » avoid the complications of most previous measurements of nanotube free-carrier generation, including tube–tube/tube–electrode contact, dielectric screening by nearby excitons and many-body interactions. At low photon fluence (approximately 0.05 excitons per μm length of tubes), we directly observe free carriers on excitation of the first and second carbon nanotube exciton transitions.« less

Exploiting Bounded Signal Flow for Graph Orientation Based on Cause-Effect Pairs

NASA Astrophysics Data System (ADS)

Dorn, Britta; Hüffner, Falk; Krüger, Dominikus; Niedermeier, Rolf; Uhlmann, Johannes

We consider the following problem: Given an undirected network and a set of sender-receiver pairs, direct all edges such that the maximum number of "signal flows" defined by the pairs can be routed respecting edge directions. This problem has applications in communication networks and in understanding protein interaction based cell regulation mechanisms. Since this problem is NP-hard, research so far concentrated on polynomial-time approximation algorithms and tractable special cases. We take the viewpoint of parameterized algorithmics and examine several parameters related to the maximum signal flow over vertices or edges. We provide several fixed-parameter tractability results, and in one case a sharp complexity dichotomy between a linear-time solvable case and a slightly more general NP-hard case. We examine the value of these parameters for several real-world network instances. For many relevant cases, the NP-hard problem can be solved to optimality. In this way, parameterized analysis yields both deeper insight into the computational complexity and practical solving strategies.

Modeling boundary-layer transition in direct and large-eddy simulations using parabolized stability equations

NASA Astrophysics Data System (ADS)

Lozano-Durán, A.; Hack, M. J. P.; Moin, P.

2018-02-01

We examine the potential of the nonlinear parabolized stability equations (PSE) to provide an accurate yet computationally efficient treatment of the growth of disturbances in H-type transition to turbulence. The PSE capture the nonlinear interactions that eventually induce breakdown to turbulence and can as such identify the onset of transition without relying on empirical correlations. Since the local PSE solution at the onset of transition is a close approximation of the Navier-Stokes equations, it provides a natural inflow condition for direct numerical simulations (DNS) and large-eddy simulations (LES) by avoiding nonphysical transients. We show that a combined PSE-DNS approach, where the pretransitional region is modeled by the PSE, can reproduce the skin-friction distribution and downstream turbulent statistics from a DNS of the full domain. When the PSE are used in conjunction with wall-resolved and wall-modeled LES, the computational cost in both the laminar and turbulent regions is reduced by several orders of magnitude compared to DNS.

Photoinduced Spontaneous Free-Carrier Generation in Semiconducting Single-Walled Carbon Nanotubes

DOE PAGES

Park, Jaehong; Reid, Obadiah G.; Blackburn, Jeffrey L.; ...

2015-11-04

The strong quantum confinement and low dielectric screening impart single-walled carbon nanotubes with exciton-binding energies substantially exceeding kBT at room temperature. Despite these large binding energies, reported photoluminescence quantum yields are typically low and some studies suggest that photoexcitation of carbon nanotube excitonic transitions can produce free charge carriers. Here we report the direct measurement of long-lived free-carrier generation in chirality-pure, single-walled carbon nanotubes in a low dielectric solvent. Time-resolved microwave conductivity enables contactless and quantitative measurement of the real and imaginary photoconductance of individually suspended nanotubes. We found that the conditions of the microwave conductivity measurement allow us tomore » avoid the complications of most previous measurements of nanotube free-carrier generation, including tube–tube/tube–electrode contact, dielectric screening by nearby excitons and many-body interactions. At low photon fluence (approximately 0.05 excitons per μm length of tubes), we directly observe free carriers on excitation of the first and second carbon nanotube exciton transitions.« less

Continuous approximation for interaction energy of adamantane encapsulated inside carbon nanotubes

NASA Astrophysics Data System (ADS)

Baowan, Duangkamon; Hill, James M.; Bacsa, Wolfgang

2018-02-01

The interaction energy for two adjacent adamantane molecules and that of adamantane molecules encapsulated inside carbon nanotubes are investigated considering only dipole-dipole induced interaction. The Lennard-Jones potential and the continuous approximation are utilised to derive analytical expressions for these interaction energies. The equilibrium distance 3.281 Å between two adamantane molecules is determined. The smallest carbon nanotube radius b0 that can encapsulate the adamantane molecule and the radius of the tube bmax that gives the maximum suction energy, linearly depend on the adamantane radius, are calculated. For larger diameter tubes, the off axis position has been calculated, and equilibrium distance between molecule and tube wall is found to be close to the interlayer spacing in graphene.

21 CFR Appendix A to Subpart A of... - List of Applicable Laws, Regulations, and Administrative Provisions

Code of Federal Regulations, 2012 CFR

2012-04-01

... PRACTICE REPORTS, MEDICAL DEVICE QUALITY SYSTEM AUDIT REPORTS, AND CERTAIN MEDICAL DEVICE PRODUCT...://dg3.eudra.org.] Council Directive 65/65/EEC of 26 January 1965 on the approximation of provisions laid... extended, widened, and amended. Council Directive 75/319/EEC of 20 May 1975 on the approximation of...

21 CFR Appendix A to Subpart A of... - List of Applicable Laws, Regulations, and Administrative Provisions

Code of Federal Regulations, 2013 CFR

2013-04-01

... PRACTICE REPORTS, MEDICAL DEVICE QUALITY SYSTEM AUDIT REPORTS, AND CERTAIN MEDICAL DEVICE PRODUCT...://dg3.eudra.org.] Council Directive 65/65/EEC of 26 January 1965 on the approximation of provisions laid... extended, widened, and amended. Council Directive 75/319/EEC of 20 May 1975 on the approximation of...

21 CFR Appendix A to Subpart A of... - List of Applicable Laws, Regulations, and Administrative Provisions

Code of Federal Regulations, 2014 CFR

2014-04-01

... PRACTICE REPORTS, MEDICAL DEVICE QUALITY SYSTEM AUDIT REPORTS, AND CERTAIN MEDICAL DEVICE PRODUCT...://dg3.eudra.org.] Council Directive 65/65/EEC of 26 January 1965 on the approximation of provisions laid... extended, widened, and amended. Council Directive 75/319/EEC of 20 May 1975 on the approximation of...

21 CFR Appendix A to Subpart A of... - List of Applicable Laws, Regulations, and Administrative Provisions

Code of Federal Regulations, 2011 CFR

2011-04-01

... PRACTICE REPORTS, MEDICAL DEVICE QUALITY SYSTEM AUDIT REPORTS, AND CERTAIN MEDICAL DEVICE PRODUCT...://dg3.eudra.org.] Council Directive 65/65/EEC of 26 January 1965 on the approximation of provisions laid... extended, widened, and amended. Council Directive 75/319/EEC of 20 May 1975 on the approximation of...

The antiproliferative activity of di-2-pyridylketone dithiocarbamate is partly attributed to catalase inhibition: detailing the interaction by spectroscopic methods.

PubMed

Li, Cuiping; Liu, Youxun; Fu, Yun; Huang, Tengfei; Kang, Lixia; Li, Changzheng

2017-08-22

The bioactivity of drugs is attributed to their interaction with biological molecules, embodied in either their direct or indirect influence on enzyme activity and conformation. Di-2-pyridylketone hydrazine dithiocarbamate (DpdtC) exhibits significant antitumor activity in our preliminary study. We speculated that its activity may partly stem from enzyme inhibition due to strong metal chelating ability. To this end, we assessed its effect on catalase from erythrocytes and found evidence of inhibition, which was further confirmed by ROS determination in vivo. Thus, detailing the interaction between the agent and catalase via spectroscopic methods and molecular docking was required to obtain information on both the dynamics and thermodynamic parameters. The Lineweaver-Burk plot implied an uncompetitive pattern between DpdtC and catalase from beef liver, and IC 50 = ∼7 μM. The thermodynamic parameters from fluorescence quenching measurements indicated that DpdtC could bind to catalase with moderate affinity (K a = approximately 10 4 M -1 ). CD spectra revealed that DpdtC could significantly disrupt the secondary structure of catalase. Docking studies indicated that DpdtC bound to a flexible region of catalase, involving hydrogen bonds and salt bond; this was consistent with thermodynamic results from spectral investigations. Our data clearly showed that catalase inhibition of DpdtC was not due to direct chelation of iron from heme (killing), but through an allosteric effect. Thus, it can be concluded that the antiproliferative activity of DpdtC is partially attributed to its catalase inhibition.

Dynamics of motile phytoplankton in turbulence: Laboratory investigation of microscale patchiness

NASA Astrophysics Data System (ADS)

Crimaldi, J. P.; True, A.; Stocker, R.

2016-02-01

Phytoplankton represent the basis of oceanic life and play a critical role in biogeochemical cycles. While phytoplankton are traditionally studied in bulk, their collective impact stems from cell-level processes and interactions at the microscale. A fundamental element that determines these interactions is the small-scale spatial distribution of individual cells: this directly determines the local cell concentration and the probability that two cells contact or interact with each other. The traditional, bulk perspective on phytoplankton distributions is that turbulence acts to smear out patchiness and locally homogenizes the distributions. However, recent numerical simulations suggest that the action of turbulence on motile phytoplankton may be precisely the opposite: by biasing the swimming direction of cells through the action of viscous torques, turbulence is predicted to generate strong patchiness at small scales. Flow-mediated patch formation has been demonstrated experimentally in simple laminar flows, but has never been tested experimentally in turbulence. In this talk we report on preliminary laboratory experiments performed in a purpose-built flow facility that uses a pair of computer-controlled oscillating grids to generate approximately homogenous isotropic 3D turbulence. Turbulent flow characteristics and dissipation rates are first quantified using particle image velocimetry (PIV). Then, 2D distributions of the motile dinoflagellate Heterosigma akashiwo are imaged using planar laser-induced fluorescence (PLIF). Analysis of imaged phytoplankton distributions for patchiness is performed using a Voronoi tessellation approach. Results suggest that motile phytoplankton distributions differ from those of passive particles. Furthermore, computed values for the patch enhancement factor are shown to be roughly consistent with those of previous DNS predictions.

Polygenic variation maintained by balancing selection: pleiotropy, sex-dependent allelic effects and G x E interactions.

PubMed Central

Turelli, Michael; Barton, N H

2004-01-01

We investigate three alternative selection-based scenarios proposed to maintain polygenic variation: pleiotropic balancing selection, G x E interactions (with spatial or temporal variation in allelic effects), and sex-dependent allelic effects. Each analysis assumes an additive polygenic trait with n diallelic loci under stabilizing selection. We allow loci to have different effects and consider equilibria at which the population mean departs from the stabilizing-selection optimum. Under weak selection, each model produces essentially identical, approximate allele-frequency dynamics. Variation is maintained under pleiotropic balancing selection only at loci for which the strength of balancing selection exceeds the effective strength of stabilizing selection. In addition, for all models, polymorphism requires that the population mean be close enough to the optimum that directional selection does not overwhelm balancing selection. This balance allows many simultaneously stable equilibria, and we explore their properties numerically. Both spatial and temporal G x E can maintain variation at loci for which the coefficient of variation (across environments) of the effect of a substitution exceeds a critical value greater than one. The critical value depends on the correlation between substitution effects at different loci. For large positive correlations (e.g., rho(ij)2>3/4), even extreme fluctuations in allelic effects cannot maintain variation. Surprisingly, this constraint on correlations implies that sex-dependent allelic effects cannot maintain polygenic variation. We present numerical results that support our analytical approximations and discuss our results in connection to relevant data and alternative variance-maintaining mechanisms. PMID:15020487

Characterization of air contaminants formed by the interaction of lava and sea water.

PubMed

Kullman, G J; Jones, W G; Cornwell, R J; Parker, J E

1994-05-01

We made environmental measurements to characterize contaminants generated when basaltic lava from Hawaii's Kilauea volcano enters sea water. This interaction of lava with sea water produces large clouds of mist (LAZE). Island winds occasionally directed the LAZE toward the adjacent village of Kalapana and the Hawaii Volcanos National Park, creating health concerns. Environmental samples were taken to measure airborne concentrations of respirable dust, crystalline silica and other mineral compounds, fibers, trace metals, inorganic acids, and organic and inorganic gases. The LAZE contained quantifiable concentrations of hydrochloric acid (HCl) and hydrofluoric acid (HF); HCl was predominant. HCl and HF concentrations were highest in dense plumes of LAZE near the sea. The HCl concentration at this sampling location averaged 7.1 ppm; this exceeds the current occupational exposure ceiling of 5 ppm. HF was detected in nearly half the samples, but all concentrations were <1 ppm Sulfur dioxide was detected in one of four short-term indicator tube samples at approximately 1.5 ppm. Airborne particulates were composed largely of chloride salts (predominantly sodium chloride). Crystalline silica concentrations were below detectable limits, less than approximately 0.03 mg/m3 of air. Settled dust samples showed a predominance of glass flakes and glass fibers. Airborne fibers were detected at quantifiable levels in 1 of 11 samples. These fibers were composed largely of hydrated calcium sulfate. These findings suggest that individuals should avoid concentrated plumes of LAZE near its origin to prevent over exposure to inorganic acids, specifically HCl.

Aeroacoustic directivity via wave-packet analysis of mean or base flows

NASA Astrophysics Data System (ADS)

Edstrand, Adam; Schmid, Peter; Cattafesta, Louis

2017-11-01

Noise pollution is an ever-increasing problem in society, and knowledge of the directivity patterns of the sound radiation is required for prediction and control. Directivity is frequently determined through costly numerical simulations of the flow field combined with an acoustic analogy. We introduce a new computationally efficient method of finding directivity for a given mean or base flow field using wave-packet analysis (Trefethen, PRSA 2005). Wave-packet analysis approximates the eigenvalue spectrum with spectral accuracy by modeling the eigenfunctions as wave packets. With the wave packets determined, we then follow the method of Obrist (JFM, 2009), which uses Lighthill's acoustic analogy to determine the far-field sound radiation and directivity of wave-packet modes. We apply this method to a canonical jet flow (Gudmundsson and Colonius, JFM 2011) and determine the directivity of potentially unstable wave packets. Furthermore, we generalize the method to consider a three-dimensional flow field of a trailing vortex wake. In summary, we approximate the disturbances as wave packets and extract the directivity from the wave-packet approximation in a fraction of the time of standard aeroacoustic solvers. ONR Grant N00014-15-1-2403.

Renormalization-group theory of plasma microturbulence

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

Carati, D.; Chriaa, K.; Balescu, R.

