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Sample records for dependent rkky interaction

  1. RKKY interaction in bilayer graphene

    Science.gov (United States)

    Mohammadi, Yawar; Moradian, Rostam

    2015-12-01

    We study the RKKY interaction between two magnetic impurities located on the same layer (intralayer case) or on different layers (interlayer case) in undoped bilayer graphene (BLG) in the four-bands model, by directly calculating the Green functions in the eigenvalues and eigenvectors representation. Our results show that both intra- and interlayer RKKY interactions between two magnetic impurities located on the same (opposite) sublattice are always ferromagnetic (antiferromagnetic). Furthermore we find unusual long-distance decay of the RKKY interaction in BLG. The intralyer RKKY interactions between two magnetic impurities located on the same sublattice, J AnAn(R) and J BnBn(R), decay closely as 1 /R6 and 1 /R2 at large impurity distances respectively, but when they are located on opposite sublattices the RKKY interactions exhibit 1 /R4 decays approximately. In the interlayer case, the RKKY interactions between two magnetic impurities located on the same sublattice show a decay close to 1 /R4 at large impurity distances, but if two magnetic impurities be on opposite sublattices the RKKY interactions, J A1B2(R) and J B1A2(R), decay closely as 1 /R6 and 1 /R2 respectively. Both intra- and interlayer RKKY interactions have anisotropic oscillatory factors which for intralayer case is equal to that for single layer graphene (SLG). Our results at weak and strong interlayer coupling limits reduce to the RKKY interaction of SLG and that of BLG in the two-bands approximation respectively.

  2. Topological phase and edge states dependence of the RKKY interaction in zigzag silicene nanoribbon

    Science.gov (United States)

    Zare, Moslem; Parhizgar, Fariborz; Asgari, Reza

    2016-07-01

    We propose versatile materials based on the Ruderman-Kittel-Kasuya-Yosida (RKKY) interaction in a zigzag silicene nanoribbon (ZSNR) on half filling in the presence of an out-of-plane electric field. We show that the topological phase transition in the band dispersion of ZSNR can be probed by using the RKKY interaction. We find that, due to the zero-energy edge states of the ZSNR, the exchange coupling is significantly enhanced when the impurities are located on the zigzag edges, and also explore that the strength of the interaction in the topological insulator phase is much greater than that when the system is in the band insulator region. We present a model to investigate the phase of a system of two magnetic impurities located on the edge of the ZSNR and find that three different magnetic phases, spiral, ferromagnetic, and antiferromagnetic, are possible for different values of the electric field. This electrical tunability of the magnetic phases in silicene can be explored by using current experimental techniques and can be of interest in the field of spintronics.

  3. RKKY interaction for the spin-polarized electron gas

    Science.gov (United States)

    Valizadeh, Mohammad M.; Satpathy, Sashi

    2015-11-01

    We extend the original work of Ruderman, Kittel, Kasuya and Yosida (RKKY) on the interaction between two magnetic moments embedded in an electron gas to the case where the electron gas is spin-polarized. The broken symmetry of a host material introduces the Dzyaloshinsky-Moriya (DM) vector and tensor interaction terms, in addition to the standard RKKY term, so that the net interaction energy has the form ℋ = JS1 ṡS2 + D ṡS1 ×S2 + S1 ṡΓ ↔ṡS2. We find that for the spin-polarized electron gas, a nonzero tensor interaction Γ ↔ is present in addition to the scalar RKKY interaction J, while D is zero due to the presence of inversion symmetry. Explicit expressions for these are derived for the electron gas both in 2D and 3D and we show that the net magnetic interaction can be expressed as a sum of Heisenberg and Ising like terms. The RKKY interaction exhibits a beating pattern, caused by the presence of the two Fermi momenta kF↑ and kF↓, while the R-3 distance dependence of the original RKKY result for the 3D electron gas is retained. This model serves as a simple example of the magnetic interaction in systems with broken symmetry, which goes beyond the RKKY interaction.

  4. Strain-modified RKKY interaction in carbon nanotubes

    DEFF Research Database (Denmark)

    Gorman, P. D.; Duffy, J. M.; Power, Stephen R.

    2015-01-01

    For low-dimensionalmetallic structures, such as nanotubes, the exchange coupling between localized magnetic dopants is predicted to decay slowly with separation. The long-range character of this interaction plays a significant role in determining the magnetic order of the system. It has previously...... been shown that the interaction range depends on the conformation of the magnetic dopants in both graphene and nanotubes. Here we examine the Ruderman-Kittel-Kasuya-Yosida (RKKY) interaction in carbon nanotubes in the presence of uniaxial strain for a range of different impurity configurations. We show...... that strain is capable of amplifying or attenuating the RKKY interaction, significantly increasing certain interaction ranges, and acting as a switch: effectively turning on or off the interaction. We argue that uniaxial strain can be employed to significantly manipulate magnetic interactions in carbon...

  5. RKKY interaction in a chirally coupled double quantum dot system

    Energy Technology Data Exchange (ETDEWEB)

    Heine, A. W.; Tutuc, D.; Haug, R. J. [Institut für Festkörperphysik, Leibniz Universität Hannover, Appelstr. 2, 30167 Hannover (Germany); Zwicknagl, G. [Institut für Mathematische Physik, TU Braunschweig, Mendelssohnstr. 3, 38106 Braunschweig (Germany); Schuh, D. [Institut für Experimentelle und Angewandte Physik, Universität Regensburg, Universitätstr. 31, 93053 Regensburg (Germany); Wegscheider, W. [Laboratorium für Festkörperphysik, ETH Zürich, Schafmattstr. 16, 8093 Zürich, Switzerland and Institut für Experimentelle und Angewandte Physik, Universität Regensburg, Universitätstr. 31, 93053 Regens (Germany)

    2013-12-04

    The competition between the Kondo effect and the Ruderman-Kittel-Kasuya-Yoshida (RKKY) interaction is investigated in a double quantum dots system, coupled via a central open conducting region. A perpendicular magnetic field induces the formation of Landau Levels which in turn give rise to the so-called Kondo chessboard pattern in the transport through the quantum dots. The two quantum dots become therefore chirally coupled via the edge channels formed in the open conducting area. In regions where both quantum dots exhibit Kondo transport the presence of the RKKY exchange interaction is probed by an analysis of the temperature dependence. The thus obtained Kondo temperature of one dot shows an abrupt increase at the onset of Kondo transport in the other, independent of the magnetic field polarity, i.e. edge state chirality in the central region.

  6. Focusing RKKY interaction by graphene P-N junction

    Science.gov (United States)

    Zhang, Shu-Hui; Zhu, Jia-Ji; Yang, Wen; Chang, Kai

    2017-09-01

    The carrier-mediated RKKY interaction between local spins plays an important role for the application of magnetically doped graphene in spintronics and quantum computation. Previous studies largely concentrate on the influence of electronic states of uniform systems on the RKKY interaction. Here we reveal a very different way to manipulate the RKKY interaction by showing that the anomalous focusing—a well-known electron optics phenomenon in graphene P-N junctions—can be utilized to refocus the massless Dirac electrons emanating from one local spin to the other local spin. This gives rise to rich spatial interference patterns and symmetry-protected non-oscillatory RKKY interaction with a strongly enhanced magnitude. It may provide a new way to engineer the long-range spin-spin interaction in graphene.

  7. RKKY interaction in P-N junction based on surface states of 3D topological insulator

    Science.gov (United States)

    Zhang, Shuhui; Yang, Wen; Chang, Kai

    The RKKY interaction mediated by conduction electrons supplies a mechanism to realize the long-range coupling of localized spins which is desired for the spin devices. Here, we examine the controllability of RKKY interaction in P-N junction (PNJ) based on surface states of 3D topological insulator (3DTI). In this study, through quantum way but not usual classical analogy to light propagation, the intuitive picture for electron waves across the interface of PNJ is obtained, e.g., Klein tunneling, negative refraction and focusing. Moreover, we perform the numerical calculations for all kinds of RKKY interaction including the Heisenberg, Ising, and Dzyaloshinskii-Moriya terms. We find the focusing of surface states leads to the local augmentation of RKKY interaction. Most importantly, a dimension transition occurs, i.e., the decay rate of RKKY interaction from the deserved 1/R 2 to 1/ R . In addition, the quadratic gate-dependence of RKKY interaction is also beneficial to the application of 3DTI PNJ in the fields of spintronics and quantum computation. This work was supported by the MOST (Grant No. 2015CB921503, and No. 2014CB848700) and NSFC (Grant No. 11434010, No. 11274036, No. 11322542, and No. 11504018).

  8. RKKY interaction of magnetic impurities in Dirac and Weyl semimetals

    Science.gov (United States)

    Chang, Hao-Ran; Zhou, Jianhui; Wang, Shi-Xiong; Shan, Wen-Yu; Xiao, Di

    2015-12-01

    We theoretically study the Ruderman-Kittel-Kasuya-Yosida (RKKY) interaction between magnetic impurities in both Dirac and Weyl semimetals (SMs). We find that the internode process, as well as the unique three-dimensional spin-momentum locking, has significant influences on the RKKY interaction, resulting in both a Heisenberg and an Ising term, and an additional Dzyaloshinsky-Moriya term if the inversion symmetry is absent. These interactions can lead to rich spin textures and possible ferromagnetism in Dirac and time-reversal symmetry-invariant Weyl SMs. The effect of anisotropic Dirac and Weyl nodes on the RKKY interaction is also discussed. Our results provide an alternative scheme to engineer topological SMs and shed new light on the application of Dirac and Weyl SMs in spintronics.

  9. RKKY interaction between extended magnetic defect lines in graphene

    DEFF Research Database (Denmark)

    Gorman, P. D.; Duffy, J. M.; Power, Stephen;

    2014-01-01

    Of fundamental interest in the field of spintronics is the mechanism of indirect exchange coupling between magnetic impurities embedded in metallic hosts. A range of physical features, such as magnetotransport and overall magnetic moment formation, are predicated upon this magnetic coupling, ofte...... consequences for the spintronic application of magnetically-doped systems, and we illustrate this with a simple magnetoresistance device....... referred to as the Ruderman-Kittel-Kasuya-Yosida (RKKY) interaction. Recent theoretical studies on the RKKY in graphene have been motivated by possible spintronic applications of magnetically doped graphene systems. In this paper a combination of analytic and numerical techniques are used to examine...

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

    Science.gov (United States)

    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.

  11. RKKY interaction between adsorbed magnetic impurities in graphene: Symmetry and strain effects

    DEFF Research Database (Denmark)

    Gorman, P. D.; Duffy, J. M.; Ferreira, Miquel

    2013-01-01

    The growing interest in carbon-based spintronics has stimulated a number of recent theoretical studies on the Ruderman-Kittel-Kasuya-Yosida (RKKY) interaction in graphene, with the aim of determining the most energetically favorable alignments between embedded magnetic moments. The RKKY interaction...

  12. Effect of the Rashba splitting on the RKKY interaction in topological-insulator thin films

    Science.gov (United States)

    Shiranzaei, Mahroo; Cheraghchi, Hosein; Parhizgar, Fariborz

    2017-07-01

    We investigate the effect of Rashba splitting on the Ruderman-Kittel-Kasuya-Yosida (RKKY) interaction in a topological-insulator (TI) thin film both at finite and zero chemical potential. We show that the spin susceptibility of the TI thin film depends strongly on the direction of the distance vector between impurities. In addition to the well-known Heisenberg-, Ising-, and Dzyaloshinskii-Moria (DM)-like terms reported before in TIs, we find another term in the off-diagonal part of the spin-susceptibility tensor which is symmetric in contrast to the DM term. Furthermore, we show how one can tune the RKKY interaction by using electric field applied perpendicularly to the surface plane of the TI, where in the presence of such a field the RKKY interaction can be enhanced drastically for small chemical doping. We present our results for two different situations, namely intersurface pairing of magnetic impurities as well as intrasurface pairing. The behavior of these two situations is completely different, which we describe by mapping the density of states of each surface on the band dispersion.

  13. Magnetic properties in kagomé lattice with RKKY interaction: A Monte Carlo study

    Science.gov (United States)

    Masrour, R.; Jabar, A.; Benyoussef, A.; Hamedoun, M.

    2016-03-01

    The magnetic properties of the kagomé lattice have been studied with Ruderman-Kittel-Kasuya-Yosida (RKKY) exchange interactions in a spin-7/2 Ising model using Monte Carlo simulations. The RKKY interaction between the two magnetic layers is considered for different distances. The magnetizations and magnetic susceptibilities of this lattice are given for different triquadratic interactions around each triangular face. The critical temperature is obtained for a fixed size. The magnetic hysteresis cycle of kagomé lattice with RKKY interactions is obtained for different temperatures and for different crystal field with a fixed size of nonmagnetic layer.

  14. Anisotropic Surface State Mediated RKKY Interaction Between Adatoms on a Hexagonal Lattice

    Science.gov (United States)

    Einstein, Theodore; Patrone, Paul

    2012-02-01

    Motivated by recent numerical studies of Ag on Pt(111), we derive a far-field expression for the RKKY interaction mediated by surface states on a (111) FCC surface, considering the effect of anisotropy in the Fermi edge. 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 component of the aforementioned kF that is parallel to 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.

  15. RKKY interaction between adsorbed magnetic impurities in graphene: Symmetry and strain effects

    DEFF Research Database (Denmark)

    Gorman, P. D.; Duffy, J. M.; Ferreira, Miquel;

    2013-01-01

    The growing interest in carbon-based spintronics has stimulated a number of recent theoretical studies on the Ruderman-Kittel-Kasuya-Yosida (RKKY) interaction in graphene, with the aim of determining the most energetically favorable alignments between embedded magnetic moments. The RKKY interaction...... in undoped graphene decays faster than expected for conventional two-dimensional materials, and recent studies suggest that the adsorption configurations favored by many transition-metal impurities may lead to even shorter-ranged decays and possible sign-changing oscillations. Here, we show...... that these features emerge in a mathematically transparent manner when the symmetry of the configurations is included in the calculation. Furthermore, we show that by breaking the symmetry of the graphene lattice, via uniaxial strain, the decay rate, and hence the range, of the RKKY interaction can be significantly...

  16. RKKY interaction and local density of states for a triangular triple quantum dot system

    Science.gov (United States)

    Xiong, Yong-Chen; Wang, Wei-Zhong; Luo, Shi-Jun; Yang, Jun-Tao; Huang, Hai-Ming

    2016-02-01

    By means of the numerical renormalization group technique, we study the local density of states (LDOS) for a triangular triple quantum dot system, with two dots connected in parallel to the conduction leads. We find the location of the Ruderman-Kittel-Kasuya-Yosida (RKKY) peak identified in the LDOS could be illustrated as JRKKY = aΓ2 / U +bt22 / U, with U being the on-site Coulomb repulsion, Γ the dot-lead coupling, and t2 the hopping between the connected dots and the side dot. When the hopping between two connected dots t1 turns on, the spectrum weight of the RKKY peaks decreases due to the competition between the direct and the RKKY interactions. As t1 increases beyond a critical point t1c, two connected dots form a spin singlet, and decouple from both the side dot and the conduction leads, thus the Kondo and RKKY peaks could not be found. For t1 1 ≥t1 c, it drops to zero.

  17. Anisotropic Heisenberg form of RKKY interaction in the one-dimensional spin-polarized electron gas

    Science.gov (United States)

    Valizadeh, M. M.

    2016-09-01

    We study the indirect exchange interaction between two localized magnetic moments, known as Ruderman-Kittel-Kasuya-Yosida (RKKY) interaction, in a one-dimensional (1D) spin-polarized electron gas. We find explicit expressions for each term of this interaction, study their oscillatory behaviors as a function of the distance between two magnetic moments, R, and compare them with the known results for RKKY interaction in the case of 1D standard electron gas. We show this interaction can be written in an anisotropic Heisenberg form, E(R) = λ2χ xx(S1xS2x + S1yS2y) + λ2χ zzS1zS2z, coming from broken time-reversal symmetry of the host material.

  18. Indirect Exchange and Ruderman–Kittel–Kasuya–Yosida (RKKY Interactions in Magnetically-Doped Graphene

    Directory of Open Access Journals (Sweden)

    Mauro S. Ferreira

    2013-01-01

    Full Text Available Magnetically-doped graphene systems are potential candidates for application in future spintronic devices. A key step is to understand the pairwise interactions between magnetic impurities embedded in graphene that are mediated by the graphene conduction electrons. A large number of studies have been undertaken to investigate the indirect exchange, or RKKY (Ruderman-Kittel-Kasuya-Yosida, interactions in graphene. Many of these studies report a decay rate faster than expected for a two-dimensional material and the absence of the usual distance dependent oscillations. In this review we summarize the techniques used to calculate the interaction and present the key results obtained to date. The effects of more detailed parameterisations of the magnetic impurities and graphene host are considered, as are results obtained from ab initio calculations. Since the fast decay of the interaction presents an obstacle to spintronic applications, we focus in particular on the possibility of augmenting the interaction range by a number of methods including doping, spin precession and the application of strain.

  19. RKKY interaction in triangular MoS2 nanoflakes

    Science.gov (United States)

    Mastrogiuseppe, Diego; Avalos-Ovando, Oscar; Ulloa, Sergio

    Transition-metal dichalcogenides (TMDs), such as MoS2, possess unique electronic and optical properties, making them promising for optospintronics. Exfoliation and CVD growth processes produce nanoflakes of different shapes, often triangular with zigzag edges. Magnetic impurities in this material interact indirectly through the TMD conduction electrons/holes. Using an effective 3-orbital tight-binding model, we study the Ruderman-Kittel-Kasuya-Yosida interaction between magnetic impurities in p-doped triangular flakes with zigzag termination. We analyze the interaction as function of impurity separation along high symmetry directions in the nanoflake, considering hybridization to different Mo orbitals, and different fillings. The interaction is anisotropic for impurities in the interior of the flake. However, when impurities lie on the edges of the crystallite, the effective exchange is Ising-like, reflecting the presence of z2-orbitals associated with edge states. Other interactions are possible by selecting impurity positions and orbital character of the states in their neighborhood. Our results can be tested with local probes, such as spin-polarized STM Supported by NSF DMR-1508325.

  20. Realizing topological Mott insulators from the RKKY interaction

    Science.gov (United States)

    Liu, Tianhan; Douçot, Benoît; Le Hur, Karyn

    2016-05-01

    We engineer topological insulating phases in a fermion-fermion mixture on the honeycomb lattice, without resorting to artificial gauge fields or spin-orbit couplings and considering only local interactions. Essentially, upon integrating out the fast component (characterized by a larger hopping amplitude) in a finite region of dopings, we obtain an effective interaction between the slow fermions at half-filling, which acquires a Haldane mass with opposite parity in the two valleys of the Dirac cones, thus triggering a quantum anomalous Hall effect. We carefully analyze the competition between the induced Semenoff-type mass (producing charge density wave orders in real space) versus the Haldane mass (quantum anomalous Hall phase), as a function of the chemical potential of the fast fermions. If the second species involves spin-1/2 particles, this interaction may induce a quantum spin Hall phase. Such fermion-fermion mixtures can be realized in optical lattices or in graphene heterostructures.

  1. Variable range of the RKKY interaction in edged graphene

    DEFF Research Database (Denmark)

    Duffy, J M; Gorman, P D; Power, S R

    2014-01-01

    The indirect exchange interaction is one of the key factors in determining the overall alignment of magnetic impurities embedded in metallic host materials. In this work we examine the range of this interaction in magnetically doped graphene systems in the presence of armchair edges using...... a combination of analytical and numerical Green function approaches. We consider both a semi-infinite sheet of graphene with a single armchair edge, and also quasi-one-dimensional armchair-edged graphene nanoribbons (GNRs). While we find signals of the bulk decay rate in semi-infinite graphene and signals...... calculations, and the result for semi-infinite graphene can be interpreted as an intermediate case between ribbon and bulk systems....

  2. Dynamic RKKY interaction between magnetic moments in graphene nanoribbons

    Science.gov (United States)

    Guimarães, F. S. M.; Duffy, J.; Costa, A. T.; Muniz, R. B.; Ferreira, M. S.

    2016-12-01

    Graphene has been identified as a promising material with numerous applications, particularly in spintronics. In this paper we investigate the peculiar features of spin excitations of magnetic units deposited on graphene nanoribbons and how they can couple through a dynamical interaction mediated by spin currents. We examine in detail the spin lifetimes and identify a pattern caused by vanishing density of states sites in pristine ribbons with armchair borders. Impurities located on these sites become practically invisible to the interaction but can be made accessible by a gate voltage or doping. We also demonstrate that the coupling between impurities can be turned on or off using this characteristic, which may be used to control the transfer of information in transistorlike devices.

  3. Multilayer transition in a spin-1 Blume-Capel model with RKKY interaction and quantum transverse anisotropy

    Institute of Scientific and Technical Information of China (English)

    N. Tahiri; H. Ez-Zahraouy; A. Benyoussef

    2011-01-01

    Using mean-field theory, we have studied the effect of quantum transverse anieotropies with RKKY interaction on the multi-layer transition and magnetic properties of the spin-1 Blume-Capel model of a system formed by two magnetic multi-layer materials, of different thicknesses, separated by a non-magnetic spacer of thickness M. It is found that the multilayer magnetic order-disorder transition temperature depends strongly on the value of the transverse anisotropy.The multilayer transition temperature decreases when increasing the transverse anisotropy. Furthermore, there exists a critical quantum transverse anisotropy △xL beyond which the separate transitions occur in the two magnetic layers.The critical transverse anisotropy △xL decreases (increases) on increasing the non-magnetic spacer of thickness M (on increasing the crystal field), and △xL undergoes oscillations as a function of the Fermi level.

  4. Indirect Exchange and Ruderman-Kittel-Kasuya-Yosida (RKKY) Interactions in Magnetically-Doped Graphene

    DEFF Research Database (Denmark)

    Power, Stephen; Ferreira, Mauro S.

    2013-01-01

    Magnetically-doped graphene systems are potential candidates for application in future spintronic devices. A key step is to understand the pairwise interactions between magnetic impurities embedded in graphene that are mediated by the graphene conduction electrons. A large number of studies have...... presents an obstacle to spintronic applications, we focus in particular on the possibility of augmenting the interaction range by a number of methods including doping, spin precession and the application of strain....

  5. Kondo Destruction in RKKY-Coupled Kondo Lattice and Multi-Impurity Systems

    Science.gov (United States)

    Nejati, Ammar; Ballmann, Katinka; Kroha, Johann

    2017-03-01

    In a Kondo lattice, the spin exchange coupling between a local spin and the conduction electrons acquires nonlocal contributions due to conduction electron scattering from surrounding local spins and the subsequent RKKY interaction. It leads to a hitherto unrecognized interference of Kondo screening and the RKKY interaction beyond the Doniach scenario. We develop a renormalization group theory for the RKKY-modified Kondo vertex. The Kondo temperature TK(y ) is suppressed in a universal way, controlled by the dimensionless RKKY coupling parameter y . Complete spin screening ceases to exist beyond a critical RKKY strength yc even in the absence of magnetic ordering. At this breakdown point, TK(y ) remains nonzero and is not defined for larger RKKY couplings y >yc. The results are in quantitative agreement with STM spectroscopy experiments on tunable two-impurity Kondo systems. The possible implications for quantum critical scenarios in heavy-fermion systems are discussed.

  6. Evidence on the presence of Ruderman-Kittel-Kasuya-Yosida (RKKY) interaction in CoFe2O4@Au nano structure

    Science.gov (United States)

    El-Sayed, H. M.

    2016-03-01

    In this work, a straight forward method for preparing CoFe2O4/Au core shell nano composite is introduced. By this method, samples with different thickness of Au as shell were obtained. The crystal and micro structures of the prepared samples were studied using x-ray diffraction and TEM micrographs. The presence of plasmonic frequencies of gold nano particles was investigated by measuring absorbance spectra in the visible range. It was found that, the plasma frequency decreases with increasing the gold thickness. The effect of the gold thickness on the magnetization, nucleation field and magnetic loss were studied. The experimental measurements showed an oscillating behavior of the magnetic parameters with increasing gold thickness. These results could be explained in terms of the presence of Ruderman-Kittel-Kasuya-Yosida (RKKY) interaction between the ferromagnetic components via the conduction electrons of the gold metal. The heating ability of the magnetic Co-Ferrite particles under high frequency magnetic field was enhanced by the presence of the gold as a shell.

  7. Indirect exchange interaction in Rashba-spin-orbit-coupled graphene nanoflakes

    Science.gov (United States)

    Nikoofard, Hossein; Semiromi, Ebrahim Heidari

    2016-10-01

    We study the indirect exchange interaction, named Ruderman-Kittel-Kasuya-Yosida (RKKY) coupling, between localized magnetic impurities in graphene nanoflakes with zig-zag edges in the presence of the Rashba spin-orbit interaction (RSOI). We calculate the isotropic and anisotropic RKKY amplitudes by utilizing the tight-binding (TB) model. The RSOI, as a gate tunable variable, is responsible for changes of the RKKY amplitude. We conclude that there is not any switching of the magnetic order (from ferro- to antiferro-magnetic and vice versa) in such a system through the RSOI. The dependence of the RKKY amplitude on the positions of the magnetic impurities and the size of the system is studied. The symmetry breaking, which can occur due to the Rashba interaction, leads to spatial anisotropy in the RKKY amplitude and manifests as collinear and noncollinear terms. Our results show the possibility of control and manipulation of spin correlations in carbon spin-based nanodevices.

  8. Competition between Kondo effect and RKKY physics in graphene magnetism

    Science.gov (United States)

    Allerdt, A.; Feiguin, A. E.; Das Sarma, S.

    2017-03-01

    The cooperative behavior of quantum impurities on two-dimensional (2D) materials, such as graphene and bilayer graphene, is characterized by a nontrivial competition between screening (Kondo effect) and Ruderman-Kittel-Kasuya-Yosida (RKKY) magnetism. In addition, due to the small density of states at the Fermi level, impurities may not couple to the conduction electrons at all, behaving as free moments. Employing a recently developed exact numerical method to study multi-impurity lattice systems, we obtain nonperturbative results that dramatically depart from expectations based on the conventional RKKY theory. At half filling and for weak coupling, impurities remain in the local moment regime when they are on opposite sublattices, up to a critical value of the interactions when they start coupling antiferromagnetically with correlations that decay very slowly with interimpurity distance. At finite doping, away from half filling, ferromagnetism is completely absent and the physics is dominated by a competition between antiferromagnetism and Kondo effect. In bilayer graphene, impurities on opposite layers behave as free moments, unless the interaction is of the order of the hopping or larger.

  9. 并联双量子点体系中的RKKY相互作用及局域磁矩%RKKY Interaction and Local Magnetic Moment for a Parallel Double Dot System

    Institute of Scientific and Technical Information of China (English)

    熊永臣; 罗时军; 杨俊涛

    2015-01-01

    The effects of the on-site Coulomb repulsion and temperature on the local density of states (DOS) and magnetic moment in a parallel double quantum dot system were studied by means of the nu-merical renormalization group method. The results show that the Ruderman-Kittel-Kasuya-Yosida (RKKY) interaction identified in the DOS is inversely proportional to U, and as temperature decreases, the magnetic moment goes through the following regimes:free orbital regime, local moment regime, spin triplet regime and Kondo screened regime. The numerical results are consistent with the perturbation theory. The results can be used to describe the strongly correlated effects of semiconductor quantum dot devices, magnetic impurities embedded in a metallic host, magnetic molecular junction and clusters on metallic surfaces.%借助数值重整化群方法研究了并联双量子点体系中,在位库伦排斥作用及温度对体系局域态密度及磁矩的影响.计算表明:态密度中观察到的RKKY相互作用与在位库伦作用成反比关系;随着温度的变化,局域磁矩依次经历自由轨道区间、局域磁矩区间、自旋三重态区间以及Kondo屏蔽区间.计算结果和微扰理论的结果是吻合的.相关结论可以用来描述半导体量子点器件、磁性杂质、磁性分子结及相关团簇吸附问题的强关联效应.

  10. Interactive Visualization of Dependencies

    Science.gov (United States)

    Moreno, Camilo Arango; Bischof, Walter F.; Hoover, H. James

    2012-01-01

    We present an interactive tool for browsing course requisites as a case study of dependency visualization. This tool uses multiple interactive visualizations to allow the user to explore the dependencies between courses. A usability study revealed that the proposed browser provides significant advantages over traditional methods, in terms of…

  11. Interactive Visualization of Dependencies

    Science.gov (United States)

    Moreno, Camilo Arango; Bischof, Walter F.; Hoover, H. James

    2012-01-01

    We present an interactive tool for browsing course requisites as a case study of dependency visualization. This tool uses multiple interactive visualizations to allow the user to explore the dependencies between courses. A usability study revealed that the proposed browser provides significant advantages over traditional methods, in terms of…

  12. Aspects, Dependencies, and Interactions

    NARCIS (Netherlands)

    Chitchyan, R; Fabry, J.; Bergmans, Lodewijk; Südholt, M.; Consel, C.

    2007-01-01

    For Aspect-Oriented Software Development (AOSD) the topic of Aspects, Dependencies and Interactions is of high importance across the whole range of development activities – from requirements engineering through to language design. Aspect interactions must be adequately addressed all across the softw

  13. Semi-Empirical Study of the Indirect Exchange Interaction in the Rem - Al System

    Science.gov (United States)

    Shakarov, Kh. O.

    2016-05-01

    The Ruderman-Kittel-Kasuya-Yosida exchange interaction (RKKY) is semi-empirically studied for the first time in compounds of binary REM - Al systems (REM - rare-earth metals: Gd, Dy, Ho, Er) using experimental values of paramagnetic Curie point (θp) of these compounds. Prediction of the RKKY theory was confirmed, i.e. there is a direct proportional dependence of θp value on de Gennes factor for equiatomic compounds of heavy REM with aluminum, just as in the case of pure REM. Values of the indirect exchange interaction parameter were semi-empirically estimated for the studied compounds. In general, it was established that RKKY-type exchange interaction is typical for REM compounds with aluminum, just as for pure REM.

  14. Influence of zigzag edges on the Ruderman-Kittel-Kasuya-Yosida interaction between magnetic impurities in graphene nanoribbons

    Energy Technology Data Exchange (ETDEWEB)

    Akbari-Sharbaf, A., E-mail: aakbaris@uwo.ca; Cottam, M. G., E-mail: cottam@uwo.ca [Department of Physics and Astronomy, University of Western Ontario, London, Ontario N6A 3K7 (Canada)

    2014-11-21

    Localized magnetic impurity centres in graphene can interact through the π-electrons, leading to an effective Ruderman-Kittel-Kasuya-Yosida (RKKY) interaction. A RKKY-type study is presented for graphene ribbons with zigzag edges. Specifically investigations of how the edges modify the interaction between two localized magnetic moments are made by using a tight-binding Hamiltonian to describe the hopping of the π-electrons between adjacent sites and a contact term for interactions with the localized moments. In terms of a Green's function formalism for the excitation spectrum, which comprises modified bulk modes and two different types of localized edge modes, explicit analytical expressions are obtained for the RKKY interaction for any two magnetic sites on the graphene ribbon. The results enable us to determine the RKKY contributions that arise individually from the bulk-like modes and from the two types of edge modes in the zigzag geometry. The importance of these contributions varies depending on the proximity of the magnetic impurities to each other and to an edge.

  15. Ruderman-Kittel-Kasuya-Yosida interaction in silicene.

    Science.gov (United States)

    Xiao, Xiao; Liu, Yu; Wen, Weijia

    2014-07-01

    We investigate the Ruderman-Kittel-Kasuya-Yosida (RKKY) interaction between two magnetic impurities in a monolayer silicene. Due to spin-orbit (SO) coupling, the RKKY interaction can be further divided into various types according to the polarization directions of the magnetic impurities. We demonstrate that the spatial behaviors of the RKKY interaction closely relate to the external electric field, which together with the SO coupling gives rise to various phases in undoped silicene. Consequently, by probing the RKKY interaction, which contains all the information in the momentum space, differences between the topological phase and the trivial phase can be identified explicitly. Moreover, the change of chemical potential induced by the doping of silicene can also have a profound influence on the spatial behaviors of the RKKY interaction.

  16. Ruderman-Kittel-Kasuya-Yosida interaction at finite temperature: Graphene and bilayer graphene

    Science.gov (United States)

    Klier, N.; Shallcross, S.; Sharma, S.; Pankratov, O.

    2015-11-01

    We investigate the Ruderman-Kittel-Kasuya-Yosida (RKKY) interaction between magnetic impurities in both single layer and Bernal stacked bilayer graphene, finding a number of striking anomalies in the temperature dependence of this interaction. In undoped single layer graphene the strength of the RKKY interaction for substitutional impurities anomalously increases upon increasing temperature, an effect that persists up to and beyond room temperature. For impurities intercalated in the Bernal stacked bilayer and a doping that places the chemical potential near the antibonding band edge, a qualitative change of the RKKY interaction with temperature occurs: a low-temperature oscillatory interaction develops into a high-temperature antiferromagnetic coupling, accompanied by an overall increase of the interaction strength. The origin of the temperature anomalies can be traced back to specific features of the density of states: the vanishing density of states at the apex of the Dirac cone in single layer graphene, and the "kink" in the density of states at the antibonding band edge in the case of the Bernal bilayer.

  17. Theory of Temperature Dependence of the Magnetization in Rare-Earth-Transition-Metal Alloys

    DEFF Research Database (Denmark)

    Szpunar, B.; Lindgård, Per-Anker

    1977-01-01

    It is shown that the temperature dependence of the magnetic moments and Curie and ferrimagnetic compensation temperatures for Gdl-xTx (T = Co, Ni, and Fe) and Y1-xCox can be accounted for by a simple model assuming a RKKY interaction between the rare-earth moments and the transition-metal pseudo-spin......1-xCox durch ein einfaches Model1 erklärt werden können, das eine RKKY-Wechsel-wirkung zwischen den Momenten der Seltenen Erden und des Pseudo-Spins des Übergangsmetalls annimmt. Die Wechselwirkung wird durch ein effektives Legierungsmedium übermittelt, das mit der CPA-Theorie und elliptischen...

  18. SPOTing Acetyl-Lysine Dependent Interactions

    Directory of Open Access Journals (Sweden)

    Sarah Picaud

    2015-08-01

    Full Text Available Post translational modifications have been recognized as chemical signals that create docking sites for evolutionary conserved effector modules, allowing for signal integration within large networks of interactions. Lysine acetylation in particular has attracted attention as a regulatory modification, affecting chromatin structure and linking to transcriptional activation. Advances in peptide array technologies have facilitated the study of acetyl-lysine-containing linear motifs interacting with the evolutionary conserved bromodomain module, which specifically recognizes and binds to acetylated sequences in histones and other proteins. Here we summarize recent work employing SPOT peptide technology to identify acetyl-lysine dependent interactions and document the protocols adapted in our lab, as well as our efforts to characterize such bromodomain-histone interactions. Our results highlight the versatility of SPOT methods and establish an affordable tool for rapid access to potential protein/modified-peptide interactions involving lysine acetylation.

  19. Temperature dependence of the hyperfine interaction at

    Energy Technology Data Exchange (ETDEWEB)

    Lopez-Garcia, Alberto; de la Presa, Patricia; Ayala, Alejandro

    2001-06-01

    The temperature dependence of the quadrupole hyperfine parameters covering the temperature range from 293 to 1173 K was measured at {sup 181}Ta probes in SrHfO{sub 3} by perturbed angular correlation spectroscopy. A fluctuating distribution of quadrupole interactions model was applied to interpret the data. At low temperatures above {approximately}300 K a static, asymmetric, and distributed electric quadrupole interaction was detected. At intermediate temperatures ({approx}600 K) a different quadrupole interaction appears, characterized by a fluctuating distribution of axially symmetric electric field gradient tensors. Above 873 K, the unique presence of a nuclear spin relaxation mechanism shows a second change in the perturbation acting on probes. These changes in the hyperfine interaction are consistent with the structural phase transitions detected by diffraction techniques. The probe effects were also analyzed, comparing {sup 181}Ta with {sup 111}Cd experiments.

  20. Orbital and anisotropy effects on the itinerant exchange interaction in 3D Dirac semimetals

    Science.gov (United States)

    Ulloa, Sergio; Mastrogiuseppe, Diego; Sandler, Nancy

    Dirac semimetals are new materials that can be considered analogues of graphene in three dimensions. Their band structure exhibits robust Dirac points that are protected by crystalline symmetry, and strong spin-orbit interaction. These unusual properties suggest that magnetic impurities may reveal exotic behavior with potential technological importance. In metallic hosts, magnetic impurities interact through the electron gas via the Ruderman-Kittel-Kasuya-Yosida (RKKY) interaction that depends strongly on the band structure of the material. We report on the RKKY interaction in 3D Dirac semimetals, such as Na3Bi and Cd3As2. We discuss asymptotic expressions for the interaction corresponding to settings with magnetic impurities at different distances and relative angle with respect to high symmetry directions on the lattice. We show that the Fermi velocity anisotropy produces a strong renormalization of the magnitude of the interaction, and a correction to the frequency of oscillation in real space. Hybridization of the impurities to different conduction electron orbitals results in interesting anisotropic interactions which can generate spiral spin structures in doped samples

  1. Length-scale dependent phonon interactions

    CERN Document Server

    Srivastava, Gyaneshwar

    2014-01-01

    This book presents  a comprehensive description of phonons and their interactions in systems with different dimensions and length scales. Internationally-recognized leaders describe theories and measurements of phonon interactions  in relation to the design of materials with exotic properties such as metamaterials, nano-mechanical systems, next-generation electronic, photonic, and acoustic devices, energy harvesting, optical information storage, and applications of phonon lasers in a variety of fields. The emergence of techniques for control of semiconductor properties and geometry has enabled engineers to design structures in which functionality is derived from controlling electron behavior. As manufacturing techniques have greatly expanded the list of available materials and the range of attainable length scales, similar opportunities now exist for designing devices whose functionality is derived from controlling phonon behavior. However, progress in this area is hampered by gaps in our knowledge of phono...

  2. pH dependence of drug-membrane interaction

    Science.gov (United States)

    Basak, Uttam Kumar; Datta, Alokmay

    2014-04-01

    Langmuir monolayer technique has been used to understand the interaction of piroxicam, a NSAID of oxicam class with the DMPC half membrane. It has been found that drug-membrane interaction is dependent on the pH of the environment. The interaction slightly increases with pH in the range 2.5-6.5 whereas the interaction becomes stronger in the pH range 6.6-8.5. The mechanism of interaction has been explained considering the pH dependent molecular conformation and ionic state of drug and lipid molecules.

  3. Species interactions among larval mosquitoes: context dependence across habitat gradients.

    Science.gov (United States)

    Juliano, Steven A

    2009-01-01

    Biotic interactions involving mosquito larvae are context dependent, with effects of interactions on populations altered by ecological conditions. Relative impacts of competition and predation change across a gradient of habitat size and permanence. Asymmetrical competition is common and ecological context changes competitive advantage, potentially facilitating landscape-level coexistence of competitors. Predator effects on mosquito populations sometimes depend on habitat structure and on emergent effects of multiple predators, particularly interference among predators. Nonlethal effects of predators on mosquito oviposition, foraging, and life history are common, and their consequences for populations and for mosquito-borne disease are poorly understood. Context-dependent beneficial effects of detritus shredders on mosquitoes occur in container habitats, but these interactions appear to involve more than simple resource modification by shredders. Investigations of context-dependent interactions among mosquito larvae will yield greater understanding of mosquito population dynamics and provide useful model systems for testing theories of context dependence in communities.

  4. Spin-dependent effective interactions for halo nuclei

    CERN Document Server

    Garrido, E; Jensen, A S

    2003-01-01

    We discuss the spin-dependence of the effective two-body interactions appropriate for three-body computations. The only reasonable choice seems to be the fine and hyperfine interactions known for atomic electrons interacting with the nucleus. One exception is the nucleon-nucleon interaction imposing a different type of symmetry. We use the two-neutron halo nucleus 11Li as illustration. We demonstrate that models with the wrong spin-dependence are basically without predictive power. The Pauli forbidden core and valence states must be consistently treated.

  5. Low energy properties of the Kondo chain in the RKKY regime

    Science.gov (United States)

    Schimmel, D. H.; Tsvelik, A. M.; Yevtushenko, O. M.

    2016-05-01

    We study the Kondo chain in the regime of high spin concentration where the low energy physics is dominated by the Ruderman-Kittel-Kasuya-Yosida interaction. As has been recently shown (Tsvelik and Yevtushenko 2015 Phys. Rev. Lett. 115 216402), this model has two phases with drastically different transport properties depending on the anisotropy of the exchange interaction. In particular, the helical symmetry of the fermions is spontaneously broken when the anisotropy is of the easy plane type. This leads to a parametrical suppression of the localization effects. In the present paper we substantially extend the previous theory, in particular, by analyzing a competition of forward- and backward- scattering, including into the theory short range electron interactions and calculating spin correlation functions. We discuss applicability of our theory and possible experiments which could support the theoretical findings.

  6. Geometric influence on Ruderman-Kittel-Kasuya-Yosida interactions in zigzag carbon nanotubes.

    Science.gov (United States)

    Bunder, J E; Hill, James M

    2012-04-21

    We derive an analytic description of the spin susceptibility in finite length zigzag carbon nanotubes (CNT) with chirality (n, 0). The spin susceptibility is proportional to the Ruderman-Kittel-Kasuya-Yosida (RKKY) interactions which describes indirect carrier mediated exchange coupling between localized magnetic moments. We show that the strongest RKKY interactions are along the edges of the nanotube and in the thermodynamic limit at half filling with spin symmetry the shape of the susceptibility curve about the edge of the CNT can be determined solely by the lattice geometry represented by the parameter n and a parameter L which describes the nanotube length. We also show that the introduction of Zeeman splitting or doping may have no effect on the spin susceptibility, provided n is small. A detailed knowledge of magnetic interactions, such as RKKY interactions, in CNT is of vital importance to the development of nanotechnology applications.

  7. Magnetic shielding and exotic spin-dependent interactions

    CERN Document Server

    Kimball, D F Jackson; Li, Y; Thulasi, S; Pustelny, S; Budker, D; Zolotorev, M

    2016-01-01

    Experiments searching for exotic spin-dependent interactions typically employ magnetic shielding between the source of the exotic field and the interrogated spins. We explore the question of what effect magnetic shielding has on detectable signals induced by exotic fields. Our general conclusion is that for common experimental geometries and conditions, magnetic shields should not significantly reduce sensitivity to exotic spin-dependent interactions, especially when the technique of comagnetometry is used. However, exotic fields that couple to electron spin can induce magnetic fields in the interior of shields made of a soft ferro- or ferrimagnetic material. This induced magnetic field must be taken into account in the interpretation of experiments searching for new spin-dependent interactions and raises the possibility of using a flux concentrator inside magnetic shields to amplify exotic spin-dependent signals.

  8. Structural study of surfactant-dependent interaction with protein

    Energy Technology Data Exchange (ETDEWEB)

    Mehan, Sumit; Aswal, Vinod K., E-mail: vkaswal@barc.gov.in [Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400 085 (India); Kohlbrecher, Joachim [Laboratory for Neutron Scattering, Paul Scherrer Institut, CH-5232 PSI Villigen (Switzerland)

    2015-06-24

    Small-angle neutron scattering (SANS) has been used to study the complex structure of anionic BSA protein with three different (cationic DTAB, anionic SDS and non-ionic C12E10) surfactants. These systems form very different surfactant-dependent complexes. We show that the structure of protein-surfactant complex is initiated by the site-specific electrostatic interaction between the components, followed by the hydrophobic interaction at high surfactant concentrations. It is also found that hydrophobic interaction is preferred over the electrostatic interaction in deciding the resultant structure of protein-surfactant complexes.

  9. Sublattice dependent magnetic response of dual Cr doped graphene monolayer: a full potential approach

    Science.gov (United States)

    Thakur, Jyoti; Kashyap, Manish K.; Taya, Ankur; Rani, Priti; Saini, Hardev S.

    2017-01-01

    In the present scenario, many researchers are exploring the possibility of inducing a magnetic channel in graphene by introducing various types of defects. To examine the Cr-Cr interactions in dual Cr doped graphene monolayer for magnetic response and spin polarization, the first-principles density functional theory based calculations are performed. Further, the possibility of achieving 100 % spin polarization in various possible configurations of dual Cr-doping have been explored. Dual doping of Cr atoms in graphene monolayer preferring ferromagnetic ordering, generates a spin magnetic state with a local moment of 4.00 µB. Depending upon the relative position of two Cr impurities in graphene, the ground states of doped systems are found be ferromagnetic, antiferromagnetic or paramagnetic. The origin of particular magnetic state observed in all possible dual Cr-doping configurations has been explained on the basis of RKKY indirect exchange interactions.

  10. Gate-tunable indirect exchange interaction in spin-orbit-coupled mesoscopic rings

    Science.gov (United States)

    Nikoofard, H.; Heidari Semiromi, E.

    2015-05-01

    We study the carrier-mediated exchange interaction, the so-called Ruderman-Kittel-Kasuya-Yosida (RKKY) coupling, between two magnetic impurity moments embedded in a semiconductor mesoscopic ring. We treat the ring in the presence of an Aharonov-Bohm-type magnetic flux and the Rashba and Dresselhaus spin-orbit interactions (RSOI and DSOI). Energy eigenvalues of the system are obtained within a tight-binding framework and the strength of the indirect exchange interaction vs. RSOI strengths are plotted for different values of DSOI strength. The results show that the type of the impurity magnetic order, ferromagnetic (F) or antiferromagnetic (AF), depends on the RSOI and DSOI strengths. This leads to a full electrical control on the magnetic alignment of the system through, e.g., an external gate voltage.

  11. Medium mass fragments production due to momentum dependent interactions

    CERN Document Server

    Kumar, Sanjeev; Puri, Rajeev K; 10.1103/PhysRevC.78.064602

    2010-01-01

    The role of system size and momentum dependent effects are analyzed in multifragmenation by simulating symmetric reactions of Ca+Ca, Ni+Ni, Nb+Nb, Xe+Xe, Er+Er, Au+Au, and U+U at incident energies between 50 MeV/nucleon and 1000 MeV/nucleon and over full impact parameter zones. Our detailed study reveals that there exist a system size dependence when reaction is simulated with momentum dependent interactions. This dependence exhibits a mass power law behavior.

  12. On the Casimir Energy of Frequency Dependent Interactions

    CERN Document Server

    Graham, N; Weigel, H

    2014-01-01

    Vacuum polarization (or Casimir) energies can be straightforwardly computed from scattering data for static field configurations whose interactions with the fluctuating field are frequency independent. In effective theories, however,such interactions are typically frequency dependent. As a consequence, the relationship between scattering data and the Green's function is modified, which may or may not induce additional contributions to the vacuum polarization energy. We discuss several examples that naturally include frequency dependent interactions: (i) scalar electrodynamics with a static background potential, (ii) an effective theory that emerges from integrating out a heavy degree of freedom, and (iii) quantum electrodynamics coupled to a frequency dependent dielectric material. In the latter case, we argue that introducing dissipation as required by the Kramers-Kronig relations requires the consideration of the Casimir energy within a statistical mechanics formalism, while in the absence of dissipation we...

  13. Dependence of Isoscaling Parameters on Nucleon-Nucleon Cross Section and Momentum-Dependent Interaction

    Institute of Scientific and Technical Information of China (English)

    XING Yong-Zhong; HAO Huan-Feng; LIU Xiao-Bin; FANG Yu-Tian; LIU Bao-Yi

    2007-01-01

    @@ Influences of the isospin dependence of the in-medium nucleon-nucleon cross section and the momentum-dependent interaction (MDI) on the isotope scaling are investigated by using the isospin-dependent quantum molecular dynamics model (IQMD). The results show that both the isospin dependence of the in-medium nucleon-nucleon cross section and the momentum-dependent interaction affect the isoscaling parameters appreciably and independently. The influence caused by the isospin dependence of two-body collision is relatively larger than that from the MDI in the mean field. Aiming at exploring the implication of isoscaling behaviour, which the statistical equilibrium in the reaction is reached, the statistical properties in the mass distribution and the kinetic energy distribution of the fragments simulated by IQMD are presented.

  14. Spin-Lattice Order in One-Dimensional Conductors: Beyond the RKKY Effect

    Science.gov (United States)

    Schecter, Michael; Rudner, Mark S.; Flensberg, Karsten

    2015-06-01

    We investigate magnetic order in a lattice of classical spins coupled to an isotropic gas of one-dimensional conduction electrons via local exchange interactions. The frequently discussed Ruderman-Kittel-Kasuya-Yosida effective exchange model for this system predicts that spiral order is always preferred. Here we consider the problem nonperturbatively, and find that such order vanishes above a critical value of the exchange coupling that depends strongly on the lattice spacing. The critical coupling tends to zero as the lattice spacing becomes commensurate with the Fermi wave vector, signaling the breakdown of the perturbative Ruderman-Kittel-Kasuya-Yosida picture, and spiral order, even at weak coupling. We provide the exact phase diagram for arbitrary exchange coupling and lattice spacing, and discuss its stability. Our results shed new light on the problem of utilizing a spiral spin-lattice state to drive a one-dimensional superconductor into a topological phase.

  15. Identification of Redox and Glucose-Dependent Txnip Protein Interactions

    Directory of Open Access Journals (Sweden)

    Benjamin J. Forred

    2016-01-01

    Full Text Available Thioredoxin-interacting protein (Txnip acts as a negative regulator of thioredoxin function and is a critical modulator of several diseases including, but not limited to, diabetes, ischemia-reperfusion cardiac injury, and carcinogenesis. Therefore, Txnip has become an attractive therapeutic target to alleviate disease pathologies. Although Txnip has been implicated with numerous cellular processes such as proliferation, fatty acid and glucose metabolism, inflammation, and apoptosis, the molecular mechanisms underlying these processes are largely unknown. The objective of these studies was to identify Txnip interacting proteins using the proximity-based labeling method, BioID, to understand differential regulation of pleiotropic Txnip cellular functions. The BioID transgene fused to Txnip expressed in HEK293 identified 31 interacting proteins. Many protein interactions were redox-dependent and were disrupted through mutation of a previously described reactive cysteine (C247S. Furthermore, we demonstrate that this model can be used to identify dynamic Txnip interactions due to known physiological regulators such as hyperglycemia. These data identify novel Txnip protein interactions and demonstrate dynamic interactions dependent on redox and glucose perturbations, providing clarification to the pleiotropic cellular functions of Txnip.

  16. RKKY-like contributions to the magnetic anisotropy energy: 3 d adatoms on Pt(111) surface

    Science.gov (United States)

    Bouhassoune, Mohammmed; Dias, Manuel dos Santos; Zimmermann, Bernd; Dederichs, Peter H.; Lounis, Samir

    2016-09-01

    The magnetic anisotropy energy defines the energy barrier that stabilizes a magnetic moment. Utilizing density-functional-theory-based simulations and analytical formulations, we establish that this barrier is strongly modified by long-range contributions very similar to Friedel oscillations and Rudermann-Kittel-Kasuya-Yosida interactions. Thus, oscillations are expected and observed, with different decaying factors and highly anisotropic in realistic materials, which can switch nontrivially the sign of the magnetic anisotropy energy. This behavior is general, and for illustration we address the transition-metal adatoms, Cr, Mn, Fe, and Co deposited on a Pt(111) surface. We explain, in particular, the mechanisms leading to the strong site dependence of the magnetic anisotropy energy observed for Fe adatoms on a Pt(111) surface as revealed previously via first-principles-based simulations and inelastic scanning tunneling spectroscopy [A. A. Khajetoorians et al., Phys. Rev. Lett. 111, 157204 (2013), 10.1103/PhysRevLett.111.157204]. The same mechanisms are probably active for the site dependence of the magnetic anisotropy energy obtained for Fe adatoms on Pd or Rh(111) surfaces and for Co adatoms on a Rh(111) surface [P. Blonski et al., Phys. Rev. B 81, 104426 (2010), 10.1103/PhysRevB.81.104426].

  17. Evolutionary games with coordination and self-dependent interactions

    Science.gov (United States)

    Király, Balázs; Szabó, György

    2017-01-01

    Multistrategy evolutionary games are studied on a square lattice when the pair interactions are composed of coordinations between strategy pairs and an additional term with self-dependent payoff. We describe a method for determining the strength of each elementary coordination component in n -strategy potential games. Using analytical and numerical methods, the presence and absence of Ising-type order-disorder phase transitions are studied when a single pair coordination is extended by some types of self-dependent elementary games. We also introduce noise-dependent three-strategy equivalents of the n -strategy elementary coordination games.

  18. Statistical thermodynamics of fluids with orientation-dependent interactions.

    NARCIS (Netherlands)

    Besseling, N.A.M.

    1993-01-01

    The aim of the present study was to develop a lattice theory for systems, homogeneous as well as heterogeneous, containing molecules with orientation- dependent interactions such as water. It was soon recognised that the so-called Bragg-Williams mean-field approximation is not capable of reproducing

  19. From networks of protein interactions to networks of functional dependencies

    Directory of Open Access Journals (Sweden)

    Luciani Davide

    2012-05-01

    Full Text Available Abstract Background As protein-protein interactions connect proteins that participate in either the same or different functions, networks of interacting and functionally annotated proteins can be converted into process graphs of inter-dependent function nodes (each node corresponding to interacting proteins with the same functional annotation. However, as proteins have multiple annotations, the process graph is non-redundant, if only proteins participating directly in a given function are included in the related function node. Results Reasoning that topological features (e.g., clusters of highly inter-connected proteins might help approaching structured and non-redundant understanding of molecular function, an algorithm was developed that prioritizes inclusion of proteins into the function nodes that best overlap protein clusters. Specifically, the algorithm identifies function nodes (and their mutual relations, based on the topological analysis of a protein interaction network, which can be related to various biological domains, such as cellular components (e.g., peroxisome and cellular bud or biological processes (e.g., cell budding of the model organism S. cerevisiae. Conclusions The method we have described allows converting a protein interaction network into a non-redundant process graph of inter-dependent function nodes. The examples we have described show that the resulting graph allows researchers to formulate testable hypotheses about dependencies among functions and the underlying mechanisms.

  20. Saturating interactions in /sup 4/He with density dependence

    Energy Technology Data Exchange (ETDEWEB)

    Bloom, S.D.; Resler, D.A.; Moszkowski, S.A.

    1989-05-03

    With the advent of larger and faster computers, as well as modern shell model codes, nuclear structure calculations for the light nuclei (A<16) which include full 2/bar h/..omega.. model spaces are quite feasible. However, there can be serious problems in the mixing of 2/bar h/..omega.. and higher excitations into the low-lying spectra if the effective interaction is non-saturating. Furthermore, effective interactions which are both saturating and density dependent have not generally been used in previous nuclear structure calculations. Therefore, we have undertaken studies of /sup 4/He using two-body potential interactions which incorporate both saturation and density-dependence. Encouraging initial results in remedying the mixing of 0 and 2/bar h/..omega.. excitations have been obtained. We have also considered the effects of our interaction on the /sup 4/He compressibility and the centroid of the breathing mode strength. First indications are that a saturating effective interaction, with a short-range density dependent part and a long-range density independent part, comes close to matching crude predictions for the compressibility of /sup 4/He. 11 refs., 6 tabs.