1994-08-01

The dynamical renormalization-group methods are applied to the gyrokinetic equation describing drift-wave turbulence in plasmas. As in both magnetohydrodynamic and neutral turbulence, small-scale fluctuations appear to act as effective dissipative processes on large-scale phenomena. A linear renormalized gyrokinetic equation is derived. No artificial forcing is introduced into the equations and all the renormalized corrections are expressed in terms of the fluctuating electric potential. The link with the quasilinear limit and the direct interaction approximation is investigated. Simple analytical expressions for the anomalous transport coefficients are derived by using the linear renormalized gyrokinetic equation. Examples show that both quasilinear and Bohmmore » scalings can be recovered depending on the spectral amplitude of the electric potential fluctuations.« less

Heat Conduction in Ceramic Coatings: Relationship Between Microstructure and Effective Thermal Conductivity

NASA Technical Reports Server (NTRS)

Kachanov, Mark

1998-01-01

Analysis of the effective thermal conductivity of ceramic coatings and its relation to the microstructure continued. Results (obtained in Task 1) for the three-dimensional problem of heat conduction in a solid containing an inclusion (or, in particular, cavity - thermal insulator) of the ellipsoidal shape, were further advanced in the following two directions: (1) closed form expressions of H tensor have been derived for special cases of ellipsoidal cavity geometry: spheroid, crack-like spheroidal cavity and needle shaped spheroidal cavity; (2) these results for one cavity have been incorporated to construct heat energy potential for a solid with many spheroidal cavities (in the approximation of non-interacting defects). This problem constitutes a basic building block for further analyses.

Stochastic annealing simulations of defect interactions among subcascades

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

Heinisch, H.L.; Singh, B.N.

1997-04-01

The effects of the subcascade structure of high energy cascades on the temperature dependencies of annihilation, clustering and free defect production are investigated. The subcascade structure is simulated by closely spaced groups of lower energy MD cascades. The simulation results illustrate the strong influence of the defect configuration existing in the primary damage state on subsequent intracascade evolution. Other significant factors affecting the evolution of the defect distribution are the large differences in mobility and stability of vacancy and interstitial defects and the rapid one-dimensional diffusion of small, glissile interstitial loops produced directly in cascades. Annealing simulations are also performedmore » on high-energy, subcascade-producing cascades generated with the binary collision approximation and calibrated to MD results.« less

The Electronics and Data Acquisition System of the DarkSide Dark Matter Search

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

Agnes, P.; et al.

2014-12-09

It is generally inferred from astronomical measurements that Dark Matter (DM) comprises approximately 27\\% of the energy-density of the universe. If DM is a subatomic particle, a possible candidate is a Weakly Interacting Massive Particle (WIMP), and the DarkSide-50 (DS) experiment is a direct search for evidence of WIMP-nuclear collisions. DS is located underground at the Laboratori Nazionali del Gran Sasso (LNGS) in Italy, and consists of three active, embedded components; an outer water veto (CTF), a liquid scintillator veto (LSV), and a liquid argon (LAr) time projection chamber (TPC). This paper describes the data acquisition and electronic systems ofmore » the DS detectors, designed to detect the residual ionization from such collisions.« less

The Resolvent Algebra of Non-relativistic Bose Fields: Observables, Dynamics and States

NASA Astrophysics Data System (ADS)

Buchholz, Detlev

2018-05-01

The structure of the gauge invariant (particle number preserving) C*-algebra generated by the resolvents of a non-relativistic Bose field is analyzed. It is shown to form a dense subalgebra of the bounded inverse limit of a directed system of approximately finite dimensional C*-algebras. Based on this observation, it is proven that the closure of the gauge invariant algebra is stable under the dynamics induced by Hamiltonians involving pair potentials. These facts allow to proceed to a description of interacting Bosons in terms of C*-dynamical systems. It is outlined how the present approach leads to simplifications in the construction of infinite bosonic states and sheds new light on topics in many body theory.

Rings in above-threshold ionization: A quasiclassical analysis

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

Lewenstein, M.; Kulander, K.C.; Schafer, K.J.

1995-02-01

A generalized strong-field approximation is formulated to describe atoms interacting with intense laser fields. We apply it to determine angular distributions of electrons in above-threshold ionization (ATI). The theory treats the effects of an electron rescattering from its parent ion core in a systematic perturbation series. Probability amplitudes for ionization are interpreted in terms of quasiclassical electron trajectories. We demonstrate that contributions from the direct tunneling processes in the absence of rescattering are not sufficient to describe the observed ATI spectra. We show that the high-energy portion of the spectrum, including recently discovered rings (i.e., complex features in the angularmore » distributions of outgoing electrons) are due to rescattering processes. We compare our quasiclassical results with exact numerical solutions.« less

Some Fundamental Issues in Ground-State Density Functional Theory: A Guide for the Perplexed.

PubMed

Perdew, John P; Ruzsinszky, Adrienn; Constantin, Lucian A; Sun, Jianwei; Csonka, Gábor I

2009-04-14

Some fundamental issues in ground-state density functional theory are discussed without equations: (1) The standard Hohenberg-Kohn and Kohn-Sham theorems were proven for a Hamiltonian that is not quite exact for real atoms, molecules, and solids. (2) The density functional for the exchange-correlation energy, which must be approximated, arises from the tendency of electrons to avoid one another as they move through the electron density. (3) In the absence of a magnetic field, either spin densities or total electron density can be used, although the former choice is better for approximations. (4) "Spin contamination" of the determinant of Kohn-Sham orbitals for an open-shell system is not wrong but right. (5) Only to the extent that symmetries of the interacting wave function are reflected in the spin densities should those symmetries be respected by the Kohn-Sham noninteracting or determinantal wave function. Functionals below the highest level of approximations should however sometimes break even those symmetries, for good physical reasons. (6) Simple and commonly used semilocal (lower-level) approximations for the exchange-correlation energy as a functional of the density can be accurate for closed systems near equilibrium and yet fail for open systems of fluctuating electron number. (7) The exact Kohn-Sham noninteracting state need not be a single determinant, but common approximations can fail when it is not. (8) Over an open system of fluctuating electron number, connected to another such system by stretched bonds, semilocal approximations make the exchange-correlation energy and hole-density sum rule too negative. (9) The gap in the exact Kohn-Sham band structure of a crystal underestimates the real fundamental gap but may approximate the first exciton energy in the large-gap limit. (10) Density functional theory is not really a mean-field theory, although it looks like one. The exact functional includes strong correlation, and semilocal approximations often overestimate the strength of static correlation through their semilocal exchange contributions. (11) Only under rare conditions can excited states arise directly from a ground-state theory.

Reconstructing the direction of reactor antineutrinos via electron scattering in Gd-doped water Cherenkov detectors

DOE PAGES

Hellfeld, D.; Bernstein, A.; Dazeley, S.; ...

2017-01-01

The potential of elastic antineutrino-electron scattering (ν¯ e + e – → ν¯ e + e –) in a Gd-doped water Cherenkov detector to determine the direction of a nuclear reactor antineutrino flux was investigated using the recently proposed WATCHMAN antineutrino experiment as a baseline model. The expected scattering rate was determined assuming a 13 km standoff from a 3.758 GWt light water nuclear reactor. Background was estimated via independent simulations and by appropriately scaling published measurements from similar detectors. Many potential backgrounds were considered, including solar neutrinos, misidentified reactor-based inverse beta decay interactions, cosmogenic radionuclide and water-borne radon decays,more » and gamma rays from the photomultiplier tubes, detector walls, and surrounding rock. The detector response was modeled using a GEANT4-based simulation package. The results indicate that with the use of low radioactivity PMTs and sufficient fiducialization, water-borne radon and cosmogenic radionuclides pose the largest threats to sensitivity. The directional sensitivity was then analyzed as a function of radon contamination, detector depth, and detector size. Lastly, the results provide a list of theoretical conditions that, if satisfied in practice, would enable nuclear reactor antineutrino directionality in a Gd-doped water Cherenkov detector approximately 10 km from a large power reactor.« less

Countably QC-Approximating Posets

PubMed Central

Mao, Xuxin; Xu, Luoshan

2014-01-01

As a generalization of countably C-approximating posets, the concept of countably QC-approximating posets is introduced. With the countably QC-approximating property, some characterizations of generalized completely distributive lattices and generalized countably approximating posets are given. The main results are as follows: (1) a complete lattice is generalized completely distributive if and only if it is countably QC-approximating and weakly generalized countably approximating; (2) a poset L having countably directed joins is generalized countably approximating if and only if the lattice σ c(L)op of all σ-Scott-closed subsets of L is weakly generalized countably approximating. PMID:25165730

Empowerment of disability benefit claimants through an interactive website: design of a randomized controlled trial.

PubMed

Samoocha, David; Bruinvels, David J; Anema, Johannes R; Steenbeek, Romy; van der Beek, Allard J

2009-05-10

Individuals claiming a disability benefit after long-term sickness absence, have to undergo medical disability assessments. These assessments, often carried out by specialized physicians, can be complicated by wrong expectations or defensive attitudes of disability benefit claimants. It is hypothesized that empowerment of these claimants will enhance the physician-patient relationship by shifting claimants from a passive role to a more active and constructive role during disability assessments. Furthermore, empowerment of claimants may lead to a more realistic expectation and acceptance of the assessment outcome among claimants and may lead to a more accurate assessment by the physician. In a two-armed randomized controlled trial (RCT), 230 claimants will be randomized to either the intervention or control group. For the intervention group, an interactive website was designed http://www.wiagesprek.nl using an Intervention Mapping procedure. This website was tested during a pilot study among 51 claimants. The final version of the website consists of five interactive modules, in which claimants will be prepared and empowered step-by-step, prior to their upcoming disability assessment. Other website components are a forum, a personal health record, a personal diary, and information on disability assessment procedures, return to work, and coping with disease and work disability. Subjects from the control group will be directed to a website with commonly available information only. Approximately two weeks prior to their disability assessment, disability claimants will be recruited through the Dutch Workers Insurance Authority (UWV). Outcomes will be assessed at five occasions: directly after recruitment (baseline), prior to disability assessment, directly after disability assessment as well as 6 and 16 weeks after the assessment. The study's primary outcome is empowerment, measured with the Vrijbaan questionnaire. Secondary outcomes include claimants' satisfaction, perceived justice, coping strategy, and knowledge. A process evaluation will also be conducted. This study evaluates the effectiveness of an interactive website aimed at empowerment of disability claimants. It is hypothesized that by increasing empowerment, the physician-patient relationship may be enhanced and claimants' satisfaction and perceived justice can be improved. Results are expected in 2010. NTR-1414.

Empowerment of disability benefit claimants through an interactive website: design of a randomized controlled trial

PubMed Central

2009-01-01

Background Individuals claiming a disability benefit after long-term sickness absence, have to undergo medical disability assessments. These assessments, often carried out by specialized physicians, can be complicated by wrong expectations or defensive attitudes of disability benefit claimants. It is hypothesized that empowerment of these claimants will enhance the physician-patient relationship by shifting claimants from a passive role to a more active and constructive role during disability assessments. Furthermore, empowerment of claimants may lead to a more realistic expectation and acceptance of the assessment outcome among claimants and may lead to a more accurate assessment by the physician. Methods/Design In a two-armed randomized controlled trial (RCT), 230 claimants will be randomized to either the intervention or control group. For the intervention group, an interactive website was designed http://www.wiagesprek.nl using an Intervention Mapping procedure. This website was tested during a pilot study among 51 claimants. The final version of the website consists of five interactive modules, in which claimants will be prepared and empowered step-by-step, prior to their upcoming disability assessment. Other website components are a forum, a personal health record, a personal diary, and information on disability assessment procedures, return to work, and coping with disease and work disability. Subjects from the control group will be directed to a website with commonly available information only. Approximately two weeks prior to their disability assessment, disability claimants will be recruited through the Dutch Workers Insurance Authority (UWV). Outcomes will be assessed at five occasions: directly after recruitment (baseline), prior to disability assessment, directly after disability assessment as well as 6 and 16 weeks after the assessment. The study's primary outcome is empowerment, measured with the Vrijbaan questionnaire. Secondary outcomes include claimants' satisfaction, perceived justice, coping strategy, and knowledge. A process evaluation will also be conducted. Discussion This study evaluates the effectiveness of an interactive website aimed at empowerment of disability claimants. It is hypothesized that by increasing empowerment, the physician-patient relationship may be enhanced and claimants' satisfaction and perceived justice can be improved. Results are expected in 2010. Trial registration NTR-1414 PMID:19426557

Deformation in the Yakataga seismic gap, Southern Alaska, 1980- 1986 ( USA).

USGS Publications Warehouse

Savage, J.C.; Lisowski, M.

1988-01-01

A 60-by-40-km trilateration network in the Yakataga seismic gap was surveyed in 1980, 1982, 1984, and 1986 with precise electro-optical distance-measuring equipment to measure strain accumulation. The overall deformation is roughly approximated by a 0.24+ or -0.03 mu strain/yr N32oW+ or -2.4o uniaxial contraction that is uniform in time. However, the spatial distribution of deformation shows some concentration of convergence in the neighbourhood of the Chugach-St. Elias fault and of right-lateral shear across the Contact fault. A simple dislocation model of the plate interaction in the Yakataga gap fits the observed deformation reasonably well but seems to require that the motion of the Pacific plate relative to the North American plate be directed more nearly N36oW than N15oW, the generally accepted direction of relative motion for this location. However, the direction of plate motion inferred from the dislocation model depends upon details of the interaction at the plate boundary that may not have been modeled accurately. A nearby but smaller trilateration network at Icy Bay was surveyed in 1982, 1984, and 1986. This network spans the SW corner of the rupture zone of the 1979 St. Elias earthquake. The deformation at Icy Bay consists of left-lateral shear across a NE trending zone. The relation of this deformation to strain accumulation in the Yakataga gap, postseismic relaxation associated with the 1979 earthquake, or rebound from the unloading associated with the rapid recession of the Guyot glacier is not understood.-Authors

Molecular Model of a Quantum Dot Beyond the Constant Interaction Approximation

NASA Astrophysics Data System (ADS)

Temirov, Ruslan; Green, Matthew F. B.; Friedrich, Niklas; Leinen, Philipp; Esat, Taner; Chmielniak, Pawel; Sarwar, Sidra; Rawson, Jeff; Kögerler, Paul; Wagner, Christian; Rohlfing, Michael; Tautz, F. Stefan

2018-05-01

We present a physically intuitive model of molecular quantum dots beyond the constant interaction approximation. It accurately describes their charging behavior and allows the extraction of important molecular properties that are otherwise experimentally inaccessible. The model is applied to data recorded with a noncontact atomic force microscope on three different molecules that act as a quantum dot when attached to the microscope tip. The results are in excellent agreement with first-principles simulations.

Gravitational radiation quadrupole formula is valid for gravitationally interacting systems

NASA Technical Reports Server (NTRS)

Walker, M.; Will, C. M.

1980-01-01

An argument is presented for the validity of the quadrupole formula for gravitational radiation energy loss in the far field of nearly Newtonian (e.g., binary stellar) systems. This argument differs from earlier ones in that it determines beforehand the formal accuracy of approximation required to describe gravitationally self-interacting systems, uses the corresponding approximate equation of motion explicitly, and evaluates the appropriate asymptotic quantities by matching along the correct space-time light cones.

Self-Interaction Corrected Electronic Structure and Energy Gap of CuAlO2 beyond Local Density Approximation

NASA Astrophysics Data System (ADS)

Nakanishi, Akitaka

2011-05-01

We implemented a self-interaction correction (SIC) into first-principles calculation code to go beyond local density approximation and applied it to CuAlO2. Our simulation shows that the valence band width calculated within the SIC is narrower than that calculated without the SIC because the SIC makes the d-band potential deeper. The energy gap calculated within the SIC expands and is close to experimental data.

Certain approximation problems for functions on the infinite-dimensional torus: Lipschitz spaces

NASA Astrophysics Data System (ADS)

Platonov, S. S.

2018-02-01

We consider some questions about the approximation of functions on the infinite-dimensional torus by trigonometric polynomials. Our main results are analogues of the direct and inverse theorems in the classical theory of approximation of periodic functions and a description of the Lipschitz spaces on the infinite-dimensional torus in terms of the best approximation.

76 FR 67731 - Federal Open Market Committee; Domestic Policy Directive of September 20 and 21, 2011

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-02

..., Treasury securities with remaining maturities of approximately 6 years to 30 years with a total face value... total face value of $400 billion. The Committee also directs the Desk to maintain its existing policy of...- backed securities in order to maintain the total face value of domestic securities at approximately $2.6...

Basement-involved faults and deep structures in the West Philippine Basin: constrains from gravity field

NASA Astrophysics Data System (ADS)

Wang, Gang; Jiang, Suhua; Li, Sanzhong; Zhang, Huixuan; Lei, Jianping; Gao, Song; Zhao, Feiyu

2017-06-01

To reveal the basement-involved faults and deep structures of the West Philippine Basin (WPB), the gravitational responses caused by these faults are observed and analyzed based on the latest spherical gravity model: WGM2012 Model. By mapping the free-air and Bouguer gravity anomalies, several main faults and some other linear structures are located and observed in the WPB. Then, by conducting a 2D discrete multi-scale wavelet decomposition, the Bouguer anomalies are decomposed into the first- to eighth-order detail and approximation fields (the first- to eighth-order Details and Approximations). The first- to third-order Details reflect detailed and localized geological information of the crust at different depths, and of which the higher-order reflects gravity field of the deeper depth. The first- to fourth-order Approximations represent the regional gravity fields at different depths of the crust, respectively. The fourth-order Approximation represents the regional gravity fluctuation caused by the density inhomogeneity of Moho interface. Therefore, taking the fourth-order Approximation as input, and adopting Parker-Oldenburg interactive inversion, We calculated the depth of Moho interface in the WPB. Results show that the Moho interface depth in the WPB ranges approximately from 8 to 12 km, indicating that there is typical oceanic crust in the basin. In the Urdaneta Plateau and the Benham Rise, the Moho interface depths are about 14 and 16 km, respectively, which provides a piece of evidence to support that the Banham Rise could be a transitional crust caused by a large igneous province. The second-order vertical derivative and the horizontal derivatives in direction 0° and 90° are computed based on the data of the third-order Detail, and most of the basement-involved faults and structures in the WPB, such as the Central Basin Fault Zone, the Gagua Ridge, the Luzon-Okinawa Fault Zone, and the Mindanao Fault Zone are interpreted by the gravity derivatives.

Training direct care staff to increase positive interactions with individuals with developmental disabilities.

PubMed

Zoder-Martell, Kimberly A; Dufrene, Brad A; Tingstrom, Daniel H; Olmi, D Joe; Jordan, Sara S; Biskie, Erika M; Sherman, Julie C

2014-09-01

This study tested the effects of direct training on direct care staff's initiation of positive interactions with individuals with developmental disabilities who resided in an intermediate care facility. Participants included four direct care staff and their residents. Direct training included real-time prompts delivered via a one-way radio, and data were collected for immediate and sustained increases in rates of direct care staff's positive interactions. Additionally, this study evaluated the link between increased rates of positive interactions and concomitant decreases in residents' challenging behaviors. A multiple baseline design across participants was used and results indicated that all direct care staff increased their rates of positive interactions during direct training. Moreover, all but one participant continued to engage residents in positive interactions at levels above the criterion during the maintenance phase and follow-up phases. The direct care staff member who did not initially meet the criterion improved to adequate levels following one brief performance feedback session. With regard to residents' challenging behaviors, across phases, residents engaged in low levels of challenging behaviors making those results difficult to evaluate. However, improvements in residents' rate of positive interactions were noted. Copyright © 2014 Elsevier Ltd. All rights reserved.

The acetate switch.

PubMed

Wolfe, Alan J

2005-03-01

To succeed, many cells must alternate between life-styles that permit rapid growth in the presence of abundant nutrients and ones that enhance survival in the absence of those nutrients. One such change in life-style, the "acetate switch," occurs as cells deplete their environment of acetate-producing carbon sources and begin to rely on their ability to scavenge for acetate. This review explains why, when, and how cells excrete or dissimilate acetate. The central components of the "switch" (phosphotransacetylase [PTA], acetate kinase [ACK], and AMP-forming acetyl coenzyme A synthetase [AMP-ACS]) and the behavior of cells that lack these components are introduced. Acetyl phosphate (acetyl approximately P), the high-energy intermediate of acetate dissimilation, is discussed, and conditions that influence its intracellular concentration are described. Evidence is provided that acetyl approximately P influences cellular processes from organelle biogenesis to cell cycle regulation and from biofilm development to pathogenesis. The merits of each mechanism proposed to explain the interaction of acetyl approximately P with two-component signal transduction pathways are addressed. A short list of enzymes that generate acetyl approximately P by PTA-ACKA-independent mechanisms is introduced and discussed briefly. Attention is then directed to the mechanisms used by cells to "flip the switch," the induction and activation of the acetate-scavenging AMP-ACS. First, evidence is presented that nucleoid proteins orchestrate a progression of distinct nucleoprotein complexes to ensure proper transcription of its gene. Next, the way in which cells regulate AMP-ACS activity through reversible acetylation is described. Finally, the "acetate switch" as it exists in selected eubacteria, archaea, and eukaryotes, including humans, is described.

Birth/birth-death processes and their computable transition probabilities with biological applications.

PubMed

Ho, Lam Si Tung; Xu, Jason; Crawford, Forrest W; Minin, Vladimir N; Suchard, Marc A

2018-03-01

Birth-death processes track the size of a univariate population, but many biological systems involve interaction between populations, necessitating models for two or more populations simultaneously. A lack of efficient methods for evaluating finite-time transition probabilities of bivariate processes, however, has restricted statistical inference in these models. Researchers rely on computationally expensive methods such as matrix exponentiation or Monte Carlo approximation, restricting likelihood-based inference to small systems, or indirect methods such as approximate Bayesian computation. In this paper, we introduce the birth/birth-death process, a tractable bivariate extension of the birth-death process, where rates are allowed to be nonlinear. We develop an efficient algorithm to calculate its transition probabilities using a continued fraction representation of their Laplace transforms. Next, we identify several exemplary models arising in molecular epidemiology, macro-parasite evolution, and infectious disease modeling that fall within this class, and demonstrate advantages of our proposed method over existing approaches to inference in these models. Notably, the ubiquitous stochastic susceptible-infectious-removed (SIR) model falls within this class, and we emphasize that computable transition probabilities newly enable direct inference of parameters in the SIR model. We also propose a very fast method for approximating the transition probabilities under the SIR model via a novel branching process simplification, and compare it to the continued fraction representation method with application to the 17th century plague in Eyam. Although the two methods produce similar maximum a posteriori estimates, the branching process approximation fails to capture the correlation structure in the joint posterior distribution.

Efficient evaluation of the material response of tissues reinforced by statistically oriented fibres

NASA Astrophysics Data System (ADS)

Hashlamoun, Kotaybah; Grillo, Alfio; Federico, Salvatore

2016-10-01

For several classes of soft biological tissues, modelling complexity is in part due to the arrangement of the collagen fibres. In general, the arrangement of the fibres can be described by defining, at each point in the tissue, the structure tensor (i.e. the tensor product of the unit vector of the local fibre arrangement by itself) and a probability distribution of orientation. In this approach, assuming that the fibres do not interact with each other, the overall contribution of the collagen fibres to a given mechanical property of the tissue can be estimated by means of an averaging integral of the constitutive function describing the mechanical property at study over the set of all possible directions in space. Except for the particular case of fibre constitutive functions that are polynomial in the transversely isotropic invariants of the deformation, the averaging integral cannot be evaluated directly, in a single calculation because, in general, the integrand depends both on deformation and on fibre orientation in a non-separable way. The problem is thus, in a sense, analogous to that of solving the integral of a function of two variables, which cannot be split up into the product of two functions, each depending only on one of the variables. Although numerical schemes can be used to evaluate the integral at each deformation increment, this is computationally expensive. With the purpose of containing computational costs, this work proposes approximation methods that are based on the direct integrability of polynomial functions and that do not require the step-by-step evaluation of the averaging integrals. Three different methods are proposed: (a) a Taylor expansion of the fibre constitutive function in the transversely isotropic invariants of the deformation; (b) a Taylor expansion of the fibre constitutive function in the structure tensor; (c) for the case of a fibre constitutive function having a polynomial argument, an approximation in which the directional average of the constitutive function is replaced by the constitutive function evaluated at the directional average of the argument. Each of the proposed methods approximates the averaged constitutive function in such a way that it is multiplicatively decomposed into the product of a function of the deformation only and a function of the structure tensors only. In order to assess the accuracy of these methods, we evaluate the constitutive functions of the elastic potential and the Cauchy stress, for a biaxial test, under different conditions, i.e. different fibre distributions and different ratios of the nominal strains in the two directions. The results are then compared against those obtained for an averaging method available in the literature, as well as against the integration made at each increment of deformation.

Optical-model potential for electron and positron elastic scattering by atoms

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

Salvat, Francesc

2003-07-01

An optical-model potential for systematic calculations of elastic scattering of electrons and positrons by atoms and positive ions is proposed. The electrostatic interaction is determined from the Dirac-Hartree-Fock self-consistent atomic electron density. In the case of electron projectiles, the exchange interaction is described by means of the local-approximation of Furness and McCarthy. The correlation-polarization potential is obtained by combining the correlation potential derived from the local density approximation with a long-range polarization interaction, which is represented by means of a Buckingham potential with an empirical energy-dependent cutoff parameter. The absorption potential is obtained from the local-density approximation, using the Born-Ochkurmore » approximation and the Lindhard dielectric function to describe the binary collisions with a free-electron gas. The strength of the absorption potential is adjusted by means of an empirical parameter, which has been determined by fitting available absolute elastic differential cross-section data for noble gases and mercury. The Dirac partial-wave analysis with this optical-model potential provides a realistic description of elastic scattering of electrons and positrons with energies in the range from {approx}100 eV up to {approx}5 keV. At higher energies, correlation-polarization and absorption corrections are small and the usual static-exchange approximation is sufficiently accurate for most practical purposes.« less

Reduced-rank approximations to the far-field transform in the gridded fast multipole method

NASA Astrophysics Data System (ADS)

Hesford, Andrew J.; Waag, Robert C.

2011-05-01

The fast multipole method (FMM) has been shown to have a reduced computational dependence on the size of finest-level groups of elements when the elements are positioned on a regular grid and FFT convolution is used to represent neighboring interactions. However, transformations between plane-wave expansions used for FMM interactions and pressure distributions used for neighboring interactions remain significant contributors to the cost of FMM computations when finest-level groups are large. The transformation operators, which are forward and inverse Fourier transforms with the wave space confined to the unit sphere, are smooth and well approximated using reduced-rank decompositions that further reduce the computational dependence of the FMM on finest-level group size. The adaptive cross approximation (ACA) is selected to represent the forward and adjoint far-field transformation operators required by the FMM. However, the actual error of the ACA is found to be greater than that predicted using traditional estimates, and the ACA generally performs worse than the approximation resulting from a truncated singular-value decomposition (SVD). To overcome these issues while avoiding the cost of a full-scale SVD, the ACA is employed with more stringent accuracy demands and recompressed using a reduced, truncated SVD. The results show a greatly reduced approximation error that performs comparably to the full-scale truncated SVD without degrading the asymptotic computational efficiency associated with ACA matrix assembly.

Reduced-Rank Approximations to the Far-Field Transform in the Gridded Fast Multipole Method.

PubMed

Hesford, Andrew J; Waag, Robert C

2011-05-10

The fast multipole method (FMM) has been shown to have a reduced computational dependence on the size of finest-level groups of elements when the elements are positioned on a regular grid and FFT convolution is used to represent neighboring interactions. However, transformations between plane-wave expansions used for FMM interactions and pressure distributions used for neighboring interactions remain significant contributors to the cost of FMM computations when finest-level groups are large. The transformation operators, which are forward and inverse Fourier transforms with the wave space confined to the unit sphere, are smooth and well approximated using reduced-rank decompositions that further reduce the computational dependence of the FMM on finest-level group size. The adaptive cross approximation (ACA) is selected to represent the forward and adjoint far-field transformation operators required by the FMM. However, the actual error of the ACA is found to be greater than that predicted using traditional estimates, and the ACA generally performs worse than the approximation resulting from a truncated singular-value decomposition (SVD). To overcome these issues while avoiding the cost of a full-scale SVD, the ACA is employed with more stringent accuracy demands and recompressed using a reduced, truncated SVD. The results show a greatly reduced approximation error that performs comparably to the full-scale truncated SVD without degrading the asymptotic computational efficiency associated with ACA matrix assembly.

Reduced-Rank Approximations to the Far-Field Transform in the Gridded Fast Multipole Method

PubMed Central

Hesford, Andrew J.; Waag, Robert C.