  1. Interactive Approach to Negotiating Styles Dependent on Personality Traits

    Directory of Open Access Journals (Sweden)

    Anna Grabowska

    2016-03-01

    Full Text Available Purpose: This study was of a theoretical character and aimed at presenting various descriptions of the interactions between all possible pairs of four well-known negotiating styles dependent on personality traits. Methodology: This study was based on analysis of the interactions as well as authors’ experiences from their observations and analyses on human behaviors during numerous negotiations and roleplay exercises arranged at the courses for practitioners. The stress was put on analyzing the interactions occurring between people representing both different and the same negotiating styles. Findings: The attempt at describing such interactions was successful and promising for farther research. The concept constitutes a useful tool for analyzing human behavioral aspects of different types of business negotiations, within the process of their planning, conduct and evaluation. Nevertheless, the concept will be a subject of subsequent authors’ research, focusing on its improvement mainly by searching more precise features of negotiating styles and interactions between them. Practical implications: The concept can be applied to analyze many real negotiation situations as well as within the experiment to be arranged by the authors to examine those interactions within the hundreds of pairs of negotiators solving particular case studies. Thus the description of such interactions can be treated as a specifc hypothesis. Originality: In general, the suggestion for solving complex, diffcult and essential issues of negotiating styles was presented but was rarely investigated in the literature on negotiations. In particular, an original concept of describing the interactions between those styles was suggested,.

  2. Even-Odd Effects of Heisenberg Chains on Long-range Interaction and Entanglement

    CERN Document Server

    Oh, Sangchul; Hu, Xuedong

    2010-01-01

    A strongly coupled Heisenberg chain provides an important channel for quantum communication through its many-body ground state. Yet, the nature of the effective interactions and the ability to mediate long-range entanglement differs significantly for chains of opposite parity. Here, we contrast the characters of even and odd-size chains when they are coupled to external qubits. Additional parity effects emerge in both cases, depending on the positions of the attached qubits. Some striking results include (i) the emergence of maximal entanglement and (ii) Ruderman-Kittel-Kasuya-Yosida (RKKY) interactions for qubits attached to an even chain, and (iii) the ability of chains of either parity to mediate qubit entanglement that is undiminished by distance.

  3. Interactive View-Dependent Rendering of Large Isosurfaces

    Energy Technology Data Exchange (ETDEWEB)

    Gregorski, B; Duchaineau, M; Lindstrom, P; Pascucci, V; Joy, K I

    2002-11-19

    We present an algorithm for interactively extracting and rendering isosurfaces of large volume datasets in a view-dependent fashion. A recursive tetrahedral mesh refinement scheme, based on longest edge bisection, is used to hierarchically decompose the data into a multiresolution structure. This data structure allows fast extraction of arbitrary isosurfaces to within user specified view-dependent error bounds. A data layout scheme based on hierarchical space filling curves provides access to the data in a cache coherent manner that follows the data access pattern indicated by the mesh refinement.

  4. Two stages of Kondo effect and competition between RKKY and Kondo in Gd-based intermetallic compound

    Energy Technology Data Exchange (ETDEWEB)

    Vaezzadeh, Mehdi [Department of Physics, K.N.Toosi University of Technology, P.O. Box 15875-4416, Tehran (Iran, Islamic Republic of)]. E-mail: mehdi@kntu.ac.ir; Yazdani, Ahmad [Tarbiat Modares University, P.O. Box 14155-4838, Tehran (Iran, Islamic Republic of); Vaezzadeh, Majid [Department of Physics, K.N.Toosi University of Technology, P.O. Box 15875-4416, Tehran (Iran, Islamic Republic of); Daneshmand, Gissoo [Department of Physics, K.N.Toosi University of Technology, P.O. Box 15875-4416, Tehran (Iran, Islamic Republic of); Kanzeghi, Ali [Department of Physics, K.N.Toosi University of Technology, P.O. Box 15875-4416, Tehran (Iran, Islamic Republic of)

    2006-05-01

    The magnetic behavior of Gd-based intermetallic compound (Gd{sub 2}Al{sub (1-x)}Au{sub x}) in the form of the powder and needle, is investigated. All the samples are an orthorhombic crystal structure. Only the compound with x=0.4 shows the Kondo effect (other compounds have a normal behavior). Although, for the compound in the form of powder, with x=0.4, the susceptibility measurement {chi}(T) shows two different stages. Moreover for (T>T{sub K2}) a fall of the value of {chi}(T) is observable, which indicates a weak presence of ferromagnetic phase. About the two stages of Kondo effect, we observe at the first (T{sub K1}) an increase of {chi}(T) and in the second stage (T{sub K2}) a new remarkable decrease of {chi}(T) (T{sub K1}>T{sub K2}). For the sample in the form of needles, the first stage is observable only under high magnetic field. This first stage could be corresponds to a narrow resonance between Kondo cloud and itinerant electron. The second stage, which is remarkably visible for the sample in the form of the powder, can be attribute to a complete polarization of Kondo cloud. Observation of these two Kondo stages could be due to the weak presence of RKKY contribution.

  5. Dilute RKKY model for NMR line broadening in the hidden-order state of URu2Si2

    Science.gov (United States)

    Walstedt, R. E.; Kambe, S.; Tokunaga, Y.; Sakai, H.

    2016-01-01

    A well-known analytic model for Lorentzian broadening of metallic NMR lines by dilute localized magnetic centers embedded in a lattice has been applied to the case of the twofold-symmetry magnetism in URu2Si2 reported by R. Okazaki et al. [Science 331, 439 (2011), 10.1126/science.1197358]. The observed Lorentzian spectra are accounted for with a simple formula giving the 29Si NMR linewidth in terms of the susceptibility of the magnetic-broadening centers and a Ruderman-Kittel-Kasuya-Yosida (RKKY) coupling parameter. The concentration of such centers is estimated as c ˜0.01 . A numerical simulation of these effects confirms Lorentzian broadening with no measurable NMR shift and a width in reasonable agreement with the analytical model. The simulation shows further that domain effects on these spectra are largely absent. A four-site extended model of the broadening centers gives an estimate of the twofold susceptibility within a factor of 2 of the torque value of the susceptibility. Hypothetical superlattice effects are shown to be easily smoothed over by convolution with background Lorentzian broadening.

  6. Monojet searches for momentum-dependent dark matter interactions

    CERN Document Server

    Barducci, Daniele; Desai, Nishita; Frigerio, Michele; Fuks, Benjamin; Goudelis, Andreas; Kulkarni, Suchita; Polesello, Giacomo; Sengupta, Dipan

    2016-01-01

    We consider minimal dark matter scenarios featuring momentum-dependent couplings of the dark sector to the Standard Model. We derive constraints from existing LHC searches in the monojet channel, estimate the future LHC sensitivity for an integrated luminosity of 300 fb$^{-1}$, and compare with models exhibiting conventional momentum-independent interactions with the dark sector. In addition to being well motivated by (composite) pseudo-Goldstone dark matter scenarios, momentum-dependent couplings are interesting as they weaken direct detection constraints. For a specific dark matter mass, the LHC turns out to be sensitive to smaller signal cross-sections in the momentum-dependent case, by virtue of the harder jet transverse-momentum distribution.

  7. Incorporating Context Dependency of Species Interactions in Species Distribution Models.

    Science.gov (United States)

    Lany, Nina K; Zarnetske, Phoebe L; Gouhier, Tarik C; Menge, Bruce A

    2017-07-01

    Species distribution models typically use correlative approaches that characterize the species-environment relationship using occurrence or abundance data for a single species. However, species distributions are determined by both abiotic conditions and biotic interactions with other species in the community. Therefore, climate change is expected to impact species through direct effects on their physiology and indirect effects propagated through their resources, predators, competitors, or mutualists. Furthermore, the sign and strength of species interactions can change according to abiotic conditions, resulting in context-dependent species interactions that may change across space or with climate change. Here, we incorporated the context dependency of species interactions into a dynamic species distribution model. We developed a multi-species model that uses a time-series of observational survey data to evaluate how abiotic conditions and species interactions affect the dynamics of three rocky intertidal species. The model further distinguishes between the direct effects of abiotic conditions on abundance and the indirect effects propagated through interactions with other species. We apply the model to keystone predation by the sea star Pisaster ochraceus on the mussel Mytilus californianus and the barnacle Balanus glandula in the rocky intertidal zone of the Pacific coast, USA. Our method indicated that biotic interactions between P. ochraceus and B. glandula affected B. glandula dynamics across >1000 km of coastline. Consistent with patterns from keystone predation, the growth rate of B. glandula varied according to the abundance of P. ochraceus in the previous year. The data and the model did not indicate that the strength of keystone predation by P. ochraceus varied with a mean annual upwelling index. Balanus glandula cover increased following years with high phytoplankton abundance measured as mean annual chlorophyll-a. M. californianus exhibited the same

  8. Steady State and Dynamics of Joule Heating in Magnetic Tunnel Junctions Observed via the Temperature Dependence of RKKY Coupling

    Science.gov (United States)

    Chavent, A.; Ducruet, C.; Portemont, C.; Vila, L.; Alvarez-Hérault, J.; Sousa, R.; Prejbeanu, I. L.; Dieny, B.

    2016-09-01

    Understanding quantitatively the heating dynamics in magnetic tunnel junctions submitted to current pulses is very important in the context of spin-transfer-torque magnetic random-access memory development. Here we provide a method to probe the heating of magnetic tunnel junctions using the Ruderman-Kittel-Kasuya-Yoshida coupling of a synthetic ferrimagnetic storage layer as a thermal sensor. The temperature increase versus applied bias voltage is measured thanks to the decrease of the spin-flop field with temperature. This method allows distinguishing spin-transfer torque effects from the influence of temperature on the switching field. The heating dynamics is then studied in real time by probing the conductance variation due to spin-flop rotation during heating. This approach provides a method for measuring fast heating in spintronic devices, particularly magnetic random-access memory using thermally assisted or spin-transfer torque writing.

  9. Framework to study dynamic dependencies in networks of interacting processes.

    Science.gov (United States)

    Chicharro, Daniel; Ledberg, Anders

    2012-10-01

    The analysis of dynamic dependencies in complex systems such as the brain helps to understand how emerging properties arise from interactions. Here we propose an information-theoretic framework to analyze the dynamic dependencies in multivariate time-evolving systems. This framework constitutes a fully multivariate extension and unification of previous approaches based on bivariate or conditional mutual information and Granger causality or transfer entropy. We define multi-information measures that allow us to study the global statistical structure of the system as a whole, the total dependence between subsystems, and the temporal statistical structure of each subsystem. We develop a stationary and a nonstationary formulation of the framework. We then examine different decompositions of these multi-information measures. The transfer entropy naturally appears as a term in some of these decompositions. This allows us to examine its properties not as an isolated measure of interdependence but in the context of the complete framework. More generally we use causal graphs to study the specificity and sensitivity of all the measures appearing in these decompositions to different sources of statistical dependence arising from the causal connections between the subsystems. We illustrate that there is no straightforward relation between the strength of specific connections and specific terms in the decompositions. Furthermore, causal and noncausal statistical dependencies are not separable. In particular, the transfer entropy can be nonmonotonic in dependence on the connectivity strength between subsystems and is also sensitive to internal changes of the subsystems, so it should not be interpreted as a measure of connectivity strength. Altogether, in comparison to an analysis based on single isolated measures of interdependence, this framework is more powerful to analyze emergent properties in multivariate systems and to characterize functionally relevant changes in the

  10. Superdeformed rotational bands with density dependent pairing interactions

    Energy Technology Data Exchange (ETDEWEB)

    Terasaki, J. [Service de Physique Nucleaire Theorique, Brussels (Belgium); Heenen, P.H. [Service de Physique Nucleaire Theorique, Brussels (Belgium); Bonche, P. [SPhT - CE Saclay, 91191 Gif-sur-Yvette Cedex (France); Dobaczewski, J. [Institute of Theoretical Physics, Warsaw University, Hoza 69, PL-00-681 Warsaw (Poland); Flocard, H. [Division de Physique Theorique, Institut de Physique Nucleaire, 91406 Orsay Cedex (France)

    1995-10-09

    The cranked Hartree-Fock-Bogoliubov method, applied in a previous study to SD bands of even Hg and Pb isotopes, is extended by including pairing correlations described by a zero-range density-dependent interaction. This more realistic description of the pairing channel modifies the balance between the neutron and proton pairing energies and introduces an orbital variation of the pairing gaps. This results in a retarded alignment, significantly improving the agreement with data in both the A=150 and 190 mass regions. The behavior expected for SD bands in odd-N or odd-Z nuclei is discussed on the basis of the quasiparticle routhians calculated for the even-even isotopes. (orig.).

  11. Superdeformed rotational bands with density dependent pairing interactions

    Science.gov (United States)

    Terasaki, J.; Heenen, P.-H.; Bonche, P.; Dobaczewski, J.; Flocard, H.

    1995-02-01

    The cranked Hartree-Fock-Bogoliubov method, applied in a previous study to SD bands of even Hg and Pb isotopes, is extended by including pairing correlations described by a zero-range density-dependent interaction. This more realistic description of the pairing channel modifies the balance between the neutron and proton pairing energies and introduces an orbital variation of the pairing gaps. This results in a retarded alignment, significantly improving the agreement with data in both the A = 150 and 190 mass regions. The behavior expected for SD bands in odd- N or odd- Z nuclei is discussed on the basis of the quasiparticle routhians calculated for the even-even isotopes.

  12. Analyse en d\\'ependances \\`a l'aide des grammaires d'interaction

    CERN Document Server

    Marchand, Jonathan; Perrier, Guy

    2009-01-01

    This article proposes a method to extract dependency structures from phrase-structure level parsing with Interaction Grammars. Interaction Grammars are a formalism which expresses interactions among words using a polarity system. Syntactical composition is led by the saturation of polarities. Interactions take place between constituents, but as grammars are lexicalized, these interactions can be translated at the level of words. Dependency relations are extracted from the parsing process: every dependency is the consequence of a polarity saturation. The dependency relations we obtain can be seen as a refinement of the usual dependency tree. Generally speaking, this work sheds new light on links between phrase structure and dependency parsing.

  13. Hidden symmetry and enhanced Rudermann-Kittel-Kasuya-Yosida interaction in P-N junctions of two-dimensional materials

    Science.gov (United States)

    Yang, Wen; Zhang, Shuhui; Zhu, Jiaji; Chang, Kai

    Correlation between magnetic atoms (spins) in non-magnetic two-dimensional (2D) systems and materials is one of the central issues in condensed matter physics. Engineering this correlation relies heavily on the carrier-mediated Rudermann-Kittel- Kasuya-Yosida (RKKY) interaction. However, tailoring and direct detection of spin-spin correlation has been limited to spins separated by a few nanometers due to the rapid 1 /R2 decay of RKKY interaction with inter-spin distance R. Here we reveal a hidden symmetry - absent from the Hamiltonian - in planar P-N junctions, which could qualitatively change the spatial scaling of various response functions in a wide range of 2D systems and materials. In particular, it allows RKKY interaction to attain 1 / R decay, the slowest decay in extended systems. This dramatically enhances RKKY interaction and enables long-range correlation between distant spins, with applications in nanoscale magnetism, spintronics, and solid-state quantum computation. This work was supported by the MOST (Grant No. 2015CB921503, and No. 2014CB848700) and NSFC (Grant No. 11434010, No. 11274036, No. 11322542, and No. 11404043).

  14. Nonbonded interactions in membrane active cyclic biopolymers. IV - Cation dependence

    Science.gov (United States)

    Radhakrishnan, R.; Srinivasan, S.; Prasad, C. V.; Brinda, S. R.; Macelroy, R. D.; Sundaram, K.

    1980-01-01

    Interactions of valinomycin and form of its analogs in several conformations with the central ions Li(+), Na(+), K(+), Rb(+) and Cs(+) are investigated as part of a study of the specific preference of valinomycin for potassium and the mechanisms of carrier-mediated ion transport across membranes. Ion binding energies and conformational potential energies are calculated taking into account polarization energy formulas and repulsive energy between the central ion and the ligand atoms for conformations representing various stages in ion capture and release for each of the two ring chiralities of valinomycin and its analogs. Results allow the prediction of the chirality and conformation most likely to be observed for a given analog, and may be used to synthesize analogs with a desired rigidity or flexibility. The binding energies with the alkali metal cations are found to decrease with increasing ion size, and to be smaller than the corresponding ion hydration energies. It is pointed out that the observed potassium preference may be explainable in terms of differences between binding and hydration energies. Binding energies are also noted to depend on ligand conformation.

  15. Location-dependent excitatory synaptic interactions in pyramidal neuron dendrites.

    Directory of Open Access Journals (Sweden)

    Bardia F Behabadi

    Full Text Available Neocortical pyramidal neurons (PNs receive thousands of excitatory synaptic contacts on their basal dendrites. Some act as classical driver inputs while others are thought to modulate PN responses based on sensory or behavioral context, but the biophysical mechanisms that mediate classical-contextual interactions in these dendrites remain poorly understood. We hypothesized that if two excitatory pathways bias their synaptic projections towards proximal vs. distal ends of the basal branches, the very different local spike thresholds and attenuation factors for inputs near and far from the soma might provide the basis for a classical-contextual functional asymmetry. Supporting this possibility, we found both in compartmental models and electrophysiological recordings in brain slices that the responses of basal dendrites to spatially separated inputs are indeed strongly asymmetric. Distal excitation lowers the local spike threshold for more proximal inputs, while having little effect on peak responses at the soma. In contrast, proximal excitation lowers the threshold, but also substantially increases the gain of distally-driven responses. Our findings support the view that PN basal dendrites possess significant analog computing capabilities, and suggest that the diverse forms of nonlinear response modulation seen in the neocortex, including uni-modal, cross-modal, and attentional effects, could depend in part on pathway-specific biases in the spatial distribution of excitatory synaptic contacts onto PN basal dendritic arbors.

  16. Peculiarities of hearing impairment depending on interaction with acoustic stimuli

    Science.gov (United States)

    Myshchenko, Iryna; Nazarenko, Vasyl; Kolganov, Anatoliy; Tereshchenko, Pavlo

    2015-01-01

    Aims: The functional state of the auditory analyzer of several operators groups was study. The objective of this study was to determine some characteristics of hearing impairment in relation with features of acoustic stimuli and informative significance of noise. Materials and Methods: 236 employees (middle age 35.4 ± 0.74 years) were divided into four groups according to features of noise perception at the workplaces. The levels of permanent shifts of acoustic thresholds were estimated using audiometric method. Statistical Analysis Used: Common statistical methods were used in research. Mean quantity and mean absolute errors were calculated. Statistical significance between operators' groups was calculated with 0.05 confidential intervals. Results: The peculiarities of hearing impairment in observed groups were different. Operators differentiating acoustic signals had peak of hearing impairment in the field of language frequencies, while the employees who work with noise background at the workplaces had maximal hearing threshold on the 4000 Hz frequency (P ≤ 0.05). Conclusions: Hearing impairment depends both on energy and human interaction with acoustic irritant. The distinctions in hearing impairment may be related with the necessity of recognizing of acoustic signals and their frequency characteristics. PMID:26957812

  17. Inheritance of Polycomb-dependent chromosomal interactions in Drosophila

    Science.gov (United States)

    Bantignies, Frédéric; Grimaud, Charlotte; Lavrov, Sergey; Gabut, Mathieu; Cavalli, Giacomo

    2003-01-01

    Maintenance of cell identity is a complex task that involves multiple layers of regulation, acting at all levels of chromatin packaging, from nucleosomes to folding of chromosomal domains in the cell nucleus. Polycomb-group (PcG) and trithorax-group (trxG) proteins maintain memory of chromatin states through binding at cis-regulatory elements named PcG response elements or cellular memory modules. Fab-7 is a well-defined cellular memory module involved in regulation of the homeotic gene Abdominal-B (Abd-B). In addition to its action in cis, we show here by three-dimensional FISH that the Fab-7 element leads to association of transgenes with each other or with the endogenous Fab-7, even when inserted in different chromosomes. These long-distance interactions enhance PcG-mediated silencing. They depend on PcG proteins, on DNA sequence homology, and on developmental progression. Once long-distance pairing is abolished by removal of the endogenous Fab-7, the derepressed chromatin state induced at the transgene locus can be transmitted through meiosis into a large fraction of the progeny, even after reintroduction of the endogenous Fab-7. Strikingly, meiotic inheritance of the derepressed state involves loss of pairing between endogenous and transgenic Fab-7. This suggests that transmission of nuclear architecture through cell division might contribute to inheritance of chromatin states in eukaryotes. PMID:14522946

  18. A trapped ion with time-dependent frequency interaction with a laser field

    Energy Technology Data Exchange (ETDEWEB)

    MartInez, J M Vargas; Moya-Cessa, H [INAOE, Apartado Postal 51 y 216, 72000 Puebla (Mexico)

    2004-06-01

    We analyse the problem of a trapped ion with time-dependent frequency interacting with a laser field. By using a set of unitary time-dependent transformations we show that this system is equivalent to the interaction between a quantized field and a double level with time-dependent interaction parameters. In passing, we show that in the on-resonance case different vibrational transitions may be achieved by using time-dependent parameters.

  19. Exposure-dependent misclassification of exposure in interaction analyses

    DEFF Research Database (Denmark)

    Lundberg, Mats; Hallqvist, J; Diderichsen, Finn

    1999-01-01

    The objectives of this paper are to analyze the consequences of exposure misclassification on effect estimates in interaction analysis, and to develop a mathematical equation for the potentially biased estimate. The main point is to identify situations in which misclassification of the first expo...

  20. Neutron diffraction test on spin-dependent short range interaction

    CERN Document Server

    Voronin, V V

    2008-01-01

    In this short note we discuss the possibility to get the constraint on the parameters of short range pseudomagnetic interaction of free neutron with matter from the crystal-diffraction experiment. It is demonstrated that for range of $\\lambda<10^{-6}$m this constraint can be a few order better than in any other method.

  1. Signature of time-dependent hydrodynamic interactions on collective diffusion in colloidal monolayers

    Science.gov (United States)

    Domínguez, Alvaro

    2014-12-01

    It has been shown recently that the coefficient of collective diffusion in a colloidal monolayer is divergent due to the hydrodynamic interactions mediated by the ambient fluid in bulk. The analysis is extended to allow for time-dependent hydrodynamic interactions. Observational features specific to this time dependency are predicted. The possible experimental detection in the dynamics of the monolayer is discussed.

  2. Spin-dependent recombination and hyperfine interaction at deep defects

    Science.gov (United States)

    Ivchenko, E. L.; Bakaleinikov, L. A.; Kalevich, V. K.

    2015-05-01

    We present a theoretical study of optical electron-spin orientation and spin-dependent Shockley-Read-Hall recombination in the longitudinal magnetic field, taking into account the hyperfine coupling between the bound-electron spin and the nuclear spin of a deep paramagnetic center. The master rate equations for the coupled system are extended to describe the nuclear spin relaxation by using two distinct relaxation times, τn 1 and τn 2, respectively, for defect states with one and two (singlet) bound electrons. The general theory is developed for an arbitrary value of the nuclear spin I . The magnetic-field and excitation-power dependencies of the electron and nuclear spin polarizations are calculated for the value of I =1 /2 . In this particular case the nuclear effects can be taken into account by a simple replacement of the bound-electron spin relaxation time by an effective time dependent on free-electron and hole densities and free-electron spin polarization. The role of nuclear spin relaxation is visualized by isolines of the electron spin polarization on a two-dimensional graph with the axes log2(τn 1) and log2(τn 2) .

  3. Effect of interband interactions on the pressure dependence on transition temperature of MgB2

    Science.gov (United States)

    Ogbuu, Okechukwu A.; Abah, Obinna

    2015-12-01

    A two-band BCS model with interactions, both phonon and non-phonon induced interactions, were employed to investigate the pressure dependence on superconducting transition temperature of two-band superconductor. We derived the transition temperature and its pressure dependence within Bogoliubov--Valatin formalism for magnesium diboride superconductor. We examined the influence of interband interactions on transition temperature at varying pressure and analyzed the relevance of this calculation in magnesium diboride, MgB2.

  4. Multiparton Interactions with an x-dependent Proton Size

    CERN Document Server

    Corke, Richard

    2011-01-01

    Theoretical arguments, supported by other indirect evidence, suggest that the wave function of high-x partons should be narrower than that of low-x ones. In this article, we present a modification to the variable impact parameter framework of Pythia 8 to model this effect. In particular, a Gaussian hadronic matter profile is introduced, with a width dependent on the x value of the constituent being probed. Results are compared against the default single- and double-Gaussian profiles, as well as an intermediate overlap function.

  5. The task dependent interaction of the deactivation regions

    Institute of Scientific and Technical Information of China (English)

    ZHANG Ye; FENG ShiGang; FENG HongBo; DONG Feng; TANG YiYuan

    2008-01-01

    Although deactivation has been found frequently in former functional brain imaging researches, only recently has it become a focus of systematic study because of its not well understood physiological mechanism. However, most of the researches concentrated on the brain areas that would present de-activation, and, to our knowledge, the deactivation connectivity between these brain areas during the cognitive tasks has rarely been reported in literature. In this work, using the functional connectivity method WlCA (within-condition interregional covariance analysis), we analyzed the deactivations in two different cognitive tasks-symbol orientation and number comparison. The results revealed de-activations in the posterior cingulate, precuneus, anterior cingulate and prefrontal cortex in both tasks. However, the interaction between the deactivated regions shows many differences. Our result further indicates that the potential implication of special deactivation connectivity may be related to the dif-ferent task or attention resource. Further research is needed to clarify the exact reason.

  6. Time-dependent interactions between iboga agents and cocaine.

    Science.gov (United States)

    Maisonneuve, I M; Visker, K E; Mann, G L; Bandarage, U K; Kuehne, M E; Glick, S D

    1997-10-08

    The purpose of this study was to clarify the effects of iboga agents on cocaine-induced hyperactivity. Both inhibition and enhancement of cocaine-induced activity by ibogaine have been reported. In the present study, rats were treated with either ibogaine (40 mg/kg, i.p.), noribogaine (40 mg/kg, i.p.), 18-methoxycoronaridine (40 mg/kg, i.p.), or saline, 1 or 19 h prior to the administration of cocaine (20 mg/kg, i.p.) or saline. Motor activity was monitored thereafter for 3 h. All three iboga agents had acute inhibitory effects and delayed potentiating effects on cocaine-induced hyperactivity. These time-dependent effects, which could not be attributed to the motor activity induced by the iboga agents alone, account for divergent results reported in the literature.

  7. Temperature Dependent Variations of Phonon Interactions in Nanocrystalline Cerium Oxide

    Directory of Open Access Journals (Sweden)

    Sugandha Dogra Pandey

    2015-01-01

    Full Text Available The temperature dependent anharmonic behavior of the phonon modes of nanocrystalline CeO2 was investigated in the temperature range of 80–440 K. The anharmonic constants have been derived from the shift in phonon modes fitted to account for the anharmonic contributions as well as the thermal expansion contribution using the high pressure parameters derived from our own high pressure experimental data reported previously. The total anharmonicity has also been estimated from the true anharmonicity as well as quasiharmonic component. In the line-width variation analysis, the cubic anharmonic term was found to dominate the quartic term. Finally, the phonon lifetime also reflected the trend so observed.

  8. [Interaction of nurses and women caring informally for dependent persons].

    Science.gov (United States)

    Delicado Useros, M V; Candel Parra, E; Alfaro Espín, A; López Máñez, M; García Borge, C

    2004-03-15

    To find the attitudes that primary care nurses in Albacete have towards family carers. Qualitative research using discussion groups. Primary care in Albacete: 5 health centres, 2 rural and 3 urban. Nurses following a primary care home visit programme, of both sexes, differing experience and training, and coming from both rural and urban areas took part. Exclusion criterion: nurses in management and administrative posts at time of recruitment. They were recruited by primary care nurses in line with the profiles of participants required. Information was collected through discussion in the groups, which was recorded and later transcribed for analysis. Those taking part in the 2 discussion groups had the following characteristics: 3 men and 8 women. 5 of them were from rural health centres (HC) and 6 from urban HC; 3 had under 2 years experience in the Home Visit Programme (HVP) and 8 had over 5 years experience in it; 5 completed their nursing studies before 1990, and 6 afterwards. In the chats it was clear that the broad experience of PC nurses made them aware of the health situation and quality of life of informal carers, of the loneliness of these and the inter-personal conflicts that occur in families when a situation of dependency arises. Nurses had their educational function towards the carers assumed despite the limitations. The view that the responsibility for the care of the dependent person is the family's was predominant, and a concern for lack of resources and support was appreciated. Nurses had a view of the carer as a resource and barely perceived her as a patient.

  9. Angle-Dependent Ionization of Small Molecules by Time-Dependent Configuration Interaction and an Absorbing Potential.

    Science.gov (United States)

    Krause, Pascal; Schlegel, H Bernhard

    2015-06-04

    The angle-dependence of strong field ionization of O2, N2, CO2, and CH2O has been studied theoretically using a time-dependent configuration interaction approach with a complex absorbing potential (TDCIS-CAP). Calculation of the ionization yields as a function of the direction of polarization of the laser pulse produces three-dimensional surfaces of the angle-dependent ionization probability. These three-dimensional shapes and their variation with laser intensity can be interpreted in terms of ionization from the highest occupied molecular orbital (HOMO) and lower lying orbitals, and the Dyson orbitals for the ground and excited states of the cations.

  10. Time-dependent restricted active space Configuration Interaction for the photoionization of many-electron atoms

    CERN Document Server

    Hochstuhl, David

    2012-01-01

    We introduce the time-dependent restricted active space Configuration Interaction method to solve the time-dependent Schr\\"odinger equation for many-electron atoms, and particularly apply it to the treatment of photoionization processes in atoms. The method is presented in a very general formulation and incorporates a wide range of commonly used approximation schemes, like the single-active electron approximation, time-dependent Configuration Interaction with single-excitations, or the time-dependent R-matrix method. We proof the applicability of the method by calculating the photoionization cross sections of Helium and Beryllium.

  11. Search for exotic spin-dependent interactions with a spin-exchange relaxation-free magnetometer

    CERN Document Server

    Chu, P -H; Savukov, I M

    2016-01-01

    We propose a novel experimental approach to explore exotic spin-dependent interactions using a spin-exchange relaxation-free (SERF) magnetometer, the most sensitive non-cryogenic magnetic-field sensor. This approach studies the interactions between optically polarized electron spins located inside a vapor cell of the SERF magnetometer and unpolarized or polarized particles of external solid-state objects. The coupling of spin-dependent interactions to the polarized electron spins of the magnetometer induces the tilt of the electron spins, which can be detected with high sensitivity by a probe laser beam similarly as an external magnetic field. We estimate that by moving unpolarized or polarized objects next to the SERF Rb vapor cell, the experimental limit to the spin-dependent interactions can be significantly improved over existing experiments, and new limits on the coupling strengths can be set in the interaction range below 0.01 m.

  12. Reconstituting Protein Interaction Networks Using Parameter-Dependent Domain-Domain Interactions

    Science.gov (United States)

    2013-05-07

    that approximately 80% of eukaryotic proteins and 67% of prokaryotic proteins have multiple domains [13,14]. Most annotation databases characterize...domain annotations, Domain-domain interactions, Protein-protein interaction networks Background The living cell is a dynamic, interconnected system...detailed in Methods. Here, we illustrate its application on a well- annotated single- cell organism. We created a merged set of protein-domain annotations

  13. Gene-environment interactions and alcohol use and dependence: current status and future challenges

    NARCIS (Netherlands)

    Zwaluw, C.S. van der; Engels, R.C.M.E.

    2009-01-01

    To discuss the current status of gene-environment interaction research with regard to alcohol use and dependence. Further, we highlight the difficulties concerning gene-environment studies. Overview of the current evidence for gene-environment interactions in alcohol outcomes, and of the associated

  14. Constraints on exotic spin-dependent interactions between electrons from helium fine-structure spectroscopy

    Science.gov (United States)

    Ficek, Filip; Kimball, Derek F. Jackson; Kozlov, Mikhail G.; Leefer, Nathan; Pustelny, Szymon; Budker, Dmitry

    2017-03-01

    Agreement between theoretical calculations of atomic structure and spectroscopic measurements is used to constrain possible contribution of exotic spin-dependent interactions between electrons to the energy differences between states in helium-4. In particular, constraints on dipole-dipole interactions associated with the exchange of pseudoscalar bosons (such as axions or axion-like particles) with masses 10-2≲m ≲104eV are improved by a factor of ˜100 . The first atomic-scale constraints on several exotic velocity-dependent dipole-dipole interactions are established as well.

  15. Temperature-dependent hyperfine interactions at {sup 111}Cd-C complex in germanium

    Energy Technology Data Exchange (ETDEWEB)

    Mola, Genene Tessema [University of Kwazulu-Natal, School Chemistry and Physics, Pietermaritzburg Campus, Private Bag X01, Scottsville (South Africa)

    2013-09-15

    The temperature dependent nuclear hyperfine interaction of {sup 111}Cd-carbon complex in germanium has been studied using the perturbed {gamma}-{gamma} angular correlation (PAC) method. The parameters of the hyperfine interaction representing substitutional carbon-cadmium complex in germanium ({nu} {sub Q1}=207(1) MHz ({eta}=0.16)) shows dependence on temperature. The formation and thermal stability of the complex has been reported by the same author earlier. It was found in this study that the quadrupole coupling constant of the interaction increases at sample temperature below 293 K. The results are encouraging toward better understanding of the complex in the host matrix. (orig.)

  16. The cyclin-dependent kinase 8 module sterically blocks Mediator interactions with RNA polymerase II

    DEFF Research Database (Denmark)

    Elmlund, Hans; Baraznenok, Vera; Lindahl, Martin

    2006-01-01

    CDK8 (cyclin-dependent kinase 8), along with CycC, Med12, and Med13, form a repressive module (the Cdk8 module) that prevents RNA polymerase II (pol II) interactions with Mediator. Here, we report that the ability of the Cdk8 module to prevent pol II interactions is independent of the Cdk8......-dependent kinase activity. We use electron microscopy and single-particle reconstruction to demonstrate that the Cdk8 module forms a distinct structural entity that binds to the head and middle region of Mediator, thereby sterically blocking interactions with pol II....

  17. Constraints on exotic spin-dependent interactions between electrons from helium fine-structure spectroscopy

    CERN Document Server

    Ficek, Filip; Kozlov, Mikhail; Leefer, Nathan; Pustelny, Szymon; Budker, Dmitry

    2016-01-01

    Agreement between theoretical calculations of atomic structure and spectroscopic measurements is used to constrain possible contribution of exotic spin-dependent interactions between electrons to the energy differences between states in helium-4. In particular, constraints on dipole-dipole interactions associated with the exchange of pseudoscalar bosons (such as axions or axion-like particles, ALPs) with masses $10^{-2}~{\\rm eV} \\lesssim m \\lesssim 10^{4}~{\\rm eV}$ are improved by a factor of $\\sim 100$. The first atomic-scale constraints on several exotic velocity-dependent dipole-dipole interactions are established as well.

  18. Density-mediated, context-dependent consumer-resource interactions between ants and extrafloral nectar plants.

    Science.gov (United States)

    Chamberlain, Scott A; Holland, J Nathaniel

    2008-05-01

    Interspecific interactions are often mediated by the interplay between resource supply and consumer density. The supply of a resource and a consumer's density response to it may in turn yield context-dependent use of other resources. Such consumer-resource interactions occur not only for predator-prey and competitive interactions, but for mutualistic ones as well. For example, consumer-resource interactions between ants and extrafloral nectar (EFN) plants are often mutualistic, as EFN resources attract and reward ants which protect plants from herbivory. Yet, ants also commonly exploit floral resources, leading to antagonistic consumer-resource interactions by disrupting pollination and plant reproduction. EFN resources associated with mutualistic ant-plant interactions may also mediate antagonistic ant-flower interactions through the aggregative density response of ants on plants, which could either exacerbate ant-flower interactions or alternatively satiate and distract ants from floral resources. In this study, we examined how EFN resources mediate the density response of ants on senita cacti in the Sonoran Desert and their context-dependent use of floral resources. Removal of EFN resources reduced the aggregative density of ants on plants, both on hourly and daily time scales. Yet, the increased aggregative ant density on plants with EFN resources decreased rather than increased ant use of floral resources, including contacts with and time spent in flowers. Behavioral assays showed no confounding effect of floral deterrents on ant-flower interactions. Thus, ant use of floral resources depends on the supply of EFN resources, which mediates the potential for both mutualistic and antagonistic interactions by increasing the aggregative density of ants protecting plants, while concurrently distracting ants from floral resources. Nevertheless, only certain years and populations of study showed an increase in plant reproduction through herbivore protection or ant

  19. The Two Faces of Social Interaction Reward in Animal Models of Drug Dependence.

    Science.gov (United States)

    El Rawas, Rana; Saria, Alois

    2016-03-01

    Drug dependence is a serious health and social problem. Social factors can modify vulnerability to developing drug dependence, acting as risk factors or protective factors. Whereas stress and peer environment that encourage substance use may increase drug taking, strong attachments between family members and peer environment that do not experience drug use may protect against drug taking and, ultimately, drug dependence. The rewarding effects of drug abuse and social interaction can be evaluated using animal models. In this review we focus on evaluating social interaction reward in the conditioned place preference paradigm. We give an overview of how social interaction, if made available within the drug context, may facilitate, promote and interact with the drug's effects. However, social interaction, if offered alternatively outside the drug context, may have pronounced protective effects against drug abuse and relapse. We also address the importance of the weight difference parameter between the social partners in determining the positive or "agonistic" versus the hostile or "antagonistic" social interaction. We conclude that understanding social interaction reward and its subsequent effects on drug reward is sorely needed for therapeutic interventions against drug dependence.

  20. The Two Faces of Social Interaction Reward in Animal Models of Drug Dependence

    Science.gov (United States)

    Rawas, Rana El

    2016-01-01

    Drug dependence is a serious health and social problem. Social factors can modify vulnerability to developing drug dependence, acting as risk factors or protective factors. Whereas stress and peer environment that encourage substance use may increase drug taking, strong attachments between family members and peer environment that do not experience drug use may protect against drug taking and, ultimately, drug dependence. The rewarding effects of drug abuse and social interaction can be evaluated using animal models. In this review we focus on evaluating social interaction reward in the conditioned place preference paradigm. We give an overview of how social interaction, if made available within the drug context, may facilitate, promote and interact with the drug’s effects. However, social interaction, if offered alternatively outside the drug context, may have pronounced protective effects against drug abuse and relapse. We also address the importance of the weight difference parameter between the social partners in determining the positive or “agonistic” versus the hostile or “antagonistic” social interaction. We conclude that understanding social interaction reward and its subsequent effects on drug reward is sorely needed for therapeutic interventions against drug dependence. PMID:26088685

  1. Genome-wide analysis of interactions between ATP-dependent chromatin remodeling and histone modifications

    Directory of Open Access Journals (Sweden)

    Wang Jiang

    2009-07-01

    Full Text Available Abstract Background ATP-dependent chromatin remodeling and the covalent modification of histones play central roles in determining chromatin structure and function. Although several specific interactions between these two activities have been elaborated, the global landscape remains to be elucidated. Results In this paper, we have developed a computational method to generate the first genome-wide landscape of interactions between ATP-dependent chromatin remodeling and the covalent modification of histones in Saccharomyces cerevisiae. Our method succeeds in identifying known interactions and uncovers many previously unknown interactions between these two activities. Analysis of the genome-wide picture revealed that transcription-related modifications tend to interact with more chromatin remodelers. Our results also demonstrate that most chromatin remodeling-modification interactions act via interactions of remodelers with both histone-modifying enzymes and histone residues. We also found that the co-occurrence of both modification and remodeling has significantly different influences on multiple gene features (e.g. nucleosome occupancy compared with the presence of either one. Conclusion We gave the first genome-wide picture of ATP-dependent chromatin remodeling-histone modification interactions. We also revealed how these two activities work together to regulate chromatin structure and function. Our results suggest that distinct strategies for regulating chromatin activity are selectively employed by genes with different properties.

  2. Isospin effects of the Skyrme potential and the momentum dependent interaction at intermediate energy heavy ion collisions

    Institute of Scientific and Technical Information of China (English)

    GUO Wen-Jun; LIU Jian-Ye

    2008-01-01

    We improve the isospin dependent quantum molecular dynamical model by including isospin effects in the Skyrme potential and the momentum dependent interaction to obtain an isospin dependent Skyrme potential and an isospin dependent momentum interaction. We investigate the isospin effects of Skyrme potential and momentum dependent interaction on the isospin fractionation ratio and the dynamical mechanism in intermediate energy heavy ion collisions. It is found that the isospin dependent Skyrme potential and the isospin dependent momentum interaction produce some important isospin effects in the isospin fractionation ratio.

  3. Orbital-dependent Electron-Hole Interaction in Graphene and Associated Multi-Layer Structures

    Science.gov (United States)

    Deng, Tianqi; Su, Haibin

    2015-11-01

    We develop an orbital-dependent potential to describe electron-hole interaction in materials with structural 2D character, i.e. quasi-2D materials. The modulated orbital-dependent potentials are also constructed with non-local screening, multi-layer screening, and finite gap due to the coupling with substrates. We apply the excitonic Hamiltonian in coordinate-space with developed effective electron-hole interacting potentials to compute excitons’ binding strength at M (π band) and Γ (σ band) points in graphene and its associated multi-layer forms. The orbital-dependent potential provides a range-separated property for regulating both long- and short-range interactions. This accounts for the existence of the resonant π exciton in single- and bi-layer graphenes. The remarkable strong electron-hole interaction in σ orbitals plays a decisive role in the existence of σ exciton in graphene stack at room temperature. The interplay between gap-opening and screening from substrates shed a light on the weak dependence of σ exciton binding energy on the thickness of graphene stacks. Moreover, the analysis of non-hydrogenic exciton spectrum in quasi-2D systems clearly demonstrates the remarkable comparable contribution of orbital dependent potential with respect to non-local screening process. The understanding of orbital-dependent potential developed in this work is potentially applicable for a wide range of materials with low dimension.

  4. Relativistic symmetry of position-dependent mass particles in a Coulomb field including tensor interaction

    Institute of Scientific and Technical Information of China (English)

    M.Eshghi; M.Hamzavi; S.M.Ikhdair

    2013-01-01

    The spatially-dependent mass Dirac equation is solved exactly for attractive scalar and repulsive vector Coulomb potentials,including a tensor interaction under the spin and pseudospin symmetric limits.Closed forms of the energy eigenvalue equation and wave functions are obtained for arbitrary spin-orbit quantum number κ.Some numerical results are also given,and the effect of tensor interaction on the bound states is presented.It is shown that tensor interaction removes the degeneracy between two states in the spin doublets.We also investigate the effects of the spatially-dependent mass on the bound states under spin symmetric limit conditions in the absence of tensor interaction.

  5. Half lives of spherical proton emitters using density dependent M3Y interaction

    CERN Document Server

    Chowdhury, P R; Basu, D N

    2005-01-01

    The proton radioactivity lifetimes of spherical proton emitters from the ground and the isomeric states are calculated using the microscopic nucleon-nucleus interaction potentials. The daughter nuclei density distributions are folded with a realistic density dependent M3Y effective interaction supplemented by a zero-range pseudo-potential. The density dependence parameters of the interaction are extracted from the nuclear matter calculations. The saturation energy per nucleon used for nuclear matter calculations is determined from the co-efficient of the volume term of Bethe-Weizsacker mass formula which is evaluated by fitting the recent experimental and estimated atomic mass excesses from Audi-Wapstra-Thibault atomic mass table by minimizing the mean square deviation. The quantum mechanical tunneling probability is calculated within the WKB approximation. Spherical charge distributions are used for calculating the Coulomb interaction potentials. These calculations provide good estimates for the observed pro...

  6. Competitive effects of nuclear deformation and density dependence of $\\Lambda\\!N$ interaction

    CERN Document Server

    Isaka, M; Rijken, T h A

    2016-01-01

    Competitive effects of nuclear deformation and density dependence of $\\Lambda\\!N$-interaction in $\\Lambda$ binding energies $B_\\Lambda$ of hypernuclei are studied systematically on the basis of the baryon-baryon interaction model ESC including many-body effects. By using the $\\Lambda\\!N$ G-matrix interaction derived from ESC, we perform microscopic calculations of $B_\\Lambda$ in $\\Lambda$ hypernuclei within the framework of the antisymmetrized molecular dynamics under the averaged-density approximation. The calculated values of $B_\\Lambda$ reproduce experimental data within a few hundred keV in the wide mass regions from 9 to 51. It is found that competitive effects of nuclear deformation and density dependence of $\\Lambda\\!N$-interaction work decisively for fine tuning of $B_\\Lambda$ values.

  7. RGD-Dependent Epithelial Cell-Matrix Interactions in the Human Intestinal Crypt

    Directory of Open Access Journals (Sweden)

    Yannick D. Benoit

    2012-01-01

    Full Text Available Interactions between the extracellular matrix (ECM and integrin receptors trigger structural and functional bonds between the cell microenvironment and the cytoskeleton. Such connections are essential for adhesion structure integrity and are key players in regulating transduction of specific intracellular signals, which in turn regulate the organization of the cell microenvironment and, consequently, cell function. The RGD peptide-dependent integrins represent a key subgroup of ECM receptors involved in the maintenance of epithelial homeostasis. Here we review recent findings on RGD-dependent ECM-integrin interactions and their roles in human intestinal epithelial crypt cells.

  8. Employing an interaction picture to remove artificial correlations in multilayer multiconfiguration time-dependent Hartree simulations

    Science.gov (United States)

    Wang, Haobin; Thoss, Michael

    2016-10-01

    The multilayer multiconfiguration time-dependent Hartree (ML-MCTDH) method is implemented in the interaction picture to allow a more effective description of correlation effects. It is shown that the artificial correlation present in the original Schrödinger picture can be removed with an appropriate choice of the zeroth-order Hamiltonian. Thereby, operators in the interaction picture are obtained through time-dependent unitary transformations, which have negligible computational cost compared with other parts of the ML-MCTDH algorithm. The efficiency of the method is demonstrated by application to a model of vibrationally coupled charge transport in molecular junctions.

  9. Isospin Momentum-Dependent Interaction and Its Role on the Isospin Fractionation Ratio in Intermediate Energy Heavy Ion Collisions

    Institute of Scientific and Technical Information of China (English)

    LIU Jian-Ye; GUO Wen-Jun; XING Yong-Zhong; LEE Xi-Guo

    2005-01-01

    @@ We investigate the role of isospin momentum-dependent interaction on the isospin fractionation ratio and its dynamical mechanism in the intermediate energy heavy ion collisions, by inserting an isospin degree of freedom into the momentum-dependent interaction to obtain an isospin momentum-dependent interaction given in a form practically usable in the isospin-dependent quantum molecular dynamics model It is found that the isospin momentum-dependent interaction brings an important isospin effect into the isospin fractionation ratio. In particular, the isospin momentum-dependent interaction reduces obviously the reduction of isospin fractionation ratio. Thus the isospin dependence of momentum-dependent interaction is thus important for studying accurately the equation of state of isospin asymmetry nuclear matter.

  10. Elucidating pH-dependent collagen triple helix formation through interstrand hydroxyproline-glutamic acid interactions.

    Science.gov (United States)

    Chen, Liwei; Cai, Shuting; Lim, Jaehong; Lee, Su Seong; Lee, Song-Gil

    2015-02-09

    Here, we describe systematic explorations into the molecular basis underlying hydroxyproline-mediated interstrand interactions on the triple-helical stability of collagen-mimetic peptides containing glutamic acid residues. Our studies reveal that the triple-helical stability of these peptides relies on the existence of interstrand interactions between hydroxyprolines and glutamic acid residues that are pH dependent. These unique interactions have been used to engineer collagen peptides that form triple helices on demand through pH control. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. The importance of species identity and interactions for multifunctionality depends on how ecosystem functions are valued.

    Science.gov (United States)

    Slade, Eleanor M; Kirwan, Laura; Bell, Thomas; Philipson, Christopher D; Lewis, Owen T; Roslin, Tomas

    2017-10-01

    overall multifunctionality depended on the weight given to individual functions. Optimal multifunctionality was context-dependent, and sensitive to the valuation of services. This combination of methodological approaches allowed us to resolve the interactions and indirect effects among species that drive ecosystem functioning, revealing how multiple aspects of biodiversity can simultaneously drive ecosystem functioning. Our results highlight the importance of a multifunctionality perspective for a complete assessment of species' functional contributions. © 2017 by the Ecological Society of America.

  12. Angular Dependence of Ionization by Circularly Polarized Light Calculated with Time-Dependent Configuration Interaction with an Absorbing Potential.

    Science.gov (United States)

    Hoerner, Paul; Schlegel, H Bernhard

    2017-02-16

    The angular dependence of ionization by linear and circularly polarized light has been examined for N2, NH3, H2O, CO2, CH2O, pyrazine, methyloxirane, and vinyloxirane. Time-dependent configuration interaction with single excitations and a complex absorbing potential was used to simulate ionization by a seven cycle 800 nm cosine squared pulse with intensities ranging from 0.56 × 10(14) to 5.05 × 10(14) W cm(-2). The shapes of the ionization yield for linearly polarized light can be understood primarily in terms of the nodal structure of the highest occupied orbitals. Depending on the orbital energies, ionization from lower-lying orbitals may also make significant contributions to the shapes. The shapes of the ionization yield for circularly polarized light can be readily explained in terms of the shapes for linearly polarized light. Averaging the results for linear polarization over orientations perpendicular to the direction of propagation yields shapes that are in very good agreement with direct calculations of the ionization yield by circularly polarized light.

  13. Chemical Potential Dependence of the Dressed-Quark Propagator from an Effective Quark-Quark Interaction

    Institute of Scientific and Technical Information of China (English)

    ZONG Hong-Shi; PING Jia-Lun; SUN Wei-Min; CHANG Chao-Hsi; WANG Fan

    2002-01-01

    We exhibit a method for obtaining the low chemical potential dependence of the dressed quark propagatorfrom an effective quark-quark interaction model. Within this approach we explore the chemical potential dependenceof the dressed-quark propagator, which provides a means of determining the behavior of the chiral and deconfinementorder parameters. A comparison with the results of previous researches is given.

  14. Humans as an animal model? : studies on cue interaction, occasion setting, and context dependency

    NARCIS (Netherlands)

    Dibbets, Pauline

    2002-01-01

    The objective of the present thesis was to study human learning behaviour and to compare the results with those from animal learning studies. Three topics originating from animal learning research were examined: cue interaction, occasion setting, and context dependency. A series of experiments was f

  15. Influence of dipolar interactions on the angular-dependent coercivity of nickel nanocylinders

    Science.gov (United States)

    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.

  16. Wave-Vector Dependence of the Jahn-Teller Interactions in TmVO4

    DEFF Research Database (Denmark)

    Kjems, Jørgen; Hayes, W.; Smith, S. H.

    1975-01-01

    The resonant Jahn-Teller coupling of the B2g acoustic phonon and the Zeeman-split ground doublet in TmVO4 has been studied by inelastic neutron scattering. Tuning of the magnetic field provides a means for investigating the wave-vector dependence of the interactions. We find that the coupling is ...

  17. Temperature-dependent interactions between juvenile steelhead and Sacramento pikeminnow in laboratory streams

    Science.gov (United States)

    Carl D. Reese; Bret C. Harvey

    2002-01-01

    Abstract - We examined the temperature dependence of interactions between juvenile steelhead 'Oncorhynchus mykiss' and juvenile Sacramento pikeminnow 'Ptychocheilus grandis' in laboratory streams. Growth of dominant steelhead in water 20-23 degree C was reduced by more than 50% in trials with Sacramento pikeminnow compared with trials with steelhead...

  18. Interactive and Symbolic Data Dependence AnalysisBased on Ranges of Expressions

    Institute of Scientific and Technical Information of China (English)

    杨博; 郑丰宙; 王鼎兴; 郑纬民

    2002-01-01

    Traditional data dependence testing algorithms have become very accurate and efficient for simple subscript expressions, but they cannot handle symbolic expressions because of the complexity of data-flow and lack of the semantic information of variables in programs. In this paper, a range-based testing and query approach, called DDTQ, is proposed to eliminate data dependence between array references with symbolic subscripts. DDTQ firstly extracts data dependence information from the symbolic subscripts, a testing algorithm is then used to disprove the dependence based on the ranges of expressions. The assumed dependence that cannot be handled by the disprover will be converted into simple questions by a question engine so that the compiler can solve them by user interaction in a friendly way. The experiment on perfect benchmarks indicates that DDTQ is effective in improving the parallelizing capability of the compiler.

  19. Ferromagnetic interactions between transition-metal impurities in topological and 3D Dirac semimetals

    Science.gov (United States)

    Dietl, Tomasz

    The magnitude of ferromagnetic coupling driven by inter-band (Bloembergen-Rowland - BR) and intra-band (Ruderman-Kittel-Kasuya-Yoshida - RKKY) spin polarization is evaluated within kp theory for topological semimetals Hg1-xMnxTe and Hg1-xMnxSe as well as for 3D Dirac semimetal (Cd1-xMnx)3As2. In these systems Mn2+ ions do not introduce any carriers. Since, however, both conduction and valence bands are built from anion p-type wave functions, hybridization of Mn d levels with neighboring anion p states leads to spin-dependent p - d coupling of both electrons and holes to localized Mn spins, resulting in sizable inter-band spin polarization and, thus in large BR interactions. We demonstrate that this ferromagnetic coupling, together with antiferromagnetic superexchange, elucidate a specific dependence of spin-glass freezing temperature on x, determined experimentally for these systems. Furthermore, by employing a multi-orbital tight-binding method, we find that superexchange becomes ferromagnetic when Mn is replaced by Cr or V. Since Cr should act as an isoelectronic impurity in HgTe, this opens a road for realization of ferromagnetic topological insulators based on (Hg,Cr)Te.

  20. Effects of symmetry energy and momentum dependent interaction on low-energy reaction mechanisms

    CERN Document Server

    Zheng, H; Baran, V; Burrello, S

    2015-01-01

    We study the dipole response associated with the Pygmy Dipole Resonance (PDR) and the Isovector Giant Dipole Resonance (IVGDR), in connection with specific properties of the nuclear effective interaction (symmetry energy and momentum dependence), in the neutron-rich systems $^{68}$Ni, $^{132}$Sn and $^{208}$Pb. We perform our investigation within a microscopic transport model based on the Landau-Vlasov kinetic equation. We observe that the peak energies of PDR and IVGDR are shifted to higher values when employing momentum dependent interactions, with respect to the results obtained neglecting momentum dependence. The calculated energies are close to the experimental values and similar to the results obtained in Hartree-Fock (HF) with Random Phase Approximation (RPA) calculations.

  1. Effects of symmetry energy and momentum dependent interaction on low-energy reaction mechanisms

    Directory of Open Access Journals (Sweden)

    Zheng H.

    2016-01-01

    Full Text Available We study the dipole response associated with the Pygmy Dipole Resonance (PDR and the Isovector Giant Dipole Resonance (IVGDR, in connection with specific properties of the nuclear effective interaction (symmetry energy and momentum dependence, in the neutron-rich systems 68Ni, 132Sn and 208Pb. We perform our investigation within a microscopic transport model based on the Landau-Vlasov kinetic equation.We observe that the peak energies of PDR and IVGDR are shifted to higher values when employing momentum dependent interactions, with respect to the results obtained neglecting momentum dependence. The calculated energies are close to the experimental values and similar to the results obtained in Hartree-Fock (HF with Random Phase Approximation (RPA calculations.

  2. Mapping of protein-protein interactions within the DNA-dependent protein kinase complex.

    Science.gov (United States)

    Gell, D; Jackson, S P

    1999-01-01

    In mammalian cells, the Ku and DNA-dependent protein kinase catalytic subunit (DNA-PKcs) proteins are required for the correct and efficient repair of DNA double-strand breaks. Ku comprises two tightly-associated subunits of approximately 69 and approximately 83 kDa, which are termed Ku70 and Ku80 (or Ku86), respectively. Previously, a number of regions of both Ku subunits have been demonstrated to be involved in their interaction, but the molecular mechanism of this interaction remains unknown. We have identified a region in Ku70 (amino acid residues 449-578) and a region in Ku80 (residues 439-592) that participate in Ku subunit interaction. Sequence analysis reveals that these interaction regions share sequence homology and suggests that the Ku subunits are structurally related. On binding to a DNA double-strand break, Ku is able to interact with DNA-PKcs, but how this interaction is mediated has not been defined. We show that the extreme C-terminus of Ku80, specifically the final 12 amino acid residues, mediates a highly specific interaction with DNA-PKcs. Strikingly, these residues appear to be conserved only in Ku80 sequences from vertebrate organisms. These data suggest that Ku has evolved to become part of the DNA-PK holo-enzyme by acquisition of a protein-protein interaction motif at the C-terminus of Ku80. PMID:10446239

  3. Spin-independent interferences and spin-dependent interactions with scalar dark matter

    CERN Document Server

    Martinez, R

    2015-01-01

    We explore mechanisms of interferences under which the spin-independent interaction in dispersions of scalar dark matter with nucleus is suppressed in relation to the spin-dependent one. We offer a detailed derivation of the nuclear amplitudes based on the interactions with quarks in the framework of an nonuniversal $U(1)'$ extension of the standard model. By assuming a range of parameters compatible with collider searches, electroweak observables and indirect dark matter search, we find scenarios for destructive interferences with and without isospin symmetry. The model admits solutions with mutually interfering scalar particles, canceling the effective spin-independent coupling with only scalar interactions, which requires an extra Higgs boson with mass $M_{H}>125$ GeV. The model also possess scenarios with only vector interactions through two neutral gauge bosons, $Z$ and $Z'$, which do not exhibits interference effects. Due to the nonuniversality of the $U(1)'$ symmetry, we distinguish two family structur...

  4. Direction-dependent intermolecular interactions: catechol on TiO2(110)-1×1

    Science.gov (United States)

    Li, Shao-Chun; Diebold, Ulrike

    2009-08-01

    The adsorption of a submonolayer of catechol (C6H6O2) on the rutile TiO2(110)-1×1 surface has been investigated by Scanning Tunneling Microscopy (STM). The catechol molecules are preferentially adsorbed on the surface 5-fold coordinated Ti4+ sites, and occupy two neighboring lattice Ti sites. No preference for adsorption at surface step edges is observed at room temperature. A statistical analysis of intermolecular distances demonstrates that the interaction between the molecules strongly depends on the surface crystallographic direction: catechol molecules exhibit attractive interaction along [1-1 0], while they repel each other along the [001] direction. The attractive interaction is proposed to be caused by the coupling of π bonding electrons and the repulsive interaction is possibly mediated by substrate.

  5. RNA LEGO: magnesium-dependent formation of specific RNA assemblies through kissing interactions.

    Science.gov (United States)

    Horiya, Satoru; Li, Xianglan; Kawai, Gota; Saito, Ryota; Katoh, Akira; Kobayashi, Koh; Harada, Kazuo

    2003-07-01

    The high affinity and specificity of nucleic acid base complementarity has been proven to be a powerful method for constructing specific molecular assemblies. On the other hand, recent structural studies of RNA have revealed the wide range of tertiary interactions utilized in RNA folding, which may potentially be used as tools for the design of specific macromolecular assemblies. Here, RNA building blocks containing two hairpin loops, based on the dimerization initiation site (DIS) of HIV RNA, connected by a short linker were used to construct large RNA assemblies through hairpin loop-loop ("kissing") interactions. We show that specific linear and circular assemblies can be constructed in a magnesium-dependent manner using several non-self-complementary loop-loop interactions designed in this study. These results show that the use of RNA tertiary interactions may broaden the repertoire of nucleic acid-based nanostructures.

  6. Size-dependent Fano Interaction in the Laser-etched Silicon Nanostructures

    Directory of Open Access Journals (Sweden)

    Kumar Rajesh

    2008-01-01

    Full Text Available AbstractPhoto-excitation and size-dependent Raman scattering studies on the silicon (Si nanostructures (NSs prepared by laser-induced etching are presented here. Asymmetric and red-shifted Raman line-shapes are observed due to photo-excited Fano interaction in the quantum confined nanoparticles. The Fano interaction is observed between photo-excited electronic transitions and discrete phonons in Si NSs. Photo-excited Fano studies on different Si NSs show that the Fano interaction is high for smaller size of Si NSs. Higher Fano interaction for smaller Si NSs is attributed to the enhanced interference between photo-excited electronic Raman scattering and phonon Raman scattering.

  7. Voltage-controlled low-energy switching of nanomagnets through Ruderman-Kittel-Kasuya-Yosida interactions for magnetoelectric device applications

    Energy Technology Data Exchange (ETDEWEB)

    Ghosh, Bahniman, E-mail: bghosh@utexas.edu; Dey, Rik; Register, Leonard F.; Banerjee, Sanjay K. [Microelectronics Research Center, University of Texas at Austin, 10100 Burnet Road, Bldg. 160, Austin, Texas 78758 (United States)

    2016-07-21

    In this article, we consider through simulation low-energy switching of nanomagnets via electrostatically gated inter-magnet Ruderman-Kittel-Kasuya-Yosida (RKKY) interactions on the surface of three-dimensional topological insulators, for possible memory and nonvolatile logic applications. We model the possibility and dynamics of RKKY-based switching of one nanomagnet by coupling to one or more nanomagnets of set orientation. Potential applications to both memory and nonvolatile logic are illustrated. Sub-attojoule switching energies, far below conventional spin transfer torque (STT)-based memories and even below CMOS logic appear possible. Switching times on the order of a few nanoseconds, comparable to times for STT switching, are estimated for ferromagnetic nanomagnets, but the approach also appears compatible with the use of antiferromagnets which may allow for faster switching.

  8. Voltage-controlled low-energy switching of nanomagnets through Ruderman-Kittel-Kasuya-Yosida interactions for magnetoelectric device applications

    Science.gov (United States)

    Ghosh, Bahniman; Dey, Rik; Register, Leonard F.; Banerjee, Sanjay K.

    2016-07-01

    In this article, we consider through simulation low-energy switching of nanomagnets via electrostatically gated inter-magnet Ruderman-Kittel-Kasuya-Yosida (RKKY) interactions on the surface of three-dimensional topological insulators, for possible memory and nonvolatile logic applications. We model the possibility and dynamics of RKKY-based switching of one nanomagnet by coupling to one or more nanomagnets of set orientation. Potential applications to both memory and nonvolatile logic are illustrated. Sub-attojoule switching energies, far below conventional spin transfer torque (STT)-based memories and even below CMOS logic appear possible. Switching times on the order of a few nanoseconds, comparable to times for STT switching, are estimated for ferromagnetic nanomagnets, but the approach also appears compatible with the use of antiferromagnets which may allow for faster switching.

  9. Synergism and context dependency of interactions between arbuscular mycorrhizal fungi and rhizobia with a prairie legume.

    Science.gov (United States)

    Larimer, Anna L; Clay, Keith; Bever, James D

    2014-04-01

    Biotic interactions play primary roles in major theories of the distribution and abundance of species, yet the nature of these biotic interactions can depend upon the larger ecological community. Leguminous plants, for example, commonly associate with both arbuscular mycorrhizal fungi (AMF) and rhizobia bacteria, and the pairwise interactions may depend upon the presence or identity of the third partner. To determine if the dynamics of plant-AMF and plant-rhizobia interactions are affected by the alternate symbiont, we manipulated the presence and identity of each symbiont, as well as levels of the nutrients supplied by each symbiont (nitrogen and phosphorus), on the growth of prairie legume Amorpha canescens. We found strong synergistic effects of AMF and rhizobia inoculation on plant biomass production that were independent of nutrient levels. AMF and rhizobia responses were each influenced by the other, but not in the same direction. AMF infection increased root nodule number and mass, but rhizobia inoculation decreased AMF hyphal colonization of roots. The relative benefits of each combination of symbionts depended upon phosphorus level. The effect of nitrogen was also contingent on the biotic environment where nitrogen addition decreased nodulation, but this decrease was reduced with coinfection by AMF. Our results demonstrate a strong contingency on the co-occurrence of AMF and rhizobia for the long-term fitness of A. canescens, and suggest that the belowground community is critical for the success of this species in tallgrass prairies.

  10. Quantitative assessment of target dependence of pion fluctuation in hadronic interactions – estimation through erraticity

    Indian Academy of Sciences (India)

    Dipak Ghosh; Argha Deb; Mitali Mondal; Arindam Mondal; Sitram Pal

    2012-12-01

    Event-to-event fluctuation pattern of pions produced by proton and pion beams is studied in terms of the newly defined erraticity measures $ (p, q)$, $_{q}^{'}$ and $_{q}^{'}$ proposed by Cao and Hwa. The analysis reveals the erratic behaviour of the produced pions signifying the chaotic multiparticle production in high-energy hadron–nucleus interactions (- –AgBr interactions at 350 GeV/c and –AgBr interactions at 400 GeV/c). However, the chaoticity does not depend on whether the projectile is proton or pion. The results are compared with the results of the VENUS-generated data for the above interactions which suggests that VENUS event generator is unable to reproduce the event-to-event fluctuations of spatial patterns of final states. A comparative study of –AgBr interactions and - collisions at 400 GeV/c from NA27, with the help of a quantitative parameter for the assessment of pion fluctuation, indicates conclusively that particle production process is more chaotic for hadron–nucleus interactions than for hadron–hadron interactions.

  11. The Cyclin-Dependent Kinase Ortholog pUL97 of Human Cytomegalovirus Interacts with Cyclins

    Directory of Open Access Journals (Sweden)

    Laura Graf

    2013-12-01

    Full Text Available The human cytomegalovirus (HCMV-encoded protein kinase, pUL97, is considered a cyclin-dependent kinase (CDK ortholog, due to shared structural and functional characteristics. The primary mechanism of CDK activation is binding to corresponding cyclins, including cyclin T1, which is the usual regulatory cofactor of CDK9. This study provides evidence of direct interaction between pUL97 and cyclin T1 using yeast two-hybrid and co-immunoprecipitation analyses. Confocal immunofluorescence revealed partial colocalization of pUL97 with cyclin T1 in subnuclear compartments, most pronounced in viral replication centres. The distribution patterns of pUL97 and cyclin T1 were independent of HCMV strain and host cell type. The sequence domain of pUL97 responsible for the interaction with cyclin T1 was between amino acids 231–280. Additional co-immunoprecipitation analyses showed cyclin B1 and cyclin A as further pUL97 interaction partners. Investigation of the pUL97-cyclin T1 interaction in an ATP consumption assay strongly suggested phosphorylation of pUL97 by the CDK9/cyclin T1 complex in a substrate concentration-dependent manner. This is the first demonstration of interaction between a herpesviral CDK ortholog and cellular cyclins.

  12. Intramolecular bond length dependence of the anisotropic dispersion coefficients for H2-rare gas interactions

    Science.gov (United States)

    Wormer, Paul E. S.; Hettema, Hinne; Thakkar, Ajit J.

    1993-05-01

    Effective states arising from variational perturbation calculations in a full configuration interaction basis are used to calculate dynamic multipole polarizabilities for H2 at seven different bond lengths. These are combined with previously calculated dynamic polarizabilities for rare gas atoms to obtain the intramolecular bond length dependence of the anisotropic C6, C8, and C10 dispersion coefficients for H2-X (X=He, Ne, Ar, Kr, Xe) interactions. The results are generally in good agreement with previous semiempirical estimates where available.

  13. Context-dependency of arbuscular mycorrhizal fungi on plant-insect interactions in an agroecosystem

    Directory of Open Access Journals (Sweden)

    Nicholas A Barber

    2013-09-01

    Full Text Available Plants interact with a variety of other community members that have the potential to indirectly influence each other through a shared host plant. Arbuscular mycorrhizal fungi (AMF are generally considered plant mutualists because of their generally positive effects on plant nutrient status and growth. AMF may also have important indirect effects on plants by altering interactions with other community members. By influencing plant traits, AMF can modify aboveground interactions with both mutualists, such as pollinators, and antagonists, such as herbivores. Because herbivory and pollination can dramatically influence plant fitness, comprehensive assessment of plant-AMF interactions should include these indirect effects. To determine how AMF affect plant-insect interactions, we grew Cucumis sativus (Cucurbitaceae under five AMF inoculum treatments and control. We measured plant growth, floral production, flower size, and foliar nutrient content of half the plants, and transferred the other half to a field setting to measure pollinator and herbivore preference of wild insects. Mycorrhizal treatment had no effect on plant biomass or floral traits but significantly affected leaf nutrients, pollinator behavior, and herbivore attack. Although total pollinator visitation did not vary with AMF treatment, pollinators exhibited taxon-specific responses, with honey bees, bumble bees, and Lepidoptera all responding differently to AMF treatments. Flower number and size were unaffected by treatments, suggesting that differences in pollinator preference were driven by other floral traits. Mycorrhizae influenced leaf K and Na, but these differences in leaf nutrients did not correspond to variation in herbivore attack. Overall, we found that AMF indirectly influence both antagonistic and mutualistic insects, but impacts depend on the identity of both the fungal partner and the interacting insect, underscoring the context dependency of plant-AMF interactions.

  14. Nuclear Effects in Neutrino Interactions with Minimal Neutrino Energy Dependence -- A NuWro Truth Study

    CERN Document Server

    Pickering, Luke

    2016-01-01

    We present a Monte Carlo truth study examining nuclear effects in charged-current neutrino interactions using observables constructed in the transverse plane. Three distributions are introduced that show very weak dependence on neutrino flux and its associated uncertainty. Measurements comparing these distributions between quasi-elastic-like and single charged pion final states will provide new constraints of nuclear effects. It is suggested that the on-axis position in the NuMI beam provides the correct flux to take advantage of this reduced energy dependence in measuring nuclear effect-generated transverse imbalances.

  15. Modeling molecule-plasmon interactions using quantized radiation fields within time-dependent electronic structure theory

    Energy Technology Data Exchange (ETDEWEB)

    Nascimento, Daniel R.; DePrince, A. Eugene, E-mail: deprince@chem.fsu.edu [Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390 (United States)

    2015-12-07

    We present a combined cavity quantum electrodynamics/ab initio electronic structure approach for simulating plasmon-molecule interactions in the time domain. The simple Jaynes-Cummings-type model Hamiltonian typically utilized in such simulations is replaced with one in which the molecular component of the coupled system is treated in a fully ab initio way, resulting in a computationally efficient description of general plasmon-molecule interactions. Mutual polarization effects are easily incorporated within a standard ground-state Hartree-Fock computation, and time-dependent simulations carry the same formal computational scaling as real-time time-dependent Hartree-Fock theory. As a proof of principle, we apply this generalized method to the emergence of a Fano-like resonance in coupled molecule-plasmon systems; this feature is quite sensitive to the nanoparticle-molecule separation and the orientation of the molecule relative to the polarization of the external electric field.

  16. Vibrationally dependent electron-electron interactions in resonant electron transport through single-molecule junctions

    Science.gov (United States)

    Erpenbeck, A.; Härtle, R.; Bockstedte, M.; Thoss, M.

    2016-03-01

    We investigate the role of electronic-vibrational coupling in resonant electron transport through single-molecule junctions, taking into account that the corresponding coupling strengths may depend on the charge and excitation state of the molecular bridge. Within an effective-model Hamiltonian approach for a molecule with multiple electronic states, this requires to extend the commonly used model and include vibrationally dependent electron-electron interaction. We use Born-Markov master equation methods and consider selected models to exemplify the effect of the additional interaction on the transport characteristics of a single-molecule junction. In particular, we show that it has a significant influence on local cooling and heating mechanisms, it may result in negative differential resistance, and it may cause pronounced asymmetries in the conductance map of a single-molecule junction.

  17. Time-dependent delta-interactions for 1D Schr\\"odinger Hamiltonians

    CERN Document Server

    Hmidi, Taoufik; Nier, Francis

    2009-01-01

    The non autonomous Cauchy problem for time dependent 1D point interactions is considered. The regularity assumptions for the coupling parameter are accurately analyzed and show that the general results for non autonomous linear evolution equations in Banach spaces are far from being optimal. In the mean time, this article shows an unexpected application of paraproduct techniques, initiated by J.M. Bony for nonlinear partial differential equations, to a classical linear problem.

  18. Phosphorylation state-dependent interaction between AKAP7δ/γ and phospholamban increases phospholamban phosphorylation

    Science.gov (United States)

    Rigatti, Marc; Le, Andrew V.; Gerber, Claire; Moraru, Ion I.; Dodge-Kafka, Kimberly L.

    2016-01-01

    Changes in heart rate and contractility in response to sympathetic stimulation occur via activation of cAMP dependent protein kinase A (PKA), leading to phosphorylation of numerous substrates that alter Ca2+ cycling. Phosphorylation of these substrates is coordinated by A-kinase anchoring proteins (AKAPs), which recruit PKA to specific substrates [1]. Phosphorylation of the PKA substrate phospholamban (PLB) is a critical determinant of Ca2+ re-entry into the sarcoplasmic reticulum and is coordinated by AKAP7δ/γ [2,3]. Here, we further these findings by showing that phosphorylation of PLB requires interaction with AKAP7δ/γ and that this interaction occurs only when PLB is unphosphorylated. Additionally, we find that two mutants of PLB (R9C and Δ14), which are associated with dilated cardiomyopathy in humans, prevent association with AKAP7δ/γ and display reduced phosphorylation in vitro. This finding implicates the AKAP7δ/γ-PLB interaction in the pathology of the disease phenotype. Further exploration of the AKAP7δ/γ-PLB association demonstrated a phosphorylation state-dependence of the interaction. Computational modeling revealed that this mode of interaction allows for small amounts of AKAP and PKA (100–200nM) to regulate the phosphorylation of large quantities of PLB (50µM). Our results confirm that AKAP7γ/δ binding to PLB is important for phosphorylation of PLB, and describe a novel phosphorylation state-dependent binding mechanism that explains how phosphorylation of highly abundant PKA substrates can be regulated by AKAPs present at ~100–200 fold lower concentrations. PMID:26027516

  19. Statistical model of rough surface contact accounting for size-dependent plasticity and asperity interaction

    Science.gov (United States)

    Song, H.; Vakis, A. I.; Liu, X.; Van der Giessen, E.

    2017-09-01

    The work by Greenwood and Williamson (GW) has initiated a simple but effective method of contact mechanics: statistical modeling based on the mechanical response of a single asperity. Two main assumptions of the original GW model are that the asperity response is purely elastic and that there is no interaction between asperities. However, as asperities lie on a continuous substrate, the deformation of one asperity will change the height of all other asperities through deformation of the substrate and will thus influence subsequent contact evolution. Moreover, a high asperity contact pressure will result in plasticity, which below tens of microns is size dependent, with smaller being harder. In this paper, the asperity interaction effect is taken into account through substrate deformation, while a size-dependent plasticity model is adopted for individual asperities. The intrinsic length in the strain gradient plasticity (SGP) theory is obtained by fitting to two-dimensional discrete dislocation plasticity simulations of the flattening of a single asperity. By utilizing the single asperity response in three dimensions and taking asperity interaction into account, a statistical calculation of rough surface contact is performed. The effectiveness of the statistical model is addressed by comparison with full-detail finite element simulations of rough surface contact using SGP. Throughout the paper, our focus is on the difference of contact predictions based on size-dependent plasticity as compared to conventional size-independent plasticity.

  20. Direct Measurement of Nuclear Dependence of Charged Current Quasielasticlike Neutrino Interactions Using MINERvA

    Science.gov (United States)

    Betancourt, M.; Ghosh, A.; Walton, T.; Altinok, O.; Bellantoni, L.; Bercellie, A.; Bodek, A.; Bravar, A.; Cai, T.; Martinez Caicedo, D. A.; Carneiro, M. F.; Dytman, S. A.; Díaz, G. A.; Felix, J.; Fields, L.; Fine, R.; Galindo, R.; Gallagher, H.; Ghosh, A.; Golan, T.; Gran, R.; Harris, D. A.; Higuera, A.; Hurtado, K.; Kiveni, M.; Kleykamp, J.; Le, T.; Maher, E.; Manly, S.; Mann, W. A.; Marshall, C. M.; McFarland, K. S.; McGivern, C. L.; McGowan, A. M.; Messerly, B.; Miller, J.; Mislivec, A.; Morfín, J. G.; Mousseau, J.; Naples, D.; Nelson, J. K.; Norrick, A.; Nuruzzaman, Patrick, C. E.; Perdue, G. N.; Ramírez, M. A.; Ren, L.; Rimal, D.; Rodrigues, P. A.; Ruterbories, D.; Schellman, H.; Sobczyk, J. T.; Solano Salinas, C. J.; Sánchez Falero, S.; Valencia, E.; Wolcott, J.; Wospakrik, M.; Yaeggy, B.; Minerva Collaboration

    2017-08-01

    Charged-current νμ interactions on carbon, iron, and lead with a final state hadronic system of one or more protons with zero mesons are used to investigate the influence of the nuclear environment on quasielasticlike interactions. The transferred four-momentum squared to the target nucleus, Q2, is reconstructed based on the kinematics of the leading proton, and differential cross sections versus Q2 and the cross-section ratios of iron, lead, and carbon to scintillator are measured for the first time in a single experiment. The measurements show a dependence on the atomic number. While the quasielasticlike scattering on carbon is compatible with predictions, the trends exhibited by scattering on iron and lead favor a prediction with intranuclear rescattering of hadrons accounted for by a conventional particle cascade treatment. These measurements help discriminate between different models of both initial state nucleons and final state interactions used in the neutrino oscillation experiments.

  1. Optical probing of spin-dependent interactions in II-VI semiconductor structures

    Energy Technology Data Exchange (ETDEWEB)

    Gaj, J.A.; Golnik, A.; Goryca, M.; Kossacki, P.; Kowalik, K.; Kudelski, A.; Maslana, W.; Nawrocki, M.; Pacuski, W.; Plochocka, P.; Senellart, P. [Institute of Experimental Physics, Warsaw University, Hoza 69, 00-681 Warszawa (Poland); Cibert, J.; Ferrand, D.; Tatarenko, S. [CNRS-CEA-UJF Joint Group ' ' Nanophysique et semiconducteurs' ' , Laboratoire de Spectrometrie Physique, BP 87, 38402 Saint Martin d' Heres Cedex (France); Karczewski, G.; Kossut, J.; Kutrowski, M. [Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warszawa (Poland); Krebs, O.; Lemaitre, A.; Voisin, P. [Laboratoire de Photonique et Nanostructures, CNRS, Route de Nozay, 91460 Marcoussis (France); Wojtowicz, T.

    2006-03-15

    We present a selection of optical experiments, providing information on several spin-dependent interactions in II-VI semiconductor structures. Exciton-exciton and exciton-carrier interactions were studied by time-resolved picosecond pump-probe measurements. Several examples of recent studies involving ion-carrier exchange interaction in quantum wells and layers are discussed, concerning the quest for room temperature ferromagnetic semiconductors, spin temperature of Mn ions in (Cd,Mn)Te quantum wells, and spin relaxation in such wells under pulsed magnetic field. Finally, anisotropic electron-hole exchange in semiconductor quantum dots is discussed in the context of efforts to obtain generation of entangled photon pairs in a biexciton-exciton cascade in a semiconductor quantum dot. (copyright 2006 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  2. When ecosystem services interact: crop pollination benefits depend on the level of pest control

    Science.gov (United States)

    Lundin, Ola; Smith, Henrik G.; Rundlöf, Maj; Bommarco, Riccardo

    2013-01-01

    Pollination is a key ecosystem service which most often has been studied in isolation although effects of pollination on seed set might depend on, and interact with, other services important for crop production. We tested three competing hypotheses on how insect pollination and pest control might jointly affect seed set: independent, compensatory or synergistic effects. For this, we performed a cage experiment with two levels of insect pollination and simulated pest control in red clover (Trifolium pratense L.) grown for seed. There was a synergistic interaction between the two services: the gain in seed set obtained when simultaneously increasing pollination and pest control outweighed the sum of seed set gains obtained when increasing each service separately. This study shows that interactions can alter the benefits obtained from service-providing organisms, and this needs to be considered to properly manage multiple ecosystem services. PMID:23269852

  3. Direct Measurement of Nuclear Dependence of Charged Current Quasielasticlike Neutrino Interactions Using MINER$\

    Energy Technology Data Exchange (ETDEWEB)

    Betancourt, M.; et al.

    2017-08-25

    Charged-current νμ interactions on carbon, iron, and lead with a final state hadronic system of one or more protons with zero mesons are used to investigate the influence of the nuclear environment on quasielasticlike interactions. The transferred four-momentum squared to the target nucleus, Q2, is reconstructed based on the kinematics of the leading proton, and differential cross sections versus Q2 and the cross-section ratios of iron, lead, and carbon to scintillator are measured for the first time in a single experiment. The measurements show a dependence on the atomic number. While the quasielasticlike scattering on carbon is compatible with predictions, the trends exhibited by scattering on iron and lead favor a prediction with intranuclear rescattering of hadrons accounted for by a conventional particle cascade treatment. These measurements help discriminate between different models of both initial state nucleons and final state interactions used in the neutrino oscillation experiments.

  4. Neutron reflectometry yields distance-dependent structures of nanometric polymer brushes interacting across water.

    Science.gov (United States)

    Rodriguez-Loureiro, Ignacio; Scoppola, Ernesto; Bertinetti, Luca; Barbetta, Aurelio; Fragneto, Giovanna; Schneck, Emanuel

    2017-08-30

    The interaction between surfaces displaying end-grafted hydrophilic polymer brushes plays important roles in biology and in many wet-technological applications. In this context, the conformation of the brushes upon their mutual approach is crucial, because it affects interaction forces and the brushes' shear-tribological properties. While this aspect has been addressed by theory, experimental data on polymer conformations under confinement are difficult to obtain. Here, we study interacting planar brushes of hydrophilic polymers with defined length and grafting density. Via ellipsometry and neutron reflectometry we obtain pressure-distance curves and determine distance-dependent polymer conformations in terms of brush compression and reciprocative interpenetration. While the pressure-distance curves are satisfactorily described by the Alexander-de-Gennes model, the pronounced brush interpenetration as seen by neutron reflectometry motivates detailed simulation-based studies capable of treating brush interpenetration on a quantitative level.

  5. Generalized spin-dependent WIMP-nucleus interactions and the DAMA modulation effect

    CERN Document Server

    Scopel, Stefano; Yoon, KookHyun

    2015-01-01

    Guided by non-relativistic Effective Field Theory (EFT) we classify the most general spin-dependent interactions between a fermionic Weakly Interacting Massive Particle (WIMP) and nuclei, and within this class of models we discuss the viability of an interpretation of the DAMA modulation result in terms of a signal from WIMP elastic scatterings using a halo-independent approach. We find that, although several relativistic EFT's can lead to a spin-dependent cross section, in some cases with an explicit, non-negligible dependence on the WIMP incoming velocity, three main scenarios can be singled out in the non-relativistic limit which approximately encompass them all, and that only differ by their dependence on the transferred momentum. For two of them compatibility between DAMA and other constraints is possible for a WIMP mass below 30 GeV, but only for a WIMP velocity distribution in the halo of our Galaxy which departs from a Maxwellian. This is achieved by combining a suppression of the WIMP effective coupl...

  6. Investigating the context-dependency of plant-soil-AMF-microbe interactions along a pollution gradient

    Science.gov (United States)

    Glassman, S. I.; Casper, B. B.

    2010-12-01

    Background/Question/Methods Investigating how arbuscular mycorrhizal fungi (AMF)-plant interactions vary with edaphic conditions provides an opportunity to test the context-dependency of interspecific interactions, which is currently recognized as a major avenue of future research. We study plant-mycorrhiza symbiotic relationships along a gradient of heavy metal contamination at a recently revegetated “Superfund” site on Blue Mountain, in Palmerton, Pennsylvania. We investigated the interactions involving the native mycorrhizal fungi, non-mycorrhizal soil microbes, soil, and two plant species (a C3 and C4 grass) along the contamination gradient. The native C3 study species Deschampsia flexuosa, is dominant along the gradient and established naturally; the C4 Sorghastrum nutans, is native to Pennsylvania but not to the site and was introduced during restoration. Because C4 grasses are obligate mycotrophs, we expected S. nutans to have a different effect on and response to the soil symbiont community than the C3 grass. We carried out a full factorial greenhouse experiment using field-collected seeds of D. flexuosa and S. nutans, soil, AMF spores, and non-mycorrhizal microbes from both high and low contaminated ends of the gradient. After 11 weeks of growth in the greenhouses, we harvested above and belowground plant biomass, and quantified AMF root colonization and AMF sporulation. Results/Conclusions Our results indicate that context-dependent function is an important factor driving specific ecological interactions between plants and soil microbes. We found that soil origin significantly affected plant growth. Plants from both species grew much larger in soil from low contaminated (LC) origin than high contaminated (HC) origin. Furthermore, we found that the efficacy of AMF in promoting plant growth depended on AMF origin. Specifically, AMF from LC improved growth of D. flexuosa best in either soil background and improved survivorship of S. nutans in HC soil

  7. Interactional power: observing and identifying power in interaction analyses of adult education situations depending on power notions and data types

    Directory of Open Access Journals (Sweden)

    Sigrid Nolda

    2014-04-01

    Full Text Available Since the 1970s, various aspects of power have been at the focus of theoretical and empirical adult education research. Despite the actual interest in political and discursive aspects of power, this article emphasizes the importance of interactional studies when observing and identifying power based on various types of data. As for German interaction studies, three phases can be distinguished, characterized by a observations of failed participation based on records of classroom behaviour, b the identification of mutual power negotiation in classroom and counselling situations based on transcriptions, and c the identification of the power of physical settings in adult education classrooms and in counselling sessions based on visual data. It is presumed that observing/identifying power in adult education classrooms and counselling sessions generally depends not only on the notions of power underlying the studies but also on the data types produced and the methods applied for their interpretation. In addition, the question is raised whether the identification of power can be considered a power practice used by adult education researchers.

  8. Dependence of Interaction Free Energy between Solutes on an External Electrostatic Field

    Directory of Open Access Journals (Sweden)

    Pei-Kun Yang

    2013-07-01

    Full Text Available To explore the athermal effect of an external electrostatic field on the stabilities of protein conformations and the binding affinities of protein-protein/ligand interactions, the dependences of the polar and hydrophobic interactions on the external electrostatic field, −Eext, were studied using molecular dynamics (MD simulations. By decomposing Eext into, along, and perpendicular to the direction formed by the two solutes, the effect of Eext on the interactions between these two solutes can be estimated based on the effects from these two components. Eext was applied along the direction of the electric dipole formed by two solutes with opposite charges. The attractive interaction free energy between these two solutes decreased for solutes treated as point charges. In contrast, the attractive interaction free energy between these two solutes increased, as observed by MD simulations, for Eext = 40 or 60 MV/cm. Eext was applied perpendicular to the direction of the electric dipole formed by these two solutes. The attractive interaction free energy was increased for Eext = 100 MV/cm as a result of dielectric saturation. The force on the solutes along the direction of Eext computed from MD simulations was greater than that estimated from a continuum solvent in which the solutes were treated as point charges. To explore the hydrophobic interactions, Eext was applied to a water cluster containing two neutral solutes. The repulsive force between these solutes was decreased/increased for Eext along/perpendicular to the direction of the electric dipole formed by these two solutes.

  9. A model of urban scaling laws based on distance dependent interactions

    Science.gov (United States)

    Ribeiro, Fabiano L.; Meirelles, Joao; Ferreira, Fernando F.

    2017-01-01

    Socio-economic related properties of a city grow faster than a linear relationship with the population, in a log–log plot, the so-called superlinear scaling. Conversely, the larger a city, the more efficient it is in the use of its infrastructure, leading to a sublinear scaling on these variables. In this work, we addressed a simple explanation for those scaling laws in cities based on the interaction range between the citizens and on the fractal properties of the cities. To this purpose, we introduced a measure of social potential which captured the influence of social interaction on the economic performance and the benefits of amenities in the case of infrastructure offered by the city. We assumed that the population density depends on the fractal dimension and on the distance-dependent interactions between individuals. The model suggests that when the city interacts as a whole, and not just as a set of isolated parts, there is improvement of the socio-economic indicators. Moreover, the bigger the interaction range between citizens and amenities, the bigger the improvement of the socio-economic indicators and the lower the infrastructure costs of the city. We addressed how public policies could take advantage of these properties to improve cities development, minimizing negative effects. Furthermore, the model predicts that the sum of the scaling exponents of social-economic and infrastructure variables are 2, as observed in the literature. Simulations with an agent-based model are confronted with the theoretical approach and they are compatible with the empirical evidences.

  10. Blocking an N-terminal acetylation–dependent protein interaction inhibits an E3 ligase

    Energy Technology Data Exchange (ETDEWEB)

    Scott, Daniel C.; Hammill, Jared T.; Min, Jaeki; Rhee, David Y.; Connelly, Michele; Sviderskiy, Vladislav O.; Bhasin, Deepak; Chen, Yizhe; Ong, Su-Sien; Chai, Sergio C.; Goktug, Asli N.; Huang, Guochang; Monda, Julie K.; Low, Jonathan; Kim, Ho Shin; Paulo, Joao A.; Cannon, Joe R.; Shelat, Anang A.; Chen, Taosheng; Kelsall, Ian R.; Alpi, Arno F.; Pagala, Vishwajeeth; Wang, Xusheng; Peng, Junmin; Singh , Bhuvanesh; Harper, J. Wade; Schulman, Brenda A.; Guy, R. Kip (MSKCC); (Dundee); (SJCH); (Harvard-Med); (MXPL)

    2017-06-05

    N-terminal acetylation is an abundant modification influencing protein functions. Because ~80% of mammalian cytosolic proteins are N-terminally acetylated, this modification is potentially an untapped target for chemical control of their functions. Structural studies have revealed that, like lysine acetylation, N-terminal acetylation converts a positively charged amine into a hydrophobic handle that mediates protein interactions; hence, this modification may be a druggable target. We report the development of chemical probes targeting the N-terminal acetylation–dependent interaction between an E2 conjugating enzyme (UBE2M or UBC12) and DCN1 (DCUN1D1), a subunit of a multiprotein E3 ligase for the ubiquitin-like protein NEDD8. The inhibitors are highly selective with respect to other protein acetyl-amide–binding sites, inhibit NEDD8 ligation in vitro and in cells, and suppress anchorage-independent growth of a cell line with DCN1 amplification. Overall, our data demonstrate that N-terminal acetyl-dependent protein interactions are druggable targets and provide insights into targeting multiprotein E2–E3 ligases.

  11. Extended Synaptotagmin Interaction with the Fibroblast Growth Factor Receptor Depends on Receptor Conformation, Not Catalytic Activity.

    Science.gov (United States)

    Tremblay, Michel G; Herdman, Chelsea; Guillou, François; Mishra, Prakash K; Baril, Joëlle; Bellenfant, Sabrina; Moss, Tom

    2015-06-26

    We previously demonstrated that ESyt2 interacts specifically with the activated FGF receptor and is required for a rapid phase of receptor internalization and for functional signaling via the ERK pathway in early Xenopus embryos. ESyt2 is one of the three-member family of Extended Synaptotagmins that were recently shown to be implicated in the formation of endoplasmic reticulum (ER)-plasma membrane (PM) junctions and in the Ca(2+) dependent regulation of these junctions. Here we show that ESyt2 is directed to the ER by its putative transmembrane domain, that the ESyts hetero- and homodimerize, and that ESyt2 homodimerization in vivo requires a TM adjacent sequence but not the SMP domain. ESyt2 and ESyt3, but not ESyt1, selectively interact in vivo with activated FGFR1. In the case of ESyt2, this interaction requires a short TM adjacent sequence and is independent of receptor autophosphorylation, but dependent on receptor conformation. The data show that ESyt2 recognizes a site in the upper kinase lobe of FGFR1 that is revealed by displacement of the kinase domain activation loop during receptor activation.

  12. NRC-interacting factor directs neurite outgrowth in an activity-dependent manner.

    Science.gov (United States)

    Zhao, X-S; Fu, W-Y; Hung, K-W; Chien, W W Y; Li, Z; Fu, A K; Ip, N Y

    2015-03-19

    Nuclear hormone receptor coregulator-interacting factor 1 (NIF-1) is a zinc finger nuclear protein that was initially identified to enhance nuclear hormone receptor transcription via its interaction with nuclear hormone receptor coregulator (NRC). NIF-1 may regulate gene transcription either by modulating general transcriptional machinery or remodeling chromatin structure through interactions with specific protein partners. We previously reported that the cytoplasmic/nuclear localization of NIF-1 is regulated by the neuronal Cdk5 activator p35, suggesting potential neuronal functions for NIF-1. The present study reveals that NIF-1 plays critical roles in regulating neuronal morphogenesis at early stages. NIF-1 was prominently expressed in the nuclei of developing rat cortical neurons. Knockdown of NIF-1 expression attenuated both neurite outgrowth in cultured cortical neurons and retinoic acid (RA)-treated Neuro-2a neuroblastoma cells. Furthermore, activity-induced Ca(2+) influx, which is critical for neuronal morphogenesis, stimulated the nuclear localization of NIF-1 in cortical neurons. Suppression of NIF-1 expression reduced the up-regulation of neuronal activity-dependent gene transcription. These findings collectively suggest that NIF-1 directs neuronal morphogenesis during early developmental stages through modulating activity-dependent gene transcription.

  13. Investigation of the pH-dependence of dye-doped protein-protein interactions.

    Science.gov (United States)

    Nudelman, Roman; Gloukhikh, Ekaterina; Rekun, Antonina; Richter, Shachar

    2016-11-01

    Proteins can dramatically change their conformation under environmental conditions such as temperature and pH. In this context, Glycoprotein's conformational determination is challenging. This is due to the variety of domains which contain rich chemical characters existing within this complex. Here we demonstrate a new, straightforward and efficient technique that uses the pH-dependent properties of dyes-doped Pig Gastric Mucin (PGM) for predicting and controlling protein-protein interaction and conformation. We utilize the PGM as natural host matrix which is capable of dynamically changing its conformational shape and adsorbing hydrophobic and hydrophilic dyes under different pH conditions and investigate and control the fluorescent properties of these composites in solution. It is shown at various pH conditions, a large variety of light emission from these complexes such as red, green and white is obtained. This phenomenon is explained by pH-dependent protein folding and protein-protein interactions that induce different emission spectra which are mediated and controlled by means of dye-dye interactions and surrounding environment. This process is used to form the technologically challenging white light-emitting liquid or solid coating for LED devices. © 2016 The Protein Society.

  14. [Fluoxetine (FX) efficacy in the treatment of cocaine dependence methadone maintenance patients. Interaction with plasma levels].

    Science.gov (United States)

    Baño, M D; Agujetas, M; López, M L; Tena, T; Rodríguez, A; Lora-Tamayo, C; Guillén, J L

    1999-01-01

    The objective of this study was to assess the efficacy of fluoxetine (FX) treatment in cocaine dependent methadone (MTD) maintenance patients, to assess decrease or interruption of cocaine use and pharmacokinetic interaction between fluoxetine an methadone plasma levels. The sample was composed of 11 patients with DSM IV criteria for opioid and cocaine dependence. We added Fluoxetine (20 mg per day) during 9 weeks in Majadahonda Drug Program. All patients were in methadone program a mean of 7.5 months. We made a psychiatry interview and the baseline severity of the mood disorder was assessed with the Clinical Global Impression ICG for therapeutic improvement. Cocaine use and fluoxetine treatment was measured in urine analysis and pharmacokinetic interaction between FX-MTD were measured with plasma levels of methadone. Fluoxetine was well tolerated combined with methadone. FX-MTD interaction didn't occur, resulting in no increased of MTD plasma level to dose before and after fluoxetine treatment. After fluoxetine treatment decreased cocaine use, changed cocaine tract from injected to smoked and improvement depressive symptoms.

  15. Motor-substrate interactions in mycoplasma motility explains non-Arrhenius temperature dependence.

    Science.gov (United States)

    Chen, Jing; Neu, John; Miyata, Makoto; Oster, George

    2009-12-02

    Mycoplasmas exhibit a novel, substrate-dependent gliding motility that is driven by approximately 400 "leg" proteins. The legs interact with the substrate and transmit the forces generated by an assembly of ATPase motors. The velocity of the cell increases linearly by nearly 10-fold over a narrow temperature range of 10-40 degrees C. This corresponds to an Arrhenius factor that decreases from approximately 45 k(B)T at 10 degrees C to approximately 10 k(B)T at 40 degrees C. On the other hand, load-velocity curves at different temperatures extrapolate to nearly the same stall force, suggesting a temperature-insensitive force-generation mechanism near stall. In this article, we propose a leg-substrate interaction mechanism that explains the intriguing temperature sensitivity of this motility. The large Arrhenius factor at low temperature comes about from the addition of many smaller energy barriers arising from many substrate-binding sites at the distal end of the leg protein. The Arrhenius dependence attenuates at high temperature due to two factors: 1), the reduced effective multiplicity of energy barriers intrinsic to the multiple-site binding mechanism; and 2), the temperature-sensitive weakly facilitated leg release that curtails the power stroke. The model suggests an explanation for the similar steep, sub-Arrhenius temperature-velocity curves observed in many molecular motors, such as kinesin and myosin, wherein the temperature behavior is dominated not by the catalytic biochemistry, but by the motor-substrate interaction.

  16. Temperature dependence of water interactions with the amide carbonyls of α-helices.

    Science.gov (United States)

    Brewer, Scott H; Tang, Yuefeng; Vu, Dung M; Gnanakaran, S; Raleigh, Daniel P; Dyer, R Brian

    2012-07-03

    Hydration is a key determinant of the folding, dynamics, and function of proteins. In this study, temperature-dependent Fourier transform infrared (FTIR) spectroscopy combined with singular value decomposition (SVD) and global fitting were used to investigate both the interaction of water with α-helical proteins and the cooperative thermal unfolding of these proteins. This methodology has been applied to an isolated α-helix (Fs peptide) and to globular α-helical proteins including the helical subdomain and full-length villin headpiece (HP36 and HP67). The results suggest a unique IR signature for the interaction of water with the helical amide carbonyl groups of the peptide backbone. The IR spectra indicate a weakening of the net hydrogen bond strength of water to the backbone carbonyls with increasing temperature. This weakening of the backbone solvation occurs as a discrete transition near the maximum of the temperature-dependent hydrophobic effect, not a continuous change with increasing temperature. Possible molecular origins of this effect are discussed with respect to previous molecular dynamics simulations of the temperature-dependent solvation of the helix backbone.

  17. Earthquake simulations with time-dependent nucleation and long-range interactions

    Directory of Open Access Journals (Sweden)

    J. H. Dieterich

    1995-01-01

    Full Text Available A model for rapid simulation of earthquake sequences is introduced which incorporates long-range elastic interactions among fault elements and time-dependent earthquake nucleation inferred from experimentally derived rate- and state-dependent fault constitutive properties. The model consists of a planar two-dimensional fault surface which is periodic in both the x- and y-directions. Elastic interactions among fault elements are represented by an array of elastic dislocations. Approximate solutions for earthquake nucleation and dynamics of earthquake slip are introduced which permit computations to proceed in steps that are determined by the transitions from one sliding state to the next. The transition-driven time stepping and avoidance of systems of simultaneous equations permit rapid simulation of large sequences of earthquake events on computers of modest capacity, while preserving characteristics of the nucleation and rupture propagation processes evident in more detailed models. Earthquakes simulated with this model reproduce many of the observed spatial and temporal characteristics of clustering phenomena including foreshock and aftershock sequences. Clustering arises because the time dependence of the nucleation process is highly sensitive to stress perturbations caused by nearby earthquakes. Rate of earthquake activity following a prior earthquake decays according to Omori's aftershock decay law and falls off with distance.

  18. The self-interaction of a fluid interface, the wavevector dependent surface tension and wedge filling

    Science.gov (United States)

    Parry, Andrew O.; Rascón, Carlos

    2011-01-01

    We argue that whenever an interface, separating bulk fluid phases, adopts a non-planar configuration (induced by a confining geometry or thermal fluctuations, say), the energy cost of it will contain a non-local self-interaction term. For systems with short-ranged forces and Ising symmetry, we determine the self-interaction by integrating out bulk-like degrees of freedom from a more microscopic Landau-Ginzburg-Wilson model. The self-interaction can be written in a simple diagrammatic form involving integrals over effective two-body forces acting at the interface and consistently accounts for a number of known features of the microscopic model, including the wavevector dependence of the surface tension describing the fluctuations of a near planar interface. When applied to wedge filling transitions, the self-interaction describes the attraction between the wetting films on either side of the wedge. We show that, for sufficiently acute wedges, this can alter the order of the filling phase transition.

  19. The self-interaction of a fluid interface, the wavevector dependent surface tension and wedge filling

    Energy Technology Data Exchange (ETDEWEB)

    Parry, Andrew O [Department of Mathematics, Imperial College London, London SW7 2BZ (United Kingdom); Rascon, Carlos [Grupo Interdisciplinar de Sistemas Complejos (GISC), Departamento de Matematicas, Universidad Carlos III de Madrid, 28911 Leganes, Madrid (Spain)

    2011-01-12

    We argue that whenever an interface, separating bulk fluid phases, adopts a non-planar configuration (induced by a confining geometry or thermal fluctuations, say), the energy cost of it will contain a non-local self-interaction term. For systems with short-ranged forces and Ising symmetry, we determine the self-interaction by integrating out bulk-like degrees of freedom from a more microscopic Landau-Ginzburg-Wilson model. The self-interaction can be written in a simple diagrammatic form involving integrals over effective two-body forces acting at the interface and consistently accounts for a number of known features of the microscopic model, including the wavevector dependence of the surface tension describing the fluctuations of a near planar interface. When applied to wedge filling transitions, the self-interaction describes the attraction between the wetting films on either side of the wedge. We show that, for sufficiently acute wedges, this can alter the order of the filling phase transition.

  20. Density-dependent effective baryon-baryon interaction from chiral three-baryon forces

    Science.gov (United States)

    Petschauer, Stefan; Haidenbauer, Johann; Kaiser, Norbert; Meißner, Ulf-G.; Weise, Wolfram

    2017-01-01

    A density-dependent effective potential for the baryon-baryon interaction in the presence of the (hyper)nuclear medium is constructed, based on the leading (irreducible) three-baryon forces derived within SU(3) chiral effective field theory. We evaluate the contributions from three classes: contact terms, one-pion exchange and two-pion exchange. In the strangeness-zero sector we recover the known result for the in-medium nucleon-nucleon interaction. Explicit expressions for the ΛN in-medium potential in (asymmetric) nuclear matter are presented. Our results are suitable for implementation into calculations of (hyper)nuclear matter. In order to estimate the low-energy constants of the leading three-baryon forces we introduce the decuplet baryons as explicit degrees of freedom and construct the relevant terms in the minimal non-relativistic Lagrangian. With these, the constants are estimated through decuplet saturation. Utilizing this approximation we provide numerical results for the effect of the three-body force in symmetric nuclear matter and pure neutron matter on the ΛN interaction. A moderate repulsion that increases with density is found in comparison to the free ΛN interaction.

  1. Temperature Depended Role of Shigella flexneri Invasion Plasmid on the Interaction with Acanthamoeba castellanii

    Directory of Open Access Journals (Sweden)

    Amir Saeed

    2012-01-01

    Full Text Available Shigella flexneri is a Gram-negative bacterium causing the diarrhoeal disease shigellosis in humans. The virulence genes required for invasion are clustered on a large 220 kb plasmid encoding type three secretion system (TTSS apparatus and virulence factors such as adhesions and invasion plasmid antigens (Ipa. The bacterium is transmitted by contaminated food, water, or from person to person. Acanthamoebae are free-living amoebae (FLA which are found in diverse environments and isolated from various water sources. Different bacteria interact differently with FLA since Francisella tularensis, Vibrio cholerae, Shigella sonnei, and S. dysenteriae are able to grow inside A. castellanii. In contrast, Pseudomonas aeruginosa induces both necrosis and apoptosis to kill A. castellanii. The aim of this study is to examine the role of invasion plasmid of S. flexneri on the interaction with A. castellanii at two different temperatures. A. castellanii in the absence or presence of wild type, IpaB mutant, or plasmid-cured strain S. flexneri was cultured at 30∘C and 37∘C and the interaction was analysed by viable count of both bacteria and amoebae, electron microscopy, flow cytometry, and statistical analysis. The outcome of the interaction was depended on the temperature since the growth of A. castellanii was inhibited at 30∘C, and A. castellanii was killed by invasion plasmid mediated necrosis at 37∘C.

  2. A cancer derived mutation in the Retinoblastoma gene with a distinct defect for LXCXE dependent interactions

    Directory of Open Access Journals (Sweden)

    Demone Jordan

    2010-03-01

    Full Text Available Abstract Background The interaction between viral oncoproteins such as Simian virus 40 TAg, adenovirus E1A, and human papilloma virus E7, and the retinoblastoma protein (pRB occurs through a well characterized peptide sequence, LXCXE, on the viral protein and a well conserved groove in the pocket domain of pRB. Cellular proteins, such as histone deacetylases, also use this mechanism to interact with the retinoblastoma protein to repress transcription at cell cycle regulated genes. For these reasons this region of the pRB pocket domain is thought to play a critical role in growth suppression. Results In this study, we identify and characterize a tumor derived allele of the retinoblastoma gene (RB1 that possesses a discrete defect in its ability to interact with LXCXE motif containing proteins that compromises proliferative control. To assess the frequency of similar mutations in the RB1 gene in human cancer, we screened blood and tumor samples for similar alleles. We screened almost 700 samples and did not detect additional mutations, indicating that this class of mutation is rare. Conclusions Our work provides proof of principal that alleles encoding distinct, partial loss of function mutations in the retinoblastoma gene that specifically lose LXCXE dependent interactions, are found in human cancer.

  3. The self-interaction of a fluid interface, the wavevector dependent surface tension and wedge filling.

    Science.gov (United States)

    Parry, Andrew O; Rascón, Carlos

    2011-01-12

    We argue that whenever an interface, separating bulk fluid phases, adopts a non-planar configuration (induced by a confining geometry or thermal fluctuations, say), the energy cost of it will contain a non-local self-interaction term. For systems with short-ranged forces and Ising symmetry, we determine the self-interaction by integrating out bulk-like degrees of freedom from a more microscopic Landau-Ginzburg-Wilson model. The self-interaction can be written in a simple diagrammatic form involving integrals over effective two-body forces acting at the interface and consistently accounts for a number of known features of the microscopic model, including the wavevector dependence of the surface tension describing the fluctuations of a near planar interface. When applied to wedge filling transitions, the self-interaction describes the attraction between the wetting films on either side of the wedge. We show that, for sufficiently acute wedges, this can alter the order of the filling phase transition.

  4. Tailoring Rydberg interactions via F\\"orster resonances: state combinations, hopping and angular dependence

    CERN Document Server

    Paris-Mandoki, Asaf; Tresp, Christoph; Mirgorodskiy, Ivan; Hofferberth, Sebastian

    2016-01-01

    F\\"orster resonances provide a highly flexible tool to tune both the strength and the angular shape of interactions between two Rydberg atoms. We give a detailed explanation about how F\\"orster resonances can be found by searching through a large range of possible quantum number combinations. We apply our search method to $SS$, $SD$ and $DD$ pair states of $^{87}$Rb with principal quantum numbers from 30 to 100, taking into account the fine structure splitting of the Rydberg states. We find various strong resonances between atoms with a large difference in principal quantum numbers. We quantify the strength of these resonances by introducing a figure of merit $\\tilde C_3$ which is independent of the magnetic quantum number and geometry to classify the resonances by interaction strength. We further predict to what extent interaction exchange is possible on different resonances and point out limitations of the coherent hopping process. Finally, we discuss the angular dependence of the dipole-dipole interaction ...

  5. Self-organized network of phase oscillators coupled by activity-dependent interactions.

    Science.gov (United States)

    Aoki, Takaaki; Aoyagi, Toshio

    2011-12-01

    We investigate a network of coupled phase oscillators whose interactions evolve dynamically depending on the relative phases between the oscillators. We found that this coevolving dynamical system robustly yields three basic states of collective behavior with their self-organized interactions. The first is the two-cluster state, in which the oscillators are organized into two synchronized groups. The second is the coherent state, in which the oscillators are arranged sequentially in time. The third is the chaotic state, in which the relative phases between oscillators and their coupling weights are chaotically shuffled. Furthermore, we demonstrate that self-assembled multiclusters can be designed by controlling the weight dynamics. Note that the phase patterns of the oscillators and the weighted network of interactions between them are simultaneously organized through this coevolving dynamics. We expect that these results will provide new insight into self-assembly mechanisms by which the collective behavior of a rhythmic system emerges as a result of the dynamics of adaptive interactions.

  6. Temperature dependence of Raman-active phonons and anharmonic interactions in layered hexagonal BN

    Science.gov (United States)

    Cuscó, Ramon; Gil, Bernard; Cassabois, Guillaume; Artús, Luis

    2016-10-01

    We present a Raman scattering study of optical phonons in hexagonal BN for temperatures ranging from 80 to 600 K. The experiments were performed on high-quality, single-crystalline hexagonal BN platelets. The observed temperature dependence of the frequencies and linewidths of both Raman active E2 g optical phonons is analyzed in the framework of anharmonic decay theory, and possible decay channels are discussed in the light of density-functional theory calculations. With increasing temperature, the E2g high mode displays strong anharmonic interactions, with a linewidth increase that indicates an important contribution of four-phonon processes and a marked frequency downshift that can be attributed to a substantial effect of the four-phonon scattering processes (quartic anharmonicity). In contrast, the E2g low mode displays a very narrow linewidth and weak anharmonic interactions, with a frequency downshift that is primarily accounted for by the thermal expansion of the interlayer spacing.