2011-01-01

The fast multipole method (FMM) has been shown to have a reduced computational dependence on the size of finest-level groups of elements when the elements are positioned on a regular grid and FFT convolution is used to represent neighboring interactions. However, transformations between plane-wave expansions used for FMM interactions and pressure distributions used for neighboring interactions remain significant contributors to the cost of FMM computations when finest-level groups are large. The transformation operators, which are forward and inverse Fourier transforms with the wave space confined to the unit sphere, are smooth and well approximated using reduced-rank decompositions that further reduce the computational dependence of the FMM on finest-level group size. The adaptive cross approximation (ACA) is selected to represent the forward and adjoint far-field transformation operators required by the FMM. However, the actual error of the ACA is found to be greater than that predicted using traditional estimates, and the ACA generally performs worse than the approximation resulting from a truncated singular-value decomposition (SVD). To overcome these issues while avoiding the cost of a full-scale SVD, the ACA is employed with more stringent accuracy demands and recompressed using a reduced, truncated SVD. The results show a greatly reduced approximation error that performs comparably to the full-scale truncated SVD without degrading the asymptotic computational efficiency associated with ACA matrix assembly. PMID:21552350

Fractal structure of the interplanetary magnetic field

NASA Technical Reports Server (NTRS)

Burlaga, L. F.; Klein, L. W.

1985-01-01

Under some conditions, time series of the interplanetary magnetic field strength and components have the properties of fractal curves. Magnetic field measurements made near 8.5 AU by Voyager 2 from June 5 to August 24, 1981 were self-similar over time scales from approximately 20 sec to approximately 3 x 100,000 sec, and the fractal dimension of the time series of the strength and components of the magnetic field was D = 5/3, corresponding to a power spectrum P(f) approximately f sup -5/3. Since the Kolmogorov spectrum for homogeneous, isotropic, stationary turbulence is also f sup -5/3, the Voyager 2 measurements are consistent with the observation of an inertial range of turbulence extending over approximately four decades in frequency. Interaction regions probably contributed most of the power in this interval. As an example, one interaction region is discussed in which the magnetic field had a fractal dimension D = 5/3.

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

Plant resources and colony growth in an invasive ant: the importance of honeydew-producing Hemiptera in carbohydrate transfer across trophic levels.

PubMed

Helms, Ken R; Vinson, S Bradleigh

2008-04-01

Studies have suggested that plant-based nutritional resources are important in promoting high densities of omnivorous and invasive ants, but there have been no direct tests of the effects of these resources on colony productivity. We conducted an experiment designed to determine the relative importance of plants and honeydew-producing insects feeding on plants to the growth of colonies of the invasive ant Solenopsis invicta (Buren). We found that colonies of S. invicta grew substantially when they only had access to unlimited insect prey; however, colonies that also had access to plants colonized by honeydew-producing Hemiptera grew significantly and substantially ( approximately 50%) larger. Our experiment also showed that S. invicta was unable to acquire significant nutritional resources directly from the Hemiptera host plant but acquired them indirectly from honeydew. Honeydew alone is unlikely to be sufficient for colony growth, however, and both carbohydrates abundant in plants and proteins abundant in animals are likely to be necessary for optimal growth. Our experiment provides important insight into the effects of a common tritrophic interaction among an invasive mealybug, Antonina graminis (Maskell), an invasive host grass, Cynodon dactylon L. Pers., and S. invicta in the southeastern United States, suggesting that interactions among these species can be important in promoting extremely high population densities of S. invicta.

Looking for dark matter trails in colliding galaxy clusters

NASA Astrophysics Data System (ADS)

Harvey, David; Robertson, Andrew; Massey, Richard; Kneib, Jean-Paul

2017-02-01

If dark matter interacts, even weakly, via non-gravitational forces, simulations predict that it will be preferentially scattered towards the trailing edge of the halo during collisions between galaxy clusters. This will temporarily create a non-symmetric mass profile, with a trailing overdensity along the direction of motion. To test this hypothesis, we fit (and subtract) symmetric haloes to the weak gravitational data of 72 merging galaxy clusters observed with the Hubble Space Telescope. We convert the shear directly into excess κ and project in to a one-dimensional profile. We generate numerical simulations and find that the one-dimensional profile is well described with simple Gaussian approximations. We detect the weak lensing signal of trailing gas at a 4σ confidence, finding a mean gas fraction of Mgas/Mdm = 0.13 ± 0.035. We find no evidence for scattered dark matter particles with an estimated scattering fraction of f = 0.03 ± 0.05. Finally, we find that if we can reduce the statistical error on the positional estimate of a single dark matter halo to <2.5 arcsec, then we will be able to detect a scattering fraction of 10 per cent at the 3σ level with current surveys. This potentially interesting new method can provide an important independent test for other complimentary studies of the self-interaction cross-section of dark matter.

The yeast kinesin-5 Cin8 interacts with the microtubule in a noncanonical manner

PubMed Central

Bell, Kayla M.; Cha, Hyo Keun; Sindelar, Charles V.; Cochran, Jared C.

2017-01-01

Kinesin motors play central roles in establishing and maintaining the mitotic spindle during cell division. Unlike most other kinesins, Cin8, a kinesin-5 motor in Saccharomyces cerevisiae, can move bidirectionally along microtubules, switching directionality according to biochemical conditions, a behavior that remains largely unexplained. To this end, we used biochemical rate and equilibrium constant measurements as well as cryo-electron microscopy methodologies to investigate the microtubule interactions of the Cin8 motor domain. These experiments unexpectedly revealed that, whereas Cin8 ATPase kinetics fell within measured ranges for kinesins (especially kinesin-5 proteins), approximately four motors can bind each αβ-tubulin dimer within the microtubule lattice. This result contrasted with those observations on other known kinesins, which can bind only a single “canonical” site per tubulin dimer. Competition assays with human kinesin-5 (Eg5) only partially abrogated this behavior, indicating that Cin8 binds microtubules not only at the canonical site, but also one or more separate (“noncanonical”) sites. Moreover, we found that deleting the large, class-specific insert in the microtubule-binding loop 8 reverts Cin8 to one motor per αβ-tubulin in the microtubule. The novel microtubule-binding mode of Cin8 identified here provides a potential explanation for Cin8 clustering along microtubules and potentially may contribute to the mechanism for direction reversal. PMID:28701465

Self-interaction effects on charge-transfer collisions

DOE PAGES

Quashie, Edwin E.; Saha, Bidhan C.; Andrade, Xavier; ...

2017-04-27

In this article, we investigate the role of the self-interaction error in the simulation of collisions using time-dependent density functional theory (TDDFT) and Ehrenfest dynamics. In addition, we compare many different approximations of the exchange and correlation potential, using as a test system the collision of H + + CH 4 at 30 eV. We find that semilocal approximations, like the Perdew-Burke- Ernzerhof (PBE), and even hybrid functionals, such as the Becke, 3-parameter, Lee-Yang-Parr (B3LYP), produce qualitatively incorrect predictions for the scattering of the proton. This discrepancy appears because the self-interaction error allows the electrons to jump too easily tomore » the proton, leading to radically different forces with respect to the non-self-interacting case. Lastly, from our results, we conclude that using a functional that is self-interaction free is essential to properly describing charge-transfer collisions between ions and molecules in TDDFT.« less

Final state interactions and the transverse structure of the pion using non-perturbative eikonal methods

DOE PAGES

Gamberg, Leonard; Schlegel, Marc

2010-01-18

In the factorized picture of semi-inclusive hadronic processes the naive time reversal-odd parton distributions exist by virtue of the gauge link which renders it color gauge invariant. The link characterizes the dynamical effect of initial/final-state interactions of the active parton due soft gluon exchanges with the target remnant. Though these interactions are non-perturbative, studies of final-state interaction have been approximated by perturbative one-gluon approximation in Abelian models. We include higher-order contributions by applying non-perturbative eikonal methods incorporating color degrees of freedom in a calculation of the Boer-Mulders function of the pion. Lastly, using this framework we explore under what conditionsmore » the Boer Mulders function can be described in terms of factorization of final state interactions and a spatial distribution in impact parameter space.« less

Brownian dynamics simulations of a flexible polymer chain which includes continuous resistance and multibody hydrodynamic interactions

NASA Astrophysics Data System (ADS)

Butler, Jason E.; Shaqfeh, Eric S. G.

2005-01-01

Using methods adapted from the simulation of suspension dynamics, we have developed a Brownian dynamics algorithm with multibody hydrodynamic interactions for simulating the dynamics of polymer molecules. The polymer molecule is modeled as a chain composed of a series of inextensible, rigid rods with constraints at each joint to ensure continuity of the chain. The linear and rotational velocities of each segment of the polymer chain are described by the slender-body theory of Batchelor [J. Fluid Mech. 44, 419 (1970)]. To include hydrodynamic interactions between the segments of the chain, the line distribution of forces on each segment is approximated by making a Legendre polynomial expansion of the disturbance velocity on the segment, where the first two terms of the expansion are retained in the calculation. Thus, the resulting linear force distribution is specified by a center of mass force, couple, and stresslet on each segment. This method for calculating the hydrodynamic interactions has been successfully used to simulate the dynamics of noncolloidal suspensions of rigid fibers [O. G. Harlen, R. R. Sundararajakumar, and D. L. Koch, J. Fluid Mech. 388, 355 (1999); J. E. Butler and E. S. G. Shaqfeh, J. Fluid Mech. 468, 204 (2002)]. The longest relaxation time and center of mass diffusivity are among the quantities calculated with the simulation technique. Comparisons are made for different levels of approximation of the hydrodynamic interactions, including multibody interactions, two-body interactions, and the "freely draining" case with no interactions. For the short polymer chains studied in this paper, the results indicate a difference in the apparent scaling of diffusivity with polymer length for the multibody versus two-body level of approximation for the hydrodynamic interactions.

Brownian dynamics simulations of a flexible polymer chain which includes continuous resistance and multibody hydrodynamic interactions.

PubMed

Butler, Jason E; Shaqfeh, Eric S G

2005-01-01

Using methods adapted from the simulation of suspension dynamics, we have developed a Brownian dynamics algorithm with multibody hydrodynamic interactions for simulating the dynamics of polymer molecules. The polymer molecule is modeled as a chain composed of a series of inextensible, rigid rods with constraints at each joint to ensure continuity of the chain. The linear and rotational velocities of each segment of the polymer chain are described by the slender-body theory of Batchelor [J. Fluid Mech. 44, 419 (1970)]. To include hydrodynamic interactions between the segments of the chain, the line distribution of forces on each segment is approximated by making a Legendre polynomial expansion of the disturbance velocity on the segment, where the first two terms of the expansion are retained in the calculation. Thus, the resulting linear force distribution is specified by a center of mass force, couple, and stresslet on each segment. This method for calculating the hydrodynamic interactions has been successfully used to simulate the dynamics of noncolloidal suspensions of rigid fibers [O. G. Harlen, R. R. Sundararajakumar, and D. L. Koch, J. Fluid Mech. 388, 355 (1999); J. E. Butler and E. S. G. Shaqfeh, J. Fluid Mech. 468, 204 (2002)]. The longest relaxation time and center of mass diffusivity are among the quantities calculated with the simulation technique. Comparisons are made for different levels of approximation of the hydrodynamic interactions, including multibody interactions, two-body interactions, and the "freely draining" case with no interactions. For the short polymer chains studied in this paper, the results indicate a difference in the apparent scaling of diffusivity with polymer length for the multibody versus two-body level of approximation for the hydrodynamic interactions. (c) 2005 American Institute of Physics.

Effective Forces Between Colloidal Particles

NASA Technical Reports Server (NTRS)

Tehver, Riina; Banavar, Jayanth R.; Koplik, Joel

1999-01-01

Colloidal suspensions have proven to be excellent model systems for the study of condensed matter and its phase behavior. Many of the properties of colloidal suspensions can be investigated with a systematic variation of the characteristics of the systems and, in addition, the energy, length and time scales associated with them allow for experimental probing of otherwise inaccessible regimes. The latter property also makes colloidal systems vulnerable to external influences such as gravity. Experiments performed in micro-ravity by Chaikin and Russell have been invaluable in extracting the true behavior of the systems without an external field. Weitz and Pusey intend to use mixtures of colloidal particles with additives such as polymers to induce aggregation and form weak, tenuous, highly disordered fractal structures that would be stable in the absence of gravitational forces. When dispersed in a polarizable medium, colloidal particles can ionize, emitting counterions into the solution. The standard interaction potential in these charged colloidal suspensions was first obtained by Derjaguin, Landau, Verwey and Overbeek. The DLVO potential is obtained in the mean-field linearized Poisson-Boltzmann approximation and thus has limited applicability. For more precise calculations, we have used ab initio density functional theory. In our model, colloidal particles are charged hard spheres, the counterions are described by a continuum density field and the solvent is treated as a homogeneous medium with a specified dielectric constant. We calculate the effective forces between charged colloidal particles by integrating over the solvent and counterion degrees of freedom, taking into account the direct interactions between the particles as well as particle-counterion, counterion-counterion Coulomb, counterion entropic and correlation contributions. We obtain the effective interaction potential between charged colloidal particles in different configurations. We evaluate two- and three-body forces in the bulk as well as study the influence of soft walls. We qualitatively explain the effects of the walls on the forces and demonstrate that many-body effects are negligible in our system. With adjustments in the parameters, the DLVO pair-potential can describe the results quantitatively. Besides electrostatic interactions, entropic depletion effects that arise from (hard-core) exclusion play an important role in determining the behavior of multi-component colloidal suspensions. A standard theory for depletion forces is due to Asakura and Oosawa and is based on the ideal gas approximation. To go beyond this approximation, we have studied entropic forces in molecular dynamics simulations of systems of hard spheres (the effects of the solvent have been ignored). The effective depletion forces for these systems can be found either from equilibrium distribution functions or from direct momentum transfer calculations. Our results obtained by either method show qualitative differences from the Asakura-Oosawa forces, indicating a longer range, higher value at contact and most importantly a more complicated structure, comprising of several maxima and minima. Our calculations include the determination of effective forces between two spheres, a hard sphere and a wall, and the behavior of a hard sphere near a step-edge and a corner. We also demonstrate that such entropic forces do not necessarily satisfy pairwise additivity.

Realizing various approximate quantum cloning with XY-type exchange interactions of flux qubits

NASA Astrophysics Data System (ADS)

Li, Na; Ye, Liu

2014-03-01

In this paper, we realize all kinds of 1 → 2 approximate quantum cloning, including optimal 1 → 2 symmetric (or asymmetric) universal quantum cloning (UQC) and phase-covariant cloning (PCC), symmetric economical phase-covariant cloning (EPCC) and real state quantum cloning, with the XY-type exchange interactions of the flux qubits which are coupled by dc superconducting quantum interference devices (SQUIDs). It is shown that our schemes can be realized with the current experimental technology.

Analysis of cholera toxin-ganglioside interactions by flow cytometry.