  7. Thermochemical and kinetic evidence for nucleotide-sequence-dependent RecA-DNA interactions.

    Science.gov (United States)

    Wittung, P; Ellouze, C; Maraboeuf, F; Takahashi, M; Nordèn, B

    1997-05-01

    RecA catalyses homologous recombination in Escherichia coli by promoting pairing of homologous DNA molecules after formation of a helical nucleoprotein filament with single-stranded DNA. The primary reaction of RecA with DNA is generally assumed to be unspecific. We show here, by direct measurement of the interaction enthalpy by means of isothermal titration calorimetry, that the polymerisation of RecA on single-stranded DNA depends on the DNA sequence, with a high exothermic preference for thymine bases. This enthalpic sequence preference of thymines by RecA correlates with faster binding kinetics of RecA to thymine DNA. Furthermore, the enthalpy of interaction between the RecA x DNA filament and a second DNA strand is large only when the added DNA is complementary to the bound DNA in RecA. This result suggests a possibility for a rapid search mechanism by RecA x DNA filaments for homologous DNA molecules.

  8. Hubbard interactions in iron-based pnictides and chalcogenides: Slater parametrization, screening channels, and frequency dependence

    Science.gov (United States)

    van Roekeghem, Ambroise; Vaugier, Loïg; Jiang, Hong; Biermann, Silke

    2016-09-01

    We calculate the strength of the frequency-dependent on-site electronic interactions in the iron pnictides LaFeAsO, BaFe2As2 , BaRu2As2 , and LiFeAs and the chalcogenide FeSe from first principles within the constrained random phase approximation. We discuss the accuracy of an atomiclike parametrization of the two-index density-density interaction matrices based on the calculation of an optimal set of three independent Slater integrals, assuming that the angular part of the Fe d localized orbitals can be described within spherical harmonics as for isolated Fe atoms. We show that its quality depends on the ligand-metal bonding character rather than on the dimensionality of the lattice: it is excellent for ionic-like Fe-Se (FeSe) chalcogenides and a more severe approximation for more covalent Fe-As (LaFeAsO, BaFe2As2 ) pnictides. We furthermore analyze the relative importance of different screening channels, with similar conclusions for the different pnictides but a somewhat different picture for the benchmark oxide SrVO3: the ligand channel does not appear to be dominant in the pnictides, while oxygen screening is the most important process in the oxide. Finally, we analyze the frequency dependence of the interaction. In contrast to simple oxides, in iron pnictides its functional form cannot be simply modeled by a single plasmon, and the actual density of modes enters the construction of an effective Hamiltonian determining the low-energy properties.

  9. Efficacy of synaptic inhibition depends on multiple, dynamically interacting mechanisms implicated in chloride homeostasis.

    Directory of Open Access Journals (Sweden)

    Nicolas Doyon

    2011-09-01

    Full Text Available Chloride homeostasis is a critical determinant of the strength and robustness of inhibition mediated by GABA(A receptors (GABA(ARs. The impact of changes in steady state Cl(- gradient is relatively straightforward to understand, but how dynamic interplay between Cl(- influx, diffusion, extrusion and interaction with other ion species affects synaptic signaling remains uncertain. Here we used electrodiffusion modeling to investigate the nonlinear interactions between these processes. Results demonstrate that diffusion is crucial for redistributing intracellular Cl(- load on a fast time scale, whereas Cl(-extrusion controls steady state levels. Interaction between diffusion and extrusion can result in a somato-dendritic Cl(- gradient even when KCC2 is distributed uniformly across the cell. Reducing KCC2 activity led to decreased efficacy of GABA(AR-mediated inhibition, but increasing GABA(AR input failed to fully compensate for this form of disinhibition because of activity-dependent accumulation of Cl(-. Furthermore, if spiking persisted despite the presence of GABA(AR input, Cl(- accumulation became accelerated because of the large Cl(- driving force that occurs during spikes. The resulting positive feedback loop caused catastrophic failure of inhibition. Simulations also revealed other feedback loops, such as competition between Cl(- and pH regulation. Several model predictions were tested and confirmed by [Cl(-](i imaging experiments. Our study has thus uncovered how Cl(- regulation depends on a multiplicity of dynamically interacting mechanisms. Furthermore, the model revealed that enhancing KCC2 activity beyond normal levels did not negatively impact firing frequency or cause overt extracellular K(- accumulation, demonstrating that enhancing KCC2 activity is a valid strategy for therapeutic intervention.

  10. Long-range exchange interaction between magnetic impurities in graphene

    Science.gov (United States)

    Agarwal, M.; Mishchenko, E. G.

    2017-02-01

    The effective spin exchange RKKY coupling between impurities (adatoms) on graphene mediated by conduction electrons is studied as a function of the strength of the potential part of the on-site energy U of the electron-adatom interaction. With increasing U , the exchange coupling becomes long range, determined largely by the impurity levels with energies close to the Dirac points. When adatoms reside on opposite sublattices, their exchange coupling, normally antiferromagnetic, becomes ferromagnetic and resonantly enhanced at a specific distance where an impurity level crosses the Dirac point.

  11. RNA LEGO: magnesium-dependent assembly of RNA building blocks through loop-loop interactions.

    Science.gov (United States)

    Horiya, Satoru; Li, Xianglan; Kawai, Gota; Saito, Ryota; Katoh, Akira; Kobayashi, Koh; Harada, Kazuo

    2002-01-01

    We describe the construction of nano-molecular assemblies using RNA building blocks the human immunodeficiency virus type 1 (HIV-1) dimerization initiation site (DIS) RNA, that forms stable base pairing through a magnesium-dependent loop-loop interaction ("kissing"). RNA building blocks containing two DIS or DIS-like hairpins connected by a two nucleotide linker self-assembled to form specific structures as observed by non-denaturing polyacrylamide gel electrophoresis (PAGE). Furthermore, observation of "real time" formation of the molecular assemblies by circular dichroism (CD) spectroscopy was attempted.

  12. Spin-Spin Interactions in Organic Magnetoresistance Probed by Angle-Dependent Measurements

    Science.gov (United States)

    Wagemans, W.; Schellekens, A. J.; Kemper, M.; Bloom, F. L.; Bobbert, P. A.; Koopmans, B.

    2011-05-01

    The dependence of organic magnetoresistance (OMAR) on the orientation of the magnetic field has been investigated. In contrast with previous claims, a finite and systematic change in magnitude is observed when the orientation of the field is changed with respect to the sample. It is demonstrated that, to explain these effects, spin-spin interactions have to be included in the models previously suggested for OMAR. Dipole coupling and exchange coupling are introduced in combination with either an anisotropy of the orientation of the spin pairs or an anisotropy in the hyperfine fields.

  13. Probing the short range spin dependent interactions by polarized {sup 3}He atom beams

    Energy Technology Data Exchange (ETDEWEB)

    Yan, H. [China Academy of Engineering Physics, Institute of Nuclear Physics and Chemistry, Mianyang, Sichuan (China); Indiana University, Center for Exploration of Energy and Matter, Bloomington, IN (United States); Sun, G.A.; Gong, J.; Pang, B.B.; Wang, Y.; Yang, Y.W.; Zhang, J.; Zhang, Y. [China Academy of Engineering Physics, Institute of Nuclear Physics and Chemistry, Mianyang, Sichuan (China)

    2014-10-15

    Experiments using polarized {sup 3}He atom beams to search for short range spin dependent forces are proposed. High intensity, high polarization, small beam size {sup 3}He atom beams have been successfully produced and used in surface science researches. By incorporating background reduction designs as combination shielding by μ-metal and superconductor and double beam paths, the precision of spin rotation angle per unit length could be improved by a factor of ∝ 10{sup 4}. By this precision, in combination with a high density and low magnetic susceptibility sample source mass, and reversing one beam path if necessary, sensitivities on three different types of spin dependent interactions could be improved by as much as ∝ 10{sup 2} to ∝ 10{sup 8} over the current experiments at the millimeter range. (orig.)

  14. Enhancing Extraction of Drug-Drug Interaction from Literature Using Neutral Candidates, Negation, and Clause Dependency

    Science.gov (United States)

    Bokharaeian, Behrouz; Diaz, Alberto; Chitsaz, Hamidreza

    2016-01-01

    Motivation Supervised biomedical relation extraction plays an important role in biomedical natural language processing, endeavoring to obtain the relations between biomedical entities. Drug-drug interactions, which are investigated in the present paper, are notably among the critical biomedical relations. Thus far many methods have been developed with the aim of extracting DDI relations. However, unfortunately there has been a scarcity of comprehensive studies on the effects of negation, complex sentences, clause dependency, and neutral candidates in the course of DDI extraction from biomedical articles. Results Our study proposes clause dependency features and a number of features for identifying neutral candidates as well as negation cues and scopes. Furthermore, our experiments indicate that the proposed features significantly improve the performance of the relation extraction task combined with other kernel methods. We characterize the contribution of each category of features and finally conclude that neutral candidate features have the most prominent role among all of the three categories. PMID:27695078

  15. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.

    Science.gov (United States)

    Rose, Jed E; Behm, Frédérique M; Drgon, Tomas; Johnson, Catherine; Uhl, George R

    2010-01-01

    Improving and targeting nicotine replacement therapy (NRT) are cost-effective strategies for reducing adverse health consequences for smokers. Treatment studies document the efficacy of precessation NRT and support important roles for level of nicotine dependence and precessation smoking reduction in successful quitting. However, prior work has not identified the optimal precessation dose or means for personalizing NRT. Genome-wide association has identified groups of genomic markers associated with successful quitting, allowing us to develop a v1.0 "quit-success" genotype score. We now report influences of v1.0 quit-success genotype score, level of dependence and precessation smoking reduction in a smoking cessation trial that examined effects of 21 versus 42 mg/24 h precessation NRT. Four hundred seventy-nine smokers were randomized to 21 or 42 mg NRT, initiated 2 wks prior to target quit dates. We monitored self-reported abstinence and end-expired air carbon monoxide (CO). Genotyping used Affymetrix arrays (Santa Clara, CA, USA). The primary outcome was 10-wk continuous smoking abstinence. NRT dose, level of nicotine dependence and genotype scores displayed significant interactive effects on successful quitting. Successful abstinence also was predicted by CO reductions during precessation NRT. These results document ways in which smoking cessation strategies can be personalized based on levels of nicotine dependence, genotype scores and CO monitoring. These assessments, taken together, can help match most smokers with optimal NRT doses and help rapidly identify some who may be better treated using other methods.

  16. Scale-dependent effects of habitat area on species interaction networks: invasive species alter relationships

    Directory of Open Access Journals (Sweden)

    Sugiura Shinji

    2012-07-01

    Full Text Available Abstract Background The positive relationship between habitat area and species number is considered a fundamental rule in ecology. This relationship predicts that the link number of species interactions increases with habitat area, and structure is related to habitat area. Biological invasions can affect species interactions and area relationships. However, how these relationships change at different spatial scales has remained unexplored. We analysed understory plant–pollinator networks in seven temperate forest sites at 20 spatial scales (radius 120–2020 m to clarify scale-associated relationships between forest area and plant–pollinator networks. Results The pooled data described interactions between 18 plant (including an exotic and 89 pollinator (including an exotic species. The total number of species and the number of interaction links between plant and pollinator species were negatively correlated with forest area, with the highest correlation coefficient at radii of 1520 and 1620 m, respectively. These results are not concordant with the pattern predicted by species–area relationships. However, when associations with exotic species were excluded, the total number of species and the number of interaction links were positively correlated with forest area (the highest correlation coefficient at a radius of 820 m. The network structure, i.e., connectance and nestedness, was also related to forest area (the highest correlation coefficients at radii of 720–820 m, when associations with exotics were excluded. In the study area, the exotic plant species Alliaria petiolata, which has invaded relatively small forest patches surrounded by agricultural fields, may have supported more native pollinator species than initially expected. Therefore, this invasive plant may have altered the original relationships between forest area and plant–pollinator networks. Conclusions Our results demonstrate scale-dependent effects of forest

  17. Gli1/DNA interaction is a druggable target for Hedgehog-dependent tumors.

    Science.gov (United States)

    Infante, Paola; Mori, Mattia; Alfonsi, Romina; Ghirga, Francesca; Aiello, Federica; Toscano, Sara; Ingallina, Cinzia; Siler, Mariangela; Cucchi, Danilo; Po, Agnese; Miele, Evelina; D'Amico, Davide; Canettieri, Gianluca; De Smaele, Enrico; Ferretti, Elisabetta; Screpanti, Isabella; Uccello Barretta, Gloria; Botta, Maurizio; Botta, Bruno; Gulino, Alberto; Di Marcotullio, Lucia

    2015-01-13

    Hedgehog signaling is essential for tissue development and stemness, and its deregulation has been observed in many tumors. Aberrant activation of Hedgehog signaling is the result of genetic mutations of pathway components or other Smo-dependent or independent mechanisms, all triggering the downstream effector Gli1. For this reason, understanding the poorly elucidated mechanism of Gli1-mediated transcription allows to identify novel molecules blocking the pathway at a downstream level, representing a critical goal in tumor biology. Here, we clarify the structural requirements of the pathway effector Gli1 for binding to DNA and identify Glabrescione B as the first small molecule binding to Gli1 zinc finger and impairing Gli1 activity by interfering with its interaction with DNA. Remarkably, as a consequence of its robust inhibitory effect on Gli1 activity, Glabrescione B inhibited the growth of Hedgehog-dependent tumor cells in vitro and in vivo as well as the self-renewal ability and clonogenicity of tumor-derived stem cells. The identification of the structural requirements of Gli1/DNA interaction highlights their relevance for pharmacologic interference of Gli signaling.

  18. Dependence of magnetization on crystal fields and exchange interactions in magnetite

    Energy Technology Data Exchange (ETDEWEB)

    Ouaissa, Mohamed, E-mail: m.ouaissa@yahoo.fr [Laboratoire de Génie Physique et Environnement, Faculté des Sciences, Université Ibn Tofail, Campus Universitaire BP 133, Kénitra 14000 (Morocco); Benyoussef, Abdelilah [Laboratory of Magnetism and Physics of High Energy, Faculty of Science, Mohammed V-Agdal University, Rabat (Morocco); Abo, Gavin S. [Department of Electrical and Computer Engineering and MINT Center, The University of Alabama, Tuscaloosa, AL 35487 (United States); Ouaissa, Samia; Hafid, Mustapha [Laboratoire de Génie Physique et Environnement, Faculté des Sciences, Université Ibn Tofail, Campus Universitaire BP 133, Kénitra 14000 (Morocco); Belaiche, Mohammed [Laboratoire de Magnétisme, Matériaux Magnétiques, Microonde et Céramique, Ecole Normale Supérieure, Université Mohammed V-Agdal, B.P. 9235, Océan, Rabat (Morocco)

    2015-11-15

    In this work, we study the magnetization of magnetite (Fe{sub 3}O{sub 4}) with different exchange interactions and crystal fields using variational method based on the Bogoliubov inequality for the Gibbs free energy within the mean field theory. The magnetic behavior was investigated in the absence and presence of crystal fields. The investigations also revealed that the transition temperature depends on the crystal fields of the octahedral and tetrahedral sites. Magnetite exhibits ferrimagnetic phase with second order transition to paramagnetic phase at 850 K. This result is confirmed using the mean field theory within the Heisenberg model. Important factors that can affect the magnetic behavior of the system are exchange interactions and crystal field. Indeed, a new magnetic behavior was observed depending on these parameters. A first order phase transition from ferrimagnetic to ferromagnetic was found at low temperature, and a second order transition from ferromagnetic to paramagnetic was observed at high temperature. - Highlights: • Magnetization of magnetite versus temperature was studied by mean field theory. • The critical temperature of magnetite (Fe{sub 3}O{sub 4}) was approximately obtained. • Effect of sublattice crystal fields on the magnetization of Fe{sub 3}O{sub 4} was investigated.

  19. Ku80 interaction with apurinic/apyrimidinic sites depends on the structure of DNA ends

    Directory of Open Access Journals (Sweden)

    Kosova A. A.

    2014-01-01

    Full Text Available Aim. The identification of a protein from human cell extract which specifically interacts with the apurinic/apyrimidinic (AP site in the partial DNA duplex containing 5'and 3'-dangling ends (DDE-AP DNA and mimicking clustered DNA damage. Methods. The Schiff base-dependent cross-linking of a protein to AP DNA (borohydride trapping, MALDI-TOF-MS, chromatography, and gel electrophoresis. Results. A human cell extract protein which forms a major covalent adduct with the AP DNA duplex with dangling ends was identified as the Ku80 subunit of Ku antigen by peptide mass mapping based on MALDI-TOF-MS data. The Ku antigen purified from the HeLa cell extract was shown to form the covalent adducts with the same mobility as observed in cell extracts. Conclusions. The Ku80 subunit of Ku antigen can specifically interact with AP DNA forming the Schiff base-mediated adducts which electrophoretic mobility depends on the structure of DNA ends. The difference in electrophoretic mobility can be caused by the cross-linking of AP DNA to distinct target amino acids that appears to reflect unequal positioning of AP DNAs in the complex with Ku antigen.

  20. Cortical Representations of Cognitive Control and Working Memory Are Dependent Yet Non-Interacting.

    Science.gov (United States)

    Harding, Ian H; Harrison, Ben J; Breakspear, Michael; Pantelis, Christos; Yücel, Murat

    2016-02-01

    Cognitive control (CC) and working memory (WM) are concurrently necessary for adaptive human behavior. These processes are thought to rely on similar neural mechanisms, yet little is known of the potential competitive or cooperative brain dynamics that support their concurrent engagement during complex behavioral tasks. Here, statistical interactions (synergy/competition) and dependencies (correlations) in brain function related to CC and WM were measured using functional magnetic resonance imaging. Twenty-five healthy adults performed a novel factorial cognitive paradigm, in which a 2-back verbal WM task was combined with the multisource interference task. Overlapping main effects in neural activation were evident in all regions of the "cognitive control network," together with robust behavioral main effects. However, no significant behavioral or cortical interaction effects were apparent. Conversely, robust positive correlations between the 2 main effects were evident within many components of the network. The results offer robust evidence that the neural representations of WM and CC are statistically dependent, but do not compete. These findings support the notion that CC and WM demands may be dynamically and flexibly encoded within a common brain network to support the efficient production of adaptive behavior across diverse task contexts.

  1. Time-dependent configuration-interaction calculations of laser-driven dynamics in presence of dissipation.

    Science.gov (United States)

    Tremblay, Jean Christophe; Klamroth, Tillmann; Saalfrank, Peter

    2008-08-28

    Correlated, multielectron dynamics of "open" electronic systems within the fixed-nuclei approximation are treated here within explicitly time-dependent configuration-interaction schemes. Specifically, we present simulations of laser-pulse driven excitations of selected electronic states of LiCN in the presence of energy and phase relaxation. The evolution of the system is studied using open-system density matrix theory, which embeds naturally in the time-dependent configuration-interaction singles (doubles) formalism. Different models for dissipation based on the Lindblad semigroup formalism are presented. These models give rise to lifetimes for energy relaxation ranging from a few hundreds of femtoseconds to several nanoseconds. Pure dephasing is treated using a Kossakowski-like Gaussian model, proceeding on similar time scales. The pulse lengths employed range from very short (tens of femtoseconds) to very long (several nanoseconds). To make long-time propagations tractable, the quasiresonant approximation is used. The results show that despite the loss of efficiency, selective dipole switching can still be achieved in the presence of dissipation when using appropriately designed laser pulses.

  2. GlyphLens: View-Dependent Occlusion Management in the Interactive Glyph Visualization.

    Science.gov (United States)

    Tong, Xin; Li, Cheng; Shen, Han-Wei

    2017-01-01

    Glyph as a powerful multivariate visualization technique is used to visualize data through its visual channels. To visualize 3D volumetric dataset, glyphs are usually placed on 2D surface, such as the slicing plane or the feature surface, to avoid occluding each other. However, the 3D spatial structure of some features may be missing. On the other hand, placing large number of glyphs over the entire 3D space results in occlusion and visual clutter that make the visualization ineffective. To avoid the occlusion, we propose a view-dependent interactive 3D lens that removes the occluding glyphs by pulling the glyphs aside through the animation. We provide two space deformation models and two lens shape models to displace the glyphs based on their spatial distributions. After the displacement, the glyphs around the user-interested region are still visible as the context information, and their spatial structures are preserved. Besides, we attenuate the brightness of the glyphs inside the lens based on their depths to provide more depth cue. Furthermore, we developed an interactive glyph visualization system to explore different glyph-based visualization applications. In the system, we provide a few lens utilities that allows users to pick a glyph or a feature and look at it from different view directions. We compare different display/interaction techniques to visualize/manipulate our lens and glyphs.

  3. Kinetochore-Dependent Microtubule Rescue Ensures Their Efficient and Sustained Interactions in Early Mitosis

    Science.gov (United States)

    Gandhi, Sapan R.; Gierliński, Marek; Mino, Akihisa; Tanaka, Kozo; Kitamura, Etsushi; Clayton, Lesley; Tanaka, Tomoyuki U.

    2011-01-01

    Summary How kinetochores regulate microtubule dynamics to ensure proper kinetochore-microtubule interactions is unknown. Here, we studied this during early mitosis in Saccharomyces cerevisiae. When a microtubule shrinks and its plus end reaches a kinetochore bound to its lateral surface, the microtubule end attempts to tether the kinetochore. This process often fails and, responding to this failure, microtubule rescue (conversion from shrinkage to growth) occurs, preventing kinetochore detachment from the microtubule end. This rescue is promoted by Stu2 transfer (ortholog of vertebrate XMAP215/ch-TOG) from the kinetochore to the microtubule end. Meanwhile, microtubule rescue distal to the kinetochore is also promoted by Stu2, which is transported by a kinesin-8 motor Kip3 along the microtubule from the kinetochore. Microtubule extension following rescue facilitates interaction with other widely scattered kinetochores, diminishing long delays in collecting the complete set of kinetochores by microtubules. Thus, kinetochore-dependent microtubule rescue ensures efficient and sustained kinetochore-microtubule interactions in early mitosis. PMID:22075150

  4. Learning a novel phonological contrast depends on interactions between individual differences and training paradigm design.

    Science.gov (United States)

    Perrachione, Tyler K; Lee, Jiyeon; Ha, Louisa Y Y; Wong, Patrick C M

    2011-07-01

    Studies evaluating phonological contrast learning typically investigate either the predictiveness of specific pretraining aptitude measures or the efficacy of different instructional paradigms. However, little research considers how these factors interact--whether different students learn better from different types of instruction--and what the psychological basis for any interaction might be. The present study demonstrates that successfully learning a foreign-language phonological contrast for pitch depends on an interaction between individual differences in perceptual abilities and the design of the training paradigm. Training from stimuli with high acoustic-phonetic variability is generally thought to improve learning; however, we found high-variability training enhanced learning only for individuals with strong perceptual abilities. Learners with weaker perceptual abilities were actually impaired by high-variability training relative to a low-variability condition. A second experiment assessing variations on the high-variability training design determined that the property of this learning environment most detrimental to perceptually weak learners is the amount of trial-by-trial variability. Learners' perceptual limitations can thus override the benefits of high-variability training where trial-by-trial variability in other irrelevant acoustic-phonetic features obfuscates access to the target feature. These results demonstrate the importance of considering individual differences in pretraining aptitudes when evaluating the efficacy of any speech training paradigm. © 2011 Acoustical Society of America

  5. An interactive graphical tool for exploring sequential dependencies in categorical data

    Energy Technology Data Exchange (ETDEWEB)

    Fitzgerald, M.

    1997-12-31

    As monitoring and data storage devices have become cheaper and more readily available, it has become common practice to establish automated monitoring processes which collect enormous amounts of data. For example, in a waste storage facility, waste from several different sources may be combined and stored in a single storage container. Within this unit, many different types of chemical and microbiological reactions may take place over the course of time, not all of which are completely understood. Thus, it is important to monitor the levels of several different chemical compounds within the system, in order to ensure that the waste is being stored safely. The monitoring devices record any anomalous behavior of the system, such as when the presence of a certain chemical compound exceeds some prescribed expectation, the pressure within the container increases beyond a tolerance threshold, the temperature drops more than .5{degree}, etc. These monitoring systems may thus collect large quantities of data in fairly short periods of time. The challenge is then to utilize these massive data sets to bring about an understanding of the process and discover potential avenues of intervention. This report describes an interactive graphical tool, written in XLISP-STAT, for exploratory data analysis of dependencies in sequences of categorical data. Both global and local views of the dependency structure can be insightful, and allowing the user the flexibility to change critical parameters and switch between views in a simple, interactive, point-and-click environment can make the task of exploring dependencies among a large number of categories feasible and lead to a better understanding of the sequential properties of the data.

  6. State-dependent blocker interactions with the CFTR chloride channel: implications for gating the pore.

    Science.gov (United States)

    Linsdell, Paul

    2014-12-01

    Chloride permeation through the cystic fibrosis transmembrane conductance regulator (CFTR) Cl(-) channel is subject to voltage-dependent open-channel block by a diverse range of cytoplasmic anions. However, in most cases the ability of these blocking substances to influence the pore opening and closing process has not been reported. In the present work, patch clamp recording was used to investigate the state-dependent block of CFTR by cytoplasmic Pt(NO2)4(2-) ions. Two major effects of Pt(NO2)4(2-) were identified. First, this anion caused fast, voltage-dependent block of open channels, leading to an apparent decrease in single-channel current amplitude. Secondly, Pt(NO2)4(2-) also decreased channel open probability due to an increase in interburst closed times. Interestingly, mutations in the pore that weakened (K95Q) or strengthened (I344K, V345K) interactions with Pt(NO2)4(2-) altered blocker effects both on Cl(-) permeation and on channel gating, suggesting that both these effects are a consequence of Pt(NO2)4(2-) interaction with a single site within the pore. Experiments at reduced extracellular Cl(-) concentration hinted that Pt(NO2)4(2-) may have a third effect, possibly increasing channel activity by interfering with channel closure. These results suggest that Pt(NO2)4(2-) can enter from the cytoplasm into the pore inner vestibule of both open and closed CFTR channels, and that Pt(NO2)4(2-) bound in the inner vestibule blocks Cl(-) permeation as well as interfering with channel opening and, perhaps, channel closure. Implications for the location of the channel gate in the pore, and the operation of this gate, are discussed.

  7. Estimation of the temperature dependent interaction between uncharged point defects in Si

    Energy Technology Data Exchange (ETDEWEB)

    Kamiyama, Eiji [Department of Communication Engineering, Okayama Prefectural University, 111 Kuboki, Soja-shi, Okayama-ken 719-1197 (Japan); GlobalWafers Japan Co., Ltd., 30 Soya, Hadano, Kanagawa, 257-8566 (Japan); Vanhellemont, Jan [Department of Solid State Sciences, Ghent University, Krijgslaan 281-S1, Ghent B-9000 (Belgium); Sueoka, Koji [Department of Communication Engineering, Okayama Prefectural University, 111 Kuboki, Soja-shi, Okayama-ken 719-1197 (Japan)

    2015-01-15

    A method is described to estimate the temperature dependent interaction between two uncharged point defects in Si based on DFT calculations. As an illustration, the formation of the uncharged di-vacancy V{sub 2} is discussed, based on the temperature dependent attractive field between both vacancies. For that purpose, all irreducible configurations of two uncharged vacancies are determined, each with their weight given by the number of equivalent configurations. Using a standard 216-atoms supercell, nineteen irreducible configurations of two vacancies are obtained. The binding energies of all these configurations are calculated. Each vacancy is surrounded by several attractive sites for another vacancy. The obtained temperature dependent of total volume of these attractive sites has a radius that is closely related with the capture radius for the formation of a di-vacancy that is used in continuum theory. The presented methodology can in principle also be applied to estimate the capture radius for pair formation of any type of point defects.

  8. Time-dep endent Calculations for Two-proton Decay Width with Schematic Density-dependent Contact Pairing Interaction

    Institute of Scientific and Technical Information of China (English)

    Oishi Tomohiro

    2016-01-01

    We calculate the two-proton decay width of the 6 Be nucleus employing the schematic density-dependent contact potential for the proton-proton pairing interaction. The decay width is calculated with a time-dependent method, in which the two-proton emission is described as a time-evolution of a three-body meta-stable state. Model-dependence of the two-proton decay width has been shown by comparing the results obtained with the two different pairing models, schematic density-dependent contact and Minnesota interactions, which have zero and finite ranges, respectively.

  9. Biotic interactions overrule plant responses to climate, depending on the species' biogeography.

    Directory of Open Access Journals (Sweden)

    Astrid Welk

    Full Text Available This study presents an experimental approach to assess the relative importance of climatic and biotic factors as determinants of species' geographical distributions. We asked to what extent responses of grassland plant species to biotic interactions vary with climate, and to what degree this variation depends on the species' biogeography. Using a gradient from oceanic to continental climate represented by nine common garden transplant sites in Germany, we experimentally tested whether congeneric grassland species of different geographic distribution (oceanic vs. continental plant range type responded differently to combinations of climate, competition and mollusc herbivory. We found the relative importance of biotic interactions and climate to vary between the different components of plant performance. While survival and plant height increased with precipitation, temperature had no effect on plant performance. Additionally, species with continental plant range type increased their growth in more benign climatic conditions, while those with oceanic range type were largely unable to take a similar advantage of better climatic conditions. Competition generally caused strong reductions of aboveground biomass and growth. In contrast, herbivory had minor effects on survival and growth. Against expectation, these negative effects of competition and herbivory were not mitigated under more stressful continental climate conditions. In conclusion we suggest variation in relative importance of climate and biotic interactions on broader scales, mediated via species-specific sensitivities and factor-specific response patterns. Our results have important implications for species distribution models, as they emphasize the large-scale impact of biotic interactions on plant distribution patterns and the necessity to take plant range types into account.

  10. Magnetic interlayer coupling in multilayers of fractional dimensionality

    CERN Document Server

    Bak, Z; Gruhn, W

    2000-01-01

    Within analytical method we calculate the RKKY interaction between localized magnetic moments for a system of fractional (nonintegral) dimension. We provide the exact derivation of the spatial dependence of the RKKY exchange integral as an analytical function of dimensionality. Moreover, with the help of fractional analysis, we derive formulae for interlayer coupling in fractional multilayers. On the basis of the results obtained possibility of controlled interlayer interaction is shown.

  11. Size-dependent interaction of silica nanoparticles with lysozyme and bovine serum albumin proteins

    Science.gov (United States)

    Yadav, Indresh; Aswal, Vinod K.; Kohlbrecher, Joachim

    2016-05-01

    The interaction of three different sized (diameter 10, 18, and 28 nm) anionic silica nanoparticles with two model proteins—cationic lysozyme [molecular weight (MW) 14.7 kDa)] and anionic bovine serum albumin (BSA) (MW 66.4 kDa) has been studied by UV-vis spectroscopy, dynamic light scattering (DLS), and small-angle neutron scattering (SANS). The adsorption behavior of proteins on the nanoparticles, measured by UV-vis spectroscopy, is found to be very different for lysozyme and BSA. Lysozyme adsorbs strongly on the nanoparticles and shows exponential behavior as a function of lysozyme concentration irrespective of the nanoparticle size. The total amount of adsorbed lysozyme, as governed by the surface-to-volume ratio, increases on lowering the size of the nanoparticles for a fixed volume fraction of the nanoparticles. On the other hand, BSA does not show any adsorption for all the different sizes of the nanoparticles. Despite having different interactions, both proteins induce similar phase behavior where the nanoparticle-protein system transforms from one phase (clear) to two phase (turbid) as a function of protein concentration. The phase behavior is modified towards the lower concentrations for both proteins with increasing the nanoparticle size. DLS suggests that the phase behavior arises as a result of the nanoparticles' aggregation on the addition of proteins. The size-dependent modifications in the interaction potential, responsible for the phase behavior, have been determined by SANS data as modeled using the two-Yukawa potential accounting for the repulsive and attractive interactions in the systems. The protein-induced interaction between the nanoparticles is found to be short-range attraction for lysozyme and long-range attraction for BSA. The magnitude of attractive interaction irrespective of protein type is enhanced with increase in the size of the nanoparticles. The total (attractive+repulsive) potential leading to two-phase formation is found to be

  12. Protein-nanoparticle interactions: the effects of surface compositional and structural heterogeneity are scale dependent

    Science.gov (United States)

    Huang, Rixiang; Carney, Randy P.; Stellacci, Francesco; Lau, Boris L. T.

    2013-07-01

    Nanoparticles (NPs) in the biological environment are exposed to a large variety and concentration of proteins. Proteins are known to adsorb in a `corona' like structure on the surface of NPs. In this study, we focus on the effects of surface compositional and structural heterogeneity on protein adsorption by examining the interaction of self-assembled monolayer coated gold NPs (AuNPs) with two types of proteins: ubiquitin and fibrinogen. This work was designed to systematically investigate the role of surface heterogeneity in nanoparticle-protein interaction. We have chosen the particles as well as the proteins to provide different types (in distribution and length-scale) of heterogeneity. The goal was to unveil the role of heterogeneity and of its length-scale in the particle-protein interaction. Dynamic light scattering and circular dichroism spectroscopy were used to reveal different interactions at pH above and below the isoelectric points of the proteins, which is related to the charge heterogeneity on the protein surface. At pH 7.4, there was only a monolayer of proteins adsorbed onto the NPs and the secondary structure of proteins remained intact. At pH 4.0, large aggregates of nanoparticle-protein complexes were formed and the secondary structures of the proteins were significantly disrupted. In terms of interaction thermodynamics, results from isothermal titration calorimetry showed that ubiquitin adsorbed differently onto (1) AuNPs with charged and nonpolar terminals organized into nano-scale structure (66-34 OT), (2) AuNPs with randomly distributed terminals (66-34 brOT), and (3) AuNPs with homogeneously charged terminals (MUS). This difference in adsorption behavior was not observed when AuNPs interacted with fibrinogen. The results suggested that the interaction between the proteins and AuNPs was influenced by the surface heterogeneity on the AuNPs, and this influence depends on the scale of surface heterogeneity and the size of the proteins

  13. Scale-Dependent Fracture-Matrix Interactions And Their Impact on Radionuclide Transport - Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Detwiler, Russell

    2014-06-30

    Matrix diffusion and adsorption within a rock matrix are widely regarded as important mechanisms for retarding the transport of radionuclides and other solutes in fractured rock (e.g., Neretnieks, 1980; Tang et al., 1981; Maloszewski and Zuber, 1985; Novakowski and Lapcevic, 1994; Jardine et al., 1999; Zhou and Xie, 2003; Reimus et al., 2003a,b). When remediation options are being evaluated for old sources of contamination, where a large fraction of contaminants reside within the rock matrix, slow diffusion out of the matrix greatly increases the difficulty and timeframe of remediation. Estimating the rates of solute exchange between fractures and the adjacent rock matrix is a critical factor in quantifying immobilization and/or remobilization of DOE-relevant contaminants within the subsurface. In principle, the most rigorous approach to modeling solute transport with fracture-matrix interaction would be based on local-scale coupled advection-diffusion/dispersion equations for the rock matrix and in discrete fractures that comprise the fracture network (Discrete Fracture Network and Matrix approach, hereinafter referred to as DFNM approach), fully resolving aperture variability in fractures and matrix property heterogeneity. However, such approaches are computationally demanding, and thus, many predictive models rely upon simplified models. These models typically idealize fracture rock masses as a single fracture or system of parallel fractures interacting with slabs of porous matrix or as a mobile-immobile or multi-rate mass transfer system. These idealizations provide tractable approaches for interpreting tracer tests and predicting contaminant mobility, but rely upon a fitted effective matrix diffusivity or mass-transfer coefficients. However, because these fitted parameters are based upon simplified conceptual models, their effectiveness at predicting long-term transport processes remains uncertain. Evidence of scale dependence of effective matrix diffusion

  14. Magnetic properties and temperature-dependent half-metallicity of Co2Mn(Ga(1-x)Z(x)) (Z=Si, Ge, Sn) from first-principles calculation.

    Science.gov (United States)

    Luo, Hu-Bin; Hu, Qing-Miao; Li, Chun-Mei; Johansson, Börje; Vitos, Levente; Yang, Rui

    2013-04-17

    Using the first-principles exact muffin-tin orbitals method in combination with the coherent potential approximation, we investigated the magnetic properties, exchange interactions, and temperature-dependent half-metallicity of the Co2Mn(Ga1-xZx) (Z=Si, Ge, Sn) alloys. The total magnetic moment follows perfectly a previously proposed Slater-Pauling relation, i.e., μ0 = Nt - 24, with Nt being the number of valence electrons. The Co-Mn and Co1-Co2 (inter-sublattice) interactions are dominated by direct exchange, whereas the Co1-Co1 (intra-sublattice) interaction is characterized by superexchange. The Mn-Mn exchange interaction in Co2MnGa is of long-ranged RKKY-type. However, the Mn-Mn exchange interactions in Co2MnZ are relatively localized and can be attributed to superexchange. The Co-Mn, Co1-Co2 and Co1-Co1 total exchange interactions increase with x, whereas the Mn-Mn total exchange interactions show convex behavior. The calculated Curie temperature (TC) increases with x. The ability of Z to enhance TC follows the sequence of Si > Ge > Sn, in agreement with the experimental findings. The temperature dependence of the spin polarization at the Fermi level [P(T)] is investigated based on the disordered local moment model. P(T) drops abruptly at temperatures much lower than TC. At temperatures higher than 200 K, the composition with higher TC generally corresponds to larger P(T).

  15. Temperature dependence of the rate constant of hydrogen isotope interactions with a lithium capillary-porous system under reactor irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Tazhibayeva, Irina, E-mail: tazhibayeva@ntsc.kz [Institute of Atomic Energy NNC RK, Kurchatov (Kazakhstan); Kulsartov, Timur; Gordienko, Yuri [Institute of Atomic Energy NNC RK, Kurchatov (Kazakhstan); Mukanova, Aliya [Al’ Farabi Kazakh National University, Almaty (Kazakhstan); Ponkratov, Yuri; Barsukov, Nikolay; Tulubaev, Evgeniy [Institute of Atomic Energy NNC RK, Kurchatov (Kazakhstan); Platacis, Erik [University of Latvia (IPUL), Riga (Latvia); Kenzhin, Ergazy [Shakarim Semey State University, Semey (Kazakhstan)

    2013-10-15

    Highlights: • The experiments with Li CPS sample were carried out at reactor IVG-1.M. • The gas absorption technique was used to study hydrogen isotope interaction with lithium CPS. • The temperature dependence of constants of interaction rate was obtained for various power rates of the reactor. • Determination of the activation energies, and pre-exponents of Arrhenius dependence. • The effect of increase of the rate constant under reaction irradiation. -- Abstract: Experiments with a sample of a lithium capillary-porous system (CPS) were performed at the reactor IVG-1.M of the Institute of Atomic Energy NNC RK to study the effects of neutron irradiation on the parameters of hydrogen isotope interactions with a lithium CPS. The absorption technique was used during the experiments, and this technique allowed the temperature dependences of the hydrogen isotope interaction rate constants with the lithium CPS to be obtained under various reactor powers. The obtained dependencies were used to determine the main interaction parameters: the activation energies and the pre-exponents of the Arrhenius dependence of the hydrogen interaction rate constants with lithium and the lithium CPS. An increase of the hydrogen isotope interaction rate with the lithium CPS was observed under reactor irradiation.

  16. Interactions between parents of technology-dependent children and providers: an integrative review.

    Science.gov (United States)

    Jachimiec, Jennifer A; Obrecht, Jennifer; Kavanaugh, Karen

    2015-03-01

    This article is a review of the literature on the experiences of parents and their interactions with healthcare providers while caring for their technology-dependent child(ren) in their homes. Results are presented in the following themes: information needs, respect and partnership with healthcare providers, care coordination, and experiences with home healthcare nurses. Parents needed information and guidance and felt supported when providers recognized parents' expertise with the child's care, and offered reassurance and confirmation about their practices. Home healthcare clinicians provided supportive care in the home, but their presence created challenges for the family. By acknowledging and valuing the parents' expertise, healthcare providers can empower parents to confidently care for their child.

  17. Parametric interactions of acoustic waves in semiconductor quantum plasmas with strain dependent dielectric constants

    Science.gov (United States)

    Yadav, N.; Ghosh, S.; Agrawal, A.

    2017-05-01

    Using quantum hydrodynamic model (QHD) of semiconductor plasma for a one-component we present an analytical investigation on parametric interaction of a laser radiation in an unmagnetised material with a strain-dependent dielectric constant. The nonlinear current density and third order susceptibility are analyzed in different wave number regions in presence and absence of quantum effect. We present the qualitative behavior of threshold pump intensity with respect to wave number in presence and absence of quantum effect. The numeric estimates are made for n-BaTiO3 crystals at 77k duly irradiated by pulsed 10.6μm CO2 laser. It is found that the quantum correction through Fermi temperature and Bohm potential terms modifies the threshold characteristics.

  18. A semi-nonlocal numerical approach for modeling of temperature-dependent crack-wave interaction

    Science.gov (United States)

    Martowicz, Adam; Kijanka, Piotr; Staszewski, Wieslaw J.

    2016-04-01

    Numerical tools, which are used to simulate complex phenomena for models of complicated shapes suffer from either long computational time or accuracy. Hence, new modeling and simulation tools, which could offer reliable results within reasonable time periods, are highly demanded. Among other approaches, the nonlocal methods have appeared to fulfill these requirements quite efficiently and opened new perspectives for accurate simulations based on crude meshes of the model's degrees of freedom. In the paper, the preliminary results are shown for simulations of the phenomenon of temperature-dependent crack-wave interaction for elastic wave propagation in a model of an aluminum plate. Semi-nonlocal finite differences are considered to solve the problem of thermoelasticity - based on the discretization schemes, which were already proposed by the authors and taken from the previously published work. Numerical modeling is used to examine wave propagation primarily in the vicinity of a notch. Both displacement and temperature fields are sought in the investigated case study.

  19. Calculation of photoelectron spectra within the time-dependent configuration interaction singles scheme

    CERN Document Server

    Karamatskou, Antonia; Chen, Yi-Jen; Santra, Robin

    2014-01-01

    We present the extension of the time-dependent configuration interaction singles (TDCIS) method to the computation of the electron kinetic-energy spectrum in photoionization processes. Especially for strong and long ionizing light pulses the detection of the photoelectron poses a computational challenge because propagating the outgoing photoelectron wavepacket requires large grid sizes. Two different methods which allow for the extraction of the asymptotic photoelectron momentum are compared regarding their methodological and computational performance. The first method follows the scheme of Tong et al. \\cite{tong} where the photoelectron wavefunction is absorbed by a real splitting function. The second method after Tao and Scrinzi \\cite{scrinzi} measures the flux of the electron wavepacket through a surface at a fixed radius. With both methods the full angle- and energy-resolved photoelectron spectrum is obtained. Combined with the TDCIS scheme it is possible to analyze the dynamics of the outgoing electron i...

  20. Structure and Interaction in the pH-Dependent Phase Behavior of Nanoparticle-Protein Systems.

    Science.gov (United States)

    Yadav, Indresh; Kumar, Sugam; Aswal, Vinod K; Kohlbrecher, Joachim

    2017-02-07

    The pH-dependent structure and interaction of anionic silica nanoparticles (diameter 18 nm) with two globular model proteins, lysozyme and bovine serum albumin (BSA), have been studied. Cationic lysozyme adsorbs strongly on the nanoparticles, and the adsorption follows exponential growth as a function of lysozyme concentration, where the saturation value increases as pH approaches the isoelectric point (IEP) of lysozyme. By contrast, irrespective of pH, anionic BSA does not show any adsorption. Despite having a different nature of interactions, both proteins render a similar phase behavior where nanoparticle-protein systems transform from being one-phase (clear) to two-phase (turbid) above a critical protein concentration (CPC). The measurements have been carried out for a fixed concentration of silica nanoparticles (1 wt %) with varying protein concentrations (0-5 wt %). The CPC is found to be much higher for BSA than for lysozyme and increases for lysozyme but decreases for BSA as pH approaches their respective IEPs. The structure and interaction in these systems have been examined using dynamic light scattering (DLS) and small-angle neutron scattering (SANS). The effective hydrodynamic size of the nanoparticles measured using DLS increases with protein concentration and is related to the aggregation of the nanoparticles above the CPC. The propensity of the nanoparticles to aggregate is suppressed for lysozyme and enhanced for BSA as pH approached their respective IEPs. This behavior is understood from SANS data through the interaction potential determined by the interplay of electrostatic repulsion with a short-range attraction for lysozyme and long-range attraction for BSA. The nanoparticle aggregation is caused by charge neutralization by the oppositely charged lysozyme and through depletion for similarly charged BSA. Lysozyme-mediated attractive interaction decreases as pH approaches the IEP because of a decrease in the charge on the protein. In the case of

  1. Time-dependent drug-drug interaction alerts in care provider order entry: software may inhibit medication error reductions

    NARCIS (Netherlands)

    I.H. van der Sijs (Heleen); L.A. Lammers (Laureen); A. van den Tweel (Annemieke); J.E.C.M. Aarts (Jos); M. Berg (Marc); A.G. Vulto (Arnold); T. van Gelder (Teun)

    2009-01-01

    textabstractTime-dependent drug-drug interactions (TDDIs) are drug combinations that result in a decreased drug effect due to coadministration of a second drug. Such interactions can be prevented by separately administering the drugs. This study attempted to reduce drug administration errors due to

  2. Bacillus anthracis interacts with plasmin(ogen to evade C3b-dependent innate immunity.

    Directory of Open Access Journals (Sweden)

    Myung-Chul Chung

    Full Text Available The causative agent of anthrax, Bacillus anthracis, is capable of circumventing the humoral and innate immune defense of the host and modulating the blood chemistry in circulation to initiate a productive infection. It has been shown that the pathogen employs a number of strategies against immune cells using secreted pathogenic factors such as toxins. However, interference of B. anthracis with the innate immune system through specific interaction of the spore surface with host proteins such as the complement system has heretofore attracted little attention. In order to assess the mechanisms by which B. anthracis evades the defense system, we employed a proteomic analysis to identify human serum proteins interacting with B. anthracis spores, and found that plasminogen (PLG is a major surface-bound protein. PLG efficiently bound to spores in a lysine- and exosporium-dependent manner. We identified α-enolase and elongation factor tu as PLG receptors. PLG-bound spores were capable of exhibiting anti-opsonic properties by cleaving C3b molecules in vitro and in rabbit bronchoalveolar lavage fluid, resulting in a decrease in macrophage phagocytosis. Our findings represent a step forward in understanding the mechanisms involved in the evasion of innate immunity by B. anthracis through recruitment of PLG resulting in the enhancement of anti-complement and anti-opsonization properties of the pathogen.

  3. Density-dependent effective baryon-baryon interaction from chiral three-baryon forces

    CERN Document Server

    Petschauer, Stefan; Kaiser, Norbert; Meißner, Ulf-G; Weise, Wolfram

    2016-01-01

    A density-dependent effective potential for the baryon-baryon interaction in the presence of the (hyper)nuclear medium is constructed, based on the leading (irreducible) three-baryon forces derived within SU(3) chiral effective field theory. We evaluate the contributions from three classes: contact terms, one-pion exchange and two-pion exchange. In the strangeness-zero sector we recover the known result for the in-medium nucleon-nucleon interaction. Explicit expressions for the Lambda-nucleon in-medium potential in (asymmetric) nuclear matter are presented. Our results are suitable for implementation into calculations of (hyper)nuclear matter. In order to estimate the low-energy constants of the leading three-baryon forces we introduce the decuplet baryons as explicit degrees of freedom and construct the relevant terms in the minimal non-relativistic Lagrangian. With these, the constants are estimated through decuplet saturation. Utilizing this approximation we provide numerical results for the effect of the ...

  4. VCP phosphorylation-dependent interaction partners prevent apoptosis in Helicobacter pylori-infected gastric epithelial cells.

    Directory of Open Access Journals (Sweden)

    Cheng-Chou Yu

    Full Text Available Previous studies have demonstrated that valosin-containing protein (VCP is associated with H. pylori-induced gastric carcinogenesis. By identifying the interactome of VCP overexpressed in AGS cells using a subtractive proteomics approach, we aimed to characterize the cellular responses mediated by VCP and its functional roles in H. pylori-associated gastric cancer. VCP immunoprecipitations followed by proteomic analysis identified 288 putative interacting proteins, 18 VCP-binding proteins belonged to the PI3K/Akt signaling pathway. H. pylori infection increased the interaction between Akt and VCP, Akt-dependent phosphorylation of VCP, levels of ubiquitinated proteins, and aggresome formation in AGS cells. Furthermore, phosphorylated VCP co-localized with the aggresome, bound ubiquitinated proteins, and increased the degradation of cellular regulators to protect H. pylori-infected AGS cells from apoptosis. Our study demonstrates that VCP phosphorylation following H. pylori infection promotes both gastric epithelial cell survival, mediated by the PI3K/Akt pathway, and the degradation of cellular regulators. These findings provide novel insights into the mechanisms of H. pylori infection induced gastric carcinogenesis.

  5. Structure-dependent interactions of polyphenols with a biomimetic membrane system.

    Science.gov (United States)

    Phan, Huong T T; Yoda, Tsuyoshi; Chahal, Bindu; Morita, Masamune; Takagi, Masahiro; Vestergaard, Mun'delanji C

    2014-10-01

    Polyphenols are naturally-occurring compounds, reported to be biologically active, and through their interactions with cell membranes. Although association of the polyphenols with the bilayer has been reported, the detailed mechanism of interaction is not yet well elucidated. We report on spatio-temporal real-time membrane dynamics observed in the presence of polyphenols. Two distinct membrane dynamics, corresponding to the two classes of polyphenols used, were observed. Flavonoids (epi-gallocatechin-3-gallate, gallocatechin, theaflavin and theaflavin-3-gallate) caused lipid membrane aggregation and rigidification. As simple structural modification through opening of the aromatic C-ring into an olefin bond, present in trans-stilbenes (resveratrol and picead), completely changed the membrane properties, increasing fluidity and inducing fluctuation. There were differences in the membrane transformations within the same class of polyphenols. Structure-dependent classification of membrane dynamics may contribute to a better understanding of the physicochemical mechanism involved in the bioactivity of polyphenols. In general, an increase in the number of hydrophilic side chains (galloyl, hydroxyl, glucoside, gallate) increased the reactivity of the polyphenols. Most notable was the difference observed through a simple addition of the gallate group. Unraveling the importance of these polyphenols, at a functional group level further opens the key to tailored design of bioactive compounds as potential drug candidates.

  6. Population dependence in the interactions with neighbors for pollination: A field experiment with Taraxacum officinale.

    Science.gov (United States)

    Lázaro, Amparo; Totland, Orjan

    2010-05-01

    PREMISE OF THE STUDY. The fitness of plants depends on their immediate biotic and abiotic environmental surroundings. The floral neighborhood of individual plants is part of this immediate environment and affects the frequency and behavior of their pollinators. However, the interactions among plants for pollination might differ among populations because populations differ in floral densities and pollinator assemblages. Despite that, manipulative experiments of the floral neighborhood in different populations with a specific focus on pollinator behavior are still rare. METHODS. We introduced mixtures of two species (Salvia farinacae and Tagetes bonanza) in two populations of Taraxacum officinale and examined their effect on pollinators' foraging behavior on Taraxacum. KEY RESULTS. The effects of the heterospecific neighborhood differed among pollinator groups and between the two populations. Only honeybees consistently preferred both the most diverse (containing three species) and completely pure patches of Taraxacum in both populations. We found a strong and positive effect of patch diversity on visitation to Taraxacum in one population, whereas in the other population either no effect or a negative effect of plant diversity occurred, which we attribute to differences between populations in the ratio of pollinators to inflorescences. Pollinator visitation consistently increased with local Taraxacum density in both populations. CONCLUSIONS. Our study shows that a similar local neighborhood can differentially affect the frequency and foraging behavior of pollinators, even in closely situated populations. Experimental studies conducted in several populations would contribute to determine which factors drive the variation in pollination interactions among populations.

  7. Structures and orientation-dependent interaction forces of titania nanowires using molecular dynamics simulations

    Science.gov (United States)

    Okeke, George; Antony, S. Joseph; Hammond, Robert B.; Ahmed, Kamran

    2017-07-01

    Engineering nanowires to develop new products and processes is highly topical due to their ability to provide highly enhanced physical, chemical, mechanical, thermal and electrical properties. In this work, using molecular dynamics simulations, we report fundamental information, about the structural and thermodynamic properties of individual anatase titania (TiO2) nanowires with cross-sectional diameters between 2 and 6 nm, and aspect ratio (length to diameter) of 6:1 at temperatures ranging from 300 to 3000 K. Estimates of the melting transition temperature of the nanowires are between 2000 and 2500 K. The melting transition temperature predicted from the radial distribution functions (RDFs) shows strong agreement with those predicted from the total energy profiles. Overall, the transition temperature is in reasonable agreement with melting points predicted from experiments and simulations reported in the literature for spherical nanoparticles of similar sizes. Hence, the melting transition temperature of TiO2 nanowires modelled here can be considered as shape independent. Furthermore, for the first time based on MD simulations, interaction forces between two nanowires are reported at ambient temperature (300 K) for different orientations: parallel, perpendicular and end-to-end. It is observed that end-to-end orientations manifested the strongest attraction forces, while the parallel and perpendicular orientations displayed weaker attractions. The results reported here could form a foundation in future multiscale modelling studies of the structured titania nanowire assemblies, depending on the inter-wire interaction forces.

  8. Nanoparticle charge-transfer interactions induce surface dependent conformational changes in apolipoprotein biocorona

    CERN Document Server

    Raghavendra, Achyut J; Brown, Jared M; Podilaa, Ramakrishna

    2016-01-01

    Upon introduction into a biological system, engineered nanomaterials (ENMs) rapidly associate with a variety of biomolecules such as proteins and lipids to form a biocorona. The presence of biocorona influences nano-bio interactions considerably, and could ultimately result in altered biological responses. Apolipoprotein A-I (ApoA-I), the major constituent of high-density lipoprotein (HDL), is one of the most prevalent proteins found in ENM-biocorona irrespective of ENM nature, size, and shape. Given the importance of ApoA-I in HDL and cholesterol transport, it is necessary to understand the mechanisms of ApoA-I adsorption and the associated structural changes for assessing consequences of ENM exposure. Here, we used a comprehensive array of microscopic and spectroscopic tools to elucidate the interactions between ApoA-I and 100 nm Ag nanoparticles (AgNPs) with four different surface functional groups. We found that the protein adsorption and secondary structural changes are highly dependent on the surface fu...

  9. Interaction of sound and sight during action perception: evidence for shared modality-dependent action representations.