PubMed

Lauer, Sabine; Goldstein, Byron; Nolan, Rhiannon L; Nolan, John P

2002-02-12

Cholera toxin entry into mammalian cells is mediated by binding of the pentameric B subunit (CTB) to ganglioside GM(1) in the cell membrane. We used flow cytometry to quantitatively measure in real time the interactions of fluorescently labeled pentameric cholera toxin B-subunit (FITC-CTB) with its ganglioside receptor on microsphere-supported phospholipid membranes. A model that describes the multiple steps of this mode of recognition was developed to guide our flow cytometric experiments and extract relevant equilibrium and kinetic rate constants. In contrast to previous studies, our approach takes into account receptor cross-linking, an important feature for multivalent interactions. From equilibrium measurements, we determined an equilibrium binding constant for a single subunit of FITC-CTB binding monovalently to GM(1) presented in bilayers of approximately 8 x 10(7) M(-1) while that for binding to soluble GM(1)-pentasaccharide was found to be approximately 4 x 10(6) M(-1). From kinetic measurements, we determined the rate constant for dissociation of a single site of FITC-CTB from microsphere-supported bilayers to be (3.21 +/- 0.03) x 10(-3) s(-1), and the rate of association of a site on FITC-CTB in solution to a GM(1) in the bilayer to be (2.8 +/- 0.4) x 10(4) M(-1) s(-1). These values yield a lower estimate for the equilibrium binding constant of approximately 1 x 10(7) M(-1). We determined the equilibrium surface cross-linking constant [(1.1 +/- 0.1) x 10(-12) cm(2)] and from this value and the value for the rate constant for dissociation derived a value of approximately 3.5 x 10(-15) cm(2) s(-1) for the forward rate constant for cross-linking. We also compared the interaction of the receptor binding B-subunit with that of the whole toxin (A- and B-subunits). Our results show that the whole toxin binds with approximately 100-fold higher avidity than the pentameric B-subunit alone which is most likely due to the additional interaction of the A(2)-subunit with the membrane surface. Interaction of cholera toxin B-subunit and whole cholera toxin with gangliosides other than GM(1) revealed specific binding only to GD1(b) and asialo-GM(1). These interactions, however, are marked by low avidity and require high receptor concentrations to be observed.

Community-level demographic consequences of urbanization: an ecological network approach.

PubMed

Rodewald, Amanda D; Rohr, Rudolf P; Fortuna, Miguel A; Bascompte, Jordi

2014-11-01

Ecological networks are known to influence ecosystem attributes, but we poorly understand how interspecific network structure affect population demography of multiple species, particularly for vertebrates. Establishing the link between network structure and demography is at the crux of being able to use networks to understand population dynamics and to inform conservation. We addressed the critical but unanswered question, does network structure explain demographic consequences of urbanization? We studied 141 ecological networks representing interactions between plants and nesting birds in forests across an urbanization gradient in Ohio, USA, from 2001 to 2011. Nest predators were identified by video-recording nests and surveyed from 2004 to 2011. As landscapes urbanized, bird-plant networks were more nested, less compartmentalized and dominated by strong interactions between a few species (i.e. low evenness). Evenness of interaction strengths promoted avian nest survival, and evenness explained demography better than urbanization, level of invasion, numbers of predators or other qualitative network metrics. Highly uneven networks had approximately half the nesting success as the most even networks. Thus, nest survival reflected how urbanization altered species interactions, particularly with respect to how nest placement affected search efficiency of predators. The demographic effects of urbanization were not direct, but were filtered through bird-plant networks. This study illustrates how network structure can influence demography at the community level and further, that knowledge of species interactions and a network approach may be requisite to understanding demographic responses to environmental change. © 2014 The Authors. Journal of Animal Ecology © 2014 British Ecological Society.

Influence of dipolar interactions on the angular-dependent coercivity of nickel nanocylinders

NASA Astrophysics Data System (ADS)

Bender, P.; Krämer, F.; Tschöpe, A.; Birringer, R.

2015-04-01

In this study the influence of dipolar interactions on the orientation-dependent magnetization behavior of an ensemble of single-domain nickel nanorods was investigated. The rods were synthesized by electrodeposition of nickel into porous alumina templates. Some of the rods were released from the oxide and embedded in gelatine hydrogels (ferrogel) at a sufficiently large average interparticle distance to suppress dipolar interactions. By comparing the orientation-dependent hystereses of the two ensembles in the template and the gel-matrix it could be shown that the dipolar interactions in the template considerably alter the functional form of the angular-dependent coercivity. Analysis of the magnetization curves for an angle of 60° between the rod-axes and the field revealed a significantly reduced coercivity of the template compared to the ferrogel, which could be directly attributed to a stray field induced magnetization reversal of a steadily increasing number of rods with increasing field strength. The magnetization curve of the template could be approximated by a weighted linear superposition of the hysteresis branches of the ferrogel. The magnetization reversal process of the rods was investigated by analyzing the angular-dependent coercivity of the non-interacting nanorods. Comparison of the functional form with analytical models and micromagnetic simulations emphasized the assumption of a localized magnetization reversal. Additionally, it could be shown that the nucleation field of rods with diameters in the range 18-29 nm tends to increase with increasing diameter.

Demonstration of an X-Band Multilayer Yagi-Like Microstrip Patch Antenna With High Directivity and Large Bandwidth

NASA Technical Reports Server (NTRS)

Nessel, James A.; Zaman, Afroz; Lee, Richard Q.; Lambert, Kevin

2005-01-01

The feasibility of obtaining large bandwidth and high directivity from a multilayer Yagi-like microstrip patch antenna at 10 GHz is investigated. A measured 10-dB bandwidth of approximately 20 percent and directivity of approximately 11 dBi is demonstrated through the implementation of a vertically-stacked structure with three parasitic directors, above the driven patch, and a single reflector underneath the driven patch. Simulated and measured results are compared and show fairly close agreement. This antenna offers the advantages of large bandwidth, high directivity, and symmetrical broadside patterns, and could be applicable to satellite as well as terrestrial communications.

Small scale variability of snow properties on Antarctic sea ice

NASA Astrophysics Data System (ADS)

Wever, Nander; Leonard, Katherine; Paul, Stephan; Jacobi, Hans-Werner; Proksch, Martin; Lehning, Michael

2016-04-01

Snow on sea ice plays an important role in air-ice-sea interactions, as snow accumulation may for example increase the albedo. Snow is also able to smooth the ice surface, thereby reducing the surface roughness, while at the same time it may generate new roughness elements by interactions with the wind. Snow density is a key property in many processes, for example by influencing the thermal conductivity of the snow layer, radiative transfer inside the snow as well as the effects of aerodynamic forcing on the snowpack. By comparing snow density and grain size from snow pits and snow micro penetrometer (SMP) measurements, highly resolved density and grain size profiles were acquired during two subsequent cruises of the RV Polarstern in the Weddell Sea, Antarctica, between June and October 2013. During the first cruise, SMP measurements were done along two approximately 40 m transects with a horizontal resolution of approximately 30 cm. During the second cruise, one transect was made with approximately 7.5 m resolution over a distance of 500 m. Average snow densities are about 300 kg/m3, but the analysis also reveals a high spatial variability in snow density on sea ice in both horizontal and vertical direction, ranging from roughly 180 to 360 kg/m3. This variability is expressed by coherent snow structures over several meters. On the first cruise, the measurements were accompanied by terrestrial laser scanning (TLS) on an area of 50x50 m2. The comparison with the TLS data indicates that the spatial variability is exhibiting similar spatial patterns as deviations in surface topology. This suggests a strong influence from surface processes, for example wind, on the temporal development of density or grain size profiles. The fundamental relationship between variations in snow properties, surface roughness and changes therein as investigated in this study is interpreted with respect to large-scale ice movement and the mass balance.

Citric Acid Enhanced Copper Removal by a Novel Multi-amines Decorated Resin

PubMed Central

Ling, Chen; Liu, Fuqiang; Pei, Zhiguo; Zhang, Xiaopeng; Wei, Mengmeng; Zhang, Yanhong; Zheng, Lirong; Zhang, Jing; Li, Aimin; Xing, Baoshan

2015-01-01

Cu removal by a novel multi-amines decorated resin (PAMD) from wastewater in the absence or presence of citric acid (CA) was examined. Adsorption capacity of Cu onto PAMD markedly increased by 186% to 5.07 mmol/g in the presence of CA, up to 7 times of that onto four commercial resins under the same conditions. Preloaded and kinetic studies demonstrated adsorption of [Cu-CA] complex instead of CA site-bridging and variations of adsorbate species were qualitatively illustrated. The interaction configuration was further studied with ESI-MS, FTIR, XPS and XANES characterizations. The large enhancement of Cu adsorption in Cu-CA bi-solutes systems was attributed to mechanism change from single-site to dual-sites interaction in which cationic or neutral Cu species (Cu2+ and CuHL0) coordinated with neutral amine sites and anionic complex species (CuL− and Cu2L22−) directly interacted with protonated amine sites via electrostatic attraction, and the ratio of the two interactions was approximately 0.5 for the equimolar bi-solutes system. Moreover, commonly coexisting ions in wastewaters had no obvious effect on the superior performance of PAMD. Also, Cu and CA could be recovered completely with HCl. Therefore, PAMD has a great potential to efficiently remove heavy metal ions from wastewaters in the presence of organic acids. PMID:25962970

Interaction of viscous and inviscid instability modes in separation-bubble transition

NASA Astrophysics Data System (ADS)

Brinkerhoff, Joshua R.; Yaras, Metin I.

2011-12-01

This paper describes numerical simulations that are used to examine the interaction of viscous and inviscid instability modes in laminar-to-turbulent transition in a separation bubble. The results of a direct numerical simulation are presented in which separation of a laminar boundary-layer occurs in the presence of an adverse streamwise pressure gradient. The simulation is performed at low freestream-turbulence levels and at a flow Reynolds number and pressure distribution approximating those typically encountered on the suction side of low-pressure turbine blades in a gas-turbine engine. The simulation results reveal the development of a viscous instability upstream of the point of separation which produces streamwise-oriented vortices in the attached laminar boundary layer. These vortices remain embedded in the flow downstream of separation and are carried into the separated shear layer, where they are amplified by the local adverse pressure-gradient and contribute to the formation of coherent hairpin-like vortices. A strong interaction is observed between these vortices and the inviscid instability that typically dominates the shear layer in the separated zone. The interaction is noted to determine the spanwise extent of the vortical flow structures that periodically shed from the downstream end of the separated shear layer. The structure of the shed vortical flow structures is examined and compared with the coherent structures typically observed within turbulent boundary layers.

Direct evidence for dominant bond-directional interactions in a honeycomb lattice iridate Na 2IrO 3

DOE PAGES

Hwan Chun, Sae; Kim, Jong-Woo; Kim, Jungho; ...

2015-05-11

We show that heisenberg interactions are ubiquitous in magnetic materials and play a central role in modelling and designing quantum magnets. Bond-directional interactions offer a novel alternative to Heisenberg exchange and provide the building blocks of the Kitaev model, which has a quantum spin liquid as its exact ground state. Honeycomb iridates, A 2IrO 3 (A = Na, Li), offer potential realizations of the Kitaev magnetic exchange coupling, and their reported magnetic behaviour may be interpreted within the Kitaev framework. However, the extent of their relevance to the Kitaev model remains unclear, as evidence for bond-directional interactions has so farmore » been indirect. Here we present direct evidence for dominant bond-directional interactions in antiferromagnetic Na 2IrO 3 and show that they lead to strong magnetic frustration. Diffuse magnetic X-ray scattering reveals broken spin-rotational symmetry even above the Néel temperature, with the three spin components exhibiting short-range correlations along distinct crystallographic directions. Lastly, this spin- and real-space entanglement directly uncovers the bond-directional nature of these interactions, thus providing a direct connection between honeycomb iridates and Kitaev physics.« less

Layer Formation On Metal Surfaces In Lead-Bismuth At High Temperatures In Presence Of Zirconium

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

Loewen, Eric Paul; Yount, Hannah J.; Volk, Kevin

If the operating temperature lead–bismuth cooled fission reactor could be extended to 800 °C, they could produce hydrogen directly from water. A key issue for the deployment of this technology at these temperatures is the corrosion of the fuel cladding and structural materials by the lead–bismuth. Corrosion studies of several metals were performed to correlate the interaction layer formation rate as a function of time, temperature, and alloy compositions. The interaction layer is defined as the narrow band between the alloy substrate and the solidified lead–bismuth eutectic on the surface. Coupons of HT-9, 410, 316L, and F22 were tested atmore » 550 and 650 °C for 1000 h inside a zirconium corrosion cell. The oxygen potential ranged from approximately 10-22 to 10-19 Pa. Analyses were performed on the coupons to determine the depth of the interaction layer and the composition, at each time step (100, 300, and 1000 h). The thickness of the interaction layer on F22 at 550 °C was 25.3 µm, the highest of all the alloys tested, whereas at 650 °C, the layer thickness was only 5.6 µm, the lowest of all the alloys tested. The growth of the interaction layer on F22 at 650 °C was suppressed, owing to the presence of Zr (at 1500 wppm) in the LBE. In the case of 316L, the interaction layers of 4.9 and 10.6 µm were formed at 550 and 650 °C, respectively.« less

Validity of the two-level approximation in the interaction of few-cycle light pulses with atoms

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

Cheng Jing; Zhou Jianying

2003-04-01

The validity of the two-level approximation (TLA) in the interaction of atoms with few-cycle light pulses is studied by investigating a simple (V)-type three-level atom model. Even the transition frequency between the ground state and the third level is far away from the spectrum of the pulse; this additional transition can make the TLA inaccuracy. For a sufficiently large transition frequency or a weak coupling between the ground state and the third level, the TLA is a reasonable approximation and can be used safely. When decreasing the pulse width or increasing the pulse area, the TLA will give rise tomore » non-negligible errors compared with the precise results.« less

Validity of the two-level approximation in the interaction of few-cycle light pulses with atoms

NASA Astrophysics Data System (ADS)

Cheng, Jing; Zhou, Jianying

2003-04-01

The validity of the two-level approximation (TLA) in the interaction of atoms with few-cycle light pulses is studied by investigating a simple V-type three-level atom model. Even the transition frequency between the ground state and the third level is far away from the spectrum of the pulse; this additional transition can make the TLA inaccuracy. For a sufficiently large transition frequency or a weak coupling between the ground state and the third level, the TLA is a reasonable approximation and can be used safely. When decreasing the pulse width or increasing the pulse area, the TLA will give rise to non-negligible errors compared with the precise results.

27 CFR 9.129 - Arroyo Grande Valley.

Code of Federal Regulations, 2014 CFR

2014-04-01

... boundary proceeds approximately 0.1 mile, in a northwesterly direction, along the roadway of State Route... Manuela land grant; (2) Then northwesterly, approximately 1.5 miles, along Printz Road to its intersection with Noyes Road in the Santa Manuela land grant; (3) Then northerly, approximately 1.5 miles, along...