    Science.gov (United States)

    Alaerts, Kaat; Swinnen, Stephan P; Wenderoth, Nicole

    2009-10-01

    Seeing or hearing manual actions activates the mirror neuron system, i.e., specialized neurons within motor areas which fire not only when an action is performed but also when it is passively perceived. Although it has been shown that mirror neurons respond to either action-specific vision or sound, it remains a topic of debate whether and how vision and sound interact during action perception. Here we used transcranial magnetic stimulation to explore multimodal interactions in the human motor system, namely at the level of the primary motor cortex (M1). Corticomotor excitability in M1 was measured while subjects perceived unimodal visual (V), unimodal auditory (A), or multimodal (V+A) stimuli of a simple hand action. In addition, incongruent multimodal stimuli were included, in which incongruent vision or sound was presented simultaneously with the auditory or visual action stimulus. A selective response increase was observed to the congruent multimodal stimulus as compared to the unimodal and incongruent multimodal stimuli. These findings speak in favour of 'shared' action representations in the human motor system that are evoked in a 'modality-dependent' way, i.e., they are elicited most robustly by the simultaneous presentation of congruent auditory and visual stimuli. Multimodality in the perception of hand movements bears functional similarities to speech perception, suggesting that multimodal convergence is a generic feature of the mirror system which applies to action perception in general.

  10. Hybrid Model of the Context Dependent Vestibulo-Ocular Reflex: Implications for Vergence-Version Interactions

    Directory of Open Access Journals (Sweden)

    Mina eRanjbaran

    2015-02-01

    Full Text Available The vestibulo-ocular reflex (VOR is an involuntary eye movement evoked by head movements. It is also influenced by viewing distance. This paper presents a hybrid nonlinear bilateral model for the horizontal angular vestibulo-ocular reflex (AVOR in the dark. The model is based on known interconnections between saccadic burst circuits in the brainstem and ocular premotor areas in the vestibular nuclei during fast and slow phase intervals of nystagmus. We implemented a viable switching strategy for the timing of nystagmus events to allow emulation of real nystagmus data. The performance of the hybrid model is evaluated with simulations, and results are consistent with experimental observations. The hybrid model replicates realistic AVOR nystagmus patterns during sinusoidal or step head rotations in the dark and during interactions with vergence, e.g. fixation distance. By simply assigning proper nonlinear neural computations at the premotor level, the model replicates all reported experimental observations. This work sheds light on potential underlying neural mechanisms driving the context dependent AVOR and explains contradictory results in the literature. Moreover, context-dependent behaviors in more complex motor systems could also rely on local nonlinear neural computations.

  11. Applying Boundary Conditions Using a Time-Dependent Lagrangian for Modeling Laser-Plasma Interactions

    Science.gov (United States)

    Reyes, Jonathan; Shadwick, B. A.

    2016-10-01

    Modeling the evolution of a short, intense laser pulse propagating through an underdense plasma is of particular interest in the physics of laser-plasma interactions. Numerical models are typically created by first discretizing the equations of motion and then imposing boundary conditions. Using the variational principle of Chen and Sudan, we spatially discretize the Lagrangian density to obtain discrete equations of motion and a discrete energy conservation law which is exactly satisfied regardless of the spatial grid resolution. Modifying the derived equations of motion (e.g., enforcing boundary conditions) generally ruins energy conservation. However, time-dependent terms can be added to the Lagrangian which force the equations of motion to have the desired boundary conditions. Although some foresight is needed to choose these time-dependent terms, this approach provides a mechanism for energy to exit the closed system while allowing the conservation law to account for the loss. An appropriate time discretization scheme is selected based on stability analysis and resolution requirements. We present results using this variational approach in a co-moving coordinate system and compare such results to those using traditional second-order methods. This work was supported by the U. S. Department of Energy under Contract No. DE-SC0008382 and by the National Science Foundation under Contract No. PHY- 1104683.

  12. Distance-dependent interactions between gold nanoparticles and fluorescent molecules with DNA as tunable spacers

    Energy Technology Data Exchange (ETDEWEB)

    Chhabra, Rahul; Sharma, Jaswinder; Lin Su; Yan Hao; Lindsay, Stuart; Liu Yan [Biodesign Institute, Arizona State University, Tempe, AZ 85287 (United States); Wang Haining; Zou Shengli, E-mail: stuart.lindsay@asu.ed, E-mail: yan_liu@asu.ed [Department of Chemistry, University of Central Florida, Orlando, FL 32816 (United States)

    2009-12-02

    Using stoichiometrically controlled 1:1 functionalization of gold nanoparticles with fluorescent dye molecules in which the dye molecule is held away from the particle surface by a rigid DNA spacer allows precise determination of the distance-dependent effect of the metal nanoparticles on fluorescence intensity. Two dyes were studied, Cy3 and Cy5, with two sizes of nanoparticles, 5 and 10 nm. The larger the particle, the more quenching of the photoluminescence (PL) intensity, due to increased overlap of the dye's emission spectrum with the Au surface plasmon resonance. Fluorescence is quenched significantly for distances somewhat larger than the particle diameter, in good agreement with the predictions of an electrodynamics model based on interacting dipoles. The distance dependence of surface energy transfer behavior, i.e. quenching efficiency, is proportional to 1/d{sup 4}, which involves no consideration of the size of the particle and the spectral overlap of the dye and AuNp. This surface energy transfer model is found qualitatively and agrees with the electrodynamic model, though the exponent is greater than 4 for the smaller nanoparticles (5 nm), and smaller than 4 for the larger nanoparticles (10 nm).

  13. Hybrid model of the context dependent vestibulo-ocular reflex: implications for vergence-version interactions.

    Science.gov (United States)

    Ranjbaran, Mina; Galiana, Henrietta L

    2015-01-01

    The vestibulo-ocular reflex (VOR) is an involuntary eye movement evoked by head movements. It is also influenced by viewing distance. This paper presents a hybrid nonlinear bilateral model for the horizontal angular vestibulo-ocular reflex (AVOR) in the dark. The model is based on known interconnections between saccadic burst circuits in the brainstem and ocular premotor areas in the vestibular nuclei during fast and slow phase intervals of nystagmus. We implemented a viable switching strategy for the timing of nystagmus events to allow emulation of real nystagmus data. The performance of the hybrid model is evaluated with simulations, and results are consistent with experimental observations. The hybrid model replicates realistic AVOR nystagmus patterns during sinusoidal or step head rotations in the dark and during interactions with vergence, e.g., fixation distance. By simply assigning proper nonlinear neural computations at the premotor level, the model replicates all reported experimental observations. This work sheds light on potential underlying neural mechanisms driving the context dependent AVOR and explains contradictory results in the literature. Moreover, context-dependent behaviors in more complex motor systems could also rely on local nonlinear neural computations.

  14. Neuron-astrocyte interaction enhance GABAergic synaptic transmission in a manner dependent on key metabolic enzymes.

    Directory of Open Access Journals (Sweden)

    Przemysław eKaczor

    2015-04-01

    Full Text Available GABA is the major inhibitory neurotransmitter in the adult brain and mechanisms of GABAergic inhibition have been intensely investigated in the past decades. Recent studies provided evidence for an important role of astrocytes in shaping GABAergic currents. One of the most obvious, but yet poorly understood, mechanisms of the cross-talk between GABAergic currents and astrocytes is metabolism including neurotransmitter homeostasis. In particular, how modulation of GABAergic currents by astrocytes depends on key enzymes involved in cellular metabolism remains largely unknown. To address this issue, we have considered two simple models of neuronal cultures: nominally astrocyte-free neuronal culture (NC and neuronal-astrocytic co-cultures (ANCC and miniature Inhibitory Postsynaptic Currents (mIPSCs were recorded in control conditions and in the presence of respective enzyme blockers. We report that enrichment of neuronal culture with astrocytes results in a marked increase in mIPSC frequency. This enhancement of GABAergic activity was accompanied by increased number of GAD65 and vGAT puncta, indicating that at least a part of the frequency enhancement was due to increased number of synaptic contacts. Inhibition of glutamine synthetase (with MSO strongly reduced mIPSC frequency in ANCC but had no effect in NC. Moreover, treatment of ANCC with inhibitor of glycogen phosphorylase (BAYU6751 or with selective inhibitor of astrocytic Krebs cycle,fluoroacetate, resulted in a marked reduction of mIPSC frequency in ANCC having no effect in NC. We conclude that GABAergic synaptic transmission strongly depends on neuron-astrocyte interaction in a manner dependent on key metabolic enzymes as well as on the Krebs cycle.

  15. Interlayer-interaction dependence of latent heat in the Heisenberg model on a stacked triangular lattice with competing interactions.

    Science.gov (United States)

    Tamura, Ryo; Tanaka, Shu

    2013-11-01

    We study the phase transition behavior of a frustrated Heisenberg model on a stacked triangular lattice by Monte Carlo simulations. The model has three types of interactions: the ferromagnetic nearest-neighbor interaction J(1) and antiferromagnetic third nearest-neighbor interaction J(3) in each triangular layer and the ferromagnetic interlayer interaction J([perpendicular]). Frustration comes from the intralayer interactions J(1) and J(3). We focus on the case that the order parameter space is SO(3)×C(3). We find that the model exhibits a first-order phase transition with breaking of the SO(3) and C(3) symmetries at finite temperature. We also discover that the transition temperature increases but the latent heat decreases as J([perpendicular])/J(1) increases, which is opposite to the behavior observed in typical unfrustrated three-dimensional systems.

  16. A theoretical scheme for generation of Gazeau-Klauder coherent states via intensity-dependent degenerate Raman interaction

    CERN Document Server

    Yadollahi, F; 10.1016/j.optcom.2010.09.062

    2010-01-01

    A theoretical scheme is presented for generating Gazeau-Klauder coherent states(GKCSs) via the generalization of degenerate Raman interaction with coupling constant to intensity-dependent coupling. Firstly, we prove that in the intensity-dependent degenerate Raman interaction, under particular conditions, the modified efective Hamiltonian can be used instead of Hamiltonian in the interaction picture, for describing the atom-field interaction. We suppose that the cavity field is initially prepared in a nonlinear CS, which is not temporally stable. As we will observe, after the occurrence of the interaction between atom and field, the generated state involves a superposition of GKCSs which are temporally stable and initial nonlinear CS. Under specific conditions which may be prepared, the generated state just includes GKCS. So, in this way we produced the GKCS, successfully.

  17. Microscopic calculation and LDA of the spatial dependence of the pairing field with bare and induced interactions

    CERN Document Server

    Pastore, A; Broglia, R A; Vigezzi, E

    2008-01-01

    The bare nucleon-nucleon interaction is essential for the production of pair correlations in nuclei, but an important contribution also arises from the induced interaction resulting from the exchange of collective vibrations between nucleons moving in time reversal states close to the Fermi energy. The pairing field resulting from the summed interaction is strongly peaked at the nuclear surface. It is possible to reproduce the detailed spatial dependence of this field using a Local Density Approximation (LDA) and a contact interaction, with parameters which are quite different from those commonly used in more phenomenological approaches.

  18. Pest control of aphids depends on landscape complexity and natural enemy interactions

    Directory of Open Access Journals (Sweden)

    Emily A. Martin

    2015-07-01

    Full Text Available Aphids are a major concern in agricultural crops worldwide, and control by natural enemies is an essential component of the ecological intensification of agriculture. Although the complexity of agricultural landscapes is known to influence natural enemies of pests, few studies have measured the degree of pest control by different enemy guilds across gradients in landscape complexity. Here, we use multiple natural-enemy exclosures replicated in 18 fields across a gradient in landscape complexity to investigate (1 the strength of natural pest control across landscapes, measured as the difference between pest pressure in the presence and in the absence of natural enemies; (2 the differential contributions of natural enemy guilds to pest control, and the nature of their interactions across landscapes. We show that natural pest control of aphids increased up to six-fold from simple to complex landscapes. In the absence of pest control, aphid population growth was higher in complex than simple landscapes, but was reduced by natural enemies to similar growth rates across all landscapes. The effects of enemy guilds were landscape-dependent. Particularly in complex landscapes, total pest control was supplied by the combined contribution of flying insects and ground-dwellers. Birds had little overall impact on aphid control. Despite evidence for intraguild predation of flying insects by ground-dwellers and birds, the overall effect of enemy guilds on aphid control was complementary. Understanding pest control services at large spatial scales is critical to increase the success of ecological intensification schemes. Our results suggest that, where aphids are the main pest of concern, interactions between natural enemies are largely complementary and lead to a strongly positive effect of landscape complexity on pest control. Increasing the availability of seminatural habitats in agricultural landscapes may thus benefit not only natural enemies, but also the

  19. Pest control of aphids depends on landscape complexity and natural enemy interactions.

    Science.gov (United States)

    Martin, Emily A; Reineking, Björn; Seo, Bumsuk; Steffan-Dewenter, Ingolf

    2015-01-01

    Aphids are a major concern in agricultural crops worldwide, and control by natural enemies is an essential component of the ecological intensification of agriculture. Although the complexity of agricultural landscapes is known to influence natural enemies of pests, few studies have measured the degree of pest control by different enemy guilds across gradients in landscape complexity. Here, we use multiple natural-enemy exclosures replicated in 18 fields across a gradient in landscape complexity to investigate (1) the strength of natural pest control across landscapes, measured as the difference between pest pressure in the presence and in the absence of natural enemies; (2) the differential contributions of natural enemy guilds to pest control, and the nature of their interactions across landscapes. We show that natural pest control of aphids increased up to six-fold from simple to complex landscapes. In the absence of pest control, aphid population growth was higher in complex than simple landscapes, but was reduced by natural enemies to similar growth rates across all landscapes. The effects of enemy guilds were landscape-dependent. Particularly in complex landscapes, total pest control was supplied by the combined contribution of flying insects and ground-dwellers. Birds had little overall impact on aphid control. Despite evidence for intraguild predation of flying insects by ground-dwellers and birds, the overall effect of enemy guilds on aphid control was complementary. Understanding pest control services at large spatial scales is critical to increase the success of ecological intensification schemes. Our results suggest that, where aphids are the main pest of concern, interactions between natural enemies are largely complementary and lead to a strongly positive effect of landscape complexity on pest control. Increasing the availability of seminatural habitats in agricultural landscapes may thus benefit not only natural enemies, but also the effectiveness of

  20. Cellular behavior in micropatterned hydrogels by bioprinting system depended on the cell types and cellular interaction.

    Science.gov (United States)

    Hong, Soyoung; Song, Seung-Joon; Lee, Jae Yeon; Jang, Hwanseok; Choi, Jaesoon; Sun, Kyung; Park, Yongdoo

    2013-08-01

    The fabrication of patterned microstructures within three-dimensional (3D) matrices is a challenging subject in tissue engineering and regenerative medicine. A 3D, free-moving bioprinting system was developed and hydrogels were patterned by varying the process parameters of z-axis moving velocity and ejection velocity. The patterning of hydrogel based microfibers in a 3D matrigel was achieved with dimensions of 4.5 mm length and widths from 79 to 200 μm. Hyaluronan-based hydrogels mixed with fibroblasts (L929), mouse endothelial cells (MS1), or human mesenchymal stem cells (hMSCs) were patterned using a 3D moving axis bioprinter and cell behavior was monitored in culture for up to 16 days. L929 and MS1 cells and hMSCs in patterned hydrogel revealed cell-cell interactions and a morphological dependency on cell types. HMSCs formed spheres through cell aggregation, while L929 cells increased in cellular mass without cell aggregation and MS1 dispersed into the matrix instead of aggregating. The aggregation of hMSCs was attenuated by treatment with Rho kinase (ROCK) inhibitor and cadherin antibody. This reflected the close relationship between cell aggregation and migration with RhoA and cell-cell adhesion molecules. Angiogenic-specific gene expression profiles showed that expression of CD105 decreased to 22% in the ROCK inhibitor group compared to control group. These results showed that cell-based patterns in a 3D matrix are highly dependent on both cell aggregation and migration over time.

  1. Temperature dependence of the effective interdimer exchange interaction in a weakly coupled antiferromagnetic dimer copper compound

    Science.gov (United States)

    Calvo, Rafael; Santana, Vinicius T.; Nascimento, Otaciro R.

    2017-08-01

    We report a variation with temperature T of the effective interdimeric interaction Jeff' in the antiferromagnetic (AFM) copper dimeric organic compound Cu2[TzTs] 4 (N -thiazol-2-yl-toluenesulfonamidate CuII). This T dependence was obtained from measurements of the effects in the electron paramagnetic resonance (EPR) spectra of the proposed quantum phase transition associated with the exchange-narrowing processes. Cu2[TzTs] 4 contains exchange-coupled pairs of CuII spins SA and SB (S =1 /2 ), with intradimeric AFM exchange coupling J0=(-115 ±1 ) cm-1 (Hex=-J0SA.SB ). The variation of the EPR linewidth of single crystals with field orientation around a "magic angle" where the transitions intersect and the integrated signal intensity of the so-called U peak of the powder spectrum were measured as a function of T . Modeling these data using arguments of exchange narrowing in the adiabatic regime considering the angular variation of the single-crystal spectra and a geometric description, we find that the effective interdimeric coupling | Jeff'| associated with the exchange frequency ωex is negligible for T ≪| J0/kB| when the units are uncoupled and | Jeff'|=(0.080 ±0.005 ) cm-1 (| Jeff'/J0|=7.0 × 10-4 ) at 298 K. Within this T interval, two ranges of | Jeff'| with linear temperature variation but different slopes, with a kink at ˜80 K, are observed and discussed. This T dependence arises from the growing population of the triplet state, and its relevance to the properties of various arrays of dimeric units is discussed. Our experimental procedures and results are compared with those of previous works in ion radical salts and dimeric metal compounds. The relation between the effective coupling | Jeff'| and the real interdimeric exchange coupling | J'| related to the chemical paths connecting neighbor units is discussed.

  2. Fundamental x-ray interaction limits in diagnostic imaging detectors: frequency-dependent Swank noise.

    Science.gov (United States)

    Hajdok, G; Battista, J J; Cunningham, I A

    2008-07-01

    A frequency-dependent x-ray Swank factor based on the "x-ray interaction" modulation transfer function and normalized noise power spectrum is determined from a Monte Carlo analysis. This factor was calculated in four converter materials: amorphous silicon (a-Si), amorphous selenium (a-Se), cesium iodide (CsI), and lead iodide (PbI2) for incident photon energies between 10 and 150 keV and various converter thicknesses. When scaled by the quantum efficiency, the x-ray Swank factor describes the best possible detective quantum efficiency (DQE) a detector can have. As such, this x-ray interaction DQE provides a target performance benchmark. It is expressed as a function of (Fourier-based) spatial frequency and takes into consideration signal and noise correlations introduced by reabsorption of Compton scatter and photoelectric characteristic emissions. It is shown that the x-ray Swank factor is largely insensitive to converter thickness for quantum efficiency values greater than 0.5. Thus, while most of the tabulated values correspond to thick converters with a quantum efficiency of 0.99, they are appropriate to use for many detectors in current use. A simple expression for the x-ray interaction DQE of digital detectors (including noise aliasing) is derived in terms of the quantum efficiency, x-ray Swank factor, detector element size, and fill factor. Good agreement is shown with DQE curves published by other investigators for each converter material, and the conditions required to achieve this ideal performance are discussed. For high-resolution imaging applications, the x-ray Swank factor indicates: (i) a-Si should only be used at low-energy (e.g., mammography); (ii) a-Se has the most promise for any application below 100 keV; and (iii) while quantum efficiency may be increased at energies just above the K edge in CsI and PbI2, this benefit is offset by a substantial drop in the x-ray Swank factor, particularly at high spatial frequencies.

  3. Spin-orbit coupling effects, interactions and superconducting transport in nanostructures

    Energy Technology Data Exchange (ETDEWEB)

    Schulz, Andreas

    2010-05-15

    In the present thesis we study the electronic properties of several low dimensional nanoscale systems. In the first part, we focus on the combined effect of spin-orbit coupling (SOI) and Coulomb interaction in carbon nanotubes (CNTs) as well as quantum wires. We derive low energy theories for both systems, using the bosonization technique and obtain analytic expressions for the correlation functions that allow us to compute basically all observables of interest. We first focus on CNTs and show that a four channel Luttinger liquid theory can still be applied when SOI effects are taken into account. Compared to previous formulations, the low-energy Hamiltonian is characterized by different Luttinger parameters and plasmon velocities. Notably, the charge and spin modes are coupled. Our theory allows us to compute an asymptotically exact expression for the spectral function of a metallic carbon nanotube. We find modifications to the previously predicted structure of the spectral function that can in principle be tested by photoemission spectroscopy experiments. We develop a very similar low energy description for an interacting quantum wire subject to Rashba spin-orbit coupling (RSOC). We derive a two component Luttinger liquid Hamiltonian in the presence of RSOC, taking into account all e-e interaction processes allowed by the conservation of total momentum. The effective low energy Hamiltonian includes an additional perturbation due to intraband backscattering processes with band flip. Within a one-loop RG scheme, this perturbation is marginally irrelevant. The fixed point model is then still a two channel Luttinger liquid, albeit with a non standard form due to SOI. Again, the charge and spin mode are coupled. Using our low energy theory, we address the problem of the RKKY interaction in an interacting Rashba wire. The coupling of spin and charge modes due to SO effects implies several modifications, e.g. the explicit dependence of the power-law decay exponent of

  4. Temperature dependence of magnetic moments of nanoparticles and their dipole interaction in magnetic fluids

    Energy Technology Data Exchange (ETDEWEB)

    Lebedev, A.V.

    2015-01-15

    Magnetic susceptibility measurements were carried out for magnetite-based fluids over a wide temperature range. The fluids were stabilized with commonly used surfactants (fatty acids) and new surfactants (polypropylene glycol and tallow acids). The coefficients of temperature dependence of the particle magnetic moments were determined by fitting of the measured and calculated values of magnetic susceptibility. The influence of the inter-particle dipole–dipole interaction on the susceptibility was taken into account in the framework of A.O. Ivanov's model. The corrections for thermal expansion were determined by density measurements of the carrier fluid. The obtained values of temperature coefficients correlate to the solidification temperature of the fluid samples. For fluids with a low solidification temperature the value of the temperature coefficient of particle magnetization coincides with its value for bulk magnetite. - Highlights: • Susceptibility measurements made for magnetic fluids over a wide temperature range. • Temperature coefficients of particle magnetization found from susceptibility data. • The value of coefficients correlates to the solidification temperature of the fluid. • For the lowest solidification temperature the coefficient corresponds to that of bulk magnetite.

  5. Cognitive endophenotypes, gene-environment interactions and experience-dependent plasticity in animal models of schizophrenia.

    Science.gov (United States)

    Burrows, Emma L; Hannan, Anthony J

    2016-04-01

    Schizophrenia is a devastating brain disorder caused by a complex and heterogeneous combination of genetic and environmental factors. In order to develop effective new strategies to prevent and treat schizophrenia, valid animal models are required which accurately model the disorder, and ideally provide construct, face and predictive validity. The cognitive deficits in schizophrenia represent some of the most debilitating symptoms and are also currently the most poorly treated. Therefore it is crucial that animal models are able to capture the cognitive dysfunction that characterizes schizophrenia, as well as the negative and psychotic symptoms. The genomes of mice have, prior to the recent gene-editing revolution, proven the most easily manipulable of mammalian laboratory species, and hence most genetic targeting has been performed using mouse models. Importantly, when key environmental factors of relevance to schizophrenia are experimentally manipulated, dramatic changes in the phenotypes of these animal models are often observed. We will review recent studies in rodent models which provide insight into gene-environment interactions in schizophrenia. We will focus specifically on environmental factors which modulate levels of experience-dependent plasticity, including environmental enrichment, cognitive stimulation, physical activity and stress. The insights provided by this research will not only help refine the establishment of optimally valid animal models which facilitate development of novel therapeutics, but will also provide insight into the pathogenesis of schizophrenia, thus identifying molecular and cellular targets for future preclinical and clinical investigations.

  6. Concentration Dependent Ion-Protein Interaction Patterns Underlying Protein Oligomerization Behaviours

    Science.gov (United States)

    Batoulis, Helena; Schmidt, Thomas H.; Weber, Pascal; Schloetel, Jan-Gero; Kandt, Christian; Lang, Thorsten

    2016-04-01

    Salts and proteins comprise two of the basic molecular components of biological materials. Kosmotropic/chaotropic co-solvation and matching ion water affinities explain basic ionic effects on protein aggregation observed in simple solutions. However, it is unclear how these theories apply to proteins in complex biological environments and what the underlying ionic binding patterns are. Using the positive ion Ca2+ and the negatively charged membrane protein SNAP25, we studied ion effects on protein oligomerization in solution, in native membranes and in molecular dynamics (MD) simulations. We find that concentration-dependent ion-induced protein oligomerization is a fundamental chemico-physical principle applying not only to soluble but also to membrane-anchored proteins in their native environment. Oligomerization is driven by the interaction of Ca2+ ions with the carboxylate groups of aspartate and glutamate. From low up to middle concentrations, salt bridges between Ca2+ ions and two or more protein residues lead to increasingly larger oligomers, while at high concentrations oligomers disperse due to overcharging effects. The insights provide a conceptual framework at the interface of physics, chemistry and biology to explain binding of ions to charged protein surfaces on an atomistic scale, as occurring during protein solubilisation, aggregation and oligomerization both in simple solutions and membrane systems.

  7. Density matrix based time-dependent configuration interaction approach to ultrafast spin-flip dynamics

    CERN Document Server

    Wang, H; Kühn, O

    2016-01-01

    Recent developments in attosecond spectroscopy yield access to the correlated motion of electrons on their intrinsic time scales. Spin-flip dynamics is usually considered in the context of valence electronic states, where spin-orbit coupling is weak and processes related to the electron spin are usually driven by nuclear motion. However, for core-excited states, where the core hole has a nonzero angular momentum, spin-orbit coupling is strong enough to drive spin-flips on a much shorter time scale. Using density matrix based time-dependent restricted active space configuration interaction including spin-orbit coupling, we address an unprecedentedly short spin-crossover for the example of L-edge (2p$\\rightarrow$3d) excited states of a prototypical Fe(II) complex. This process occurs on a time scale, which is faster than that of Auger decay ($\\sim$4\\,fs) treated here explicitly. Modest variations of carrier frequency and pulse duration can lead to substantial changes in the spin-state yield, suggesting its cont...

  8. Direction dependence of the magneto-optical absorption in nanowires with Rashba interaction

    Energy Technology Data Exchange (ETDEWEB)

    Sakr, M.R., E-mail: msakr@alexu.edu.eg

    2016-09-16

    We study the directional dependence of the absorption spectrum of ballistic nanowires in the presence of gate-controlled Rashba spin–orbit interaction and an in-plane magnetic field. In the weak Rashba regime, our analytical and numerical results show that the absorption peaks associated with the first and third intersubband transitions exhibit frequency shifts and strong amplitude modulations as the direction of the magnetic field changes. If the field is parallel to the nanowire axis, these peaks disappear and the resonance frequencies of the whole absorption spectrum are given merely in terms of the Zeeman splitting and the energy scale characterizing the confinement potential. The second transition has an absorption peak that suffers an opposite frequency shift with amplitude that is largely direction independent. The amplitude modulation and frequency shift of the absorption spectrum is periodic in the angle that the magnetic field makes with the nanowire axis. - Highlights: • Absorption spectrum of the nanowire is calculated in the weak Rashba regime. • First and third absorption peaks show amplitude and frequency modulation. • They disappear if the magnetic field is along the wire axis, forbidden transitions. • The second transition peak shows frequency shift with minor amplitude modulation. • The frequency and amplitude modulations are periodic in the direction of the field.

  9. Competing effects of nuclear deformation and density dependence of the Λ N interaction in BΛ values of hypernuclei

    Science.gov (United States)

    Isaka, M.; Yamamoto, Y.; Rijken, Th. A.

    2016-10-01

    Competitive effects of nuclear deformation and density dependence of Λ N interaction in Λ binding energies BΛ of hypernuclei are studied systematically on the basis of the baryon-baryon interaction model ESC (extended soft core) including many-body effects. By using the Λ N G -matrix interaction derived from ESC, we perform microscopic calculations of BΛ in Λ hypernuclei within the framework of the antisymmetrized molecular dynamics under the averaged-density approximation. The calculated values of BΛ reproduce experimental data within a few hundred keV in the wide mass regions from 9 to 51. It is found that competitive effects of nuclear deformation and density dependence of Λ N interaction work decisively for fine-tuning of BΛ values.

  10. An Envelope Soliton in a Nonlinear Chain with the Power-Law Dependence of Long-Range Interaction

    Institute of Scientific and Technical Information of China (English)

    王登龙; 颜晓红; 唐翌

    2003-01-01

    We study the Fermi-Pasta-Ulam lattice model in the presence ora power-law dependence of long-range interaction by virtue of the method of multiple scales. Our results show that an envelope soliton still appears, but it is of different property for the group velocity compared with that of the soliton in the model when long-range interaction is absent.

  11. DNA replication checkpoint signaling depends on a Rad53-Dbf4 N-terminal interaction in Saccharomyces cerevisiae.

    Science.gov (United States)

    Chen, Ying-Chou; Kenworthy, Jessica; Gabrielse, Carrie; Hänni, Christine; Zegerman, Philip; Weinreich, Michael

    2013-06-01

    Dbf4-dependent kinase (DDK) and cyclin-dependent kinase (CDK) are essential to initiate DNA replication at individual origins. During replication stress, the S-phase checkpoint inhibits the DDK- and CDK-dependent activation of late replication origins. Rad53 kinase is a central effector of the replication checkpoint and both binds to and phosphorylates Dbf4 to prevent late-origin firing. The molecular basis for the Rad53-Dbf4 physical interaction is not clear but occurs through the Dbf4 N terminus. Here we found that both Rad53 FHA1 and FHA2 domains, which specifically recognize phospho-threonine (pT), interacted with Dbf4 through an N-terminal sequence and an adjacent BRCT domain. Purified Rad53 FHA1 domain (but not FHA2) bound to a pT Dbf4 peptide in vitro, suggesting a possible phospho-threonine-dependent interaction between FHA1 and Dbf4. The Dbf4-Rad53 interaction is governed by multiple contacts that are separable from the Cdc5- and Msa1-binding sites in the Dbf4 N terminus. Importantly, abrogation of the Rad53-Dbf4 physical interaction blocked Dbf4 phosphorylation and allowed late-origin firing during replication checkpoint activation. This indicated that Rad53 must stably bind to Dbf4 to regulate its activity.

  12. Context-dependent planktivory: interacting effects of turbidity and predation risk on adaptive foraging

    Science.gov (United States)

    Pangle, Kevin L.; Malinich, Timothy D.; Bunnell, David B.; DeVries, Dennis R.; Ludsin, Stuart A.

    2012-01-01

    By shaping species interactions, adaptive phenotypic plasticity can profoundly influence ecosystems. Predicting such outcomes has proven difficult, however, owing in part to the dependence of plasticity on the environmental context. Of particular relevance are environmental factors that affect sensory performance in organisms in ways that alter the tradeoffs associated with adaptive phenotypic responses. We explored the influence of turbidity, which simultaneously and differentially affects the sensory performance of consumers at multiple trophic levels, on the indirect effect of a top predator (piscivorous fish) on a basal prey resource (zooplankton) that is mediated through changes in the plastic foraging behavior of an intermediate consumer (zooplanktivorous fish). We first generated theoretical predictions of the adaptive foraging response of a zooplanktivore across wide gradients of turbidity and predation risk by a piscivore. Our model predicted that predation risk can change the negative relationship between intermediate consumer foraging and turbidity into a humped-shaped (unimodal) one in which foraging is low in both clear and highly turbid conditions due to foraging-related risk and visual constraints, respectively. Consequently, the positive trait-mediated indirect effect (TMIE) of the top predator on the basal resource is predicted to peak at low turbidity and decline thereafter until it reaches an asymptote of zero at intermediate turbidity levels (when foraging equals that which is predicted when the top predator is absent). We used field observations and a laboratory experiment to test our model predictions. In support, we found humped-shaped relationships between planktivory and turbidity for several zooplanktivorous fishes from diverse freshwater ecosystems with predation risk. Further, our experiment demonstrated that predation risk reduced zooplanktivory by yellow perch (Perca flavescens) at a low turbidity, but had no effect on consumption at

  13. Dependence of the rate of LiF ion pairing on the description of molecular interaction

    Energy Technology Data Exchange (ETDEWEB)

    Pluharova, Eva; Baer, Marcel D.; Schenter, Gregory K.; Jungwirth, Pavel; Mundy, Christopher J.

    2016-03-03

    We present an analysis of the dynamics of ion-pairing of Lithium Fluoride (LiF) in aqueous solvent using both detailed molecular simulation as well as reduced models within a Gener- alized Langevin Equation (GLE) framework. We explored the sensitivity of the ion-pairing phenomena to the details of descriptions of molecular interaction, comparing two empirical potentials to explicit quantum based density functional theory. We find quantitative differences in the potentials of mean force for ion-pairing as well as time dependent frictions that lead to variations in the rate constant and reactive flux correlation functions. These details reflect differences in solvent response to ion-pairing between different representations of molecular interaction and influence anharmonicity of the dynamic response. We find that the short time anharmonic response is recovered with a GLE parameterization. Recovery of the details of long time response may require extensions to the reduced model. We show that the utility of using a reduced model leads to a straight forward application of variational transition state the- ory concepts to the condensed phase system. The significance of this is reflected in the analysis of committor distributions and the variation of planar hypersurfaces, leading to an improved understanding of factors that determine the rate of LiF ion-pairing. CJM and GKS are supported by the U.S. Department of Energy‘s (DOE) Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences. Pacific Northwest Na- tional Laboratory (PNNL) is operated for the Department of Energy by Battelle. MDB is grateful for the support of Laboratory Directed Research and Development funding under the auspices of PNNL’s Laboratory Initiative Materials Synthesis and Simulation across Scales (MS3). Additional computing resources were generously allocated by PNNL’s Institutional Computing program. EP acknowledges support from PNNL’s Alternate Sponsored

  14. Fermionic particles with position-dependent mass in the presence of inversely quadratic Yukawa potential and tensor interaction

    Indian Academy of Sciences (India)

    M K Bahar; F Yasuk

    2013-02-01

    Approximate solutions of the Dirac equation with position-dependent mass are presented for the inversely quadratic Yukawa potential and Coulomb-like tensor interaction by using the asymptotic iteration method. The energy eigenvalues and the corresponding normalized eigenfunctions are obtained in the case of position-dependent mass and arbitrary spin-orbit quantum number k state and approximation on the spin-orbit coupling term.

  15. Seed harvesting by a generalist consumer is context-dependent: Interactive effects across multiple spatial scales

    Science.gov (United States)

    Ostoja, Steven M.; Schupp, Eugene W.; Klinger, Rob

    2013-01-01

    Granivore foraging decisions affect consumer success and determine the quantity and spatial pattern of seed survival. These decisions are influenced by environmental variation at spatial scales ranging from landscapes to local foraging patches. In a field experiment, the effects of seed patch variation across three spatial scales on seed removal by western harvester ants Pogonomyrmex occidentalis were evaluated. At the largest scale we assessed harvesting in different plant communities, at the intermediate scale we assessed harvesting at different distances from ant mounds, and at the smallest scale we assessed the effects of interactions among seed species in local seed neighborhoods on seed harvesting (i.e. resource–consumer interface). Selected seed species were presented alone (monospecific treatment) and in mixture with Bromus tectorum (cheatgrass; mixture treatment) at four distances from P. occidentalis mounds in adjacent intact sagebrush and non-native cheatgrass-dominated communities in the Great Basin, Utah, USA. Seed species differed in harvest, with B. tectorum being least preferred. Large and intermediate scale variation influenced harvest. More seeds were harvested in sagebrush than in cheatgrass-dominated communities (largest scale), and the quantity of seed harvested varied with distance from mounds (intermediate-scale), although the form of the distance effect differed between plant communities. At the smallest scale, seed neighborhood affected harvest, but the patterns differed among seed species considered. Ants harvested fewer seeds from mixed-seed neighborhoods than from monospecific neighborhoods, suggesting context dependence and potential associational resistance. Further, the effects of plant community and distance from mound on seed harvest in mixtures differed from their effects in monospecific treatments. Beyond the local seed neighborhood, selection of seed resources is better understood by simultaneously evaluating removal at

  16. Temperature dependent CO2 behavior in microporous 1-D channels of a metal-organic framework with multiple interaction sites

    Science.gov (United States)

    Kim, Dongwook; Park, Jaehun; Kim, Yung Sam; Lah, Myoung Soo

    2017-01-01

    The MOF with the encapsulated CO2 molecule shows that the CO2 molecule is ligated to the unsaturated Cu(II) sites in the cage using its Lewis basic oxygen atom via an angular η1-(OA) coordination mode and also interacts with Lewis basic nitrogen atoms of the tetrazole ligands using its Lewis acidic carbon atom. Temperature dependent structure analyses indicate the simultaneous weakening of both interactions as temperature increases. Infrared spectroscopy of the MOF confirmed that the CO2 interaction with the framework is temperature dependent. The strength of the interaction is correlated to the separation of the two bending peaks of the bound CO2 rather than the frequency shift of the asymmetric stretching peak from that of free CO2. The encapsulated CO2 in the cage is weakly interacting with the framework at around ambient temperatures and can have proper orientation for wiggling out of the cage through the narrow portals so that the reversible uptake can take place. On the other hand, the CO2 in the cage is restrained at a specific orientation at 195 K since it interacts with the framework strong enough using the multiple interaction sites so that adsorption process is slightly restricted and desorption process is almost clogged.

  17. Analysis of context dependence in social interaction networks of a massively multiplayer online role-playing game.

    Science.gov (United States)

    Son, Seokshin; Kang, Ah Reum; Kim, Hyun-chul; Kwon, Taekyoung; Park, Juyong; Kim, Huy Kang

    2012-01-01

    Rapid advances in modern computing and information technology have enabled millions of people to interact online via various social network and gaming services. The widespread adoption of such online services have made possible analysis of large-scale archival data containing detailed human interactions, presenting a very promising opportunity to understand the rich and complex human behavior. In collaboration with a leading global provider of Massively Multiplayer Online Role-Playing Games (MMORPGs), here we present a network science-based analysis of the interplay between distinct types of user interaction networks in the virtual world. We find that their properties depend critically on the nature of the context-interdependence of the interactions, highlighting the complex and multilayered nature of human interactions, a robust understanding of which we believe may prove instrumental in the designing of more realistic future virtual arenas as well as provide novel insights to the science of collective human behavior.

  18. Impact of density-dependent symmetry energy and Coulomb interactions on the evolution of intermediate mass fragments

    Indian Academy of Sciences (India)

    Karan Singh Vinayak; Suneel Kumar

    2014-03-01

    Within the framework of isospin-dependent quantum molecular dynamics (IQMD) model, we demonstrate the evolution of intermediate mass fragments in heavy-ion collisions. In this paper, we study the time evolution, impact parameter, and excitation energy dependence of IMF production for the different forms of density-dependent symmetry energy. The IMF production and charge distribution show a minor but considerable sensitivity towards various forms of densitydependent symmetry energy. The Coulomb interactions affect the IMF production significantly at peripheral collisions. The IMF production increases with the stiffness of symmetry energy.

  19. A simple dependence between protein evolution rate and the number of protein-protein interactions

    Directory of Open Access Journals (Sweden)

    Hirsh Aaron E

    2003-05-01

    Full Text Available Abstract Background It has been shown for an evolutionarily distant genomic comparison that the number of protein-protein interactions a protein has correlates negatively with their rates of evolution. However, the generality of this observation has recently been challenged. Here we examine the problem using protein-protein interaction data from the yeast Saccharomyces cerevisiae and genome sequences from two other yeast species. Results In contrast to a previous study that used an incomplete set of protein-protein interactions, we observed a highly significant correlation between number of interactions and evolutionary distance to either Candida albicans or Schizosaccharomyces pombe. This study differs from the previous one in that it includes all known protein interactions from S. cerevisiae, and a larger set of protein evolutionary rates. In both evolutionary comparisons, a simple monotonic relationship was found across the entire range of the number of protein-protein interactions. In agreement with our earlier findings, this relationship cannot be explained by the fact that proteins with many interactions tend to be important to yeast. The generality of these correlations in other kingdoms of life unfortunately cannot be addressed at this time, due to the incompleteness of protein-protein interaction data from organisms other than S. cerevisiae. Conclusions Protein-protein interactions tend to slow the rate at which proteins evolve. This may be due to structural constraints that must be met to maintain interactions, but more work is needed to definitively establish the mechanism(s behind the correlations we have observed.

  20. The APP-Interacting Protein FE65 is Required for Hippocampus-Dependent Learning and Long-Term Potentiation

    Science.gov (United States)

    Wang, Yan; Zhang, Ming; Moon, Changjong; Hu, Qubai; Wang, Baiping; Martin, George; Sun, Zhongsheng; Wang, Hongbing

    2009-01-01

    FE65 is expressed predominantly in the brain and interacts with the C-terminal domain of [beta]-amyloid precursor protein (APP). We examined hippocampus-dependent memory and in vivo long-term potentiation (LTP) at the CA1 synapses with isoform-specific FE65 knockout (p97FE65[superscript -/-]) mice. When examined using the Morris water maze,…

  1. Calix-arene silver nanoparticles interactions with surfactants are charge, size and critical micellar concentration dependent.

    Science.gov (United States)

    Tauran, Yannick; Brioude, Arnaud; Shahgaldian, Patrick; Cumbo, Alessandro; Kim, Beomjoon; Perret, Florent; Coleman, Anthony W; Montasser, Imed

    2012-10-04

    The interactions of silver nanoparticles capped by various calix[n]arenes bearing sulphonate groups at the para and/or phenolic faces with cationic, neutral and anionic surfactants have been studied. Changes in the plasmonic absorption show that only the calix[4]arene derivatives sulphonated at the para-position interact and then only with cationic surfactants. The interactions follow the CMC values of the surfactants either as simple molecules or mixed micelles.

  2. NEM and MFEM Simulation of Interaction between Time-dependent Waves and Obstacles

    Science.gov (United States)

    Perminov, V. A.; Rein, T. S.; Karabtcev, S. N.

    2015-04-01

    Fundamental research challenge of structural integrity and construction resistance while interacting with fluid or gas is of high importance when estimating their efficiency and lifetime. The paper presents the simulation results of interaction between incompressible ideal fluid and an escarpment at the bottom, and interaction between viscous incompressible fluid and an obstacle above fluid surface. Flow patterns at different times and chronograms of hydrodynamic loads on solid walls of computational domain, horizontal and vertical obstacles are displayed.

  3. A Novel Experimental Technique to Monitor the Time-Dependent Water and Ions Uptake when Shale Interacts with Aqueous Solutions

    Science.gov (United States)

    AL-Bazali, Talal

    2013-09-01

    The time-dependent water and ions uptake when shale interacts with aqueous solutions is quantified using a combination of immersion and gravimetric techniques. Results show that when shale interacts with salt solutions, water uptake into shale goes through three distinct stages; water movement out of shale (due to chemical osmosis), water movement into shale (due to diffusion osmosis) and stationary state (equilibrium stage). This work shows that chemical osmosis dominates water movement in early times while diffusion osmosis takes over later. In addition, it is shown that the amount of water movement due to chemical osmosis depends on the chemical potential gradient while the amount of water movement due to diffusion osmosis is highly related to the ionic concentration imbalance. In addition, the amount of ions uptake into shale at equilibrium is shown to depend on the type and concentration of salt solution. Furthermore, this work shows that potassium ion has a strengthening effect on shale while sodium and calcium ions have a weakening effect on shale. Results also show that the shale's compressive strength alteration is greatly influenced by the type and concentration of the salt solution. Furthermore, the shale's compressive strength alteration is shown to be time dependent and correlates very well with the time-dependent flux of water and ions. Finally, it is shown that chemical osmosis and diffusion osmosis take place simultaneously when shale interacts with water-based muds. The overall impact on shale stability is governed by the net water flow resulting from chemical osmosis and diffusion osmosis.

  4. Protein interactions with HER-family receptors can have different characteristics depending on the hosting cell line.

    Science.gov (United States)

    Barta, Pavel; Malmberg, Jennie; Melicharova, Ludmila; Strandgård, John; Orlova, Anna; Tolmachev, Vladimir; Laznicek, Milan; Andersson, Karl

    2012-05-01

    Cell lines are common model systems in the development of therapeutic proteins and in the research on cellular functions and dysfunctions. In this field, the protein interaction assay is a frequently used tool for assessing the adequacy of a protein for diagnostic and therapeutic purposes. In this study, we investigated the extent to which the interaction characteristics depend on the choice of cell line for HER-family receptors. The interaction characteristics of two therapeutic antibodies (trastuzumab and cetuximab) and one Affibody molecule (ZHER2:342), interacting with the intended receptor were characterized with high precision using an automated real-time interaction method, in different cell lines (HaCaT, A431, HEP-G2, SKOV3, PC3, DU-145). Clear differences in binding affinity and kinetics, up to one order of magnitude, were found for the interaction of the same protein binding to the same receptor on different cells for all three proteins. For HER-family receptors, it is therefore important to refer to the measured affinity for a protein-receptor interaction together with the hosting cell line. The ability to accurately measure affinity and kinetics of a protein-receptor interaction on cell lines of different origins may increase the understanding of underlying receptor biology, and impact the selection of candidates in the development of therapeutic or diagnostic agents.

  5. Spatial heterogeneity, frequency-dependent selection and polymorphism in host-parasite interactions

    Directory of Open Access Journals (Sweden)

    Tellier Aurélien

    2011-11-01

    Full Text Available Abstract Background Genomic and pathology analysis has revealed enormous diversity in genes involved in disease, including those encoding host resistance and parasite effectors (also known in plant pathology as avirulence genes. It has been proposed that such variation may persist when an organism exists in a spatially structured metapopulation, following the geographic mosaic of coevolution. Here, we study gene-for-gene relationships governing the outcome of plant-parasite interactions in a spatially structured system and, in particular, investigate the population genetic processes which maintain balanced polymorphism in both species. Results Following previous theory on the effect of heterogeneous environments on maintenance of polymorphism, we analysed a model with two demes in which the demes have different environments and are coupled by gene flow. Environmental variation is manifested by different coefficients of natural selection, the costs to the host of resistance and to the parasite of virulence, the cost to the host of being diseased and the cost to an avirulent parasite of unsuccessfully attacking a resistant host. We show that migration generates negative direct frequency-dependent selection, a condition for maintenance of stable polymorphism in each deme. Balanced polymorphism occurs preferentially if there is heterogeneity for costs of resistance and virulence alleles among populations and to a lesser extent if there is variation in the cost to the host of being diseased. We show that the four fitness costs control the natural frequency of oscillation of host resistance and parasite avirulence alleles. If demes have different costs, their frequencies of oscillation differ and when coupled by gene flow, there is amplitude death of the oscillations in each deme. Numerical simulations show that for a multiple deme island model, costs of resistance and virulence need not to be present in each deme for stable polymorphism to occur

  6. Capacitation dependent changes in the sperm plasma membrane influence porcine gamete interaction

    NARCIS (Netherlands)

    Flesch, F.M.

    2000-01-01

    Although the sperm cell was first seen through Van Leeuwenhoek’s microscope in the late seventieth century and despite much effort in the last 40 years in particular, we still do not know a great deal of the sperm cell and its interaction with the oocyte. Mammalian sperm-oocyte interaction is a comp

  7. Analysis of Phosphorylation-dependent Protein Interactions of Adhesion and Degranulation Promoting Adaptor Protein (ADAP) Reveals Novel Interaction Partners Required for Chemokine-directed T cell Migration.

    Science.gov (United States)

    Kuropka, Benno; Witte, Amelie; Sticht, Jana; Waldt, Natalie; Majkut, Paul; Hackenberger, Christian P R; Schraven, Burkhart; Krause, Eberhard; Kliche, Stefanie; Freund, Christian

    2015-11-01

    Stimulation of T cells leads to distinct changes of their adhesive and migratory properties. Signal propagation from activated receptors to integrins depends on scaffolding proteins such as the adhesion and degranulation promoting adaptor protein (ADAP)(1). Here we have comprehensively investigated the phosphotyrosine interactome of ADAP in T cells and define known and novel interaction partners of functional relevance. While most phosphosites reside in unstructured regions of the protein, thereby defining classical SH2 domain interaction sites for master regulators of T cell signaling such as SLP76, Fyn-kinase, and NCK, other binding events depend on structural context. Interaction proteomics using different ADAP constructs comprising most of the known phosphotyrosine motifs as well as the structured domains confirm that a distinct set of proteins is attracted by pY571 of ADAP, including the ζ-chain-associated protein kinase of 70 kDa (ZAP70). The interaction of ADAP and ZAP70 is inducible upon stimulation either of the T cell receptor (TCR) or by chemokine. NMR spectroscopy reveals that the N-terminal SH2 domains within a ZAP70-tandem-SH2 construct is the major site of interaction with phosphorylated ADAP-hSH3(N) and microscale thermophoresis (MST) indicates an intermediate binding affinity (Kd = 2.3 μm). Interestingly, although T cell receptor dependent events such as T cell/antigen presenting cell (APC) conjugate formation and adhesion are not affected by mutation of Y571, migration of T cells along a chemokine gradient is compromised. Thus, although most phospho-sites in ADAP are linked to T cell receptor related functions we have identified a unique phosphotyrosine that is solely required for chemokine induced T cell behavior.

  8. The archaic chaperone-usher pathways may depend on donor strand exchange for intersubunit interactions.

    Science.gov (United States)

    Wu, Miaomiao; Xu, Shihui; Zhu, Wei; Mao, Xiaohua

    2014-10-01

    Subunit-subunit interactions of the classical and alternate chaperone-usher (CU) systems have been shown to proceed through a donor strand exchange (DSE) mechanism. However, it is not known whether DSE is required for intersubunit interactions in the archaic CU system. We have previously shown that the Myxococcus xanthus Mcu system, a member of the archaic CU family that functions in spore coat formation, is likely to use the principle of donor strand complementation to medicate chaperone-subunit interactions analogous to the classical CU pathway. Here we describe the results of studies on Mcu subunit-subunit interactions. We constructed a series of N-terminal-deleted, single amino acid-mutated and donor strand-complemented Mcu subunits, and characterized their abilities to participate in subunit-subunit interactions. It appears that certain residues in both the N and C termini of McuA, a subunit of the Mcu system, play a critical role in intersubunit interactions and these interactions may involve the general principle of DSE of the classical and alternate CU systems. In addition, the specificity of the M. xanthus CU system for Mcu subunits over other spore coat proteins is demonstrated.

  9. Energy dependence of hadron spectra and multiplicities in p+p interactions

    CERN Document Server

    Puławski, Szymon

    2015-05-11

    The NA61/SHINE experiment at the CERN SPS aims to discover the critical point of strongly interacting matter and study the properties of the onset of deconfinement. In order to reach these goals measurements of hadron production properties are performed in nucleus-nucleus, proton-proton and proton-nucleus interactions as a function of collision energy and size of the colliding nuclei. Inclusive spectra of identified hadrons in p+p interactions at the SPS energies are presented as a function of transverse momentum, transverse mass and rapidity. The results are compared with the world data and theoretical models.

  10. Dependency of micro particle adhesion of dispersive and nondispersive interactions analyzed by atomic force microscopy

    CERN Document Server

    Kawal, A; Andoh, E

    1999-01-01

    The adhesion behaviour of a micro semi-sphere tip (radius of curvature of 18 nm) after making contact with various inorganic solid surfaces is analyzed. Measurement force by the AFM tip corresponds to the interactive force estimated $9 using surface energy components, dispersion and nondispersion, based on van der Waal's interaction. These components can be obtained by measuring the contact angle of standard liquids on a material surface. By using two kinds of tip $9 with different component values, analysis of the interactive mechanism and prediction of macro tip (particle) adhesion can be made. (6 refs).

  11. Time-dependent transport in interacting and noninteracting resonant-tunneling systems

    DEFF Research Database (Denmark)

    Jauho, Antti-Pekka; Wingreen, Ned S.; Meir, Yigal

    1994-01-01

    We consider a mesoscopic region coupled to two leads under the influence of external time-dependent voltages. The time dependence is coupled to source and drain contacts, the gates controlling the tunnel-barrier heights, or to the gates that define the mesoscopic region. We derive, with the Keldy...

  12. A theoretical study on the frequency-dependent electric conductivity of electrolyte solutions. II. Effect of hydrodynamic interaction.

    Science.gov (United States)

    Yamaguchi, T; Matsuoka, T; Koda, S

    2009-03-07

    The theory on the frequency-dependent electric conductivity of electrolyte solutions proposed previously by Yamaguchi et al. [J. Chem. Phys. 127, 234501 (2007)] is extended to include the hydrodynamic interaction between ions. The theory is applied to the aqueous solution of NaCl and the concentration dependence of the conductivity agrees well with that determined by experiments. The effects of the hydrodynamic and relaxation effects are highly nonadditive in the concentrated solution, because the hydrodynamic interaction between ions affects the time-dependent response of the ionic atmosphere. The decrease in the electric conductivity is divided into the contributions of ion pair distribution at various distances. The long-range ionic atmosphere plays a major role at the concentration as low as 0.01 mol/kg, whereas the contribution of the contact ion pair region is important at 1 mol/kg. The magnitude of the contribution of the contact ion pair region is scarcely dependent on the presence of the hydrodynamic interaction. The transport number of cation is calculated to be a decreasing function of concentration as is observed in experiments.

  13. Comparing the epidermal growth factor interaction with four different cell lines: intriguing effects imply strong dependency of cellular context.

    Directory of Open Access Journals (Sweden)

    Hanna Björkelund

    Full Text Available The interaction of the epidermal growth factor (EGF with its receptor (EGFR is known to be complex, and the common over-expression of EGF receptor family members in a multitude of tumors makes it important to decipher this interaction and the following signaling pathways. We have investigated the affinity and kinetics of (125I-EGF binding to EGFR in four human tumor cell lines, each using four culturing conditions, in real time by use of LigandTracer®.Highly repeatable and precise measurements show that the overall apparent affinity of the (125I-EGF - EGFR interaction is greatly dependent on cell line at normal culturing conditions, ranging from K(D ≈ 200 pM on SKBR3 cells to K(D≈8 nM on A431 cells. The (125I-EGF - EGFR binding curves (irrespective of cell line have strong signs of multiple simultaneous interactions. Furthermore, for the cell lines A431 and SKOV3, gefitinib treatment increases the (125I-EGF - EGFR affinity, in particular when the cells are starved. The (125I-EGF - EGFR interaction on cell line U343 is sensitive to starvation while as on SKBR3 it is insensitive to gefitinib and starvation.The intriguing pattern of the binding characteristics proves that the cellular context is important when deciphering how EGF interacts with EGFR. From a general perspective, care is advisable when generalizing ligand-receptor interaction results across multiple cell-lines.