27 CFR 9.139 - Santa Lucia Highlands.

Code of Federal Regulations, 2014 CFR

2014-04-01

... boundary follows Limekiln Creek for approximately 1.25 miles northeast to the 100 foot elevation. (2) Then following the 100 foot contour in a southeasterly direction for approximately 1 mile, where the boundary... approximately 6.50 miles, to the point where the 160 foot elevation crosses River Road. (6) Then following River...

27 CFR 9.139 - Santa Lucia Highlands.

Code of Federal Regulations, 2012 CFR

2012-04-01

... boundary follows Limekiln Creek for approximately 1.25 miles northeast to the 100 foot elevation. (2) Then following the 100 foot contour in a southeasterly direction for approximately 1 mile, where the boundary... approximately 6.50 miles, to the point where the 160 foot elevation crosses River Road. (6) Then following River...

27 CFR 9.139 - Santa Lucia Highlands.

Code of Federal Regulations, 2013 CFR

2013-04-01

... boundary follows Limekiln Creek for approximately 1.25 miles northeast to the 100 foot elevation. (2) Then following the 100 foot contour in a southeasterly direction for approximately 1 mile, where the boundary... approximately 6.50 miles, to the point where the 160 foot elevation crosses River Road. (6) Then following River...

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.

DNA-DNA interaction beyond the ground state

NASA Astrophysics Data System (ADS)

Lee, D. J.; Wynveen, A.; Kornyshev, A. A.

2004-11-01

The electrostatic interaction potential between DNA duplexes in solution is a basis for the statistical mechanics of columnar DNA assemblies. It may also play an important role in recombination of homologous genes. We develop a theory of this interaction that includes thermal torsional fluctuations of DNA using field-theoretical methods and Monte Carlo simulations. The theory extends and rationalizes the earlier suggested variational approach which was developed in the context of a ground state theory of interaction of nonhomologous duplexes. It shows that the heuristic variational theory is equivalent to the Hartree self-consistent field approximation. By comparison of the Hartree approximation with an exact solution based on the QM analogy of path integrals, as well as Monte Carlo simulations, we show that this easily analytically-tractable approximation works very well in most cases. Thermal fluctuations do not remove the ability of DNA molecules to attract each other at favorable azimuthal conformations, neither do they wash out the possibility of electrostatic “snap-shot” recognition of homologous sequences, considered earlier on the basis of ground state calculations. At short distances DNA molecules undergo a “torsional alignment transition,” which is first order for nonhomologous DNA and weaker order for homologous sequences.

Ray-theory approach to electrical-double-layer interactions.

PubMed

Schnitzer, Ory

2015-02-01

A novel approach is presented for analyzing the double-layer interaction force between charged particles in electrolyte solution, in the limit where the Debye length is small compared with both interparticle separation and particle size. The method, developed here for two planar convex particles of otherwise arbitrary geometry, yields a simple asymptotic approximation limited to neither small zeta potentials nor the "close-proximity" assumption underlying Derjaguin's approximation. Starting from the nonlinear Poisson-Boltzmann formulation, boundary-layer solutions describing the thin diffuse-charge layers are asymptotically matched to a WKBJ expansion valid in the bulk, where the potential is exponentially small. The latter expansion describes the bulk potential as superposed contributions conveyed by "rays" emanating normally from the boundary layers. On a special curve generated by the centers of all circles maximally inscribed between the two particles, the bulk stress-associated with the ray contributions interacting nonlinearly-decays exponentially with distance from the center of the smallest of these circles. The force is then obtained by integrating the traction along this curve using Laplace's method. We illustrate the usefulness of our theory by comparing it, alongside Derjaguin's approximation, with numerical simulations in the case of two parallel cylinders at low potentials. By combining our result and Derjaguin's approximation, the interaction force is provided at arbitrary interparticle separations. Our theory can be generalized to arbitrary three-dimensional geometries, nonideal electrolyte models, and other physical scenarios where exponentially decaying fields give rise to forces.

Interplanetary and Geomagnetic Consequences of Interacting CMEs of 13 - 14 June 2012

NASA Astrophysics Data System (ADS)

Srivastava, Nandita; Mishra, Wageesh; Chakrabarty, D.

2018-01-01

We report on the kinematics of two interacting CMEs observed on 13 and 14 June 2012. The two CMEs originated from the same active region NOAA 11504. After their launches which were separated by several hours, they were observed to interact at a distance of 100 R_{⊙} from the Sun. The interaction led to a moderate geomagnetic storm at the Earth with minimum D_{st} index of approximately -86 nT. The kinematics of the two CMEs is estimated using data from the Sun Earth Connection Coronal and Heliospheric Investigation (SECCHI) instrument onboard the Solar Terrestrial Relations Observatory (STEREO). Assuming a head-on collision scenario, we find that the collision is inelastic in nature. Further, the signatures of their interaction are examined using the in situ observations obtained by Wind and the Advance Composition Explorer (ACE) spacecraft. It is also found that this interaction event led to the strongest sudden storm commencement (SSC) ({≈ }150 nT) of the present Solar Cycle 24. The SSC was of long duration, approximately 20 hours. The role of interacting CMEs in enhancing the geoeffectiveness is examined.

Accelerated solution of discrete ordinates approximation to the Boltzmann transport equation via model reduction

DOE PAGES

Tencer, John; Carlberg, Kevin; Larsen, Marvin; ...

2017-06-17

Radiation heat transfer is an important phenomenon in many physical systems of practical interest. When participating media is important, the radiative transfer equation (RTE) must be solved for the radiative intensity as a function of location, time, direction, and wavelength. In many heat-transfer applications, a quasi-steady assumption is valid, thereby removing time dependence. The dependence on wavelength is often treated through a weighted sum of gray gases (WSGG) approach. The discrete ordinates method (DOM) is one of the most common methods for approximating the angular (i.e., directional) dependence. The DOM exactly solves for the radiative intensity for a finite numbermore » of discrete ordinate directions and computes approximations to integrals over the angular space using a quadrature rule; the chosen ordinate directions correspond to the nodes of this quadrature rule. This paper applies a projection-based model-reduction approach to make high-order quadrature computationally feasible for the DOM for purely absorbing applications. First, the proposed approach constructs a reduced basis from (high-fidelity) solutions of the radiative intensity computed at a relatively small number of ordinate directions. Then, the method computes inexpensive approximations of the radiative intensity at the (remaining) quadrature points of a high-order quadrature using a reduced-order model constructed from the reduced basis. Finally, this results in a much more accurate solution than might have been achieved using only the ordinate directions used to compute the reduced basis. One- and three-dimensional test problems highlight the efficiency of the proposed method.« less

Accelerated solution of discrete ordinates approximation to the Boltzmann transport equation via model reduction

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

Tencer, John; Carlberg, Kevin; Larsen, Marvin

Radiation heat transfer is an important phenomenon in many physical systems of practical interest. When participating media is important, the radiative transfer equation (RTE) must be solved for the radiative intensity as a function of location, time, direction, and wavelength. In many heat-transfer applications, a quasi-steady assumption is valid, thereby removing time dependence. The dependence on wavelength is often treated through a weighted sum of gray gases (WSGG) approach. The discrete ordinates method (DOM) is one of the most common methods for approximating the angular (i.e., directional) dependence. The DOM exactly solves for the radiative intensity for a finite numbermore » of discrete ordinate directions and computes approximations to integrals over the angular space using a quadrature rule; the chosen ordinate directions correspond to the nodes of this quadrature rule. This paper applies a projection-based model-reduction approach to make high-order quadrature computationally feasible for the DOM for purely absorbing applications. First, the proposed approach constructs a reduced basis from (high-fidelity) solutions of the radiative intensity computed at a relatively small number of ordinate directions. Then, the method computes inexpensive approximations of the radiative intensity at the (remaining) quadrature points of a high-order quadrature using a reduced-order model constructed from the reduced basis. Finally, this results in a much more accurate solution than might have been achieved using only the ordinate directions used to compute the reduced basis. One- and three-dimensional test problems highlight the efficiency of the proposed method.« less

Comparative In Situ Measurements of Plasma Instabilities in the Equatorial and Auroral Electrojets

NASA Technical Reports Server (NTRS)

Pfaff, Robert F.

2008-01-01

This presentation provides a comparison of in situ measurements of plasma instabilities gathered by rocket-borne probes in the equatorial and auroral electrojets. Specifically, using detailed measurements of the DC electric fields, current density, and plasma number density within the unstable daytime equatorial electrojet from Brazil (Guara Campaign) and in the auroral electrojet from Sweden (ERRIS Campaign), we present comparative observations and general conclusions regarding the observed physical properties of Farley-Buneman two-stream waves and large scale, gradient drift waves. The two stream observations reveal coherent-like waves propagating near the E x B direction but at reduced speeds (nearer to the presumed acoustic velocity) with wavelengths of approximately 5-10m in both the equatorial and auroral electrojet, as measured using the spaced-receiver technique. The auroral electrojet data generally shows extensions to shorter wavelengths, in concert with the fact that these waves are driven harder. With respect to gradient-drift driven waves, observations of this instability are much more pronounced in the equatorial electrojet, given the more favorable geometry for growth provided by the vertical gradient and horizontal magnetic field lines. We present new analysis of Guara rocket observations of electric field and plasma density data that reveal considerable structuring in the middle and lower portion of the electrojet (90-105 km) where the ambient plasma density gradient is unstable. Although the electric field amplitudes are largest (approximately 10-15 mV/m) in the zonal direction, considerable structure (approximately 5-10 mV/m) is also observed in the vertical electric field component as well, implying that the dominant large scale waves involve significant vertical interaction and coupling within the narrow altitude range where they are observed. Furthermore, a detailed examination of the phase of the waveforms show that on some, but not all occasions, locally enhanced eastward fields are associated with locally enhanced upwards (polarization) electric fields. The measurements are discussed in terms of theories involving the non-linear evolution and structuring of plasma waves.

AOFA- THREE-DIMENSIONAL SUPERSONIC VISCOUS FLOW

NASA Technical Reports Server (NTRS)

Rakich, J. V.

1994-01-01

This program, which is called 'AOFA', determines the complete viscous and inviscid flow around a body of revolution at a given angle of attack and traveling at supersonic speeds. The viscous calculations from this program agree with experimental values for surface and pitot pressures and with surface heating rates. At high speeds, lee-side flows are important because the local heating is difficult to correlate and because the shed vortices can interact with vehicle components such as a canopy or a vertical tail. This program should find application in the design analysis of any high speed vehicle. Lee-side flows are difficult to calculate because thin-boundary-layer theory is not applicable and the concept of matching inviscid and viscous flow is questionable. This program uses the parabolic approximation to the compressible Navier-Stokes equations and solves for the complete inviscid and viscous regions of flow, including the pressure. The parabolic approximation results from the assumption that the stress derivatives in the streamwise direction are small in comparison with derivatives in the normal and circumferential directions. This assumption permits the equation to be solved by an implicit finite difference marching technique which proceeds downstream from the initial data point, provided the inviscid portion of flow is supersonic. The viscous cross-flow separation is also determined as part of the solution. To use this method it is necessary to first determine an initial data point in a region where the inviscid portion of the flow is supersonic. Input to this program consists of two parts. Problem description is conveyed to the program by namelist input. Initial data is acquired by the program as formatted data. Because of the large amount of run time this program can consume the program includes a restart capability. Output is in printed format and magnetic tape for further processing. This program is written in FORTRAN IV and has been implemented on a CDC 7600 with a central memory requirement of approximately 35K (octal) of 60 bit words.

Electron-Phonon and Electron-Electron Interactions in Individual Suspended Carbon Nanotubes

NASA Astrophysics Data System (ADS)

Cronin, Stephen

2010-03-01

The fabrication of pristine, nearly defect-free, suspended carbon nanotubes (CNTs) enables the observation of several phenomena not seen before in carbon nanotubes, including breakdown of the Born-Oppenheimer approximation^1, mode selective electron-phonon coupling^2, and a Mott insulator transition^3. Raman spectroscopy of these nanotubes under applied gate and bias potentials reveals exceptionally strong electron-phonon coupling, arising from Kohn anomalies, which result in mode selective electron-phonon coupling, negative differential conductance (NDC), and non-equilibrium phonon populations^2,4. Due to the extremely long electron lifetimes, we observe a breakdown of the Born-Oppenheimer approximation, as deduced from the gate voltage-induced changes in the vibrational energies of suspended carbon nanotubes^1. We also report strikingly large variations in the Raman intensity of pristine metallic CNTs in response to gate voltages, which are attributed to a Mott insulating state of the strongly correlated electrons^3. As will be shown, preparing clean, defect-free devices is an essential prerequisite for studying the rich low-dimensional physics of CNTs. (1.) Bushmaker, A.W., Deshpande, V.V., Hsieh, S., Bockrath, M.W., and Cronin, S.B., ``Direct Observation of Born-Oppenheimer Approximation Breakdown in Carbon Nanotubes.'' Nano Letters, 9, 607 (2009). (2.) Bushmaker, A.W., Deshpande, V.V., Bockrath, M.W., and Cronin, S.B., ``Direct Observation of Mode Selective Electron-Phonon Coupling in Suspended Carbon Nanotubes.'' Nano Letters, 7, 3618 (2007) (3.) Bushmaker, A.W., Deshpande, V.V., Hsieh, S., Bockrath, M.W., and Cronin, S.B., ``Large Modulations in the Intensity of Raman-Scattered Light from Pristine Carbon Nanotubes.'' Physical Review Letters, 103, 067401 (2009). (4.) Bushmaker, A.W., Deshpande, V.V., Hsieh, S., Bockrath, M.W., and Cronin, S.B., ``Gate Voltage Controlled Non-Equilibrium and Non-Ohmic Behavior in Suspended Carbon Nanotubes.'' Nano Letters, 9, 2862 (2009)

Metaphor, Metonymy, and Their Interaction in the Production of Semantic Approximations by Monolingual Children: A Corpus Analysis

ERIC Educational Resources Information Center

Pérez-Hernández, Lorena; Duvignau, Karine

2016-01-01

The present study looks into the largely unexplored territory of the cognitive underpinnings of semantic approximations in child language. The analysis of a corpus of 233 semantic approximations produced by 101 monolingual French-speaking children from 1;8 to 4;2 years of age leads to a classification of a significant number of them as instances…

Spectroscopic accuracy directly from quantum chemistry: application to ground and excited states of beryllium dimer.