  14. Diet-dependent modular dynamic interactions of the equine cecal microbiota

    DEFF Research Database (Denmark)

    Kristoffersen, Camilla; Jensen, Rasmus Bovbjerg; Avershina, Ekaterina

    2016-01-01

    Knowledge on dynamic interactions in microbiota is pivotal for understanding the role of bacteria in the gut. We herein present comprehensive dynamic models of the horse cecal microbiota, which include short-chained fatty acids, carbohydrate metabolic networks, and taxonomy. Dynamic models were...... diets. We observed marked differences in the microbial dynamic interaction patterns for Fibrobacter succinogenes, Lachnospiraceae, Streptococcus, Treponema, Anaerostipes, and Anaerovibrio between the two diet groups. Fluctuations and microbiota interactions were the most pronounced for the starch rich...... sugars for the starch-rich diet and monosaccharides for the fiber-rich diet. In conclusion, diet may not only affect the composition of the cecal microbiota, but also dynamic interactions and metabolic cross-feeding....

  15. Probe Spin-Velocity Dependent New Interactions by Spin Relaxation Times of Polarized $^{3}He$ Gas

    CERN Document Server

    Zhang, Y; Peng, S M; Fu, C B; Guo, Hao; Liu, B Q; Yan, H

    2014-01-01

    We have studied how to constrain the $\\alpha\\vec{\\sigma}\\cdot\\vec{v}$ type interactions with the relaxation time of spin polarized noble gases in magnetic fields. Using the longest $T_{2}$ measured in the laboratory and the earth as the source, we obtained constraints on three new interactions. We present a new experimental upper bound to the vector-axial-vector($V_{VA}$) type interaction for ranges between $1\\sim10^{8}$m. In combination with the previous result, we set the most stringent experiment limits on $g_{V}g_{A}$ ranging from $\\sim\\mu m$ to $\\sim10^{8}$m. We improve the laboratory limit to the axial-axial-vector($V_{AA}$) type interaction by $\\sim2$ orders or more for distances below $\\sim1$cm. To our best knowledge, we report the first experiment upper limit on torsion induced by the earth on its surface.

  16. Interaction mining and skill-dependent recommendations for multi-objective team composition

    OpenAIRE

    Dorn C.; Skopik F.; Schall D.; Dustdar S.

    2011-01-01

    Web-based collaboration and virtual environments supported by various Web 2.0 concepts enable the application of numerous monitoring, mining and analysis tools to study human interactions and team formation processes. The composition of an effective team requires a balance between adequate skill fulfillment and sufficient team connectivity. The underlying interaction structure reflects social behavior and relations of individuals and determines to a large degree how well people can be expecte...

  17. Amino acid behavior in aqueous amide solutions: Temperature dependence of the L-phenylalanine–N,N-dimethylformamide interaction

    Energy Technology Data Exchange (ETDEWEB)

    Kustov, Andrey V., E-mail: kustov@isuct.ru

    2013-08-20

    Highlights: • Thermodynamics of amino acid solvation in aqueous DMF solutions was studied at 288–318 K. • The pair interaction parameters were compared with those for urea solutions. • For hydrophobic solutes enthalpies and entropies of interaction reveal strong temperature changes. • The relationship between the temperature dependence of solvation and solute–solute interactions was found. - Abstract: We have studied thermodynamics of the L-phenylalanine (Phe) pair interaction with denaturing agents – urea (U) and dimethylformamide (DMF) at 288–318 K. Our study does indicate that enthalpies and entropies of the Phe–U interaction reveal the anomalous temperature dependence which does not occur for DMF solutions. The anomalous Phe behavior in U solutions appears to be closely related to peculiarities of U hydration. One more result is in the fact that for hydrophobic solutes such as L-phenylalanine and substituted amides it is not justified to use the results obtained at 298 K for predicting the solute behavior at physiological temperatures.

  18. Residue Specific and Chirality Dependent Interactions between Carbon Nanotubes and Flagellin.

    Science.gov (United States)

    Macwan, Isaac G; Zhao, Zihe; Sobh, Omar T; Mukerji, Ishita; Dharmadhikari, Bhushan; Patra, Prabir K

    2016-01-01

    Flagellum is a lash-like cellular appendage found in many single-celled living organisms. The flagellin protofilaments contain 11-helix dual turn structure in a single flagellum. Each flagellin consists of four sub-domains - two inner domains (D0, D1) and two outer domains (D2, D3). While inner domains predominantly consist of α-helices, the outer domains are primarily beta sheets with D3. In flagellum, the outermost sub-domain is the only one that is exposed to the native environment. This study focuses on the interactions of the residues of D3 of an R-type flagellin with 5nm long chiral (5,15) and arm-chair (12,12) single-walled carbon nanotubes (SWNT) using molecular dynamics simulation. It presents the interactive forces between the SWNT and the residues of D3 from the perspectives of size and chirality of the SWNT. It is found that the metallic (arm-chair) SWNT interacts the most with glycine and threonine residues through van der Waals and hydrophobic interactions, whereas the semiconducting (chiral) SWNT interacts largely with the area of protein devoid of glycine by van der Waals, hydrophobic interactions, and hydrogen bonding. This indicates a crucial role that glycine plays in distinguishing metallic from semiconducting SWNTs.

  19. Structure and interaction in the polymer-dependent reentrant phase behavior of a charged nanoparticle solution.

    Science.gov (United States)

    Kumar, Sugam; Ray, D; Aswal, V K; Kohlbrecher, J

    2014-10-01

    Small-angle neutron scattering (SANS) studies have been carried out to examine the evolution of interaction and structure in a nanoparticle (silica)-polymer (polyethylene glycol) system. The nanoparticle-polymer solution interestingly shows a reentrant phase behavior where the one-phase charged stabilized nanoparticles go through a two-phase system (nanoparticle aggregation) and back to one-phase as a function of polymer concentration. Such phase behavior arises because of the nonadsorption of polymer on nanoparticles and is governed by the interplay of polymer-induced attractive depletion with repulsive nanoparticle-nanoparticle electrostatic and polymer-polymer interactions in different polymer concentration regimes. At low polymer concentrations, the electrostatic repulsion dominates over the depletion attraction. However, the increase in polymer concentration enhances the depletion attraction to give rise to the nanoparticle aggregation in the two-phase system. Further, the polymer-polymer repulsion at high polymer concentrations is believed to be responsible for the reentrance to one-phase behavior. The SANS data in polymer contrast-matched conditions have been modeled by a two-Yukawa potential accounting for both repulsive and attractive parts of total interaction potential between nanoparticles. Both of these interactions (repulsive and attractive) are found to be long range. The magnitude and the range of the depletion interaction increase with the polymer concentration leading to nanoparticle clustering. At higher polymer concentrations, the increased polymer-polymer repulsion reduces the depletion interaction leading to reentrant phase behavior. The nanoparticle clusters in the two-phase system are characterized by the surface fractal with simple cubic packing of nanoparticles within the clusters. The effect of varying ionic strength and polymer size in tuning the interaction has also been examined.

  20. Absence of spin dependence in the final state interaction of the d(pol) p --> 3He eta reaction

    CERN Document Server

    Papenbrock, M; Burmeister, I; Chiladze, D; Dymov, S; Fritzsch, C; Gebel, R; Goslawski, P; Hartmann, M; Kacharava, A; Keshelashvili, I; Khoukaz, A; Kulessa, P; Kulikov, A; Lorentz, B; Mchedlishvili, D; Mersmann, T; Merzliakov, S; Mielke, M; Mikirtychiants, S; Ohm, H; Prasuhn, D; Rathmann, F; Rausmann, T; Serdyuk, V; Ströher, H; Täschner, A; Trusov, S; Valdau, Y; Wilkin, C

    2014-01-01

    The deuteron tensor analysing power t_{20} of the d(pol) p --> 3He eta reaction has been measured at the COSY-ANKE facility in small steps in excess energy Q up to Q = 11 MeV. Despite the square of the production amplitude varying by over a factor of five through this range, t_{20} shows little or no energy dependence. This is evidence that the final state interaction causing the energy variation is not influenced by the spin configuration in the entrance channel. The weak angular dependence observed for t_{20} provides useful insight into the amplitude structure near threshold.

  1. Combined nonmetallic electronegativity equalisation and point-dipole interaction model for the frequency-dependent polarisability

    Science.gov (United States)

    Smalø, Hans S.; Åstrand, Per-Olof; Mayer, Alexandre

    2013-07-01

    A molecular mechanics model for the frequency-dependent polarisability is presented. It is a combination of a recent model for the frequency dependence in a charge-dipole model [Nanotechnology 19, 025203, 2008] and a nonmetallic modification of the electronegativity equalisation model rephrased as atom-atom charge-transfer terms [J. Chem. Phys. 131, 044101, 2009]. An accurate model for the frequency-dependent polarisability requires a more accurate partitioning into charge and dipole contributions than the static polarisability, which has resulted in several modifications of the charge-transfer model. Results are presented for hydrocarbons, including among others, alkanes, polyenes and aromatic systems. Although their responses to an electric field are quite different in terms of the importance of charge-transfer contributions, it is demonstrated that their frequency-dependent polarisabilities can be described with the same model and the same set of atom-type parameters.

  2. Interactions between bicarbonate, potassium, and magnesium, and sulfur-dependent induction of luminescence in Vibrio fischeri.

    Science.gov (United States)

    Tabei, Yosuke; Era, Mariko; Ogawa, Akane; Morita, Hiroshi

    2012-06-01

    In spite of its central importance in research efforts, the relationship between seawater compounds and bacterial luminescence has not previously been investigated in detail. Thus, in this study, we investigated the effect of cations (Na(+) , K(+) , NH(4) (+) , Mg(2+) , and Ca(2+) ) and anions (Cl(-) , HCO(3) (-) , CO(3) (2-) , and NO(3) (-) ) on the induction of both inorganic (sulfate, sulfite, and thiosulfate) and organic (L-cysteine and L-cystine) sulfur-dependent luminescence in Vibrio fischeri. We found that HCO(3) (-) (bicarbonate) and CO(3) (2-) (carbonate), in the form of various compounds, had a stimulatory effect on sulfur-dependent luminescence. The luminescence induced by bicarbonate was further promoted by the addition of magnesium. Potassium also increased sulfur-dependent luminescence when sulfate or thiosulfate was supplied as the sole sulfur source, but not when sulfite, L-cysteine, or L-cystine was supplied. The positive effect of potassium was accelerated by the addition of magnesium and/or calcium. Furthermore, the additional supply of magnesium improved the induction of sulfite- or L-cysteine-dependent luminescence, but not the l-cystine-dependent type. These results suggest that sulfur-dependent luminescence of V. fischeri under nutrient-starved conditions is mainly controlled by bicarbonate, carbonate, and potassium. In addition, our results indicate that an additional supply of magnesium is effective for increasing V. fischeri luminescence.

  3. Density dependence of relaxation dynamics in glass formers, and the dependence of their fragility on the softness of inter-particle interactions

    Indian Academy of Sciences (India)

    ANSHUL D S PARMAR; PALLABI KUNDU; SRIKANTH SASTRY

    2017-07-01

    Fragility, quantifying the rapidity of variation of relaxation times, is analysed for a series of model glass formers, which differ in the softness of their interparticle interactions. In an attempt to rationalize experimental observations in colloidal suspensions that softer interactions lead to stronger (less fragile) glassformers, we study the variation of relaxation dynamics with density, rather than temperature, as a control parameter.We employ density-temperature scaling, analyzed in recent studies, to address the question.We find that while employing inverse density in place of temperature leads to the conclusion that softer interactions lead to stronger behaviour, the use of scaled variables involving temperature and density lead to the opposite conclusion, similarly to earlier investigations where temperature variation of relaxation dynamics was analysed for the same systems. We rationalize our results by considering the Adam-Gibbs (AG) fragility, which incorporates the density dependence of the configurational entropy and an activation energy that may arise from other propertiesof a glass former.Within the framework of the Adam-Gibbs relation, by employing density temperature scaling for the analysis, we find that softer particles make more fragile glasses, as deduced from dynamical quantities, which is found to be consistent with the Adam-Gibbs fragility.

  4. Chalcogen-height dependent magnetic interactions and magnetic order switching in FeSexTe1-x.

    Science.gov (United States)

    Moon, Chang-Youn; Choi, Hyoung Joon

    2010-02-05

    Magnetic properties of iron chalcogenide superconducting materials are investigated using density-functional calculations. We find that the stability of magnetic phases is very sensitive to the height of chalcogen species from the Fe plane: while FeTe with optimized Te height has the double-stripe (pi, 0) magnetic ordering, the single-stripe (pi, pi) ordering becomes the ground state when Te is lowered below a critical height by, e.g., Se doping. This behavior is understood by opposite Te-height dependences of the superexchange interaction and a longer range magnetic interaction mediated by itinerant electrons. We also demonstrate a linear temperature dependence of the macroscopic magnetic susceptibility in the single-stripe phase in contrast with the constant behavior in the double-stripe phase. Our findings provide a comprehensive and unified view on the magnetism in FeSexTe1-x and iron pnictide superconductors.

  5. Temperature Dependent Interaction Non-Additivity in the Inorganic Ionic Clusters

    CERN Document Server

    Chaban, Vitaly V

    2015-01-01

    Interaction non-additivity in the chemical context means that binding of certain atom to a reference atom cannot be fully predicted from the interactions of these two atoms with other atoms. This constitutes one of key phenomena determining an identity of our world, which would have been much poorer otherwise. Ionic systems provide a good example of the interaction non-additivity in most cases due to electron transfer and delocalization effects. We report Born-Oppenheimer molecular dynamics (BOMD) simulations of LiCl, NaCl, and KCl at 300, 1500, and 2000 K. We show that our observations originate from interplay of thermal motion during BOMD and cation nature. In the case of alkali cations, ionic nature plays a more significant role than temperature. Our results bring fundamental understanding of electronic effects in the condensed phase of ionic systems and foster progress in physical chemistry and engineering.

  6. MEASUREMENT OF BUBBLE-BUBBLE INTERACTION DEPENDED ON REYNOLDS NUMBER USING STEREOSCOPIC BUBBLE-TRACKING TECHNIQUE

    Institute of Scientific and Technical Information of China (English)

    QU Jian-wu; MURAI Yuichi; YAMAMOTO Fujio

    2005-01-01

    Bubble-bubble interaction in free rising bubbly flows is experimentally investigated in the present study.The velocity vectors of the bubbles are measured by a stereoscopic bubble-tracking technique and then the relative velocity vectors of two nearest-neighbor bubbles are calculated with high statistical reliability.With the measurement data at Reynolds number ranging from 5 to 75, the vertical attraction and the horizontal repulsion are confirmed for Re<10 as known by the past study based on Navier-Stokes simulation.The new finding of the present measurement is that the bubbles of Re>30 have repulsive velocity bothin the horizontal and the vertical directions as those rise closely.Moreover, the three-dimensional structure of the bubble-bubble interaction is discussed with the data analysis of the interaction vector fields.

  7. Temperature-dependent raman spectroscopy of lithium triflate-PEO complexes: phase equilibrium and component interactions.

    Science.gov (United States)

    Alloin, Fannie; Hirankumar, Gurusamy; Pagnier, Thierry

    2009-12-31

    Poly(ethylene oxide) and complexes of lithium trifluorosulfonate-poly(ethylene oxide) (LiTf-PEO) with 4 PEO)(3)LiTf defined compound has been deduced from the experimental data. Subtraction of the Raman spectrum due to (PEO)(3)LiTf in each sample allowed us to determine for the first time the composition and the Li(+)-Tf(-) and Li(+)-PEO interactions in the part of the polymer not crystallized as (PEO)(3)LiTf. It is shown that the local interactions between cation and anion or between cation and PEO chain persist even in the melted state, up to near the liquidus temperature. In particular, the Li(+)-PEO interactions decrease significantly just below the liquidus temperature with a simultaneous strong increase in the ion pair concentration.

  8. Stable BLOCH oscillations of cold atoms with time-dependent interaction.

    Science.gov (United States)

    Gaul, C; Lima, R P A; Díaz, E; Müller, C A; Domínguez-Adame, F

    2009-06-26

    We investigate Bloch oscillations of interacting cold atoms in a mean-field framework. In general, atom-atom interaction causes dephasing and destroys Bloch oscillations. Here we show that Bloch oscillations are persistent if the interaction is modulated harmonically with suitable frequency and phase. For other modulations, Bloch oscillations are rapidly damped. We explain this behavior in terms of collective coordinates whose Hamiltonian dynamics permits one to predict a whole family of stable solutions. In order to describe also the unstable cases, we carry out a stability analysis for Bogoliubov excitations. Using Floquet theory, we are able to predict the unstable modes as well as their growth rate, found to be in excellent agreement with numerical simulations.

  9. Identification of Posttranslational Modification-Dependent Protein Interactions Using Yeast Surface Displayed Human Proteome Libraries.

    Science.gov (United States)

    Bidlingmaier, Scott; Liu, Bin

    2015-01-01

    The identification of proteins that interact specifically with posttranslational modifications such as phosphorylation is often necessary to understand cellular signaling pathways. Numerous methods for identifying proteins that interact with posttranslational modifications have been utilized, including affinity-based purification and analysis, protein microarrays, phage display, and tethered catalysis. Although these techniques have been used successfully, each has limitations. Recently, yeast surface-displayed human proteome libraries have been utilized to identify protein fragments with affinity for various target molecules, including phosphorylated peptides. When coupled with fluorescently activated cell sorting and high throughput methods for the analysis of selection outputs, yeast surface-displayed human proteome libraries can rapidly and efficiently identify protein fragments with affinity for any soluble ligand that can be fluorescently detected, including posttranslational modifications. In this review we compare the use of yeast surface display libraries to other methods for the identification of interactions between proteins and posttranslational modifications and discuss future applications of the technology.

  10. Er sensitization by a thin Si layer: Interaction-distance dependence

    DEFF Research Database (Denmark)

    Julsgaard, Brian; Lu, Ying-Wei; Jensen, Rasmus Vincentz Skougaard

    2011-01-01

    From photoluminescence measurements on sensitized erbium in a-Si/SiO2:Er/SiO2 multilayers, we determine the characteristic interaction length of the sensitization process from the silicon-layer sensitizer to the erbium-ion receiver to be 0.22±0.02 nm. By using sufficiently low temperatures in the...... in the fabrication steps, we ensure that diffusion of erbium ions does not affect our results. In addition, we demonstrate that saturation of the erbium 4I13/2→ 4I15/2 transition may lead to an exaggerated estimate of the interaction distance....

  11. Interaction of the phospholipid scramblase 1 with HIV-1 Tat results in the repression of Tat-dependent transcription

    Energy Technology Data Exchange (ETDEWEB)

    Kusano, Shuichi, E-mail: skusano@m2.kufm.kagoshima-u.ac.jp; Eizuru, Yoshito

    2013-04-19

    Highlights: •PLSCR1 specifically interacted with HIV-1 Tat in vitro and in vivo. •PLSCR1 repressed Tat-dependent transactivation of the HIV-1 LTR. •Suppression of PLSCR1 expression enhanced the levels of HIV-1 transcripts. •PLSCR1 reduced the nuclear localization of Tat. -- Abstract: Human phospholipid scramblase 1 (PLSCR1) is an interferon (IFN)-stimulated gene and possesses an IFN-mediated antiviral function. We show here that PLSCR1 directly interacts with human immunodeficiency virus type-1 (HIV-1) Tat. This interaction occurs both in vitro and in vivo through amino acids 160–250 of PLSCR1. Overexpression of PLSCR1 efficiently represses the Tat-dependent transactivation of the HIV-1 long terminal repeat (LTR) and reduces the nuclear translocation of Tat. In addition, shRNA-mediated suppression of endogenous PLSCR1 expression enhances the levels of gag mRNA in an HIV-1-infected T-cell line. These findings indicate that PLSCR1 negatively regulates the Tat-dependent transactivation of the HIV-1 LTR during HIV-1 infection.

  12. INO80 and gamma-H2AX interaction links ATP-dependent chromatin remodeling to DNA damage repair.

    Science.gov (United States)

    Morrison, Ashby J; Highland, Jessica; Krogan, Nevan J; Arbel-Eden, Ayelet; Greenblatt, Jack F; Haber, James E; Shen, Xuetong

    2004-12-17

    While the role of ATP-dependent chromatin remodeling in transcription is well established, a link between chromatin remodeling and DNA repair has remained elusive. We have found that the evolutionarily conserved INO80 chromatin remodeling complex directly participates in the repair of a double-strand break (DSB) in yeast. The INO80 complex is recruited to a HO endonuclease-induced DSB through a specific interaction with the DNA damage-induced phosphorylated histone H2A (gamma-H2AX). This interaction requires Nhp10, an HMG-like subunit of the INO80 complex. The loss of Nhp10 or gamma-H2AX results in reduced INO80 recruitment to the DSB. Finally, components of the INO80 complex show synthetic genetic interactions with the RAD52 DNA repair pathway, the main pathway for DSB repair in yeast. Our findings reveal a new role of ATP-dependent chromatin remodeling in nuclear processes and suggest that an ATP-dependent chromatin remodeling complex can read a DNA repair histone code.

  13. Comparative aspects of spin-dependent interaction potentials for spin-1/2 and spin-1 matter fields

    CERN Document Server

    Malta, P C; Veiga, K; Helayël-Neto, J A

    2015-01-01

    This paper sets out to establish a comparative study between classes of spin- and velocity-dependent current-current interaction potentials for spin-1/2 and spin-1 matter sources in the non-relativistic regime. Both (neutral massive) scalar and vector particles are considered to mediate the interactions between scalar, pseudo-scalar, vector and pseudo-vector matter currents. We contemplate specific cases in which our results may describe the electromagnetic interaction with a massive (Proca-type) photon exchanged between two spin-1/2 or two spin-1 carriers. We highlight the similarities and peculiarities of the potentials for the two different types of charged matter and also focus our attention to the comparison between two different field representations for spin-1 matter particles. We believe that our results may contribute to a further discussion of the relation between charge, spin and extensibility.

  14. Arabidopsis cysteine proteinase inhibitor AtCYSb interacts with a Ca(2+)-dependent nuclease, AtCaN2.

    Science.gov (United States)

    Guo, Kunyuan; Bu, Yuanyuan; Takano, Tetsuo; Liu, Shenkui; Zhang, Xinxin

    2013-11-01

    Plant cysteine proteinase inhibitors (cystatins) play important roles in plant defense mechanisms. Some proteins that interact with cystatins may defend against abiotic stresses. Here, we showed that AtCaN2, a Ca(2+)-dependent nuclease in Arabidopsis, is transcribed in senescent leaves and stems and interacts with an Arabidopsis cystatin (AtCYSb) in a yeast two-hybrid screen. The interaction between AtCYSb and AtCaN2 was confirmed by in vitro pull-down assay and bimolecular fluorescence complementation. Agarose gel electrophoresis showed that the nuclease activity of AtCaN2 against λDNA was inhibited by AtCYSb, which suggests that AtCYSb regulates nucleic acid degradation in cells.

  15. CHIP-MYTH: a novel interactive proteomics method for the assessment of agonist-dependent interactions of the human β₂-adrenergic receptor.

    Science.gov (United States)

    Kittanakom, Saranya; Barrios-Rodiles, Miriam; Petschnigg, Julia; Arnoldo, Anthony; Wong, Victoria; Kotlyar, Max; Heisler, Lawrence E; Jurisica, Igor; Wrana, Jeffrey L; Nislow, Corey; Stagljar, Igor

    2014-03-21

    G-protein coupled receptors (GPCRs) are involved in a variety of disease processes and comprise major drug targets. However, the complexity of integral membrane proteins such as GPCRs makes the identification of their interacting partners and subsequent drug development challenging. A comprehensive understanding of GPCR protein interaction networks is needed to design effective therapeutic strategies to inhibit these drug targets. Here, we developed a novel split-ubiquitin membrane yeast two-hybrid (MYTH) technology called CHIP-MYTH, which allows the unbiased characterization of interaction partners of full-length GPCRs in a drug-dependent manner. This was achieved by coupling DNA microarray technology to the MYTH approach, which allows a quantitative evaluation of interacting partners of a given integral membrane protein in the presence or absence of drug. As a proof of principle, we applied the CHIP-MYTH approach to the human β2-adrenergic receptor (β2AR), a target of interest in the treatment of asthma, chronic obstructive pulmonary disease (COPD), neurological disease, cardiovascular disease, and obesity. A CHIP-MYTH screen was performed in the presence or absence of salmeterol, a long-acting β2AR-agonist. Our results suggest that β2AR activation with salmeterol can induce the dissociation of heterotrimeric G-proteins, Gαβγ, into Gα and Gβγ subunits, which in turn activates downstream signaling cascades. Using CHIP-MYTH, we confirmed previously known and identified novel β2AR interactors involved in GPCR-mediated signaling cascades. Several of these interactions were confirmed in mammalian cells using LUminescence-based Mammalian IntERactome (LUMIER) and co-immunoprecipitation assays. In summary, the CHIP-MYTH approach is ideal for conducting comprehensive protein-protein interactions (PPI) screenings of full-length GPCRs in the presence or absence of drugs, thus providing a valuable tool to further our understanding of GPCR-mediated signaling

  16. Interaction mining and skill-dependent recommendations for multi-objective team composition.

    Science.gov (United States)

    Dorn, Christoph; Skopik, Florian; Schall, Daniel; Dustdar, Schahram

    2011-10-01

    Web-based collaboration and virtual environments supported by various Web 2.0 concepts enable the application of numerous monitoring, mining and analysis tools to study human interactions and team formation processes. The composition of an effective team requires a balance between adequate skill fulfillment and sufficient team connectivity. The underlying interaction structure reflects social behavior and relations of individuals and determines to a large degree how well people can be expected to collaborate. In this paper we address an extended team formation problem that does not only require direct interactions to determine team connectivity but additionally uses implicit recommendations of collaboration partners to support even sparsely connected networks. We provide two heuristics based on Genetic Algorithms and Simulated Annealing for discovering efficient team configurations that yield the best trade-off between skill coverage and team connectivity. Our self-adjusting mechanism aims to discover the best combination of direct interactions and recommendations when deriving connectivity. We evaluate our approach based on multiple configurations of a simulated collaboration network that features close resemblance to real world expert networks. We demonstrate that our algorithm successfully identifies efficient team configurations even when removing up to 40% of experts from various social network configurations.

  17. Dependence of Xmax and multiplicity of electron and muon on different high energy interaction models

    Directory of Open Access Journals (Sweden)

    G Rastegarzadeh

    2010-06-01

    Full Text Available Different high energy interaction models are the applied in CORSIKA code to simulate Extensive Air Showers (EAS generated by Cosmic Rays (CR. In this work the effects of QGSJET01, QGSJETII, DPMJET, SIBYLL models on Xmax and multiplicity of secondary electrons and muons at observation level are studied.

  18. Elders' Usability, Dependability, and Flow Experiences on Embodied Interactive Video Games

    Science.gov (United States)

    Hwang, Ming-Yueh; Hong, Jon-Chao; Hao, Yung-wei; Jong, Jyh-Tsorng

    2011-01-01

    Daily physical activities may slow down the deterioration of cognitive aging. This study intended to develop embodiment interactive video games with friendly human-machine interface to break through the elder's literacy, cognitive aging, and psychomotor hindrances toward technology. Another objective was to understand, through field experiments…

  19. Heritability of insulin sensitivity and lipid profile depend on BMI : evidence for gene-obesity interaction

    NARCIS (Netherlands)

    Wang, X.; Ding, X.; Su, S.; Spector, T. D.; Mangino, M.; Iliadou, A.; Snieder, H.

    2009-01-01

    Evidence from candidate gene studies suggests that obesity may modify genetic susceptibility to type 2 diabetes and dyslipidaemia. On an aggregate level, gene-obesity interactions are expected to result in different heritability estimates at different obesity levels. However, this hypothesis has nev

  20. Dendritic cell interaction with Candida albicans critically depends on N-linked mannan.

    NARCIS (Netherlands)

    Cambi, A.; Netea, M.G.; Mora-Montes, H.M.; Gow, N.A.; Hato, S.V.; Lowman, D.W.; Kullberg, B.J.; Torensma, R.; Williams, D.L.; Figdor, C.G.

    2008-01-01

    The fungus Candida albicans is the most common cause of mycotic infections in immunocompromised hosts. Little is known about the initial interactions between Candida and immune cell receptors, because a detailed characterization at the structural level is lacking. Antigen-presenting dendritic cells

  1. The Frequency-Predictability Interaction in Reading: It Depends Where You're Coming from

    Science.gov (United States)

    Hand, Christopher J.; Miellet, Sebastien; O'Donnell, Patrick J.; Sereno, Sara C.

    2010-01-01

    A word's frequency of occurrence and its predictability from a prior context are key factors determining how long the eyes remain on that word in normal reading. Past reaction-time and eye movement research can be distinguished by whether these variables, when combined, produce interactive or additive results, respectively. Our study addressed…

  2. Macroeconomic policy interaction: State dependency and implications for financial stability in UK: A systemic review

    Directory of Open Access Journals (Sweden)

    Muhammad Ali Nasir

    2016-12-01

    Full Text Available The association between economic and financial stabilities and influence of macroeconomic policies on the financial sector creates scope of active policy role in financial stability. As a contribution to the existing body of knowledge, this study has analysed the implications of macroeconomic policy interaction/coordination for financial stability, proxied by financial assets, i.e. equity and bonds price oscillation. The critical review and analysis of the existing literature on the subject suggests that there is also ample evidence of interdependence between monetary and fiscal policies and this interrelation necessitates coordination between them for the sake of financial stability. There is also a case for analysing the symmetry of financial markets responses to macroeconomic policy interaction. On methodological and empirical grounds, it is vital to test the robustness of policy recommendations to overcome the limitation of a single empirical approach (Jeffrey–Lindley’s paradox. Hence, the Frequentist and Bayesian approaches should be used in commentary manner. The policy interaction and optimal policy combination should also be analysed in the context of institutional design and major financial events to gain insight into the implications of policy interaction in the periods of stable economic and financial environments as well as period of financial and economic distress.

  3. Heritability of insulin sensitivity and lipid profile depend on BMI : evidence for gene-obesity interaction

    NARCIS (Netherlands)

    Wang, X.; Ding, X.; Su, S.; Spector, T. D.; Mangino, M.; Iliadou, A.; Snieder, H.

    2009-01-01

    Evidence from candidate gene studies suggests that obesity may modify genetic susceptibility to type 2 diabetes and dyslipidaemia. On an aggregate level, gene-obesity interactions are expected to result in different heritability estimates at different obesity levels. However, this hypothesis has

  4. An age-dependent interaction with leptin unmasks ghrelin's bone-protective effects

    Science.gov (United States)

    The mutual interplay between energy homeostasis and bone metabolism is an important emerging concept. Ghrelin and leptin antagonize each other in regulating energy balance, but the role of this interaction in bone metabolism is unknown. Using ghrelin receptor and leptin-deficient mice, we show that ...

  5. Interaction of PAMAM dendrimers with bovine insulin depends on nanoparticle end-groups

    Energy Technology Data Exchange (ETDEWEB)

    Nowacka, Olga; Milowska, Katarzyna, E-mail: milowska@biol.uni.lodz.pl; Bryszewska, Maria

    2015-06-15

    We have looked at the interactions between polyamidoamine (PAMAM) dendrimers with different terminal groups (−COOH, −NH{sub 2}, −OH) and bovine insulin. The influence of PAMAM dendrimers on insulin was tested by measuring zeta potential and fluorescence quenching. The secondary structure of insulin in the presence of dendrimers was examined by circular dichroism. The effect of dendrimers on dithiotreitol-induced aggregation of insulin was investigated by spectrophotometry. Dendrimers quenched the fluorescence of insulin, but did not change its secondary structure. Thus dendrimers neither induce hormone aggregation nor inhibit the aggregation process induced by dithiotreitol (DTT), except at 0.01 µmol/l. Dendrimers–insulin interactions are mainly electrostatic. - Highlight: • The interactions between PAMAM dendrimers and insulin were investigated. • The PAMAM dendrimers can quench the fluorescence of insulin. • The PAMAM dendrimers did not change the secondary structure of insulin. • Dendrimers did not induce aggregation of hormone. • Dendrimers–insulin interaction is mainly electrostatic.

  6. Resolution-of-identity stochastic time-dependent configuration interaction for dissipative electron dynamics in strong fields.

    Science.gov (United States)

    Klinkusch, Stefan; Tremblay, Jean Christophe

    2016-05-14

    In this contribution, we introduce a method for simulating dissipative, ultrafast many-electron dynamics in intense laser fields. The method is based on the norm-conserving stochastic unraveling of the dissipative Liouville-von Neumann equation in its Lindblad form. The N-electron wave functions sampling the density matrix are represented in the basis of singly excited configuration state functions. The interaction with an external laser field is treated variationally and the response of the electronic density is included to all orders in this basis. The coupling to an external environment is included via relaxation operators inducing transition between the configuration state functions. Single electron ionization is represented by irreversible transition operators from the ionizing states to an auxiliary continuum state. The method finds its efficiency in the representation of the operators in the interaction picture, where the resolution-of-identity is used to reduce the size of the Hamiltonian eigenstate basis. The zeroth-order eigenstates can be obtained either at the configuration interaction singles level or from a time-dependent density functional theory reference calculation. The latter offers an alternative to explicitly time-dependent density functional theory which has the advantage of remaining strictly valid for strong field excitations while improving the description of the correlation as compared to configuration interaction singles. The method is tested on a well-characterized toy system, the excitation of the low-lying charge transfer state in LiCN.

  7. Rapidity dependence of multiplicity fluctuations and correlations in high-energy nucleus–nucleus interactions

    Indian Academy of Sciences (India)

    Dipak Ghosh; Argha Deb; Swarnapratim Bhattacharyya; Utpal Datta

    2011-08-01

    The multiplicity fluctuations of the produced pions were studied using scaled variance method in 16O–AgBr interactions at 2.1 AGeV, 24Mg–AgBr interactions at 4.5 AGeV, 12C–AgBr interactions at 4.5 AGeV, 16O–AgBr interactions at 60 AGeV and 32S–AgBr interactions at 200 AGeV at two different binning conditions. In the first binning condition, the rapidity interval was varied in steps of one centring about the central rapidity until it reached 14. In the second case, the rapidity interval was increased in steps of 1.6 up to 14.4. Multiplicity distributions and their scaled variances were presented as a function of the dependence on the rapidity width for both the binning conditions. Multiplicity fluctuations were found to increase with the increase of rapidity interval and later found to saturate at larger rapidity window for all the interactions and in both the binning conditions. Multiplicity fluctuations were found to increase with the energy of the projectile beam. The values of the scaled variances were found to be greater than one in all the cases in both the binning conditions indicating the presence of correlation during the multiparticle production process in high-energy nucleus–nucleus interactions. Experimental results were compared with the results obtained from the Monte Carlo simulated events for all the interactions. The Monte Carlo simulated data showed very small values of scaled variance suggesting very small fluctuations for the simulated events. Experimental results obtained from 16O–AgBr interactions at 60 AGeV and 32S–AgBr interactions at 200 AGeV were compared with the events generated by Lund Monte Carlo code (FRITIOF model). FRITIOF model failed to explain the multiplicity fluctuations of pions emitted from 16O–AgBr interactions at 60 AGeV for both the binning conditions. However, the experimental data agreed well with the FRITIOF model for 32S–AgBr interactions at 200 AGeV.

  8. Novel role of phosphorylation-dependent interaction between FtsZ and FipA in mycobacterial cell division.

    Directory of Open Access Journals (Sweden)

    Kamakshi Sureka

    Full Text Available The bacterial divisome is a multiprotein complex. Specific protein-protein interactions specify whether cell division occurs optimally, or whether division is arrested. Little is known about these protein-protein interactions and their regulation in mycobacteria. We have investigated the interrelationship between the products of the Mycobacterium tuberculosis gene cluster Rv0014c-Rv0019c, namely PknA (encoded by Rv0014c and FtsZ-interacting protein A, FipA (encoded by Rv0019c and the products of the division cell wall (dcw cluster, namely FtsZ and FtsQ. M. smegmatis strains depleted in components of the two gene clusters have been complemented with orthologs of the respective genes of M. tuberculosis. Here we identify FipA as an interacting partner of FtsZ and FtsQ and establish that PknA-dependent phosphorylation of FipA on T77 and FtsZ on T343 is required for cell division under oxidative stress. A fipA knockout strain of M. smegmatis is less capable of withstanding oxidative stress than the wild type and showed elongation of cells due to a defect in septum formation. Localization of FtsQ, FtsZ and FipA at mid-cell was also compromised. Growth and survival defects under oxidative stress could be functionally complemented by fipA of M. tuberculosis but not its T77A mutant. Merodiploid strains of M. smegmatis expressing the FtsZ(T343A showed inhibition of FtsZ-FipA interaction and Z ring formation under oxidative stress. Knockdown of FipA led to elongation of M. tuberculosis cells grown in macrophages and reduced intramacrophage growth. These data reveal a novel role of phosphorylation-dependent protein-protein interactions involving FipA, in the sustenance of mycobacterial cell division under oxidative stress.

  9. Filled and empty states of carbon nanotubes in water: Dependence on nanotube diameter, wall thickness and dispersion interactions

    Indian Academy of Sciences (India)

    Malay Rana; Amalendu Chandra

    2007-09-01

    We have carried out a series of molecular dynamics simulations of water containing a narrow carbon nanotube as a solute to investigate the filling and emptying of the nanotube and also the modifications of the density and hydrogen bond distributions of water inside and also in the vicinity of the outer surfaces of the nanotube. Our primary goal is to look at the effects of varying nanotube diameter, wall thickness and also solute-solvent interactions on the solvent structure in the confined region also near the outer surfaces of the solute. The thickness of the walls is varied by considering single and multi-walled nanotubes and the interaction potential is varied by tuning the attractive strength of the 12-6 pair interaction potential between a carbon atom of the nanotubes and a water molecule. The calculations are done for many different values of the tuning parameter ranging from fully Lennard-Jones to pure repulsive pair interactions. It is found that both the solvation characteristics and hydrogen bond distributions can depend rather strongly on the strength of the attractive part of the solute-water interaction potential. The thickness of the nanotube wall, however, is found to have only minor effects on the density profiles, hydrogen bond network and the wetting characteristics. This indicates that the long range electrostatic interactions between water molecules inside and on the outer side of the nanotube do not make any significant contribution to the overall solvation structure of these hydrophobic solutes. The solvation characteristics are primarily determined by the balance between the loss of energy due to hydrogen bond network disruption, cavity repulsion potential and offset of the same by attractive component of the solute-water interactions. Our studies with different system sizes show that the essential features of wetting and dewetting characteristics of narrow nanotubes for different diameter and interaction potentials are also present in

  10. Phosphorylation-dependent 14-3-3 protein interactions regulate CFTR biogenesis.

    Science.gov (United States)

    Liang, Xiubin; Da Paula, Ana Carina; Bozóky, Zoltán; Zhang, Hui; Bertrand, Carol A; Peters, Kathryn W; Forman-Kay, Julie D; Frizzell, Raymond A

    2012-03-01

    Cystic fibrosis transmembrane conductance regulator (CFTR) is a cAMP/protein kinase A (PKA)-regulated chloride channel whose phosphorylation controls anion secretion across epithelial cell apical membranes. We examined the hypothesis that cAMP/PKA stimulation regulates CFTR biogenesis posttranslationally, based on predicted 14-3-3 binding motifs within CFTR and forskolin-induced CFTR expression. The 14-3-3β, γ, and ε isoforms were expressed in airway cells and interacted with CFTR in coimmunoprecipitation assays. Forskolin stimulation (15 min) increased 14-3-3β and ε binding to immature and mature CFTR (bands B and C), and 14-3-3 overexpression increased CFTR bands B and C and cell surface band C. In pulse-chase experiments, 14-3-3β increased the synthesis of immature CFTR, reduced its degradation rate, and increased conversion of immature to mature CFTR. Conversely, 14-3-3β knockdown decreased CFTR B and C bands (70 and 55%) and elicited parallel reductions in cell surface CFTR and forskolin-stimulated anion efflux. In vitro, 14-3-3β interacted with the CFTR regulatory region, and by nuclear magnetic resonance analysis, this interaction occurred at known PKA phosphorylated sites. In coimmunoprecipitation assays, forskolin stimulated the CFTR/14-3-3β interaction while reducing CFTR's interaction with coat protein complex 1 (COP1). Thus 14-3-3 binding to phosphorylated CFTR augments its biogenesis by reducing retrograde retrieval of CFTR to the endoplasmic reticulum. This mechanism permits cAMP/PKA stimulation to make more CFTR available for anion secretion.

  11. Spin-dependent Seebeck effect in Aharonov-Bohm rings with Rashba and Dresselhaus spin-orbit interactions

    Science.gov (United States)

    Liu, Bin; Li, Yunyun; Zhou, Jun; Nakayama, Tsuneyoshi; Li, Baowen

    2016-06-01

    We theoretically investigate the spin-dependent Seebeck effect in an Aharonov-Bohm mesoscopic ring in the presence of both Rashba and Dresselhaus spin-orbit interactions under magnetic flux perpendicular to the ring. We apply the Green's function method to calculate the spin Seebeck coefficient employing the tight-binding Hamiltonian. It is found that the spin Seebeck coefficient is proportional to the slope of the energy-dependent transmission coefficients. We study the strong dependence of spin Seebeck coefficient on the Fermi energy, magnetic flux, strength of spin-orbit coupling, and temperature. Maximum spin Seebeck coefficients can be obtained when the strengths of Rashba and Dresselhaus spin-orbit couplings are slightly different. The spin Seebeck coefficient can be reduced by increasing temperature and disorder.

  12. Nuclear spin dependent parity violating electron-nucleus interaction in heavy atoms. The anapole moment and the perturbation of the hadronic vector neutral current by the hyperfine interaction

    Energy Technology Data Exchange (ETDEWEB)

    Bouchiat, C.; Piketty, C.A. (Lab. de Physique Theorique, Ecole Normale Superieure, 75 - Paris (France))

    1991-10-24

    We present first a computation of the nuclear anapole moment of thallium by a method developed previously by the authors. Then we perform a detailed analysis of the spin dependent parity violating electron-nucleon potential generated by the hyperfine coupling perturbation upon the pseudoscalar interaction of the electron with the weak charge of the nucleus. This effect is found to be of order {alpha}G{sub F}A{sup 2/3} and represents, depending upon the nucleus, (10-70)% of the anapole moment contribution. In the case of thallium, it compensates almost exactly the contribution associated with the axial hadronic neutral current. This fact, together with other arguments given in the paper, makes thallium a favoured candidate for the anapole moment search provided accurate enough experiments can be performed. (orig.).

  13. Nuclear spin dependent parity violating electron-nucleus interaction in heavy atoms. The anapole moment and the perturbation of the hadronic vector neutral current by the hyperfine interaction

    Science.gov (United States)

    Bouchiat, C.; Piketty, C. A.

    1991-10-01

    We present first a computation of the nuclear anapole moment of thallium by a method developed previously by the authors. Then we perform a detailed analysis of the spin dependent parity violating electron-nucleon potential generated by the hyperfine coupling perturbation upon the pseudoscalar interaction of the electron with the weak charge of the nucleus. This effect is found to be of order αG FA {2}/{3} and represents, depending upon the nucleus, (10-70)% of the anapole moment contribution. In the case of thallium, it compensates almost exactly the contribution associated with the axial hadronic neutral current. This fact, together with other arguments given in the paper, makes thallium a favoured candidate for the anapole moment search provided accurate enough experiments can be performed.

  14. Chemical Potential Dependence of the Dressed—Quark Propagator from an Effective Quark—Quark Interaction

    Institute of Scientific and Technical Information of China (English)

    ZONGHong-Shi; PINGJia-Lun; 等

    2002-01-01

    We exhibit a method for obtaining the low chemical potential dependence of the dressed quark propagator from the dressed-quark propagator,which provides a means of determining the behavior of the chiral and deconfinement order parameters.A comparison with the results of previous researches is given.

  15. Interaction of plant chimeric calcium/calmodulin-dependent protein kinase with a homolog of eukaryotic elongation factor-1alpha

    Science.gov (United States)

    Wang, W.; Poovaiah, B. W.

    1999-01-01

    A chimeric Ca2+/calmodulin-dependent protein kinase (CCaMK) was previously cloned and characterized in this laboratory. To investigate the biological functions of CCaMK, the yeast two-hybrid system was used to isolate genes encoding proteins that interact with CCaMK. One of the cDNA clones obtained from the screening (LlEF-1alpha1) has high similarity with the eukaryotic elongation factor-1alpha (EF-1alpha). CCaMK phosphorylated LlEF-1alpha1 in a Ca2+/calmodulin-dependent manner. The phosphorylation site for CCaMK (Thr-257) was identified by site-directed mutagenesis. Interestingly, Thr-257 is located in the putative tRNA-binding region of LlEF-1alpha1. An isoform of Ca2+-dependent protein kinase (CDPK) phosphorylated multiple sites of LlEF-1alpha1 in a Ca2+-dependent but calmodulin-independent manner. Unlike CDPK, CCaMK phosphorylated only one site, and this site is different from CDPK phosphorylation sites. This suggests that the phosphorylation of EF-1alpha by these two kinases may have different functional significance. Although the phosphorylation of LlEF-1alpha1 by CCaMK is Ca2+/calmodulin-dependent, in vitro binding assays revealed that CCaMK binds to LlEF-1alpha1 in a Ca2+-independent manner. This was further substantiated by coimmunoprecipitation of CCaMK and EF-1alpha using the protein extract from lily anthers. Dissociation of CCaMK from EF-1alpha by Ca2+ and phosphorylation of EF-1alpha by CCaMK in a Ca2+/calmodulin-dependent manner suggests that these interactions may play a role in regulating the biological functions of EF-1alpha.

  16. Interaction of plant chimeric calcium/calmodulin-dependent protein kinase with a homolog of eukaryotic elongation factor-1alpha

    Science.gov (United States)

    Wang, W.; Poovaiah, B. W.

    1999-01-01

    A chimeric Ca2+/calmodulin-dependent protein kinase (CCaMK) was previously cloned and characterized in this laboratory. To investigate the biological functions of CCaMK, the yeast two-hybrid system was used to isolate genes encoding proteins that interact with CCaMK. One of the cDNA clones obtained from the screening (LlEF-1alpha1) has high similarity with the eukaryotic elongation factor-1alpha (EF-1alpha). CCaMK phosphorylated LlEF-1alpha1 in a Ca2+/calmodulin-dependent manner. The phosphorylation site for CCaMK (Thr-257) was identified by site-directed mutagenesis. Interestingly, Thr-257 is located in the putative tRNA-binding region of LlEF-1alpha1. An isoform of Ca2+-dependent protein kinase (CDPK) phosphorylated multiple sites of LlEF-1alpha1 in a Ca2+-dependent but calmodulin-independent manner. Unlike CDPK, CCaMK phosphorylated only one site, and this site is different from CDPK phosphorylation sites. This suggests that the phosphorylation of EF-1alpha by these two kinases may have different functional significance. Although the phosphorylation of LlEF-1alpha1 by CCaMK is Ca2+/calmodulin-dependent, in vitro binding assays revealed that CCaMK binds to LlEF-1alpha1 in a Ca2+-independent manner. This was further substantiated by coimmunoprecipitation of CCaMK and EF-1alpha using the protein extract from lily anthers. Dissociation of CCaMK from EF-1alpha by Ca2+ and phosphorylation of EF-1alpha by CCaMK in a Ca2+/calmodulin-dependent manner suggests that these interactions may play a role in regulating the biological functions of EF-1alpha.

  17. Energy dependence of negatively charged pion production in proton-proton interactions at the CERN SPS

    CERN Document Server

    AUTHOR|(SzGeCERN)663936; Dominik, Wojciech; Gaździck, Marek

    2016-01-01

    This thesis presents inclusive spectra of the negatively charged pions produced in inelastic proton-proton interactions measured at five beam momenta: 20, 31, 40, 80 and 158 GeV/c. The measurements were conducted in the NA61/SHINE experiment at CERN using a system of five Time Projection Chambers. The negatively charged pion spectra were calculated based on the negatively charged hadron spectra. Contribution of hadrons other than the primary pions was removed using EPOS simulations. The results were corrected for effects related to detection, acceptance, reconstruction efficiency and the analysis technique. Two-dimensional spectra were derived as a function of rapidity and transverse momentum or transverse mass. The spectra were parametrised by widths of the rapidity distributions, inverse slope parameters of the transverse mass distributions, mean transverse masses and the total pion multiplicities. The negatively charged pion spectra in proton-proton interactions belong to a broad NA61/SHINE programme of se...

  18. Evidence for a Sex-Dependent MAOA× Childhood Stress Interaction in the Neural Circuitry of Aggression.

    Science.gov (United States)

    Holz, Nathalie; Boecker, Regina; Buchmann, Arlette F; Blomeyer, Dorothea; Baumeister, Sarah; Hohmann, Sarah; Jennen-Steinmetz, Christine; Wolf, Isabella; Rietschel, Marcella; Witt, Stephanie H; Plichta, Michael M; Meyer-Lindenberg, Andreas; Schmidt, Martin H; Esser, Günter; Banaschewski, Tobias; Brandeis, Daniel; Laucht, Manfred

    2016-03-01

    Converging evidence emphasizes the role of an interaction between monoamine oxidase A (MAOA) genotype, environmental adversity, and sex in the pathophysiology of aggression. The present study aimed to clarify the impact of this interaction on neural activity in aggression-related brain systems. Functional magnetic resonance imaging was performed in 125 healthy adults from a high-risk community sample followed since birth. DNA was genotyped for the MAOA-VNTR (variable number of tandem repeats). Exposure to childhood life stress (CLS) between the ages of 4 and 11 years was assessed using a standardized parent interview, aggression by the Youth/Young Adult Self-Report between the ages of 15 and 25 years, and the VIRA-R (Vragenlijst Instrumentele En Reactieve Agressie) at the age of 15 years. Significant interactions were obtained between MAOA genotype, CLS, and sex relating to amygdala, hippocampus, and anterior cingulate cortex (ACC) response, respectively. Activity in the amygdala and hippocampus during emotional face-matching increased with the level of CLS in male MAOA-L, while decreasing in male MAOA-H, with the reverse pattern present in females. Findings in the opposite direction in the ACC during a flanker NoGo task suggested that increased emotional activity coincided with decreased inhibitory control. Moreover, increasing amygdala activity was associated with higher Y(A)SR aggression in male MAOA-L and female MAOA-H carriers. Likewise, a significant association between amygdala activity and reactive aggression was detected in female MAOA-H carriers. The results point to a moderating role of sex in the MAOA× CLS interaction for intermediate phenotypes of emotional and inhibitory processing, suggesting a possible mechanism in conferring susceptibility to violence-related disorders.

  19. BEAM LIFETIME DEPENDENCE ON THE BEAM-GAS INTERACTIONS IN RHIC.

    Energy Technology Data Exchange (ETDEWEB)

    TRBOJEVIC,D.; HSUEH,H.C.; MACKAY,W.; DREES,A.; FLILLER,R.

    2001-06-18

    In the Relativistic Heavy ion Collider (RHIC) much larger background signals were occurring at BRAMS, one of the four experiments. This was especially pronounced at the time when vacuum conditions deteriorated due to the beam ionization profile monitor replacements. Recording the beam intensities during the store provided the beam lifetime. Predictions from the beam gas interactions to the above measured values are compared The ionization gauges simultaneously recorded the vacuum pressure data.

  20. The dependence of proton correlations on integral characteristics of eA interactions

    Energy Technology Data Exchange (ETDEWEB)

    Degtyarenko, P.V. (ITEP, Moscow (Russian Federation)); Doroshkevich, E.A. (ITEP, Moscow (Russian Federation)); Efremenko, Yu.V. (ITEP, Moscow (Russian Federation)); Gavrilov, V.B. (ITEP, Moscow (Russian Federation)); Kossov, M.V. (ITEP, Moscow (Russian Federation)); Leksin, G.A. (ITEP, Moscow (Russian Federation)); Stavinsky, A.V. (ITEP, Moscow (Russian Federation)); Vlassov, A.V. (ITEP, Moscow (Russian Federation))

    1994-12-01

    We report the results of analysis of correlations of the product protons from inelastic eA collisions at small Q[sup 2]. The experimental data were measured by the ARGUS detector. The correlation effect at small relative momenta q (interference and final state interaction) is closely associated with the angular correlations due to momentum conservation. The examined correlations in eA collisions also show features similar to correlations in hA collisions. (orig.)

  1. The dependence of proton correlations on integral characteristics of eA interactions

    Science.gov (United States)

    Degtyarenko, P. V.; Doroshkevich, E. A.; Efremenko, Yu. V.; Gavrilov, V. B.; Kossov, M. V.; Leksin, G. A.; Stavinsky, A. V.; Vlassov, A. V.

    1994-09-01

    We report the results of analysis of correlations of the product protons from inelastic eA collisions at small Q 2. The experimental data were measured by the ARGUS detector. The correlation effect at small relative momenta q (interference and final state interaction) is closely associated with the angular correlations due to momentum conservation. The examined correlations in eA collisions also show features similar to correlations in hA collisions.

  2. Size-dependent interactions of silica nanoparticles with a flat silica surface.

    Science.gov (United States)

    Seo, Jihoon; Kim, Joo Hyun; Lee, Myoungjae; Moon, Jinok; Yi, Dong Kee; Paik, Ungyu

    2016-12-01

    We have investigated the surface chemistry of SiO2 nanoparticles (NPs) with different sizes and their corresponding interactions with a flat substrate of surface curvature ∼0. As the size of the NPs increases, the SiO2 surface is increasingly covered with H-bonded silanol groups, thereby increasing the ζ-potential and shifting the isoelectric point higher in pH. Interactions between the SiO2 NPs and the flat SiO2 surface were analyzed in situ using quartz crystal microbalance with dissipation (QCM-D) method, and the results were interpreted based on an extended Derjaguin-Landau-Verwey-Overbeek theory. At very low ionic strength (1mM NaCl), there was no particle adsorption onto the surface due to the highly repulsive energy barriers to this interaction. On the other hand, QCM-D results showed that the significant adsorption of SiO2 NPs onto a flat SiO2 surface occurred under conditions of high ionic strength (100mM NaCl). Interestingly, the adsorption behaviors of three different-sized SiO2 NPs on the surface varied considerably with size. SiO2 NPs with small size have high adsorption affinity with the flat SiO2 surface due to an extremely low energy barrier for the interactions, whereas relatively large SiO2 NPs have very weak adsorption affinity with the flat surface due to the repulsive energy barrier formed by the increase in the electrostatic and hydration repulsion energy.