PubMed

Sharma, Sandeep; Yanai, Takeshi; Booth, George H; Umrigar, C J; Chan, Garnet Kin-Lic

2014-03-14

We combine explicit correlation via the canonical transcorrelation approach with the density matrix renormalization group and initiator full configuration interaction quantum Monte Carlo methods to compute a near-exact beryllium dimer curve, without the use of composite methods. In particular, our direct density matrix renormalization group calculations produce a well-depth of D(e) = 931.2 cm(-1) which agrees very well with recent experimentally derived estimates D(e) = 929.7±2 cm(-1) [J. M. Merritt, V. E. Bondybey, and M. C. Heaven, Science 324, 1548 (2009)] and D(e) = 934.6 cm(-1) [K. Patkowski, V. Špirko, and K. Szalewicz, Science 326, 1382 (2009)], as well the best composite theoretical estimates, D(e) = 938±15 cm(-1) [K. Patkowski, R. Podeszwa, and K. Szalewicz, J. Phys. Chem. A 111, 12822 (2007)] and D(e) = 935.1±10 cm(-1) [J. Koput, Phys. Chem. Chem. Phys. 13, 20311 (2011)]. Our results suggest possible inaccuracies in the functional form of the potential used at shorter bond lengths to fit the experimental data [J. M. Merritt, V. E. Bondybey, and M. C. Heaven, Science 324, 1548 (2009)]. With the density matrix renormalization group we also compute near-exact vertical excitation energies at the equilibrium geometry. These provide non-trivial benchmarks for quantum chemical methods for excited states, and illustrate the surprisingly large error that remains for 1 ¹Σ(g)⁻ state with approximate multi-reference configuration interaction and equation-of-motion coupled cluster methods. Overall, we demonstrate that explicitly correlated density matrix renormalization group and initiator full configuration interaction quantum Monte Carlo methods allow us to fully converge to the basis set and correlation limit of the non-relativistic Schrödinger equation in small molecules.

The Dynamical Mean Field Study of Competition between Ferromagnetism and Disorder in Ferromagnetic Semiconductors

NASA Astrophysics Data System (ADS)

Aryanpour, Karan

2003-03-01

We employ the Dynamical Mean Field Approximation (DMFA) to study the Janko-Zarand model [1] for the combination of large spin-orbit coupling and spatial disorder effects in GaAs doped with Mn. In this model the electronic dispersion and the spin-orbit coupling are simultaneously diagonalized and therefore, the Hamiltonian for the pure system takes a surprisingly simple form. The price for this simplicity is that the quantization axis for the spin must be rotated along the direction of momentum. This chiral basis greatly complicates the form of the hole-impurity interaction at a single site i. In the DMFA, since all the crossing Feynman diagrams for the hole-impurity interaction vanish, the problem simplifies to the local diagrams for the holes scattering off of a single Mn impurity site only. The diagrammatics for the self-energy reduces to the local Green functions and potentials in the non-chiral basis in which they have very simple forms. We first calculate the initial green function G(k) in the chiral basis and then rotate G(k) back into the non chiral basis and coarse grain it over all the k momenta. The hole-impurity interaction is greatly simplified in the non-chiral basis and can be averaged over all the spin configurations and orientations of the Mn atoms on the lattice.The self energy may be extracted from the averaged Green function, and used to recalculate the initial cluster Green function, etc. completing the DMFA self-consistent loop. We intend to calculate the spin and charge transport coefficients, and spectra such as the AC susceptibility and the ARPES which may be directly compared with experiment. [1] Phys. Rev. Lett.89,047201/1-4 (2002)

Thermal states of neutron stars with a consistent model of interior

NASA Astrophysics Data System (ADS)

Fortin, M.; Taranto, G.; Burgio, G. F.; Haensel, P.; Schulze, H.-J.; Zdunik, J. L.

2018-04-01

We model the thermal states of both isolated neutron stars and accreting neutron stars in X-ray transients in quiescence and confront them with observations. We use an equation of state calculated using realistic two-body and three-body nucleon interactions, and superfluid nucleon gaps obtained using the same microscopic approach in the BCS approximation. Consistency with low-luminosity accreting neutron stars is obtained, as the direct Urca process is operating in neutron stars with mass larger than 1.1 M⊙ for the employed equation of state. In addition, proton superfluidity and sufficiently weak neutron superfluidity, obtained using a scaling factor for the gaps, are necessary to explain the cooling of middle-aged neutron stars and to obtain a realistic distribution of neutron star masses.

A simple molecular orbital treatment of current distributions in quantum transport through molecular junctions

NASA Astrophysics Data System (ADS)

Jhan, Sin-Mu; Jin, Bih-Yaw

2017-11-01

A simple molecular orbital treatment of local current distributions inside single molecular junctions is developed in this paper. Using the first-order perturbation theory and nonequilibrium Green's function techniques in the framework of Hückel theory, we show that the leading contributions to local current distributions are directly proportional to the off-diagonal elements of transition density matrices. Under the orbital approximation, the major contributions to local currents come from a few dominant molecular orbital pairs which are mixed by the interactions between the molecule and electrodes. A few simple molecular junctions consisting of single- and multi-ring conjugated systems are used to demonstrate that local current distributions inside molecular junctions can be decomposed by partial sums of a few leading contributing transition density matrices.

Vectorlike fermions and Higgs effective field theory revisited

DOE PAGES

Chen, Chien-Yi; Dawson, S.; Furlan, Elisabetta

2017-07-10

Heavy vectorlike quarks (VLQs) appear in many models of beyond the Standard Model physics. Direct experimental searches require these new quarks to be heavy, ≳ 800 – 1000 GeV . Here, we perform a global fit of the parameters of simple VLQ models in minimal representations of S U ( 2 ) L to precision data and Higgs rates. One interesting connection between anomalous Z bmore » $$\\bar{b}$$ interactions and Higgs physics in VLQ models is discussed. Finally, we present our analysis in an effective field theory (EFT) framework and show that the parameters of VLQ models are already highly constrained. Exact and approximate analytical formulas for the S and T parameters in the VLQ models we consider are available in the Supplemental Material as Mathematica files.« less

Quantum Effects at a Proton Relaxation at Low Temperatures

NASA Astrophysics Data System (ADS)

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

2016-11-01

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

Rapid calculation method for Frenkel-type two-exciton states in one to three dimensions

NASA Astrophysics Data System (ADS)

Ajiki, Hiroshi

2014-07-01

Biexciton and two-exciton dissociated states of Frenkel-type excitons are well described by a tight-binding model with a nearest-neighbor approximation. Such two-exciton states in a finite-size lattice are usually calculated by numerical diagonalization of the Hamiltonian, which requires an increasing amount of computational time and memory as the lattice size increases. I develop here a rapid, memory-saving method to calculate the energies and wave functions of two-exciton states by employing a bisection method. In addition, an attractive interaction between two excitons in the tight-binding model can be obtained directly so that the biexciton energy agrees with the observed energy, without the need for the trial-and-error procedure implemented in the numerical diagonalization method.

Three-dimensional Image Reconstruction in J-PET Using Filtered Back-projection Method

NASA Astrophysics Data System (ADS)

Shopa, R. Y.; Klimaszewski, K.; Kowalski, P.; Krzemień, W.; Raczyński, L.; Wiślicki, W.; Białas, P.; Curceanu, C.; Czerwiński, E.; Dulski, K.; Gajos, A.; Głowacz, B.; Gorgol, M.; Hiesmayr, B.; Jasińska, B.; Kisielewska-Kamińska, D.; Korcyl, G.; Kozik, T.; Krawczyk, N.; Kubicz, E.; Mohammed, M.; Pawlik-Niedźwiecka, M.; Niedźwiecki, S.; Pałka, M.; Rudy, Z.; Sharma, N. G.; Sharma, S.; Silarski, M.; Skurzok, M.; Wieczorek, A.; Zgardzińska, B.; Zieliński, M.; Moskal, P.

We present a method and preliminary results of the image reconstruction in the Jagiellonian PET tomograph. Using GATE (Geant4 Application for Tomographic Emission), interactions of the 511 keV photons with a cylindrical detector were generated. Pairs of such photons, flying back-to-back, originate from e+e- annihilations inside a 1-mm spherical source. Spatial and temporal coordinates of hits were smeared using experimental resolutions of the detector. We incorporated the algorithm of the 3D Filtered Back Projection, implemented in the STIR and TomoPy software packages, which differ in approximation methods. Consistent results for the Point Spread Functions of ~5/7,mm and ~9/20, mm were obtained, using STIR, for transverse and longitudinal directions, respectively, with no time of flight information included.

Single-ion hydration thermodynamics from clusters to bulk solutions: Recent insights from molecular modeling

DOE PAGES

Vlcek, Lukas; Chialvo, Ariel A.

2016-01-03

The importance of single-ion hydration thermodynamic properties for understanding the driving forces of aqueous electrolyte processes, along with the impossibility of their direct experimental measurement, have prompted a large number of experimental, theoretical, and computational studies aimed at separating the cation and anion contributions. Here we provide an overview of historical approaches based on extrathermodynamic assumptions and more recent computational studies of single-ion hydration in order to evaluate the approximations involved in these methods, quantify their accuracy, reliability, and limitations in the light of the latest developments. Finally, we also offer new insights into the factors that influence the accuracymore » of ion–water interaction models and our views on possible ways to fill this substantial knowledge gap in aqueous physical chemistry.« less

Empirical study on social groups in pedestrian evacuation dynamics

NASA Astrophysics Data System (ADS)

von Krüchten, Cornelia; Schadschneider, Andreas

2017-06-01

Pedestrian crowds often include social groups, i.e. pedestrians that walk together because of social relationships. They show characteristic configurations and influence the dynamics of the entire crowd. In order to investigate the impact of social groups on evacuations we performed an empirical study with pupils. Several evacuation runs with groups of different sizes and different interactions were performed. New group parameters are introduced which allow to describe the dynamics of the groups and the configuration of the group members quantitatively. The analysis shows a possible decrease of evacuation times for large groups due to self-ordering effects. Social groups can be approximated as ellipses that orientate along their direction of motion. Furthermore, explicitly cooperative behaviour among group members leads to a stronger aggregation of group members and an intermittent way of evacuation.

Observations of electron phase-space holes driven during magnetic reconnection in a laboratory plasma

NASA Astrophysics Data System (ADS)

Fox, W.; Porkolab, M.; Egedal, J.; Katz, N.; Le, A.

2012-03-01

This work presents detailed experimental observations of electron phase-space holes driven during magnetic reconnection events on the Versatile Toroidal Facility. The holes are observed to travel on the order of or faster than the electron thermal speed, and are of large size scale, with diameter of order 60 Debye lengths. In addition, they have 3D spheroidal structure with approximately unity aspect ratio. We estimate the direct anomalous resistivity due to ion interaction with the holes and find it to be too small to affect the reconnection rate; however, the holes may play a role in reining in a tail of accelerated electrons and they indicate the presence of other processes in the reconnection layer, such as electron energization and electron beam formation.

Estimation of conformational entropy in protein-ligand interactions: a computational perspective.

PubMed

Polyansky, Anton A; Zubac, Ruben; Zagrovic, Bojan

2012-01-01

Conformational entropy is an important component of the change in free energy upon binding of a ligand to its target protein. As a consequence, development of computational techniques for reliable estimation of conformational entropies is currently receiving an increased level of attention in the context of computational drug design. Here, we review the most commonly used techniques for conformational entropy estimation from classical molecular dynamics simulations. Although by-and-large still not directly used in practical drug design, these techniques provide a golden standard for developing other, computationally less-demanding methods for such applications, in addition to furthering our understanding of protein-ligand interactions in general. In particular, we focus on the quasi-harmonic approximation and discuss different approaches that can be used to go beyond it, most notably, when it comes to treating anharmonic and/or correlated motions. In addition to reviewing basic theoretical formalisms, we provide a concrete set of steps required to successfully calculate conformational entropy from molecular dynamics simulations, as well as discuss a number of practical issues that may arise in such calculations.

Numerical investigation of the dynamics of Janus magnetic particles in a rotating magnetic field

NASA Astrophysics Data System (ADS)

Kim, Hui Eun; Kim, Kyoungbeom; Ma, Tae Yeong; Kang, Tae Gon

2017-02-01

We investigated the rotational dynamics of Janus magnetic particles suspended in a viscous liquid, in the presence of an externally applied rotating magnetic field. A previously developed two-dimensional direct simulation method, based on the finite element method and a fictitious domain method, is employed to solve the magnetic particulate flow. As for the magnetic problem, the two Maxwell equations are converted to a differential equation using the magnetic potential. The magnetic forces acting on the particles are treated by a Maxwell stress tensor formulation, enabling us to consider the magnetic interactions among the particles without any approximation. The dynamics of a single particle in the rotating field is studied to elucidate the effect of the Mason number and the magnetic susceptibility on the particle motions. Then, we extended our interest to a two-particle problem, focusing on the effect of the initial configuration of the particles on the particle motions. In three-particle interaction problems, the particle dynamics and the fluid flow induced by the particle motions are significantly affected by the particle configuration and the orientation of each particle.

CDK1 Is a Synthetic Lethal Target for KRAS Mutant Tumours

PubMed Central

Costa-Cabral, Sara; Brough, Rachel; Konde, Asha; Aarts, Marieke; Campbell, James; Marinari, Eliana; Riffell, Jenna; Bardelli, Alberto; Torrance, Christopher; Lord, Christopher J.; Ashworth, Alan

2016-01-01

Activating KRAS mutations are found in approximately 20% of human cancers but no RAS-directed therapies are currently available. Here we describe a novel, robust, KRAS synthetic lethal interaction with the cyclin dependent kinase, CDK1. This was discovered using parallel siRNA screens in KRAS mutant and wild type colorectal isogenic tumour cells and subsequently validated in a genetically diverse panel of 26 colorectal and pancreatic tumour cell models. This established that the KRAS/CDK1 synthetic lethality applies in tumour cells with either amino acid position 12 (p.G12V, pG12D, p.G12S) or amino acid position 13 (p.G13D) KRAS mutations and can also be replicated in vivo in a xenograft model using a small molecule CDK1 inhibitor. Mechanistically, CDK1 inhibition caused a reduction in the S-phase fraction of KRAS mutant cells, an effect also characterised by modulation of Rb, a master control of the G1/S checkpoint. Taken together, these observations suggest that the KRAS/CDK1 interaction is a robust synthetic lethal effect worthy of further investigation. PMID:26881434

On Variation of Polyandry in a Bush-Cricket, Metrioptera roeselii, in Northern Europe

PubMed Central

Kaňuch, Peter; Kiehl, Berrit; Low, Matthew; Cassel-Lundhagen, Anna

2013-01-01

Patterns of polyandry in nuptial-gift-giving insects are often explained in terms of sexually antagonistic coevolution. However, the potential influence of environmental constraints and life-history traits on polyandry in these species is still largely unexplored. As an initial step in examining the role of these factors, this study measured the number of matings (spermatodoses per female) of female Roesel's bush-crickets, Metrioptera roeselii Hagenbach (Orthoptera: Tettigoniidae), along a latitudinal gradient in northern Europe (16 sites, 53.89–60.47° N). Females contained between 0 and 5 spermatodoses (mean ± SE: 1.7 ± 0.08; N = 114), with the degree of polyandry generally increasing at higher latitudes (approximately 0.12–0.3 matings per degree of latitude). As expected, female body size also had an influence on polyandry; the number of matings increased from small to moderately large individuals before declining. The field-based results suggested that there were potentially interesting interactions between environment, life-history traits, and patterns of polyandry in nuptial-gift-giving insect species, and these potentially interesting interactions are used to outline future research directions.