  3. Interaction of the antibiotic norfloxacin with ionic micelles: pH-dependent binding.

    Science.gov (United States)

    Muniz, Gabriel Silva Vignoli; Teixeira, Letícia Regina; Louro, Sonia Renaux Wanderley

    2014-11-01

    The interaction of the antimicrobial drug norfloxacin (NFX) with anionic sodium dodecyl sulfate (SDS) and cationic cetyltrimethylammonium bromide (CTAB) micelles was studied using the intrinsic spectroscopic properties of NFX to obtain association constants and molecular modifications. Nonionic Tween(®) 20 micelles were also investigated, but the spectroscopic properties of NFX did not detect interactions with these micelles, and quenching by iodide suggested a weak association constant around 47 M(-1). For SDS and CTAB, UV-Vis absorption spectroscopy, steady-state and time-resolved fluorometry were monitored as a function of surfactant concentration ranging from the premicellar to micellar region. It was found that cationic (pH 4.0) and zwitterionic NFX (pH 7.4) associate with SDS micelles, with binding constants equal to 5.4 × 10(3) and 1.7 × 10(3) M(-1), respectively. Premicellar interaction slightly decreases the critical micelle concentration of SDS. Association of anionic NFX (pH 10.6) is very weak. The fluorescence spectrum and lifetime showed that SDS-associated NFX is cationic and that the heterocycle penetrates the interfacial environment of decreased polarity. Cationic CTAB micelles do not bind cationic NFX, and the association constant with zwitterionic NFX is two orders of magnitude lower than that of SDS micelles. From a pharmacological point of view, it is important that at neutral pH, NFX presented a two orders of magnitude higher affinity for anionic than for cationic sites, and did not interact significantly with nonionic or zwitterionic micelle interfaces.

  4. Identification of Cell Cycle Dependent Interaction Partners of the Septins by Quantitative Mass Spectrometry.

    Directory of Open Access Journals (Sweden)

    Christian Renz

    Full Text Available The septins are a conserved family of GTP-binding proteins that, in the baker's yeast, assemble into a highly ordered array of filaments at the mother bud neck. These filaments undergo significant structural rearrangements during the cell cycle. We aimed at identifying key components that are involved in or regulate the transitions of the septins. By combining cell synchronization and quantitative affinity-purification mass-spectrometry, we performed a screen for specific interaction partners of the septins at three distinct stages of the cell cycle. A total of 83 interaction partners of the septins were assigned. Surprisingly, we detected DNA-interacting/nuclear proteins and proteins involved in ribosome biogenesis and protein synthesis predominantly present in alpha-factor arrested that do not display an assembled septin structure. Furthermore, two distinct sets of regulatory proteins that are specific for cells at S-phase with a stable septin collar or at mitosis with split septin rings were identified. Complementary methods like SPLIFF and immunoprecipitation allowed us to more exactly define the spatial and temporal characteristics of selected hits of the AP-MS screen.

  5. Nucleotide excision repair is associated with the replisome and its efficiency depends on a direct interaction between XPA and PCNA.

    Directory of Open Access Journals (Sweden)

    Karin M Gilljam

    Full Text Available Proliferating cell nuclear antigen (PCNA is an essential protein for DNA replication, DNA repair, cell cycle regulation, chromatin remodeling, and epigenetics. Many proteins interact with PCNA through the PCNA interacting peptide (PIP-box or the newly identified AlkB homolog 2 PCNA interacting motif (APIM. The xeroderma pigmentosum group A (XPA protein, with a central but somewhat elusive role in nucleotide excision repair (NER, contains the APIM sequence suggesting an interaction with PCNA. With an in vivo based approach, using modern techniques in live human cells, we show that APIM in XPA is a functional PCNA interacting motif and that efficient NER of UV lesions is dependent on an intact APIM sequence in XPA. We show that XPA(-/- cells complemented with XPA containing a mutated APIM sequence have increased UV sensitivity, reduced repair of cyclobutane pyrimidine dimers and (6-4 photoproducts, and are consequently more arrested in S phase as compared to XPA(-/- cells complemented with wild type XPA. Notably, XPA colocalizes with PCNA in replication foci and is loaded on newly synthesized DNA in undamaged cells. In addition, the TFIIH subunit XPD, as well as XPF are loaded on DNA together with XPA, and XPC and XPG colocalize with PCNA in replication foci. Altogether, our results suggest a presence of the NER complex in the vicinity of the replisome and a novel role of NER in post-replicative repair.

  6. p35 regulates the CRM1-dependent nucleocytoplasmic shuttling of nuclear hormone receptor coregulator-interacting factor 1 (NIF-1.

    Directory of Open Access Journals (Sweden)

    Xiao-Su Zhao

    Full Text Available Cyclin-dependent kinase 5 (Cdk5 is a proline-directed serine/threonine kinase, which plays critical roles in a wide spectrum of neuronal functions including neuronal survival, neurite outgrowth, and synapse development and plasticity. Cdk5 activity is controlled by its specific activators: p35 or p39. While knockout studies reveal that Cdk5/p35 is critical for neuronal migration during early brain development, functions of Cdk5/p35 have been unraveled through the identification of the interacting proteins of p35, most of which are Cdk5/p35 substrates. However, it remains unclear whether p35 can regulate neuronal functions independent of Cdk5 activity. Here, we report that a nuclear protein, nuclear hormone receptor coregulator (NRC-interacting factor 1 (NIF-1, is a new interacting partner of p35. Interestingly, p35 regulates the functions of NIF-1 independent of Cdk5 activity. NIF-1 was initially discovered as a transcriptional regulator that enhances the transcriptional activity of nuclear hormone receptors. Our results show that p35 interacts with NIF-1 and regulates its nucleocytoplasmic trafficking via the nuclear export pathway. Furthermore, we identified a nuclear export signal on p35; mutation of this site or blockade of the CRM1/exportin-dependent nuclear export pathway resulted in the nuclear accumulation of p35. Intriguingly, blocking the nuclear export of p35 attenuated the nuclear accumulation of NIF-1. These findings reveal a new p35-dependent mechanism in transcriptional regulation that involves the nucleocytoplasmic shuttling of transcription regulators.

  7. p35 regulates the CRM1-dependent nucleocytoplasmic shuttling of nuclear hormone receptor coregulator-interacting factor 1 (NIF-1).

    Science.gov (United States)

    Zhao, Xiao-Su; Fu, Wing-Yu; Chien, Winnie W Y; Li, Zhen; Fu, Amy K Y; Ip, Nancy Y

    2014-01-01

    Cyclin-dependent kinase 5 (Cdk5) is a proline-directed serine/threonine kinase, which plays critical roles in a wide spectrum of neuronal functions including neuronal survival, neurite outgrowth, and synapse development and plasticity. Cdk5 activity is controlled by its specific activators: p35 or p39. While knockout studies reveal that Cdk5/p35 is critical for neuronal migration during early brain development, functions of Cdk5/p35 have been unraveled through the identification of the interacting proteins of p35, most of which are Cdk5/p35 substrates. However, it remains unclear whether p35 can regulate neuronal functions independent of Cdk5 activity. Here, we report that a nuclear protein, nuclear hormone receptor coregulator (NRC)-interacting factor 1 (NIF-1), is a new interacting partner of p35. Interestingly, p35 regulates the functions of NIF-1 independent of Cdk5 activity. NIF-1 was initially discovered as a transcriptional regulator that enhances the transcriptional activity of nuclear hormone receptors. Our results show that p35 interacts with NIF-1 and regulates its nucleocytoplasmic trafficking via the nuclear export pathway. Furthermore, we identified a nuclear export signal on p35; mutation of this site or blockade of the CRM1/exportin-dependent nuclear export pathway resulted in the nuclear accumulation of p35. Intriguingly, blocking the nuclear export of p35 attenuated the nuclear accumulation of NIF-1. These findings reveal a new p35-dependent mechanism in transcriptional regulation that involves the nucleocytoplasmic shuttling of transcription regulators.

  8. Interaction of the mu-opioid receptor with GPR177 (Wntless inhibits Wnt secretion: potential implications for opioid dependence

    Directory of Open Access Journals (Sweden)

    Stagljar Igor

    2010-03-01

    Full Text Available Abstract Background Opioid agonist drugs produce analgesia. However, long-term exposure to opioid agonists may lead to opioid dependence. The analgesic and addictive properties of opioid agonist drugs are mediated primarily via the mu-opioid receptor (MOR. Opioid agonists appear to alter neuronal morphology in key brain regions implicated in the development of opioid dependence. However, the precise role of the MOR in the development of these neuronal alterations remains elusive. We hypothesize that identifying and characterizing novel MOR interacting proteins (MORIPs may help to elucidate the underlying mechanisms involved in the development of opioid dependence. Results GPR177, the mammalian ortholog of Drosophila Wntless/Evi/Sprinter, was identified as a MORIP in a modified split ubiquitin yeast two-hybrid screen. GPR177 is an evolutionarily conserved protein that plays a critical role in mediating Wnt protein secretion from Wnt producing cells. The MOR/GPR177 interaction was validated in pulldown, coimmunoprecipitation, and colocalization studies using mammalian tissue culture cells. The interaction was also observed in rodent brain, where MOR and GPR177 were coexpressed in close spatial proximity within striatal neurons. At the cellular level, morphine treatment caused a shift in the distribution of GPR177 from cytosol to the cell surface, leading to enhanced MOR/GPR177 complex formation at the cell periphery and the inhibition of Wnt protein secretion. Conclusions It is known that chronic morphine treatment decreases dendritic arborization and hippocampal neurogenesis, and Wnt proteins are essential for these processes. We therefore propose that the morphine-mediated MOR/GPR177 interaction may result in decreased Wnt secretion in the CNS, resulting in atrophy of dendritic arbors and decreased neurogenesis. Our results demonstrate a previously unrecognized role for GPR177 in regulating cellular response to opioid drugs.

  9. The temperature dependence of the Hofmeister series: thermodynamic fingerprints of cosolute-protein interactions.

    Science.gov (United States)

    Senske, Michael; Constantinescu-Aruxandei, Diana; Havenith, Martina; Herrmann, Christian; Weingärtner, Hermann; Ebbinghaus, Simon

    2016-11-02

    The Hofmeister series is a universal homologous series to rank ion-specific effects on biomolecular properties such as protein stability or aggregation propensity. Although this ranking is widely used, outliers and exceptions are discussed controversially and a molecular level understanding is still lacking. Studying the thermal unfolding equilibrium of RNase A, we here show that this ambiguity arises from the oversimplified approach to determine the ion rankings. Instead of measuring salt effects on a single point of the protein folding stability curve (e.g. the melting point Tm), we here consider the salt induced shifts of the entire protein 'stability curve' (the temperature dependence of the unfolding free energy change, ΔGu(T)). We found multiple intersections of these curves, pinpointing a widely ignored fact: the Hofmeister cation and anion rankings are temperature dependent. We further developed a novel classification scheme of cosolute effects based on their thermodynamic fingerprints, reaching beyond salt effects to non-electrolytes.

  10. Time-dependent density functional theory for many-electron systems interacting with cavity photons.

    Science.gov (United States)

    Tokatly, I V

    2013-06-07

    Time-dependent (current) density functional theory for many-electron systems strongly coupled to quantized electromagnetic modes of a microcavity is proposed. It is shown that the electron-photon wave function is a unique functional of the electronic (current) density and the expectation values of photonic coordinates. The Kohn-Sham system is constructed, which allows us to calculate the above basic variables by solving self-consistent equations for noninteracting particles. We suggest possible approximations for the exchange-correlation potentials and discuss implications of this approach for the theory of open quantum systems. In particular we show that it naturally leads to time-dependent density functional theory for systems coupled to the Caldeira-Leggett bath.

  11. Spin-dependent two-body interactions from gravitational self-force computations

    CERN Document Server

    Bini, Donato; Geralico, Andrea

    2015-01-01

    We analytically compute, through the eight-and-a-half post-Newtonian order and the fourth-order in spin, the gravitational self-force correction to Detweiler's gauge invariant redshift function for a small mass in circular orbit around a Kerr black hole. Using the first law of mechanics for black hole binaries with spin [L.~Blanchet, A.~Buonanno and A.~Le Tiec, Phys.\\ Rev.\\ D {\\bf 87}, 024030 (2013)] we transcribe our results into a knowledge of various spin-dependent couplings, as encoded within the spinning effective-one-body model of T.~Damour and A.~Nagar [Phys.\\ Rev.\\ D {\\bf 90}, 044018 (2014)]. We also compare our analytical results to the (corrected) numerical self-force results of A.~G.~Shah, J.~L.~Friedman and T.~S.~Keidl [Phys.\\ Rev.\\ D {\\bf 86}, 084059 (2012)], from which we show how to directly extract physically relevant spin-dependent couplings.

  12. Relativistic study of the energy-dependent Coulomb potential including Coulomb-like tensor interaction

    CERN Document Server

    Hamzavi, Majid

    2012-01-01

    The exact Dirac equation for the energy-dependent Coulomb (EDC) potential including a Coulomb-like tensor (CLT) potential has been studied in the presence of spin and pseudospin (p-spin) symmetries with arbitrary spin-orbit quantum number The energy eigenvalues and corresponding eigenfunctions are obtained in the framework of asymptotic iteration method (AIM). Some numerical results are obtained in the presence and absence of EDC and CLT potentials.

  13. Effect of Different Display Types on Vection and Its Interaction With Motion Direction and Field Dependence

    Directory of Open Access Journals (Sweden)

    Behrang Keshavarz

    2017-05-01

    Full Text Available Illusory self-motion (vection can be generated by visual stimulation. The purpose of the present study was to compare behavioral vection measures including intensity ratings, duration, and onset time across different visual display types. Participants were exposed to a pattern of alternating black-and-white horizontal or vertical bars that moved either in vertical or horizontal direction, respectively. Stimuli were presented on four types of displays in randomized order: (a large field of view dome projection, (b combination of three computer screens, (c single computer screen, (d large field of view flat projection screen. A Computer Rod and Frame Test was used to measure field dependence, a cognitive style indicating the person’s tendency to rely on external cues (i.e., field dependent or internal cues (i.e., field independent with respect to the perception of one’s body position in space. Results revealed that all four displays successfully generated at least moderately strong vection. However, shortest vection onset, longest vection duration, and strongest vection intensity showed for the dome projection and the combination of three screens. This effect was further pronounced in field independent participants, indicating that field dependence can alter vection.

  14. Applying Boundary Conditions Using a Time-Dependent Lagrangian for Modeling Laser-Plasma Interactions

    Science.gov (United States)

    Reyes, J. Paxon; Shadwick, B. A.

    2015-11-01

    Describing a cold-Maxwell fluid system with a spatially-discrete, unbounded Lagrangian is problematic for numerical modeling since boundary conditions must be applied after the variational step. Accurate solutions may still be attained, but do not technically satisfy the derived energy conservation law. The size of the numerical domain, the order accuracy of the discrete approximations used, and the type of boundary conditions applied influence the behavior of the artificially-bounded system. To encode the desired boundary conditions of the equations of motion, we include time-dependent terms into the discrete Lagrangian. Although some foresight is needed to choose these time-dependent terms, this approach provides a mechanism for energy to exit the closed system while allowing the conservation law to account for the energy loss. Results of a spatially-discrete, time-dependent Lagrangian system (with approximations of second-order accuracy in space and fourth order in time) will be presented. The fields and total energy will be compared with models of the same accuracy using a time-independent variational approach as well as a non-variational approach. This work was supported by the U. S. Department of Energy under Contract No. DE-SC0008382 and by the National Science Foundation under Contract No. PHY- 1104683.

  15. Protein denaturation with guanidine hydrochloride or urea provides a different estimate of stability depending on the contributions of electrostatic interactions.

    Science.gov (United States)

    Monera, O. D.; Kay, C. M.; Hodges, R. S.

    1994-01-01

    The objective of this study was to address the question of whether or not urea and guanidine hydrochloride (GdnHCl) give the same estimates of the stability of a particular protein. We previously suspected that the estimates of protein stability from GdnHCl and urea denaturation data might differ depending on the electrostatic interactions stabilizing the proteins. Therefore, 4 coiled-coil analogs were designed, where the number of intrachain and interchain electrostatic attractions (A) were systematically changed to repulsions (R): 20A, 15A5R, 10A10R, and 20R. The GdnHCl denaturation data showed that the 4 coiled-coil analogs, which had electrostatic interactions ranging from 20 attractions to 20 repulsions, had very similar [GdnHCl]1/2 values (average of congruent to 3.5 M) and, as well, their delta delta Gu values were very close to 0 (0.2 kcal/mol). In contrast, urea denaturation showed that the [urea]1/2 values proportionately decreased with the stepwise change from 20 electrostatic attractions to 20 repulsions (20A, 7.4 M; 15A5R, 5.4 M; 10A10R, 3.2 M; and 20R, 1.4 M), and the delta delta Gu values correspondingly increased with the increasing differences in electrostatic interactions (20A-15A5R, 1.5 kcal/mol; 20A-10A10R, 3.7 kcal/mol; and 20A-20R, 5.8 kcal/mol). These results indicate that the ionic nature of GdnHCl masks electrostatic interactions in these model proteins, a phenomenon that was absent when the unchanged urea was used. Thus, GdnHCl and urea denaturations may give vastly different estimates of protein stability, depending on how important electrostatic interactions are to the protein. PMID:7703845

  16. Information entropy of a time-dependent three-level trapped ion interacting with a laser field

    Science.gov (United States)

    Abdel-Aty, Mahmoud

    2005-10-01

    Trapped and laser-cooled ions are increasingly used for a variety of modern high-precision experiments, frequency standard applications and quantum information processing. Therefore, in this communication we present a comprehensive analysis of the pattern of information entropy arising in the time evolution of an ion interacting with a laser field. A general analytic approach is proposed for a three-level trapped-ion system in the presence of the time-dependent couplings. By working out an exact analytic solution, we conclusively analyse the general properties of the von Neumann entropy and quantum information entropy. It is shown that the information entropy is affected strongly by the time-dependent coupling and exhibits long time periodic oscillations. This feature attributed to the fact that in the time-dependent region Rabi oscillation is time dependent. Using parameters corresponding to a specific three-level ionic system, a single beryllium ion in a RF-(Paul) trap, we obtain illustrative examples of some novel aspects of this system in the dynamical evolution. Our results establish an explicit relation between the exact information entropy and the entanglement between the multi-level ion and the laser field. We show that different nonclassical effects arise in the dynamics of the ionic population inversion, depending on the initial states of the vibrational motion/field and on the values of Lamb-Dicke parameter η.

  17. Microbial interactions with the cyanobacterium Microcystis aeruginosa and their dependence on temperature

    DEFF Research Database (Denmark)

    Dziallas, Claudia; Grossart, Hans-Peter

    2012-01-01

    was greatly driven by temperature as seen by DNA Wngerprinting. However, the associated microbes also closely interacted with the cyanobacteria indicating changing ecological consequence of the associated bacterial community with temperature. Whereas concentration of dissolved organic carbon in cyanobacterial...... and their associated community often masked this temperature effect. Both macro- and microenvironment of active cyanobacterial strains were characterized by high pH and oxygen values creating a unique habitat that potentially affects microbial diversity and function. For example, archaea including ‘anaerobic...

  18. Regulatory R region of the CFTR chloride channel is a dynamic integrator of phospho-dependent intra- and intermolecular interactions.

    Science.gov (United States)

    Bozoky, Zoltan; Krzeminski, Mickael; Muhandiram, Ranjith; Birtley, James R; Al-Zahrani, Ateeq; Thomas, Philip J; Frizzell, Raymond A; Ford, Robert C; Forman-Kay, Julie D

    2013-11-19

    Intrinsically disordered proteins play crucial roles in regulatory processes and often function as protein interaction hubs. Here, we present a detailed characterization of a full-length disordered hub protein region involved in multiple dynamic complexes. We performed NMR, CD, and fluorescence binding studies on the nonphosphorylated and highly PKA-phosphorylated human cystic fibrosis transmembrane conductance regulator (CFTR) regulatory region, a ∼200-residue disordered segment involved in phosphorylation-dependent regulation of channel trafficking and gating. Our data provide evidence for dynamic, phosphorylation-dependent, multisite interactions of various segments of the regulatory region for its intra- and intermolecular partners, including the CFTR nucleotide binding domains 1 and 2, a 42-residue peptide from the C terminus of CFTR, the SLC26A3 sulphate transporter and antisigma factor antagonist (STAS) domain, and 14-3-3β. Because of its large number of binding partners, multivalent binding of individually weak sites facilitates rapid exchange between free and bound states to allow the regulatory region to engage with different partners and generate a graded or rheostat-like response to phosphorylation. Our results enrich the understanding of how disordered binding segments interact with multiple targets. We present structural models consistent with our data that illustrate this dynamic aspect of phospho-regulation of CFTR by the disordered regulatory region.

  19. Palmitoylation-dependent CDKL5–PSD-95 interaction regulates synaptic targeting of CDKL5 and dendritic spine development

    Science.gov (United States)

    Zhu, Yong-Chuan; Li, Dan; Wang, Lu; Lu, Bin; Zheng, Jing; Zhao, Shi-Lin; Zeng, Rong; Xiong, Zhi-Qi

    2013-01-01

    The X-linked gene cyclin-dependent kinase-like 5 (CDKL5) is mutated in severe neurodevelopmental disorders, including some forms of atypical Rett syndrome, but the function and regulation of CDKL5 protein in neurons remain to be elucidated. Here, we show that CDKL5 binds to the scaffolding protein postsynaptic density (PSD)-95, and that this binding promotes the targeting of CDKL5 to excitatory synapses. Interestingly, this binding is not constitutive, but governed by palmitate cycling on PSD-95. Furthermore, pathogenic mutations that truncate the C-terminal tail of CDKL5 diminish its binding to PSD-95 and synaptic accumulation. Importantly, down-regulation of CDKL5 by RNA interference (RNAi) or interference with the CDKL5–PSD-95 interaction inhibits dendritic spine formation and growth. These results demonstrate a critical role of the palmitoylation-dependent CDKL5–PSD-95 interaction in localizing CDKL5 to synapses for normal spine development and suggest that disruption of this interaction by pathogenic mutations may be implicated in the pathogenesis of CDKL5-related disorders. PMID:23671101

  20. Multiple Pairwise Analysis of Non-homologous Centromere Coupling Reveals Preferential Chromosome Size-Dependent Interactions and a Role for Bouquet Formation in Establishing the Interaction Pattern.

    Science.gov (United States)

    Lefrançois, Philippe; Rockmill, Beth; Xie, Pingxing; Roeder, G Shirleen; Snyder, Michael

    2016-10-01

    During meiosis, chromosomes undergo a homology search in order to locate their homolog to form stable pairs and exchange genetic material. Early in prophase, chromosomes associate in mostly non-homologous pairs, tethered only at their centromeres. This phenomenon, conserved through higher eukaryotes, is termed centromere coupling in budding yeast. Both initiation of recombination and the presence of homologs are dispensable for centromere coupling (occurring in spo11 mutants and haploids induced to undergo meiosis) but the presence of the synaptonemal complex (SC) protein Zip1 is required. The nature and mechanism of coupling have yet to be elucidated. Here we present the first pairwise analysis of centromere coupling in an effort to uncover underlying rules that may exist within these non-homologous interactions. We designed a novel chromosome conformation capture (3C)-based assay to detect all possible interactions between non-homologous yeast centromeres during early meiosis. Using this variant of 3C-qPCR, we found a size-dependent interaction pattern, in which chromosomes assort preferentially with chromosomes of similar sizes, in haploid and diploid spo11 cells, but not in a coupling-defective mutant (spo11 zip1 haploid and diploid yeast). This pattern is also observed in wild-type diploids early in meiosis but disappears as meiosis progresses and homologous chromosomes pair. We found no evidence to support the notion that ancestral centromere homology plays a role in pattern establishment in S. cerevisiae post-genome duplication. Moreover, we found a role for the meiotic bouquet in establishing the size dependence of centromere coupling, as abolishing bouquet (using the bouquet-defective spo11 ndj1 mutant) reduces it. Coupling in spo11 ndj1 rather follows telomere clustering preferences. We propose that a chromosome size preference for centromere coupling helps establish efficient homolog recognition.

  1. Interactions between Leishmania braziliensis and Macrophages Are Dependent on the Cytoskeleton and Myosin Va

    Directory of Open Access Journals (Sweden)

    Elisama Azevedo

    2012-01-01

    Full Text Available Leishmaniasis is a neglected tropical disease with no effective vaccines. Actin, microtubules and the actin-based molecular motor myosin Va were investigated for their involvement in Leishmania braziliensis macrophage interactions. Results showed a decrease in the association index when macrophages were without F-actin or microtubules regardless of the activation state of the macrophage. In the absence of F-actin, the production of NO in non-activated cells increased, while in activated cells, the production of NO was reduced independent of parasites. The opposite effect of an increased NO production was observed in the absence of microtubules. In activated cells, the loss of cytoskeletal components inhibited the release of IL-10 during parasite interactions. The production of IL-10 also decreased in the absence of actin or microtubules in non-activated macrophages. Only the disruption of actin altered the production of TNF-α in activated macrophages. The expression of myosin Va tail resulted in an acute decrease in the association index between transfected macrophages and L. braziliensis promastigotes. These data reveal the importance of F-actin, microtubules, and myosin-Va suggesting that modulation of the cytoskeleton may be a mechanism used by L. braziliensis to overcome the natural responses of macrophages to establish infections.

  2. Protein encapsulation in liposomes: efficiency depends on interactions between protein and phospholipid bilayer.

    Directory of Open Access Journals (Sweden)

    Winterhalter Mathias

    2002-05-01

    Full Text Available Abstract Background We investigated the encapsulation mechanism of enzymes into liposomes. The existing protocols to achieve high encapsulation efficiencies are basically optimized for chemically stable molecules. Enzymes, however, are fragile and encapsulation requires in addition the preservation of their functionality. Using acetylcholinesterase as a model, we found that most protocols lead to a rapid denaturation of the enzyme with loss in the functionality and therefore inappropriate for such an application. The most appropriate method is based on lipid film hydration but had a very low efficiency. Results To improve it and to propose a standard procedure for enzyme encapsulation, we separate each step and we studied the effect of each parameter on encapsulation: lipid and buffer composition and effect of the different physical treatment as freeze-thaw cycle or liposomes extrusion. We found that by increasing the lipid concentration, increasing the number of freeze-thaw cycles and enhancing the interactions of the enzyme with the liposome lipid surface more than 40% of the initial total activity can be encapsulated. Conclusion We propose here an optimized procedure to encapsulate fragile enzymes into liposomes. Optimal encapsulation is achieved by induction of a specific interaction between the enzyme and the lipid surface.

  3. Strong Delayed Interactive Effects of Metal Exposure and Warming: Latitude-Dependent Synergisms Persist Across Metamorphosis.

    Science.gov (United States)

    Debecker, Sara; Dinh, Khuong V; Stoks, Robby

    2017-02-21

    As contaminants are often more toxic at higher temperatures, predicting their impact under global warming remains a key challenge for ecological risk assessment. Ignoring delayed effects, synergistic interactions between contaminants and warming, and differences in sensitivity across species' ranges could lead to an important underestimation of the risks. We addressed all three mechanisms by studying effects of larval exposure to zinc and warming before, during, and after metamorphosis in Ischnura elegans damselflies from high- and low-latitude populations. By integrating these mechanisms into a single study, we could identify two novel patterns. First, during exposure zinc did not affect survival, whereas it induced mild to moderate postexposure mortality in the larval stage and at metamorphosis, and very strongly reduced adult lifespan. This severe delayed effect across metamorphosis was especially remarkable in high-latitude animals, as they appeared almost insensitive to zinc during the larval stage. Second, the well-known synergism between metals and warming was manifested not only during the larval stage but also after metamorphosis, yet notably only in low-latitude damselflies. These results highlight that a more complete life-cycle approach that incorporates the possibility of delayed interactions between contaminants and warming in a geographical context is crucial for a more realistic risk assessment in a warming world.

  4. Protein kinase C interaction with calcium: a phospholipid-dependent process.

    LENUS (Irish Health Repository)

    Bazzi, M D

    1990-08-21

    The calcium-binding properties of calcium- and phospholipid-dependent protein kinase C (PKC) were investigated by equilibrium dialysis in the presence and the absence of phospholipids. Calcium binding to PKC displayed striking and unexpected behavior; the free proteins bound virtually no calcium at intracellular calcium concentrations and bound limited calcium (about 1 mol\\/mol of PKC) at 200 microM calcium. However, in the presence of membranes containing acidic phospholipids, PKC bound at least eight calcium ions per protein. The presence of 1 microM phorbol dibutyrate (PDBu) in the dialysis buffer had little effect on these calcium-binding properties. Analysis of PKC-calcium binding by gel filtration under equilibrium conditions gave similar results; only membrane-associated PKC bound significant amounts of calcium. Consequently, PKC is a member of what may be a large group of proteins that bind calcium in a phospholipid-dependent manner. The calcium concentrations needed to induce PKC-membrane binding were similar to those needed for calcium binding (about 40 microM calcium at the midpoint). However, the calcium concentration required for PKC-membrane binding was strongly influenced by the phosphatidylserine composition of the membranes. Membranes with higher percentages of phosphatidylserine required lower concentrations of calcium. These properties suggested that the calcium sites may be generated at the interface between PKC and the membrane. Calcium may function as a bridge between PKC and phospholipids. These studies also suggested that calcium-dependent PKC-membrane binding and PKC function could be regulated by a number of factors in addition to calcium levels and diacylglycerol content of the membrane.

  5. Interaction between two sliders in a system with rate- and state-dependent friction

    Institute of Scientific and Technical Information of China (English)

    HE; Changrong; (何昌荣)

    2003-01-01

    This study examines slip recurrence patterns in a two-block spring-slider model with rate- and state-dependent friction. Both weak and strong heterogeneities are considered with different settings of coupling stiffness. The results show that the recurrence pattern of slips strongly depends on the degree of coupling between the two blocks. With strong coupling between the two blocks (e.g., kc/ki max >~1), the slip pattern of the system is simple and characterized by periodical stick-slips, with the two blocks slipping together. With strong heterogeneity in friction strength, period-2 motion is found for moderate coupling stiffness (kc/ki max=0.4) between the two blocks. More complicated patterns are found with weak coupling stiffness (kc/ki max=0.2) and strong heterogeneity. With strong heterogeneity, very weak coupling leads to chaotic slip patterns. With coupling stiffness kc=5 ki max and strong heterogeneity, chaotic slip patterns are not found, in contrast with the results by Huang and Turcotte who employed the classical static/kinetic friction law.

  6. Phase transition of strongly interacting matter with a chemical potential dependent Polyakov loop potential

    CERN Document Server

    Shao, Guo-yun; Di Toro, Massimo; Colonna, Maria; Gao, Xue-yan; Gao, Ning

    2016-01-01

    We construct a hadron-quark two-phase model based on the Walecka-quantum hadrodynamics and the improved Polyakov-Nambu--Jona-Lasinio model with an explicit chemical potential dependence of Polyakov-loop potential ($\\mu$PNJL model). With respect to the original PNJL model, the confined-deconfined phase transition is largely affected at low temperature and large chemical potential. Using the two-phase model, we investigate the equilibrium transition between hadronic and quark matter at finite chemical potentials and temperatures. The numerical results show that the transition boundaries from nuclear to quark matter move towards smaller chemical potential (lower density) when the $\\mu$-dependent Polyakov loop potential is taken. In particular, for charge asymmetric matter, we compute the local asymmetry of $u, d$ quarks in the hadron-quark coexisting phase, and analyse the isospin-relevant observables possibly measurable in heavy-ion collision (HIC) experiments. In general new HIC data on the location and proper...

  7. Energy Dependence of the πN Amplitude and the Three-Nucleon Interaction

    Science.gov (United States)

    Saito, T.-Y.; Afnan, I. R.

    1995-08-01

    By calculating the contribution of the ππ three-body force to the three-nucleon binding energy in terms of the πN amplitude using perturbation theory, we are able to determine the importance of the energy dependence and the contribution of the different partial waves of the πN amplitude to the three-nucleon force. A separable representation of the non-pole πN amplitude allows us to write the three-nucleon force in terms of the amplitude for NN → NN*, propagation of the NNN* system, and the amplitude for NN* → NN , with N* being the πN quasi-particle amplitude in a given state. The division of the πN amplitude into a pole and non-pole part gives a procedure for the determination of the πNN form factor within the model. The total contribution of the three-body force to the binding energy of the triton for the separable approximation to the Paris nucleon-nucleon potential (PEST) is found to be very small mainly as a result of the energy dependence of the πN amplitude, the cancellation between the S- and P-wave πN amplitudes, and the soft πNN form factor.

  8. Opioid antinociception, tolerance and dependence: interactions with the N-methyl-D-aspartate system in mice.

    Science.gov (United States)

    Dykstra, Linda A; Fischer, Bradford D; Balter, Rebecca E; Henry, Fredrick E; Schmidt, Karl T; Miller, Laurence L

    2011-09-01

    This study explored the involvement of N-methyl-D-aspartate (NMDA) in the effects of μ-opioid agonists. A hot-plate procedure was used to assess antinociception and tolerance in mice in which the NR1 subunit of the NMDA receptor was reduced [knockdown (KD)] to approximately 10%, and in mice treated with the NMDA antagonist, (-)-6-phosphonomethyl-deca-hydroisoquinoline-3-carboxylic acid (LY235959). The μ opioid agonists, morphine, l-methadone and fentanyl, were approximately three-fold less potent in the NR1 KD mice than in wild-type (WT) controls; however, the development of morphine tolerance and dependence did not differ markedly in the NR1 KD and the WT mice. Acute administration of the NMDA antagonist, LY235959, produced dose-dependent, leftward shifts in the morphine dose-effect curve in the WT mice, but not in the NR1 KD mice. Chronic administration of LY235959 during the morphine tolerance regimen did not attenuate the development of tolerance in the NR1 KD or the WT mice. These results indicate that the NR1 subunit of the NMDA receptor does not play a prominent role in μ opioid tolerance.

  9. Temperature dependence of band gaps in semiconductors: electron-phonon interaction

    Energy Technology Data Exchange (ETDEWEB)

    Kremer, Reinhard K.; Cardona, M.; Lauck, R. [MPI for Solid State Research, Stuttgart (Germany); Bhosale, J.; Ramdas, A.K. [Physics Dept., Purdue University, West Lafayette, IN (United States); Burger, A. [Fisk University, Dept. of Life and Physical Sciences, Nashville, TN (United States); Munoz, A. [MALTA Consolider Team, Dept. de Fisica Fundamental II, Universidad de La Laguna, Tenerife (Spain); Instituto de Materiales y Nanotecnologia, Universidad de La Laguna, Tenerife (Spain); Romero, A.H. [CINVESTAV, Dept. de Materiales, Unidad Queretaro, Mexico (Mexico); MPI fuer Mikrostrukturphysik, Halle an der Saale (Germany)

    2013-07-01

    We investigate the temperature dependence of the energy gap of several semiconductors with chalcopyrite structure and re-examine literature data and analyze own high-resolution reflectivity spectra in view of our new ab initio calculations of their phonon properties. This analysis leads us to distinguish between materials with d-electrons in the valence band (e.g. CuGaS{sub 2}, AgGaS{sub 2}) and those without d-electrons (e.g. ZnSnAs{sub 2}). The former exhibit a rather peculiar non-monotonic temperature dependence of the energy gap which, so far, has resisted cogent theoretical description. We demonstrate it can well be fitted by including two Bose-Einstein oscillators with weights of opposite sign leading to an increase at low-T and a decrease at higher T's. We find that the energy of the former correlates well with characteristic peaks in the phonon density of states associated with low-energy vibrations of the d-electron constituents.

  10. The energy dependence of the $\\pi$N amplitude and the three-nucleon interaction

    CERN Document Server

    Saitô, T; Saito, T Y

    1994-01-01

    By calculating the contribution of the \\pi-\\pi three-body force to the three-nucleon binding energy in terms of the \\pi N amplitude using perturbation theory, we are able to determine the importance of the energy dependence and the contribution of the different partial waves of the \\pi N amplitude to the three-nucleon force. A separable representation of the non-pole \\pi N amplitude allows us to write the three-nucleon force in terms of the amplitude for NN\\rightarrow NN^*, propagation of the NNN^* system, and the amplitude for NN^*\\rightarrow NN, with N^* being the \\pi N quasi-particle amplitude in a given state. The division of the \\pi N amplitude into a pole and non-pole gives a procedure for the determination of the \\pi NN form factor within the model. The total contribution of the three-body force to the binding energy of the triton for the separable approximation to the Paris nucleon-nucleon potential (PEST) is found to be very small mainly as a result of the energy dependence of the \\pi N amplitude, th...

  11. M. tuberculosis sliding β-clamp does not interact directly with the NAD+-dependent DNA ligase.

    Directory of Open Access Journals (Sweden)

    Vandna Kukshal

    Full Text Available The sliding β-clamp, an important component of the DNA replication and repair machinery, is drawing increasing attention as a therapeutic target. We report the crystal structure of the M. tuberculosis β-clamp (Mtbβ-clamp to 3.0 Å resolution. The protein crystallized in the space group C222(1 with cell-dimensions a = 72.7, b = 234.9 & c = 125.1 Å respectively. Mtbβ-clamp is a dimer, and exhibits head-to-tail association similar to other bacterial clamps. Each monomer folds into three domains with similar structures respectively and associates with its dimeric partner through 6 salt-bridges and about 21 polar interactions. Affinity experiments involving a blunt DNA duplex, primed-DNA and nicked DNA respectively show that Mtbβ-clamp binds specifically to primed DNA about 1.8 times stronger compared to the other two substrates and with an apparent K(d of 300 nM. In bacteria like E. coli, the β-clamp is known to interact with subunits of the clamp loader, NAD(+-dependent DNA ligase (LigA and other partners. We tested the interactions of the Mtbβ-clamp with MtbLigA and the γ-clamp loader subunit through radioactive gel shift assays, size exclusion chromatography, yeast-two hybrid experiments and also functionally. Intriguingly while Mtbβ-clamp interacts in vitro with the γ-clamp loader, it does not interact with MtbLigA unlike in bacteria like E. coli where it does. Modeling studies involving earlier peptide complexes reveal that the peptide-binding site is largely conserved despite lower sequence identity between bacterial clamps. Overall the results suggest that other as-yet-unidentified factors may mediate interactions between the clamp, LigA and DNA in mycobacteria.

  12. An interactive Tool for Writer Identification based on Offline Text Dependent Approach

    Directory of Open Access Journals (Sweden)

    Saranya K

    2013-01-01

    Full Text Available Writer identification is the process of identifying the writer of the document based on their handwriting. The growth of computational engineering, artificial intelligence and pattern recognition fields owes greatly to one of the highly challenged problem of handwriting identification. This paper proposes the computational intelligence technique to develop discriminative model for writer identification based on handwritten documents. Scanned images of handwritten documents are segmented into words and these words are further segmented into characters for word level and character level writer identification. A set of features are extracted from the segmented words and characters. Feature vectors are trained using support vector machine and obtained 94.27% accuracy for word level, 90.10% for character level. An interactive tool has been developed based on the word level writer identification model.

  13. The effects of spin-dependent interactions on polarisation of bright polariton solitons

    CERN Document Server

    Sich, M; Chana, J K; Skolnick, M S; Krizhanovskii, D N; Gorbach, A V; Hartley, R; Skryabin, D V; Gavrilov, S V; Cerda-Mendez, E A; Biermann, K; Hey, R; Santos, P V

    2013-01-01

    We report on the spin properties of bright polariton solitons supported by an external pump to compensate losses. We observe robust circularly polarised solitons when a circularly polarised pump is applied, a result attributed to phase synchronisation between nondegenerate TE and TM polarised polariton modes at high momenta. For the case of a linearly polarised pump either s+ or s- circularly polarised bright solitons can be switched on in a controlled way by a s+ or s- writing beam respectively. This feature arises directly from the widely differing interaction strengths between co- and cross-circularly polarised polaritons. In the case of orthogonally linearly polarised pump and writing beams, the soliton emission on average is found to be unpolarised, suggesting strong spatial evolution of the soliton polarisation, a conclusion supported by polarisation correlation measurements. The observed results are in agreement with theory, which predicts stable circularly polarised solitons and unstable linearly pola...

  14. Study of the Dependence of Photoenhanced Nonlinear Acoustic Surface Wave Interactions on the Wavelength of Light.

    Science.gov (United States)

    1977-05-10

    CenterRockwell International SC5027.4FR 5.0 APPEND IX a) Participating Sci enti fic Personnel: Dr. Edgar A. Kraut Dr. T. C. Lim Mr. Fran k J. Morin Mr. John...Research Triangle Park, North Carolina 27709 JUN 23 19fl _ / L~. Co-Inve stigators F— 0 . Edgar A. Kraut Dr. Te g C. Lim ___________ 4nr...INTERACTIONS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ON THE WAVELENGTH OF LIGHT~ I sc~o~i.~ p. /7 QR(a,) ~~~~~O~~TRA~~’T O R GRA NT NUMBER(S) Dr. Edgar A

  15. Context-dependent interaction leads to emergent search behavior in social aggregates

    CERN Document Server

    Torney, Colin; Couzin, Iain D

    2009-01-01

    Locating the source of an advected chemical signal is a common challenge facing many living organisms. When the advecting medium is characterized by either high Reynolds number or high Peclet number the task becomes highly non-trivial due to the generation of heterogenous, dynamically changing filamental concentrations which do not decrease monotonically with distance to the source. Defining search strategies which are effective in these environments has important implications for the understanding of animal behavior and for the design of biologically inspired technology. Here we present a strategy which is able to solve this task without the higher intelligence required to assess spatial gradient direction, measure the diffusive properties of the flow field or perform complex calculations. Instead our method is based on the collective behavior of autonomous individuals following simple social interaction rules which are modified according to the local conditions they are experiencing. Through these context-d...

  16. Inverse Temperature Dependence in Static Quenching versus Calorimetric Exploration: Binding Interaction of Chloramphenicol to β-Lactoglobulin.

    Science.gov (United States)

    Ghosh, Narayani; Mondal, Ramakanta; Mukherjee, Saptarshi

    2015-07-28

    The binding interaction between the whey protein bovine β-lactoglobulin (βLG) with the well-known antibiotic chloramphenicol (Clp) is explored by monitoring the intrinsic fluorescence of βLG. Steady-state and time-resolved fluorescence spectral data reveal that quenching of βLG fluorescence proceeds through ground state complex formation, i.e., static quenching mechanism. However, the drug-protein binding constant is found to vary proportionately with temperature. This anomalous result is explained on the basis of the Arrhenius theory which states that the rate constant varies proportionally with temperature. Thermodynamic parameters like ΔH, ΔS, ΔG, and the stoichiometry for the binding interaction have been estimated by isothermal titration calorimetric (ITC) study. Thermodynamic data show that the binding phenomenon is mainly an entropy driven process suggesting the major role of hydrophobic interaction forces in the Clp-βLG binding. Constant pressure heat capacity change (ΔCp) has been calculated from enthalpy of binding at different temperatures which reveals that hydrophobic interaction is the major operating force. The inverse temperature dependence in static quenching is however resolved from ITC data which show that the binding constant regularly decreases with increase in temperature. The modification of native protein conformation due to binding of drug has been monitored by circular dichroism (CD) spectroscopy. The probable binding location of Clp inside βLG is explored from AutoDock based blind docking simulation.

  17. VEGF-A isoforms differentially regulate ATF-2–dependent VCAM-1 gene expression and endothelial–leukocyte interactions

    Science.gov (United States)

    Fearnley, Gareth W.; Odell, Adam F.; Latham, Antony M.; Mughal, Nadeem A.; Bruns, Alexander F.; Burgoyne, Nicholas J.; Homer-Vanniasinkam, Shervanthi; Zachary, Ian C.; Hollstein, Monica C.; Wheatcroft, Stephen B.; Ponnambalam, Sreenivasan

    2014-01-01

    Vascular endothelial growth factor A (VEGF-A) regulates many aspects of vascular physiology. VEGF-A stimulates signal transduction pathways that modulate endothelial outputs such as cell migration, proliferation, tubulogenesis, and cell–cell interactions. Multiple VEGF-A isoforms exist, but the biological significance of this is unclear. Here we analyzed VEGF-A isoform–specific stimulation of VCAM-1 gene expression, which controls endothelial–leukocyte interactions, and show that this is dependent on both ERK1/2 and activating transcription factor-2 (ATF-2). VEGF-A isoforms showed differential ERK1/2 and p38 MAPK phosphorylation kinetics. A key feature of VEGF-A isoform–specific ERK1/2 activation and nuclear translocation was increased phosphorylation of ATF-2 on threonine residue 71 (T71). Using reverse genetics, we showed ATF-2 to be functionally required for VEGF-A–stimulated endothelial VCAM-1 gene expression. ATF-2 knockdown blocked VEGF-A–stimulated VCAM-1 expression and endothelial–leukocyte interactions. ATF-2 was also required for other endothelial cell outputs, such as cell migration and tubulogenesis. In contrast, VCAM-1 was essential only for promoting endothelial–leukocyte interactions. This work presents a new paradigm for understanding how soluble growth factor isoforms program complex cellular outputs and responses by modulating signal transduction pathways. PMID:24966171

  18. SARM modulates MyD88-mediated TLR activation through BB-loop dependent TIR-TIR interactions.

    Science.gov (United States)

    Carlsson, Emil; Ding, Jeak Ling; Byrne, Bernadette

    2016-02-01

    Toll-like receptors (TLRs) recognise invading pathogens and initiate an innate immune response by recruiting intracellular adaptor proteins via heterotypic Toll/interleukin-1 receptor (TIR) domain interactions. Of the five TIR domain-containing adaptor proteins identified, Sterile α- and armadillo-motif-containing protein (SARM) is functionally unique; suppressing immune signalling instead of promoting it. Here we demonstrate that the recombinantly expressed and purified SARM TIR domain interacts with both the major human TLR adaptors, MyD88 and TRIF. A single glycine residue located in the BB-loop of the SARM TIR domain, G601, was identified as essential for interaction. A short peptide derived from this motif was also found to interact with MyD88 in vitro. SARM expression in HEK293 cells was found to significantly suppress lipopolysaccharide (LPS)-mediated upregulation of inflammatory cytokines, IL-8 and TNF-α, an effect lost in the G601A mutant. The same result was observed with cytokine activation initiated by MyD88 expression and stimulation of TLR2 with lipoteichoic acid (LTA), suggesting that SARM is capable of suppressing both TRIF- and MyD88- dependent TLR signalling. Our findings indicate that SARM acts on a broader set of target proteins than previously thought, and that the BB-loop motif is functionally important, giving further insight into the endogenous mechanisms used to suppress inflammation in immune cells. Copyright © 2015 Elsevier B.V. All rights reserved.

  19. Phosphorylation-dependent interactions between Crb2 and Chk1 are essential for DNA damage checkpoint.

    Directory of Open Access Journals (Sweden)

    Meng Qu

    2012-07-01

    Full Text Available In response to DNA damage, the eukaryotic genome surveillance system activates a checkpoint kinase cascade. In the fission yeast Schizosaccharomyces pombe, checkpoint protein Crb2 is essential for DNA damage-induced activation of downstream effector kinase Chk1. The mechanism by which Crb2 mediates Chk1 activation is unknown. Here, we show that Crb2 recruits Chk1 to double-strand breaks (DSBs through a direct physical interaction. A pair of conserved SQ/TQ motifs in Crb2, which are consensus phosphorylation sites of upstream kinase Rad3, is required for Chk1 recruitment and activation. Mutating both of these motifs renders Crb2 defective in activating Chk1. Tethering Crb2 and Chk1 together can rescue the SQ/TQ mutations, suggesting that the main function of these phosphorylation sites is promoting interactions between Crb2 and Chk1. A 19-amino-acid peptide containing these SQ/TQ motifs is sufficient for Chk1 binding in vitro when one of the motifs is phosphorylated. Remarkably, the same peptide, when tethered to DSBs by fusing with either recombination protein Rad22/Rad52 or multi-functional scaffolding protein Rad4/Cut5, can rescue the checkpoint defect of crb2Δ. The Rad22 fusion can even bypass the need for Rad9-Rad1-Hus1 (9-1-1 complex in checkpoint activation. These results suggest that the main role of Crb2 and 9-1-1 in DNA damage checkpoint signaling is recruiting Chk1 to sites of DNA lesions.

  20. Carrier dependent ferromagnetism in chromium doped topological insulator Cr{sub y}(Bi{sub x}Sb{sub 1−x}){sub 2−y}Te{sub 3}

    Energy Technology Data Exchange (ETDEWEB)

    Li, Bin; Fan, Qingyan; Ji, Fuhao; Liu, Zhen; Pan, Hong; Qiao, S., E-mail: qiaoshan@fudan.edu.cn

    2013-10-30

    To understand the mechanism of ferromagnetism in topological insulator, we studied the structural, magnetic and transport characters of Cr{sub y}(Bi{sub x}Sb{sub 1−x}){sub 2−y}Te{sub 3} single crystals. The Curie temperature T{sub C}, which is determined from magnetization and anomalous Hall effect (AHE) measurements by Arrott plots, is found to be proportional to y{sub Cr}⁎p{sup 1/3}, where p is the hole density. This fact supports a scenario of Ruderman–Kittel–Kasuya–Yoshida (RKKY) interaction with mean-field approximation.

  1. On the importance of direct detection combined limits for spin independent and spin dependent dark matter interactions

    CERN Document Server

    Marcos, Cristina; Robles, Sandra

    2015-01-01

    In this work we show how the inclusion of dark matter (DM) direct detection upper bounds in a theoretically consistent manner can affect the allowed parameter space of a DM model. Traditionally the limits from DM direct detection experiments on the elastic scattering cross section of DM particles as a function of their mass are extracted under simplifying assumptions. Relaxing those assumptions related to the DM particle nature, such as the proton to neutron ratio of the interactions, or the possibility of having similar contributions from the spin independent (SI) and spin dependent (SD) interactions vary significantly the upper limits. Furthermore, it is known that astrophysical and nuclear uncertainties can also affect the upper bounds. To exemplify the impact of including these bounds properly we analyse two well motivated and popular DM scenarios: neutralinos in the NMSSM and a Z' portal with Dirac DM. We show how the allowed parameter space of these models is subject to important variations when one inc...

  2. Totally asymmetric simple exclusion process with a time-dependent boundary: interaction between vehicles and pedestrians at intersections

    CERN Document Server

    Ito, Hidetaka

    2014-01-01

    Interaction between vehicles and pedestrians is seen in many areas such as crosswalks and intersections. In this paper, we study a totally asymmetric simple exclusion process with a bottleneck at a boundary caused by an interaction. Due to the time-dependent effect originating from the speed of pedestrians, the flow of the model varies even if the average hopping probability at the last site is the same. We analyze the phenomenon by using two types of approximations: (2+1)-cluster approximation and isolated rarefaction wave approximation. The approximate results capture intriguing features of the model. Moreover, we discuss the situation where vehicles turn right at the intersection by adding a traffic light at the boundary condition. The result suggests that pedestrian scrambles are valid to eliminate traffic congestion in the right turn lane.

  3. Effect of interacting second- and third-order stimulus-dependent correlations on population-coding asymmetries

    Science.gov (United States)

    Montangie, Lisandro; Montani, Fernando

    2016-10-01

    Spike correlations among neurons are widely encountered in the brain. Although models accounting for pairwise interactions have proved able to capture some of the most important features of population activity at the level of the retina, the evidence shows that pairwise neuronal correlation analysis does not resolve cooperative population dynamics by itself. By means of a series expansion for short time scales of the mutual information conveyed by a population of neurons, the information transmission can be broken down into firing rate and correlational components. In a proposed extension of this framework, we investigate the information components considering both second- and higher-order correlations. We show that the existence of a mixed stimulus-dependent correlation term defines a new scenario for the interplay between pairwise and higher-than-pairwise interactions in noise and signal correlations that would lead either to redundancy or synergy in the information-theoretic sense.

  4. A novel twist on molecular interactions between thioredoxin and nicotinamide adenine dinucleotide phosphate-dependent thioredoxin reductase

    DEFF Research Database (Denmark)

    Kirkensgaard, Kristine Groth; Hägglund, Per; Shahpiri, Azar;

    2013-01-01

    dinucleotide (FAD)-binding domain of HvNTR2 to strongly affect the interaction with Trx. In particular, Trp42 and Met43 play key roles for recognition of the endogenous HvTrxh2. Trx from Arabidopsis thaliana is also efficiently recycled by HvNTR2 but turnover in this case appears to be less dependent...... on these two residues, suggesting a distinct mode for NTR:Trx recognition. Comparison between the HvNTR2:HvTrxh2 model and the crystal structure of the Escherichia coli NTR:Trx complex reveals major differences in interactions involving the FAD- and NADPH-binding domains as supported by our experiments...

  5. Hydrologic and biologic influences on stream network nutrient concentrations: Interactions of hydrologic turnover and concentration-dependent nutrient uptake

    Science.gov (United States)

    Mallard, John; McGlynn, Brian; Covino, Tim

    2016-04-01

    Stream networks lie in a crucial landscape position between terrestrial ecosystems and downstream water bodies. As such, whether inferring terrestrial watershed processes from watershed outlet nutrient signals or predicting the effect of observed terrestrial processes on stream nutrient signals, it is requisite to understand how stream networks can modulate terrestrial nutrient inputs. To date integrated understanding and modeling of physical and biological influences on nutrient concentrations at the stream network scale have been limited. However, watershed scale groundwater - surface water exchange (hydrologic turnover), concentration-variable biological uptake, and the interaction between the two can strongly modify stream water nutrient concentrations. Stream water and associated nutrients are lost to and replaced from groundwater with distinct nutrient concentrations while in-stream nutrients can also be retained by biological processes at rates that vary with concentration. We developed an empirically based network scale model to simulate the interaction between hydrologic turnover and concentration-dependent nutrient uptake across stream networks. Exchange and uptake parameters were measured using conservative and nutrient tracer addition experiments in the Bull Trout Watershed, central Idaho. We found that the interaction of hydrologic turnover and concentration-dependent uptake combined to modify and subsequently stabilize in-stream concentrations, with specific concentrations dependent on the magnitude of hydrologic turnover, groundwater concentrations, and the shape of nutrient uptake kinetic curves. We additionally found that by varying these physical and biological parameters within measured ranges we were able to generate a spectrum of stream network concentration distributions representing a continuum of shifting magnitudes of physical and biological influences on in-stream concentrations. These findings elucidate the important and variable role of

  6. Redox-Dependent Conformational Dynamics of Decameric 2-Cysteine Peroxiredoxin and its Interaction with Cyclophilin 20-3.