Structural and functional determinants of conserved lipid interaction domains of inward rectifying Kir6.2 channels.

PubMed

Cukras, Catherine A; Jeliazkova, Iana; Nichols, Colin G

2002-06-01

All members of the inward rectifiier K(+) (Kir) channel family are activated by phosphoinositides and other amphiphilic lipids. To further elucidate the mechanistic basis, we examined the membrane association of Kir6.2 fragments of K(ATP) channels, and the effects of site-directed mutations of these fragments and full-length Kir6.2 on membrane association and K(ATP) channel activity, respectively. GFP-tagged Kir6.2 COOH terminus and GFP-tagged pleckstrin homology domain from phospholipase C delta1 both associate with isolated membranes, and association of each is specifically reduced by muscarinic m1 receptor-mediated phospholipid depletion. Kir COOH termini are predicted to contain multiple beta-strands and a conserved alpha-helix (residues approximately 306-311 in Kir6.2). Systematic mutagenesis of D307-F315 reveals a critical role of E308, I309, W311 and F315, consistent with residues lying on one side of a alpha-helix. Together with systematic mutation of conserved charges, the results define critical determinants of a conserved domain that underlies phospholipid interaction in Kir channels.

Momentum-resolved radio-frequency spectroscopy of a spin-orbit-coupled atomic Fermi gas near a Feshbach resonance in harmonic traps

NASA Astrophysics Data System (ADS)

Peng, Shi-Guo; Liu, Xia-Ji; Hu, Hui; Jiang, Kaijun

2012-12-01

We theoretically investigate the momentum-resolved radio-frequency spectroscopy of a harmonically trapped atomic Fermi gas near a Feshbach resonance in the presence of equal Rashba and Dresselhaus spin-orbit coupling. The system is qualitatively modeled as an ideal gas mixture of atoms and molecules, in which the properties of molecules, such as the wave function, binding energy, and effective mass, are determined from the two-particle solution of two interacting atoms. We calculate separately the radio-frequency response from atoms and molecules at finite temperatures by using the standard Fermi golden rule and take into account the effect of harmonic traps within local density approximation. The total radio-frequency spectroscopy is discussed as functions of temperature and spin-orbit coupling strength. Our results give a qualitative picture of radio-frequency spectroscopy of a resonantly interacting spin-orbit-coupled Fermi gas and can be directly tested in atomic Fermi gases of 40K atoms at Shanxi University and 6Li atoms at the Massachusetts Institute of Technology.

Elemental abundances in corotating events

NASA Technical Reports Server (NTRS)

Vonrosenvinge, T. T.; Mcguire, R. E.

1986-01-01

Large, persistent solar-wind streams in 1973 and 1974 produced corotating interaction regions which accelerated particles to energies of a few MeV/nucleon. The proton to helium ratio (H/He) reported was remarkably constant at a value (22 + or - 5) equal to that in the solar wind (32 + or - 3), suggesting that particles were being accelerated directly out of the solar wind. Preliminary results from a similar study approximately 11 years (i.e., one solar cycle) later are reported. Corotating events were identified by surveying the solar wind data, energetic particle time-histories and anisotropies. This data was all obtained from the ISEE-3/ICE spacecraft. These events also show H/He ratios similar to that in the solar wind. In addition, other corotating events were examined at times when solar flare events could have injected particles into the corresponding corotating interaction regions. It was found that in these cases there is evidence for H/He ratios which are significantly different from that of the solar wind but which are consistent with the range of values found in solar flare events.

Search for sterile neutrino mixing using three years of IceCube DeepCore data

NASA Astrophysics Data System (ADS)

Aartsen, M. G.; Ackermann, M.; Adams, J.; Aguilar, J. A.; Ahlers, M.; Ahrens, M.; Al Samarai, I.; Altmann, D.; Andeen, K.; Anderson, T.; Ansseau, I.; Anton, G.; Archinger, M.; Argüelles, C.; Auffenberg, J.; Axani, S.; Bai, X.; Barwick, S. W.; Baum, V.; Bay, R.; Beatty, J. J.; Becker Tjus, J.; Becker, K.-H.; BenZvi, S.; Berley, D.; Bernardini, E.; Besson, D. Z.; Binder, G.; Bindig, D.; Blaufuss, E.; Blot, S.; Bohm, C.; Börner, M.; Bos, F.; Bose, D.; Böser, S.; Botner, O.; Braun, J.; Brayeur, L.; Bretz, H.-P.; Bron, S.; Burgman, A.; Carver, T.; Casier, M.; Cheung, E.; Chirkin, D.; Christov, A.; Clark, K.; Classen, L.; Coenders, S.; Collin, G. H.; Conrad, J. M.; Cowen, D. F.; Cross, R.; Day, M.; de André, J. P. A. M.; De Clercq, C.; del Pino Rosendo, E.; Dembinski, H.; De Ridder, S.; Desiati, P.; de Vries, K. D.; de Wasseige, G.; de With, M.; DeYoung, T.; Díaz-Vélez, J. C.; di Lorenzo, V.; Dujmovic, H.; Dumm, J. P.; Dunkman, M.; Eberhardt, B.; Ehrhardt, T.; Eichmann, B.; Eller, P.; Euler, S.; Evenson, P. A.; Fahey, S.; Fazely, A. R.; Feintzeig, J.; Felde, J.; Filimonov, K.; Finley, C.; Flis, S.; Fösig, C.-C.; Franckowiak, A.; Friedman, E.; Fuchs, T.; Gaisser, T. K.; Gallagher, J.; Gerhardt, L.; Ghorbani, K.; Giang, W.; Gladstone, L.; Glauch, T.; Glüsenkamp, T.; Goldschmidt, A.; Gonzalez, J. G.; Grant, D.; Griffith, Z.; Haack, C.; Hallgren, A.; Halzen, F.; Hansen, E.; Hansmann, T.; Hanson, K.; Hebecker, D.; Heereman, D.; Helbing, K.; Hellauer, R.; Hickford, S.; Hignight, J.; Hill, G. C.; Hoffman, K. D.; Hoffmann, R.; Hoshina, K.; Huang, F.; Huber, M.; Hultqvist, K.; In, S.; Ishihara, A.; Jacobi, E.; Japaridze, G. S.; Jeong, M.; Jero, K.; Jones, B. J. P.; Kang, W.; Kappes, A.; Karg, T.; Karle, A.; Katz, U.; Kauer, M.; Keivani, A.; Kelley, J. L.; Kheirandish, A.; Kim, J.; Kim, M.; Kintscher, T.; Kiryluk, J.; Kittler, T.; Klein, S. R.; Kohnen, G.; Koirala, R.; Kolanoski, H.; Konietz, R.; Köpke, L.; Kopper, C.; Kopper, S.; Koskinen, D. J.; Kowalski, M.; Krings, K.; Kroll, M.; Krückl, G.; Krüger, C.; Kunnen, J.; Kunwar, S.; Kurahashi, N.; Kuwabara, T.; Kyriacou, A.; Labare, M.; Lanfranchi, J. L.; Larson, M. J.; Lauber, F.; Lennarz, D.; Lesiak-Bzdak, M.; Leuermann, M.; Lu, L.; Lünemann, J.; Madsen, J.; Maggi, G.; Mahn, K. B. M.; Mancina, S.; Mandelartz, M.; Maruyama, R.; Mase, K.; Maunu, R.; McNally, F.; Meagher, K.; Medici, M.; Meier, M.; Menne, T.; Merino, G.; Meures, T.; Miarecki, S.; Micallef, J.; Momenté, G.; Montaruli, T.; Moulai, M.; Nahnhauer, R.; Naumann, U.; Neer, G.; Niederhausen, H.; Nowicki, S. C.; Nygren, D. R.; Obertacke Pollmann, A.; Olivas, A.; O'Murchadha, A.; Palczewski, T.; Pandya, H.; Pankova, D. V.; Peiffer, P.; Penek, Ö.; Pepper, J. A.; Pérez de los Heros, C.; Pieloth, D.; Pinat, E.; Price, P. B.; Przybylski, G. T.; Quinnan, M.; Raab, C.; Rädel, L.; Rameez, M.; Rawlins, K.; Reimann, R.; Relethford, B.; Relich, M.; Resconi, E.; Rhode, W.; Richman, M.; Riedel, B.; Robertson, S.; Rongen, M.; Rott, C.; Ruhe, T.; Ryckbosch, D.; Rysewyk, D.; Sabbatini, L.; Sanchez Herrera, S. E.; Sandrock, A.; Sandroos, J.; Sarkar, S.; Satalecka, K.; Schlunder, P.; Schmidt, T.; Schoenen, S.; Schöneberg, S.; Schumacher, L.; Seckel, D.; Seunarine, S.; Soldin, D.; Song, M.; Spiczak, G. M.; Spiering, C.; Stachurska, J.; Stanev, T.; Stasik, A.; Stettner, J.; Steuer, A.; Stezelberger, T.; Stokstad, R. G.; Stößl, A.; Ström, R.; Strotjohann, N. L.; Sullivan, G. W.; Sutherland, M.; Taavola, H.; Taboada, I.; Tatar, J.; Tenholt, F.; Ter-Antonyan, S.; Terliuk, A.; Tešić, G.; Tilav, S.; Toale, P. A.; Tobin, M. N.; Toscano, S.; Tosi, D.; Tselengidou, M.; Tung, C. F.; Turcati, A.; Unger, E.; Usner, M.; Vandenbroucke, J.; van Eijndhoven, N.; Vanheule, S.; van Rossem, M.; van Santen, J.; Vehring, M.; Voge, M.; Vogel, E.; Vraeghe, M.; Walck, C.; Wallace, A.; Wallraff, M.; Wandkowsky, N.; Waza, A.; Weaver, Ch.; Weiss, M. J.; Wendt, C.; Westerhoff, S.; Whelan, B. J.; Wickmann, S.; Wiebe, K.; Wiebusch, C. H.; Wille, L.; Williams, D. R.; Wills, L.; Wolf, M.; Wood, T. R.; Woolsey, E.; Woschnagg, K.; Xu, D. L.; Xu, X. W.; Xu, Y.; Yanez, J. P.; Yodh, G.; Yoshida, S.; Zoll, M.; IceCube Collaboration

2017-06-01

We present a search for a light sterile neutrino using three years of atmospheric neutrino data from the DeepCore detector in the energy range of approximately 10-60 GeV. DeepCore is the low-energy subarray of the IceCube Neutrino Observatory. The standard three-neutrino paradigm can be probed by adding an additional light (Δ m412˜1 eV2 ) sterile neutrino. Sterile neutrinos do not interact through the standard weak interaction and, therefore, cannot be directly detected. However, their mixing with the three active neutrino states leaves an imprint on the standard atmospheric neutrino oscillations for energies below 100 GeV. A search for such mixing via muon neutrino disappearance is presented here. The data are found to be consistent with the standard three-neutrino hypothesis. Therefore, we derive limits on the mixing matrix elements at the level of |Uμ 4|2<0.11 and |Uτ 4|2<0.15 (90% C.L.) for the sterile neutrino mass splitting Δ m412=1.0 eV2 .

Electron beam cooling in intense focussed laser pulses

NASA Astrophysics Data System (ADS)

Yoffe, Samuel R.; Noble, Adam; Macleod, Alexander J.; Jaroszynski, Dino A.

2017-05-01

In the coming years, a new generation of high-power laser facilities (such as the Extreme Light Infrastructure) will become operational, for which it is important to understand how the interaction with intense laser pulses affects the bulk properties of relativistic electron bunches. At such high field intensities, we expect both radiation reaction and quantum effects to have a dominant role to play in determining the dynamics. The reduction in relative energy spread (beam cooling) at the expense of mean beam energy predicted by classical theories of radiation reaction has been shown to occur equally in the longitudinal and transverse directions, whereas this symmetry is broken when the theory is extended to approximate certain quantum effects. The reduction in longitudinal cooling suggests that the effects of radiation reaction could be better observed in measurements of the transverse distribution, which for real-world laser pulses motivates the investigation of the angular dependence of the interaction. Using a stochastic single-photon emission model with a (Gaussian beam) focussed pulse, we find strong angular dependence of the stochastic heating.

The Effect of Cumulus Cloud Field Anisotropy on Domain-Averaged Solar Fluxes and Atmospheric Heating Rates

NASA Technical Reports Server (NTRS)

Hinkelman, Laura M.; Evans, K. Franklin; Clothiaux, Eugene E.; Ackerman, Thomas P.; Stackhouse, Paul W., Jr.

2006-01-01

Cumulus clouds can become tilted or elongated in the presence of wind shear. Nevertheless, most studies of the interaction of cumulus clouds and radiation have assumed these clouds to be isotropic. This paper describes an investigation of the effect of fair-weather cumulus cloud field anisotropy on domain-averaged solar fluxes and atmospheric heating rate profiles. A stochastic field generation algorithm was used to produce twenty three-dimensional liquid water content fields based on the statistical properties of cloud scenes from a large eddy simulation. Progressively greater degrees of x-z plane tilting and horizontal stretching were imposed on each of these scenes, so that an ensemble of scenes was produced for each level of distortion. The resulting scenes were used as input to a three-dimensional Monte Carlo radiative transfer model. Domain-average transmission, reflection, and absorption of broadband solar radiation were computed for each scene along with the average heating rate profile. Both tilt and horizontal stretching were found to significantly affect calculated fluxes, with the amount and sign of flux differences depending strongly on sun position relative to cloud distortion geometry. The mechanisms by which anisotropy interacts with solar fluxes were investigated by comparisons to independent pixel approximation and tilted independent pixel approximation computations for the same scenes. Cumulus anisotropy was found to most strongly impact solar radiative transfer by changing the effective cloud fraction, i.e., the cloud fraction when the field is projected on a surface perpendicular to the direction of the incident solar beam.