    Science.gov (United States)

    Liebthal, Michael; Strüve, Marcel; Li, Xin; Hertle, Yvonne; Maynard, Daniel; Hellweg, Thomas; Viehhauser, Andrea; Dietz, Karl-Josef

    2016-07-01

    2-Cysteine peroxiredoxins (2-CysPrxs) switch between functions as a thiol peroxidase, chaperone, an interaction partner and possibly a proximity-based oxidase in a redox-dependent manner. In photosynthetic eukaryotes, 2-CysPrx localizes to the plastid, functions in the context of photosynthesis and enables an ascorbate peroxidase-independent water-water cycle for detoxifying H2O2 The high degree of evolutionary conservation of 2-CysPrx suggests that the switching is an essential characteristic and needed to transduce redox information to downstream pathways and regulation. The study aimed at exploring the dissociation behavior of 2-CysPrx and its interactions with cyclophilin depending on bulk phase conditions. Isothermal titration microcalorimetry (ITC), dynamic light scattering and size exclusion chromatography (SEC) proved the previously suggested model that reduced 2-CysPrx below a critical transition concentration (CTC) exists in its dimeric state, and above the CTC adopts the decameric state. The presence of cyclophilin 20-3 (Cyp20-3) affected the CTC of a 2-CysPrx decamer suggesting interaction which was further quantified by direct titration of 2-CysPrx with Cyp20-3, and in overlays. Finally catalytic inactivation assays showed the higher catalytic efficiency of 2-CysPrx at pH 8 compared with pH 7.2, but also revealed increased inactivation by hyperoxidation at pH 8. Interestingly, calculation of the average turnover number until inactivation gave rather similar values of 243 and 268 catalytic cycles at pH 8 and pH 7.2, respectively. These quantitative data support a model where 2-CysPrx and Cyp20-3, by interaction, form a redox-sensitive regulatory module in the chloroplast which is under control of the photosynthesis-linked stromal pH value, the redox state and additional stromal protein factor(s).

  7. Charge-dependent non-bonded interaction methods for use in quantum mechanical modeling of condensed phase reactions

    Science.gov (United States)

    Kuechler, Erich R.

    Molecular modeling and computer simulation techniques can provide detailed insight into biochemical phenomena. This dissertation describes the development, implementation and parameterization of two methods for the accurate modeling of chemical reactions in aqueous environments, with a concerted scientific effort towards the inclusion of charge-dependent non-bonded non-electrostatic interactions into currently used computational frameworks. The first of these models, QXD, modifies interactions in a hybrid quantum mechanical/molecular (QM/MM) mechanical framework to overcome the current limitations of 'atom typing' QM atoms; an inaccurate and non-intuitive practice for chemically active species as these static atom types are dictated by the local bonding and electrostatic environment of the atoms they represent, which will change over the course of the simulation. The efficacy QXD model is demonstrated using a specific reaction parameterization (SRP) of the Austin Model 1 (AM1) Hamiltonian by simultaneously capturing the reaction barrier for chloride ion attack on methylchloride in solution and the solvation free energies of a series of compounds including the reagents of the reaction. The second, VRSCOSMO, is an implicit solvation model for use with the DFTB3/3OB Hamiltonian for biochemical reactions; allowing for accurate modeling of ionic compound solvation properties while overcoming the discontinuous nature of conventional PCM models when chemical reaction coordinates. The VRSCOSMO model is shown to accurately model the solvation properties of over 200 chemical compounds while also providing smooth, continuous reaction surfaces for a series of biologically motivated phosphoryl transesterification reactions. Both of these methods incorporate charge-dependent behavior into the non-bonded interactions variationally, allowing the 'size' of atoms to change in meaningful ways with respect to changes in local charge state, as to provide an accurate, predictive and

  8. Spin-dependent electron-phonon interaction in SmFeAsO by low-temperature Raman spectroscopy.

    Science.gov (United States)

    Zhang, L; Guan, P F; Feng, D L; Chen, X H; Xie, S S; Chen, M W

    2010-11-03

    The interplay between spin dynamics and lattice vibration has been suggested as an important part of the puzzle of high-temperature superconductivity. Here, we report the strong interaction between spin fluctuation and phonon in SmFeAsO, a parent compound of the iron arsenide family of superconductors, revealed by low-temperature Raman spectroscopy. Anomalous zone-boundary-phonon Raman scattering from spin superstructure was observed at temperatures below the antiferromagnetic ordering point, which offers compelling evidence on spin-dependent electron-phonon coupling in pnictides.

  9. Remarkable Dependence of the Final Charge Separation Efficiency on the Donor-Acceptor Interaction in Photoinduced Electron Transfer.

    Science.gov (United States)

    Higashino, Tomohiro; Yamada, Tomoki; Yamamoto, Masanori; Furube, Akihiro; Tkachenko, Nikolai V; Miura, Taku; Kobori, Yasuhiro; Jono, Ryota; Yamashita, Koichi; Imahori, Hiroshi

    2016-01-11

    The unprecedented dependence of final charge separation efficiency as a function of donor-acceptor interaction in covalently-linked molecules with a rectilinear rigid oligo-p-xylene bridge has been observed. Optimization of the donor-acceptor electronic coupling remarkably inhibits the undesirable rapid decay of the singlet charge-separated state to the ground state, yielding the final long-lived, triplet charge-separated state with circa 100% efficiency. This finding is extremely useful for the rational design of artificial photosynthesis and organic photovoltaic cells toward efficient solar energy conversion.

  10. Benchmarks for electronically excited states: Time-dependent density functional theory and density functional theory based multireference configuration interaction

    DEFF Research Database (Denmark)

    Silva-Junior, Mario R.; Schreiber, Marko; Sauer, Stephan P. A.;

    2008-01-01

    Time-dependent density functional theory (TD-DFT) and DFT-based multireference configuration interaction (DFT/MRCI) calculations are reported for a recently proposed benchmark set of 28 medium-sized organic molecules. Vertical excitation energies, oscillator strengths, and excited-state dipole...... moments are computed using the same geometries (MP2/6-31G*) and basis set (TZVP) as in our previous ab initio benchmark study on electronically excited states. The results from TD-DFT (with the functionals BP86, B3LYP, and BHLYP) and from DFT/MRCI are compared against the previous high-level ab initio...

  11. Laser-induced electron dynamics including photoionization: A heuristic model within time-dependent configuration interaction theory.

    Science.gov (United States)

    Klinkusch, Stefan; Saalfrank, Peter; Klamroth, Tillmann

    2009-09-21

    We report simulations of laser-pulse driven many-electron dynamics by means of a simple, heuristic extension of the time-dependent configuration interaction singles (TD-CIS) approach. The extension allows for the treatment of ionizing states as nonstationary states with a finite, energy-dependent lifetime to account for above-threshold ionization losses in laser-driven many-electron dynamics. The extended TD-CIS method is applied to the following specific examples: (i) state-to-state transitions in the LiCN molecule which correspond to intramolecular charge transfer, (ii) creation of electronic wave packets in LiCN including wave packet analysis by pump-probe spectroscopy, and, finally, (iii) the effect of ionization on the dynamic polarizability of H(2) when calculated nonperturbatively by TD-CIS.

  12. Patterns formations in a diffusive ratio-dependent predator-prey model of interacting populations

    Science.gov (United States)

    Camara, B. I.; Haque, M.; Mokrani, H.

    2016-11-01

    The present investigation deals with the analysis of the spatial pattern formation of a diffusive predator-prey system with ratio-dependent functional response involving the influence of intra-species competition among predators within two-dimensional space. The appropriate condition of Turing instability around the interior equilibrium point of the present model has been determined. The emergence of complex patterns in the diffusive predator-prey model is illustrated through numerical simulations. These results are based on the existence of bifurcations of higher codimension such as Turing-Hopf, Turing-Saddle-node, Turing-Transcritical bifurcation, and the codimension- 3 ​Turing-Takens-Bogdanov bifurcation. The paper concludes with discussions of our results in ecology.

  13. Boundary-Dependent Chaotic Regions for a Bose-Einstein Condensate Interacting with Laser Field

    Institute of Scientific and Technical Information of China (English)

    ZHU Qian-Quan; HAI Wen-Hua; DENG Hai-Ming

    2007-01-01

    Spatial chaos of a Bose-Einstein condensate perturbed by a weak laser standing wave and a weak laser S pulse is studied. By using the perturbed chaotic solution we investigate the new type of Melnikov chaotic regions, which depend on an integration constant CQ determined by the boundary conditions. It is shown that when the |c0| values are small, the chaotic region corresponds to small values of laser wave vector k, and the chaotic region for the larger k values is related to the large |c0| values. The result is confirmed numerically by finding the chaotic and regular orbits on the Poincaré section for the two different parameter regions. Thus, for a fixed c0 the adjustment of k from a small value to large value can transform the chaotic region into the regular one or on the contrary, which suggests a feasible method for eliminating or generating Melnikov chaos.

  14. The $Q^{2}$ Dependence of Dijet Cross Sections in $\\gamma p$ Interactions at HERA

    CERN Document Server

    Breitweg, J; Derrick, Malcolm; Krakauer, D A; Magill, S; Musgrave, B; Pellegrino, A; Repond, J; Stanek, R; Yoshida, R; Mattingly, M C K; Abbiendi, G; Anselmo, F; Antonioli, P; Bari, G; Basile, M; Bellagamba, L; Boscherini, D; Bruni, A; Bruni, G; Cara Romeo, G; Castellini, G; Cifarelli, Luisa; Cindolo, F; Contin, A; Coppola, N; Corradi, M; De Pasquale, S; Giusti, P; Iacobucci, G; Laurenti, G; Levi, G; Margotti, A; Massam, Thomas; Nania, R; Palmonari, F; Pesci, A; Polini, A; Sartorelli, G; Zamora-Garcia, Yu E; Zichichi, A; Amelung, C; Bornheim, A; Brock, I; Coboken, K; Crittenden, James Arthur; Deffner, R; Hartmann, H; Heinloth, K; Hilger, E; Irrgang, P; Jakob, H P; Kappes, A; Katz, U F; Kerger, R; Paul, E; Schnurbusch, H; Stifutkin, A; Tandler, J; Voss, K C; Weber, A; Wieber, H; Bailey, D S; Barret, O; Brook, N H; Foster, B; Heath, G P; Heath, H F; McFall, J D; Piccioni, D; Rodrigues, E; Scott, J; Tapper, R J; Capua, M; Mastroberardino, A; Schioppa, M; Susinno, G; Jeoung, H Y; Kim, J Y; Lee, J H; Lim, I T; Ma, K J; Pac, M Y; Caldwell, A; Liu, W; Liu, X; Mellado, B; Paganis, S; Sacchi, R; Sampson, S; Sciulli, F; Chwastowski, J; Eskreys, Andrzej; Figiel, J; Klimek, K H; Olkiewicz, K; Piotrzkowski, K; Przybycien, M B; Stopa, P; Zawiejski, L; Adamczyk, L; Bednarek, B; Jelen, K; Kisielewska, D; Kowal, A M; Kowalski, T; Rulikowska-Zarebska, E; Suszycki, L; Szuba, D; Kotanski, Andrzej; Bauerdick, L A T; Behrens, U; Bienlein, J K; Burgard, C; Desler, K; Drews, G; Fox-Murphy, A; Fricke, U; Göbel, F; Göttlicher, P; Graciani, R; Haas, T; Hain, W; Hartner, G F; Hasell, D; Hebbel, K; Johnson, K F; Kasemann, M; Koch, W; Kötz, U; Kowalski, H; Lindemann, L; Löhr, B; Martínez, M; Milite, M; Monteiro, T; Moritz, M; Notz, D; Pelucchi, F; Petrucci, M C; Rohde, M; Saull, P R B; Savin, A A; Schneekloth, U; Selonke, F; Sievers, M; Stonjek, S; Tassi, E; Wolf, G; Wollmer, U; Youngman, C; Zeuner, W; Coldewey, C; Grabosch, H J; López-Duran-Viani, A; Meyer, A; Schlenstedt, S; Straub, P B; Barbagli, G; Gallo, E; Pelfer, P G; Maccarrone, G D; Votano, L; Bamberger, Andreas; Benen, A; Eisenhardt, S; Markun, P; Raach, H; Wölfle, S; Bussey, Peter J; Doyle, A T; Lee, S W; MacDonald, N; McCance, G J; Saxon, D H; Sinclair, L E; Skillicorn, Ian O; Waugh, R; Bohnet, I; Gendner, N; Holm, U; Meyer-Larsen, A; Salehi, H; Wick, K; Dannheim, D; Garfagnini, A; Gialas, I; Gladilin, L K; Kcira, D; Klanner, Robert; Lohrmann, E; Poelz, G; Zetsche, F; Goncalo, R; Long, K R; Miller, D B; Tapper, A D; Walker, R; Mallik, U; Cloth, P; Filges, D; Ishii, T; Kuze, M; Nagano, K; Tokushuku, K; Yamada, S; Yamazaki, Y; Ahn, S H; An Shiz Hong; Hong, S J; Lee, S B; Nam, S W; Park, S K; Lim, H; Park, I H; Son, D; Barreiro, F; García, G; Glasman, C; González, O; Labarga, L; Del Peso, J; Redondo, I; Terron, J; Barbi, M S; Corriveau, F; Hanna, D S; Ochs, A; Padhi, S; Riveline, M; Stairs, D G; Wing, M; Tsurugai, T; Bashkirov, V; Dolgoshein, B A; Dementev, R K; Ermolov, P F; Golubkov, Yu A; Katkov, I I; Khein, L A; Korotkova, N A; Korzhavina, I A; Kuzmin, V A; Lukina, O Yu; Proskuryakov, A S; Shcheglova, L M; Solomin, A N; Vlasov, N N; Zotkin, S A; Bokel, C; Botje, M; Brümmer, N; Engelen, J; Grijpink, S; Koffeman, E; Kooijman, P M; Schagen, S; Van Sighem, A; Tiecke, H G; Tuning, N; Velthuis, J J; Vossebeld, Joost Herman; Wiggers, L; De Wolf, E; Bylsma, B; Durkin, L S; Gilmore, J; Ginsburg, C M; Kim, C L; Ling, T Y; Nylander, P; Boogert, S; Cooper-Sarkar, A M; Devenish, R C E; Grosse-Knetter, J; Matsushita, T; Ruske, O; Sutton, M R; Walczak, R; Bertolin, A; Brugnera, R; Carlin, R; Dal Corso, F; Dosselli, U; Dusini, S; Limentani, S; Morandin, M; Posocco, M; Stanco, L; Stroili, R; Voci, C; Iannotti, L; Oh, B Y; Okrasinski, J R; Toothacker, W S; Whitmore, J J; Iga, Y; D'Agostini, Giulio; Marini, G; Nigro, A; Cormack, C; Hart, J C; McCubbin, N A; Shah, T P; Epperson, D E; Heusch, C A; Sadrozinski, H F W; Seiden, A; Wichmann, R; Williams, D C; Pavel, N; Abramowicz, H; Dagan, S; Kananov, S; Kreisel, A; Levy, A; Abe, T; Fusayasu, T; Umemori, K; Yamashita, T; Hamatsu, R; Hirose, T; Inuzuka, M; Kitamura, S; Nishimura, T; Arneodo, M; Cartiglia, N; Cirio, R; Costa, M; Ferrero, M I; Maselli, S; Monaco, V; Peroni, C; Ruspa, M; Solano, A; Staiano, A; Dardo, M; Bailey, D C; Fagerstroem, C P; Galea, R; Koop, T; Levman, G M; Martin, J F; Orr, R S; Polenz, S; Sabetfakhri, A; Simmons, D; Butterworth, J M; Catterall, C D; Hayes, M E; Heaphy, E A; Jones, T W; Lane, J B; West, B J; Ciborowski, J; Ciesielski, R; Grzelak, G; Nowak, R J; Pawlak, J M; Pawlak, R; Smalska, B; Tymieniecka, T; Wróblewski, A K; Zakrzewski, J A; Adamus, M; Gadaj, T; Deppe, O; Eisenberg, Y; Hochman, D; Karshon, U; Badgett, W F; Chapin, D; Cross, R; Foudas, C; Mattingly, S E K; Reeder, D D; Smith, W H; Vaiciulis, A W; Wildschek, T; Wodarczyk, M; Deshpande, A A; Dhawan, S K; Hughes, V W; Bhadra, S; Cole, J E; Frisken, W R; Hall-Wilton, R; Khakzad, M; Menary, S R; Schmidke, W B

    2000-01-01

    The dependence of the photon structure on the photon virtuality, Q^2, isstudied by measuring the reaction e^+p\\to e^+ + {\\rm jet} + {\\rm jet} + {\\rm X}at photon-proton centre-of-mass energies 134 5.5 GeV in the final state.The dijet cross section has been measured as a function of the fractionalmomentum of the photon participating in the hard process, x_gamma. The ratio ofthe dijet cross section with x_gamma 0.75decreases as Q^2 increases. The data are compared with the predictions of NLOpQCD and leading-order Monte Carlo programs using various parton distributionfunctions of the photon. The measurements can be interpreted in terms of aresolved photon component that falls with Q^2 but remains present at values ofQ^2 up to 4.5 GeV^2. However, none of the models considered gives a gooddescription of the data.

  15. Decellularized matrix from tumorigenic human mesenchymal stem cells promotes neovascularization with galectin-1 dependent endothelial interaction.

    Directory of Open Access Journals (Sweden)

    Jorge S Burns

    Full Text Available BACKGROUND: Acquisition of a blood supply is fundamental for extensive tumor growth. We recently described vascular heterogeneity in tumours derived from cell clones of a human mesenchymal stem cell (hMSC strain (hMSC-TERT20 immortalized by retroviral vector mediated human telomerase (hTERT gene expression. Histological analysis showed that cells of the most vascularized tumorigenic clone, -BD11 had a pericyte-like alpha smooth muscle actin (ASMA+ and CD146+ positive phenotype. Upon serum withdrawal in culture, -BD11 cells formed cord-like structures mimicking capillary morphogenesis. In contrast, cells of the poorly tumorigenic clone, -BC8 did not stain for ASMA, tumours were less vascularized and serum withdrawal in culture led to cell death. By exploring the heterogeneity in hMSC-TERT20 clones we aimed to understand molecular mechanisms by which mesenchymal stem cells may promote neovascularization. METHODOLOGY/PRINCIPAL FINDINGS: Quantitative qRT-PCR analysis revealed similar mRNA levels for genes encoding the angiogenic cytokines VEGF and Angiopoietin-1 in both clones. However, clone-BD11 produced a denser extracellular matrix that supported stable ex vivo capillary morphogenesis of human endothelial cells and promoted in vivo neovascularization. Proteomic characterization of the -BD11 decellularized matrix identified 50 extracellular angiogenic proteins, including galectin-1. siRNA knock down of galectin-1 expression abrogated the ex vivo interaction between decellularized -BD11 matrix and endothelial cells. More stable shRNA knock down of galectin-1 expression did not prevent -BD11 tumorigenesis, but greatly reduced endothelial migration into -BD11 cell xenografts. CONCLUSIONS: Decellularized hMSC matrix had significant angiogenic potential with at least 50 angiogenic cell surface and extracellular proteins, implicated in attracting endothelial cells, their adhesion and activation to form tubular structures. hMSC -BD11 surface galectin-1

  16. Quantifying size-dependent interactions between fluorescently labeled polystyrene nanoparticles and mammalian cells

    Science.gov (United States)

    2012-01-01

    Background Nanoparticles (NPs) are currently used in a wide variety of fields such as technology, medicine and industry. Due to the novelty of these applications and to ensure their success, a precise characterization of the interactions between NPs and cells is essential. Findings The current study explores the uptake of polystyrene NPs by 1321N1 human astrocytoma and A549 human lung carcinoma cell lines. In this work we show for the first time a comparison of the uptake rates of fluorescently labeled carboxylated polystyrene (PS) NPs of different sizes (20, 40 and 100 nm) in two different cell types, keeping the number of NPs per unit volume constant for all sizes. We propose a reliable methodology to control the dose of fluorescently labeled NPs, by counting individual NPs using automated particle detection from 3D confocal microscopy images. The possibility of detecting individual NPs also allowed us to calculate the size of each nanoparticle and compare the fluorescence of single NPs across different sizes, thereby providing a robust platform for normalization of NP internalization experiments as measured by flow cytometry. Conclusions Our findings show that 40 nm NPs are internalized faster than 20 nm or 100 nm particles in both cell lines studied, suggesting that there is a privileged size gap in which the internalization of NPs is higher. PMID:23006133

  17. Quantifying size-dependent interactions between fluorescently labeled polystyrene nanoparticles and mammalian cells

    Directory of Open Access Journals (Sweden)

    Varela Juan A

    2012-09-01

    Full Text Available Abstract Background Nanoparticles (NPs are currently used in a wide variety of fields such as technology, medicine and industry. Due to the novelty of these applications and to ensure their success, a precise characterization of the interactions between NPs and cells is essential. Findings The current study explores the uptake of polystyrene NPs by 1321N1 human astrocytoma and A549 human lung carcinoma cell lines. In this work we show for the first time a comparison of the uptake rates of fluorescently labeled carboxylated polystyrene (PS NPs of different sizes (20, 40 and 100 nm in two different cell types, keeping the number of NPs per unit volume constant for all sizes. We propose a reliable methodology to control the dose of fluorescently labeled NPs, by counting individual NPs using automated particle detection from 3D confocal microscopy images. The possibility of detecting individual NPs also allowed us to calculate the size of each nanoparticle and compare the fluorescence of single NPs across different sizes, thereby providing a robust platform for normalization of NP internalization experiments as measured by flow cytometry. Conclusions Our findings show that 40 nm NPs are internalized faster than 20 nm or 100 nm particles in both cell lines studied, suggesting that there is a privileged size gap in which the internalization of NPs is higher.

  18. Cellulose-pectin composite hydrogels: Intermolecular interactions and material properties depend on order of assembly.

    Science.gov (United States)

    Lopez-Sanchez, Patricia; Martinez-Sanz, Marta; Bonilla, Mauricio R; Wang, Dongjie; Gilbert, Elliot P; Stokes, Jason R; Gidley, Michael J

    2017-04-15

    Plant cell walls have a unique combination of strength and flexibility however, further investigations are required to understand how those properties arise from the assembly of the relevant biopolymers. Recent studies indicate that Ca(2+)-pectates can act as load-bearing components in cell walls. To investigate this proposed role of pectins, bioinspired wall models were synthesised based on bacterial cellulose containing pectin-calcium gels by varying the order of assembly of cellulose/pectin networks, pectin degree of methylesterification and calcium concentration. Hydrogels in which pectin-calcium assembly occurred prior to cellulose synthesis showed evidence for direct cellulose/pectin interactions from small-angle scattering (SAXS and SANS), had the densest networks and the lowest normal stress. The strength of the pectin-calcium gel affected cellulose structure, crystallinity and material properties. The results highlight the importance of the order of assembly on the properties of cellulose composite networks and support the role of pectin in the mechanics of cell walls. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Kinetic mixing and symmetry breaking dependent interactions of the dark photon

    Directory of Open Access Journals (Sweden)

    Biswajoy Brahmachari

    2014-10-01

    Full Text Available We examine spontaneous symmetry breaking of a renormalisable U(1×U(1 gauge theory coupled to fermions when kinetic mixing is present. We do not assume that the kinetic mixing parameter is small. A rotation plus scaling is used to remove the mixing and put the gauge kinetic terms in the canonical form. Fermion currents are also rotated in a non-orthogonal way by this basis transformation. Through suitable redefinitions the interaction is cast into a diagonal form. This framework, where mixing is absent, is used for subsequent analysis. The symmetry breaking determines the fermionic current which couples to the massless gauge boson. The strength of this coupling as well as the couplings of the massive gauge boson are extracted. This formulation is used to consider a gauged model for dark matter by identifying the massless gauge boson with the photon and the massive state to its dark counterpart. Matching the coupling of the residual symmetry with that of the photon sets a lower bound on the kinetic mixing parameter. We present analytical formulae of the couplings of the dark photon in this model and indicate some physics consequences.

  20. KIR/HLA interactions negatively affect rituximab- but not GA101 (obinutuzumab)-induced antibody-dependent cellular cytotoxicity.

    Science.gov (United States)

    Terszowski, Grzegorz; Klein, Christian; Stern, Martin

    2014-06-15

    Ab-dependent cellular cytotoxicity (ADCC) mediated by NK cells is regulated by inhibitory killer cell Ig-like receptors (KIRs), which interact with target cell HLA class I. We analyzed how KIR/HLA interactions influence ADCC induced by rituximab and by GA101, a novel type II CD20 Ab glycoengineered for increased FcgRIII binding and ADCC capacity. We found that KIR/HLA interactions strongly and selectively inhibit rituximab-induced in vitro ADCC toward target cells expressing cognate HLA KIR ligands. NK cells of donors carrying all three ligands to inhibitory KIR showed weak activation and target cell depletion capacity when incubated with rituximab and KIR-ligand matched target B cells. In contrast, NK cells from individuals missing one or more KIR ligands activated more strongly and depleted KIR ligand-matched target B cells more efficiently in the presence of rituximab. NK cells expressing a KIR for which the ligand was absent were the main effectors of ADCC in these donors. Notably, the influence of KIR/HLA interactions on NK cell activation was synergistic with the effect of the V158F FCGR3A single nucleotide polymorphism. In contrast, GA101 induced activation of NK cells irrespective of inhibitory KIR expression, and efficiency of target cell depletion was not negatively affected by KIR/HLA interactions. These data show that modification of the Fc fragment to enhance ADCC can be an effective strategy to augment the efficacy of therapeutic mAbs by recruiting NK cells irrespective of their inhibitory KIR expression.

  1. Phosphorylation-dependent protein interactions at the spindle midzone mediate cell cycle regulation of spindle elongation.

    Science.gov (United States)

    Khmelinskii, Anton; Roostalu, Johanna; Roque, Helio; Antony, Claude; Schiebel, Elmar

    2009-08-01

    The metaphase-to-anaphase transition is one of the most dramatic and highly regulated steps in cell division. At anaphase onset the protease separase dissolves sister chromatid cohesion. Simultaneously, the mitotic spindle elongates as interpolar microtubules (iMTs) slide apart at the spindle midzone, ensuring chromosome segregation. However, it remains unclear how spindle elongation is coordinated with cell cycle progression. Here we demonstrate that phosphorylation of the midzone organizer Ase1 controls localization and function of Cin8, a kinesin-5 that slides iMTs relative to each other. Phosphorylation of Ase1 by Cdk1 (cyclin-dependent kinase) inhibits Cin8 binding to iMTs, preventing bending and collapse of the metaphase spindle. In anaphase Ase1 dephosphorylation by the separase-activated phosphatase Cdc14 is necessary and sufficient for Cin8 recruitment to the midzone, where it drives spindle elongation. Our results reveal that sliding forces at the midzone are activated by separase and explain how spindle elongation is triggered with anaphase entry.

  2. Tri-trophic interactions affect density dependence of seed fate in a tropical forest palm.

    Science.gov (United States)

    Visser, Marco D; Muller-Landau, Helene C; Wright, S Joseph; Rutten, Gemma; Jansen, Patrick A

    2011-11-01

    Natural enemies, especially host-specific enemies, are hypothesised to facilitate the coexistence of plant species by disproportionately inflicting more damage at increasing host abundance. However, few studies have assessed such Janzen-Connell mechanisms on a scale relevant for coexistence and no study has evaluated potential top-down influences on the specialized pests. We quantified seed predation by specialist invertebrates and generalist vertebrates, as well as larval predation on these invertebrates, for the Neotropical palm Attalea butyracea across ten 4-ha plots spanning 20-fold variation in palm density. As palm density increased, seed attack by bruchid beetles increased, whereas seed predation by rodents held constant. But because rodent predation on bruchid larvae increased disproportionately with increasing palm density, bruchid emergence rates and total seed predation by rodents and bruchids combined were both density-independent. Our results demonstrate that top-down effects can limit the potential of host-specific insects to induce negative-density dependence in plant populations.

  3. Protein interacting with C kinase 1 (PICK1) reduces reinsertion rates of interaction partners sorted to Rab11-dependent slow recycling pathway

    DEFF Research Database (Denmark)

    Madsen, Kenneth Lindegaard; Thorsen, Thor Seneca; Rahbek-Clemmensen, Troels;

    2012-01-01

    of PICK1 co-clusters in Rab11-positive compartments. Furthermore, PICK1 inhibited Rab11-mediated recycling of the receptor in a BAR and PDZ domain-dependent manner. In contrast, transfer of the DAT C terminus to the δ-opioid receptor, which sorts to degradation, did not result in PICK1 co-clusters or any...... primarily sorts to degradation upon internalization, did not form perinuclear clusters with PICK1, and PICK1 did not affect DAT internalization/recycling. However, transfer of the PICK1-binding DAT C terminus to the β(2)-adrenergic receptor, which sorts to recycling upon internalization, led to formation...... change in internalization/recycling. Further support for a role of PICK1 determined by its PDZ cargo was obtained for the PICK1 interaction partner prolactin-releasing peptide receptor (GPR10). GPR10 co-localized with Rab11 and clustered with PICK1 upon constitutive internalization but co...

  4. Refinement and Pattern Formation in Neural Circuits by the Interaction of Traveling Waves with Spike-Timing Dependent Plasticity

    Science.gov (United States)

    Bennett, James E. M.; Bair, Wyeth

    2015-01-01

    Traveling waves in the developing brain are a prominent source of highly correlated spiking activity that may instruct the refinement of neural circuits. A candidate mechanism for mediating such refinement is spike-timing dependent plasticity (STDP), which translates correlated activity patterns into changes in synaptic strength. To assess the potential of these phenomena to build useful structure in developing neural circuits, we examined the interaction of wave activity with STDP rules in simple, biologically plausible models of spiking neurons. We derive an expression for the synaptic strength dynamics showing that, by mapping the time dependence of STDP into spatial interactions, traveling waves can build periodic synaptic connectivity patterns into feedforward circuits with a broad class of experimentally observed STDP rules. The spatial scale of the connectivity patterns increases with wave speed and STDP time constants. We verify these results with simulations and demonstrate their robustness to likely sources of noise. We show how this pattern formation ability, which is analogous to solutions of reaction-diffusion systems that have been widely applied to biological pattern formation, can be harnessed to instruct the refinement of postsynaptic receptive fields. Our results hold for rich, complex wave patterns in two dimensions and over several orders of magnitude in wave speeds and STDP time constants, and they provide predictions that can be tested under existing experimental paradigms. Our model generalizes across brain areas and STDP rules, allowing broad application to the ubiquitous occurrence of traveling waves and to wave-like activity patterns induced by moving stimuli. PMID:26308406

  5. Grain Size Dependence of Exchange-Coupling Interaction between Magnetically Soft-Hard Grains and Effective Anisotropy

    Institute of Scientific and Technical Information of China (English)

    韩广兵; 高汝伟; 傅爽; 刘汉强; 冯维存; 陈伟

    2004-01-01

    Taking α-Fe and Nd2Fe14B grains as example, the grain size dependence of the exchange-coupling interaction and effective anisotropy and also their variations depending on the ratio of magnetically soft and hard grain sizes, Ds∶ Dh, were investigated. When grain size D>Lex, the grain's anisotropy is the statistic value of the coupled and uncoupled part. The anisotropy constant of uncoupled part is the common value K1 and that of coupled part varies with the distance to the grain surface. The effective anisotropy constant between magnetically soft and hard grains, Keff, can be expressed as the sum of the products of volume fractions for soft and hard grains, respectively, and the corresponding mean anisotropy constants. The calculation results indicate that the exchange-coupling interaction is enhanced with the reduction of grain size, and the effective anisotropy decreases with reducing grain size and increasing ratio of Ds∶ Dh. In order to get high effective anisotropy constant, Keff, in composite magnetically soft-hard grains, the hard grain size should be larger than 30 nm and the soft grain size should be about 10 nm.

  6. Polymer-Ion Interaction Weakens the Strain-Rate Dependence of Extension-Induced Crystallization for Poly(ethylene oxide).

    Science.gov (United States)

    Hu, Tingting; Tian, Nan; Ali, Sarmad; Wang, Zhen; Chang, Jiarui; Huang, Ningdong; Li, Liangbin

    2016-03-01

    The crystallization of poly(ethylene oxide) (PEO)-sodium iodine (NaI) composites is investigated by differential scanning calorimetry (DSC), extensional rheology, and in situ small-angle X-ray scattering (SAXS) with the aim of demonstrating versatile roles played by polymer-ion interactions. In the isothermal quiescent crystallization process, a decrease in the crystal growth rate is observed for PEO-NaI and is attributed to slow chain movement caused by the coordination between cations and polymer. In situ SAXS on extensional flow-induced crystallization (FIC) exhibits enhanced kinetics and orientation for both PEO and PEO-NaI with increasing strain rate. However, an overall weaker strain-rate dependence of FIC is observed for PEO-NaI, which can be interpreted as a synergistic consequence of promoted nucleation under flow and impeded crystal growth by polymer-ion interaction. A possible microscopic mechanism is proposed to account for the experimental observation based on the formation of transient cross-linking points in PEO-NaI and their influence on the entanglement network of polymer under various flow fields. The disclosed strain-rate dependence and various ion effects on the behavior of PEO-salt composites contribute to a comprehensive understanding of polymer-ion solid polyelectrolytes.

  7. Metabolomic linkage reveals functional interaction between glucose-dependent insulinotropic polypeptide and ghrelin in humans.

    Science.gov (United States)

    Rudovich, Natalia N; Nikiforova, Victoria J; Otto, Baerbel; Pivovarova, Olga; Gögebakan, Ozlem; Erban, Alexander; Möhlig, Matthias; Weickert, Martin O; Spranger, Joachim; Tschöp, Matthias H; Willmitzer, Lothar; Nauck, Michael; Pfeiffer, Andreas F H

    2011-10-01

    The gastric peptide ghrelin promotes energy storage, appetite, and food intake. Nutrient intake strongly suppresses circulating ghrelin via molecular mechanisms possibly involving insulin and gastrointestinal hormones. On the basis of the growing evidence that glucose-dependent insulinotropic polypeptide (GIP) is involved in the control of fuel metabolism, we hypothesized that GIP and/or insulin, directly or via changes in plasma metabolites, might affect circulating ghrelin. Fourteen obese subjects were infused with GIP (2.0 pmol·kg(-1)·min(-1)) or placebo in the fasting state during either euglycemic hyperinsulinemic (EC) or hyperglycemic hyperinsulinemic clamps (HC). Apart from analysis of plasma ghrelin and insulin levels, GC-TOF/MS analysis was applied to create a hormone-metabolite network for each experiment. The GIP and insulin effects on circulating ghrelin were analyzed within the framework of those networks. In the HC, ghrelin levels decreased in the absence (19.2% vs. baseline, P = 0.028) as well as in the presence of GIP (33.8%, P = 0.018). Ghrelin levels were significantly lower during HC with GIP than with placebo, despite insulin levels not differing significantly. In the GIP network combining data on GIP-infusion, EC+GIP and HC+GIP experiments, ghrelin was integrated into hormone-metabolite networks through a connection to a group of long-chain fatty acids. In contrast, ghrelin was excluded from the network of experiments without GIP. GIP decreased circulating ghrelin and might have affected the ghrelin system via modification of long-chain fatty acid pools. These observations were independent of insulin and offer potential mechanistic underpinnings for the involvement of GIP in systemic control of energy metabolism.

  8. Interactions of gold nanoparticles with freshwater aquatic macrophytes are size and species dependent.

    Science.gov (United States)

    Glenn, J Brad; White, Sarah A; Klaine, Stephen J

    2012-01-01

    The partitioning of 4- and 18-nm gold nanoparticles (AuNPs) to aquatic macrophytes was investigated in vivo with exposure suspension in well water. Three morphologically distinct aquatic macrophytes were studied. Myriophyllum simulans Orch. and Egeria densa Planch. are submerged aquatic vascular plants, whereas Azolla caroliniana Willd. is a free-floating aquatic fern. Because aquatic plants absorb the majority of their nutrients from the water column, it is logical to hypothesize that they may absorb nanomaterials in suspension, potentially facilitating trophic transfer. Each plant was exposed to two different-sized gold nanospheres at a nominal concentration of 250 µg/L AuNPs for 24 h. Macrophytes were harvested at six time points (1, 3, 6, 12, 18, and 24 h), dried, and then analyzed for gold concentration via inductively coupled plasma-mass spectrometry. Concentrations were normalized to whole-plant dry tissue mass. The present study shows that absorption of AuNPs through root uptake was size and species dependent. Electron microscopy revealed that 4- and 18-nm AuNPs adsorbed to the roots of each species. Root tissue was sectioned, and transmission electron microscopy indicated that 4-nm and 18-nm AuNPs were absorbed by A. caroliniana, whereas only 4-nm AuNPs were absorbed by M. simulans. Egeria densa did not absorb AuNPs of either size. Gold nanoparticles were confirmed in tissue by using energy-dispersive X-ray spectroscopy. Absorption of AuNPs by plants may be a function of the salinity tolerance of each species.

  9. Mg2+-dependent Interactions of ATP with the Cystathionine-β-Synthase (CBS) Domains of a Magnesium Transporter*

    Science.gov (United States)

    Hirata, Yusuke; Funato, Yosuke; Takano, Yu; Miki, Hiroaki

    2014-01-01

    Ancient conserved domain protein/cyclin M (CNNM) family proteins are evolutionarily conserved Mg2+ transporters. However, their biochemical mechanism of action remains unknown. Here, we show the functional importance of the commonly conserved cystathionine-β-synthase (CBS) domains and reveal their unique binding ability to ATP. Deletion mutants of CNNM2 and CNNM4, lacking the CBS domains, are unable to promote Mg2+ efflux. Furthermore, the substitution of one amino acid residue in the CBS domains of CNNM2, which is associated with human hereditary hypomagnesemia, abrogates Mg2+ efflux. Binding analyses reveal that the CBS domains of CNNM2 bind directly to ATP and not AMP in a manner dependent on the presence of Mg2+, which is inhibited in a similar pattern by the disease-associated amino acid substitution. The requirement of Mg2+ for these interactions is a unique feature among CBS domains, which can be explained by the presence of highly electronegative surface potentials around the ATP binding site on CNNM2. These results demonstrate that the CBS domains play essential roles in Mg2+ efflux, probably through interactions with ATP. Interactions with ATP, which mostly forms complexes with Mg2+ in cells, may account for the rapid Mg2+ transport by CNNM family proteins. PMID:24706765

  10. Mg2+-dependent interactions of ATP with the cystathionine-β-synthase (CBS) domains of a magnesium transporter.

    Science.gov (United States)

    Hirata, Yusuke; Funato, Yosuke; Takano, Yu; Miki, Hiroaki

    2014-05-23

    Ancient conserved domain protein/cyclin M (CNNM) family proteins are evolutionarily conserved Mg(2+) transporters. However, their biochemical mechanism of action remains unknown. Here, we show the functional importance of the commonly conserved cystathionine-β-synthase (CBS) domains and reveal their unique binding ability to ATP. Deletion mutants of CNNM2 and CNNM4, lacking the CBS domains, are unable to promote Mg(2+) efflux. Furthermore, the substitution of one amino acid residue in the CBS domains of CNNM2, which is associated with human hereditary hypomagnesemia, abrogates Mg(2+) efflux. Binding analyses reveal that the CBS domains of CNNM2 bind directly to ATP and not AMP in a manner dependent on the presence of Mg(2+), which is inhibited in a similar pattern by the disease-associated amino acid substitution. The requirement of Mg(2+) for these interactions is a unique feature among CBS domains, which can be explained by the presence of highly electronegative surface potentials around the ATP binding site on CNNM2. These results demonstrate that the CBS domains play essential roles in Mg(2+) efflux, probably through interactions with ATP. Interactions with ATP, which mostly forms complexes with Mg(2+) in cells, may account for the rapid Mg(2+) transport by CNNM family proteins. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  11. Pore-Width-Dependent Preferential Interaction of sp2 Carbon Atoms in Cyclohexene with Graphitic Slit Pores by GCMC Simulation

    Directory of Open Access Journals (Sweden)

    Natsuko Kojima

    2011-01-01

    Full Text Available The adsorption of cyclohexene with two sp2 and four sp3 carbon atoms in graphitic slit pores was studied by performing grand canonical Monte Carlo simulation. The molecular arrangement of the cyclohexene on the graphitic carbon wall depends on the pore width. The distribution peak of the sp2 carbon is closer to the pore wall than that of the sp3 carbon except for the pore width of 0.7 nm, even though the Lennard-Jones size of the sp2 carbon is larger than that of the sp3 carbon. Thus, the difference in the interactions of the sp2 and sp3 carbon atoms of cyclohexene with the carbon pore walls is clearly observed in this study. The preferential interaction of sp2 carbon gives rise to a slight tilting of the cyclohexene molecule against the graphitic wall. This is suggestive of a π-π interaction between the sp2 carbon in the cyclohexene molecule and graphitic carbon.

  12. Experience-Dependent Plasticity in Accessory Olfactory Bulb Interneurons following Male-Male Social Interaction.

    Science.gov (United States)

    Cansler, Hillary L; Maksimova, Marina A; Meeks, Julian P

    2017-07-26

    Chemosensory information processing in the mouse accessory olfactory system guides the expression of social behavior. After salient chemosensory encounters, the accessory olfactory bulb (AOB) experiences changes in the balance of excitation and inhibition at reciprocal synapses between mitral cells (MCs) and local interneurons. The mechanisms underlying these changes remain controversial. Moreover, it remains unclear whether MC-interneuron plasticity is unique to specific behaviors, such as mating, or whether it is a more general feature of the AOB circuit. Here, we describe targeted electrophysiological studies of AOB inhibitory internal granule cells (IGCs), many of which upregulate the immediate-early gene Arc after male-male social experience. Following the resident-intruder paradigm, Arc-expressing IGCs in acute AOB slices from resident males displayed stronger excitation than nonexpressing neighbors when sensory inputs were stimulated. The increased excitability of Arc-expressing IGCs was not correlated with changes in the strength or number of excitatory synapses with MCs but was instead associated with increased intrinsic excitability and decreased HCN channel-mediated IH currents. Consistent with increased inhibition by IGCs, MCs responded to sensory input stimulation with decreased depolarization and spiking following resident-intruder encounters. These results reveal that nonmating behaviors drive AOB inhibitory plasticity and indicate that increased MC inhibition involves intrinsic excitability changes in Arc-expressing interneurons.SIGNIFICANCE STATEMENT The accessory olfactory bulb (AOB) is a site of experience-dependent plasticity between excitatory mitral cells (MCs) and inhibitory internal granule cells (IGCs), but the physiological mechanisms and behavioral conditions driving this plasticity remain unclear. Here, we report studies of AOB neuronal plasticity following male-male social chemosensory encounters. We show that the plasticity

  13. Testing for spin dependence in the final state interaction of the reaction vector dp → {sup 3}Heη

    Energy Technology Data Exchange (ETDEWEB)

    Papenbrock, Michael; Khoukaz, Alfons; Fritzsch, Christopher; Goslawski, Paul; Mielke, Malte; Schroeer, Daniel; Taeschner, Alexander [Institut fuer Kernphysik, Westfaelische Wilhelms-Universitaet, 48149 Muenster (Germany); Wilkin, Colin [Physics and Astronomy Department, UCL, London WC1E 6BT (United Kingdom); Collaboration: ANKE-Collaboration

    2014-07-01

    The dp → {sup 3}Heη reaction is known for the unexpected energy dependence of its total cross section, which rises rapidly to its plateau value within the first 1 MeV of excess energy Q. This behaviour has been ascribed to a strong final state interaction and may indicate a quasi-bound η {sup 3}He state. In order to investigate the possibility of spin-dependent contributions to the total cross section, the deuteron tensor analysing power t{sub 20} has been measured in an excess energy range from Q=0 MeV up to above Q 10 MeV at the COSY-ANKE spectrometer. This allows one to compare the magnitudes of the contributions from the two spin configurations in the entrance channel with the strong variation seen in the average production amplitude. Furthermore, a weak angular dependence of t{sub 20} was also extracted and this provides insight into the structure of the production amplitude close to threshold. Final results are presented and discussed.

  14. pH-dependent drug-drug interactions for weak base drugs: potential implications for new drug development.

    Science.gov (United States)

    Zhang, L; Wu, F; Lee, S C; Zhao, H; Zhang, L

    2014-08-01

    Absorption of an orally administered drug with pH-dependent solubility may be altered when it is coadministered with a gastric acid-reducing agent (ARA). Assessing a drug's potential for pH-dependent drug-drug interactions (DDIs), considering study design elements for such DDI studies, and interpreting and communicating study results in the drug labeling to guide drug dosing are important for drug development. We collected pertinent information related to new molecular entities approved from January 2003 to May 2013 by the US Food and Drug Administration for which clinical DDI studies with ARAs were performed. On the basis of assessments of data on pH solubility and in vivo DDIs with ARAs, we proposed a conceptual framework for assessing the need for clinical pH-dependent DDI studies for weak base drugs (WBDs). Important study design considerations include selection of ARAs and timing of dosing of an ARA relative to the WBD in a DDI study. Labeling implications for drugs having DDIs with ARAs are also illustrated.

  15. Inhibition of rat hippocampal excitability by the plant alkaloid 3-acetylaconitine mediated by interaction with voltage-dependent sodium channels.

    Science.gov (United States)

    Ameri, A

    1997-02-01

    The effects of the Aconitum alkaloid 3-acetylaconitine on neuronal activity were investigated in the slice preparation and on cultivated neurons of rat hippocampus by extracellular and patch-clamp recordings, respectively. 3-Acetylaconitine (0.01-1 microM) diminished the orthodromic and antidromic population spike in a concentration-dependent manner. The inhibitory action of the drug was preceded by a transiently enhanced excitability. The latency of onset of the inhibition was accelerated by increased stimulation frequency, whereas recovery during washout of the alkaloid was accelerated by decreased stimulation frequency. Moreover, the inhibitory effect of 3-acetylaconitine was evaluated in two different models of epileptiform activity induced either by blockade of GABA receptors by bicuculline (10 microM) or by a nominal Mg(2+)-free bathing medium. In accordance with the activity-dependent mode of action, this compound abolished the synaptically evoked population spikes in the presence of bicuculline or nominal Mg(2+)-free bathing medium, respectively. Whole-cell patch-clamp recordings revealed an interaction of 3-acetylaconitine with the voltage-dependent sodium channel. At a concentration of 1 microM, 3-acetylaconitine did not affect the peak amplitude of the sodium current, but shifted the current-voltage relationship in the hyperpolarized direction such that sodium currents were already activated at the resting potential.

  16. Interaction of Gram-negative bacteria with cationic proteins: Dependence on the surface characteristics of the bacterial cell

    Directory of Open Access Journals (Sweden)

    Isabella R Prokhorenko

    2009-03-01

    Full Text Available Isabella R Prokhorenko1, Svetlana V Zubova1, Alexandr Yu Ivanov2, Sergey V Grachev31Laboratory of Molecular Biomedicine, Institute of Basic Biological Problems; 2Institute of Cell Biophysics, Russian Academy of Sciences, Moscow, Russia; 3I.M. Sechenov’s Moscow Medical Academy, Moscow, Russia Abstract: Gram-negative bacteria can enter the bloodstream and interact with serum cationic proteins. The character of interaction will depend on the surface characteristics of bacterial cells, which are determined by bacterial chemotype and density of lipopolysaccharide (LPS packing in the cell wall. It was shown that the lysozyme treatment resulted in the increase sensitivity to hypotonic shock. Signifi cant differences to this effect were found between Escherichia coli strain D21 and D21f2 under treatment with physiological protein concentration. On the basis of electrokinetic measurements and studies of the interaction of cells with lysozyme, the hypothesis was formed that the cell wall of the E. coli strain D21f2 contains more LPS and has a higher density of their packing than the cell wall of the E. coli D21 cells. The effect of lysozyme and lactoferrin on the viability of E. coli cells of two different strains was examined. Lysozyme was found to more effectively inhibit the growth of the E. coli D21 bacteria, and lactoferrin suppressed mainly the growth of the E. coli D21f2 bacteria. These results indicate that the differences in LPS core structure of bacterial R-chemotype, which determines surface charge and density of LPS packing, plays an essential role in the mechanisms of interaction of the cationic proteins with the cell wall.Keywords: lipopolysaccharide, Escherichia coli, chemotype, lysozyme, lactoferrin, colony-forming units

  17. VEGF-A isoforms differentially regulate ATF-2-dependent VCAM-1 gene expression and endothelial-leukocyte interactions.

    Science.gov (United States)

    Fearnley, Gareth W; Odell, Adam F; Latham, Antony M; Mughal, Nadeem A; Bruns, Alexander F; Burgoyne, Nicholas J; Homer-Vanniasinkam, Shervanthi; Zachary, Ian C; Hollstein, Monica C; Wheatcroft, Stephen B; Ponnambalam, Sreenivasan

    2014-08-15

    Vascular endothelial growth factor A (VEGF-A) regulates many aspects of vascular physiology. VEGF-A stimulates signal transduction pathways that modulate endothelial outputs such as cell migration, proliferation, tubulogenesis, and cell-cell interactions. Multiple VEGF-A isoforms exist, but the biological significance of this is unclear. Here we analyzed VEGF-A isoform-specific stimulation of VCAM-1 gene expression, which controls endothelial-leukocyte interactions, and show that this is dependent on both ERK1/2 and activating transcription factor-2 (ATF-2). VEGF-A isoforms showed differential ERK1/2 and p38 MAPK phosphorylation kinetics. A key feature of VEGF-A isoform-specific ERK1/2 activation and nuclear translocation was increased phosphorylation of ATF-2 on threonine residue 71 (T71). Using reverse genetics, we showed ATF-2 to be functionally required for VEGF-A-stimulated endothelial VCAM-1 gene expression. ATF-2 knockdown blocked VEGF-A-stimulated VCAM-1 expression and endothelial-leukocyte interactions. ATF-2 was also required for other endothelial cell outputs, such as cell migration and tubulogenesis. In contrast, VCAM-1 was essential only for promoting endothelial-leukocyte interactions. This work presents a new paradigm for understanding how soluble growth factor isoforms program complex cellular outputs and responses by modulating signal transduction pathways. © 2014 Fearnley et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  18. Overdamped motion of interacting particles in general confining potentials: time-dependent and stationary-state analyses

    Science.gov (United States)

    Ribeiro, M. S.; Nobre, F. D.; Curado, E. M. F.

    2012-12-01

    By comparing numerical and analytical results, it is shown that a system of interacting particles under overdamped motion is very well described by a nonlinear Fokker-Planck equation, which can be associated with nonextensive statistical mechanics. The particle-particle interactions considered are repulsive, motivated by three different physical situations: (i) modified Bessel function, commonly used in vortex-vortex interactions, relevant for the flux-front penetration in disordered type-II superconductors; (ii) Yukawa-like forces, useful for charged particles in plasma, or colloidal suspensions; (iii) derived from a Gaussian potential, common in complex fluids, like polymer chains dispersed in a solvent. Moreover, the system is subjected to a general confining potential, φ( x) = ( α| x| z )/ z ( α > 0 , z > 1), so that a stationary state is reached after a sufficiently long time. Recent numerical and analytical investigations, considering interactions of type (i) and a harmonic confining potential ( z = 2), have shown strong evidence that a q-Gaussian distribution, P( x,t), with q = 0, describes appropriately the particle positions during their time evolution, as well as in their stationary state. Herein we reinforce further the connection with nonextensive statistical mechanics, by presenting numerical evidence showing that: (a) in the case z = 2, different particle-particle interactions only modify the diffusion parameter D of the nonlinear Fokker-Planck equation; (b) for z ≠ 2, all cases investigated fit well the analytical stationary solution P st( x), given in terms of a q-exponential (with the same index q = 0) of the general external potential φ( x). In this later case, we propose an approximate time-dependent P( x,t) (not known analytically for z ≠ 2), which is in very good agreement with the simulations for a large range of times, including the approach to the stationary state. The present work suggests that a wide variety of physical phenomena

  19. Long-range magnetic order in models for rare-earth quasicrystals

    Science.gov (United States)

    Thiem, Stefanie; Chalker, J. T.

    2015-12-01

    We take a two-step theoretical approach to study magnetism of rare-earth quasicrystals by considering Ising spins on quasiperiodic tilings, coupled via Ruderman-Kittel-Kasuya-Yosida (RKKY) interactions. First, we compute RKKY interactions from a tight-binding Hamiltonian defined on the two-dimensional quasiperiodic tilings. We find that the magnetic interactions are frustrated and strongly dependent on the local environment. This results in the formation of clusters with strong bonds at certain patterns of the tilings that repeat quasiperiodically. Second, we examine the statistical mechanics of Ising spins with these RKKY interactions, using extensive Monte Carlo simulations. Although models that have frustrated interactions and lack translational invariance might be expected to display spin-glass behavior, we show that the spin system has a phase transition to low-temperature states with long-range quasiperiodic magnetic order. Additionally, we find that in some of the systems spin clusters can fluctuate much below the ordering temperature.

  20. Temperature dependent electronic structure and magnetism of metallic systems with localized moments. Application on gadolinium; Temperaturabhaengige elektronische Struktur und Magnetismus von metallischen Systemen mit lokalisierten Momenten. Anwendung auf Gadolinium

    Energy Technology Data Exchange (ETDEWEB)

    Santos, C.A.M. dos

    2005-06-24

    This thesis focuses on the theoretical investigation of the temperature dependent electronic and magnetic properties of metallic 4f-systems with localized magnetic moments. The presented theory is based on the Kondo-lattice model, which describes the interaction between a system of 4f-localized magnetic moments and the itinerant conduction band electrons. This interaction is responsible for a remarkable temperature dependence of the electronic structure mainly induced by the subsystem of 4f-localized moments. The many-body problem provoked by the Kondo-lattice model is solved by using a moment conserving Green function technique, which takes care of several special limiting cases. This method reproduces the T=0-exact solvable limiting case of the ferromagnetically saturated semiconductor. The temperature dependent magnetic properties of the 4f-localized subsystem are evaluated by means of a modified Rudermann-Kittel-Kasuya-Yosida (RKKY) type procedure, which together with the solution of the electronic part allows for a self-consistent calculation of all the electronic and magnetic properties of the model. Results of model calculations allow to deduce the conditions for ferromagnetism in dependence of the electron density n, exchange coupling J and temperature T. The self-consistently calculated Curie temperature T{sub C} is presented and discussed in dependence of relevant parameters (J, n, and W) of the model. The second part of the thesis is concerned with the investigation of the temperature dependence of the electronic and magnetic properties of the rare-earth metal Gadolinium (Gd). The original Kondo-lattice model is extended to a multi-band Kondo-lattice model and combined with an ab-initio band structure calculation to take into account for the multi-bands in real systems. The single-particle energies of the model are taken from an augmented spherical wave (ASW) band structure calculation. The proposed method avoids the double counting of relevant

  1. Cmv2b-AGO interaction is required for the suppression of RDR-dependent antiviral silencing in Arabidopsis

    Directory of Open Access Journals (Sweden)

    Yuan-Yuan Fang

    2016-08-01

    Full Text Available Using a transient plant system, it was previously found that the suppression of Cucumber mosaic virus (CMV 2b protein relies on its double-strand (ds RNA binding capacity, but it is independent of its interaction with ARGONAUTE (AGO proteins. Thus, the biological meaning of the 2b-AGO interaction in the context of virus infection remains elusive. In this study, we created infectious clones of CMV mutants that expressed the 2b functional domains of dsRNA or AGO binding and tested the effect of these CMV mutants on viral pathogenicity. We found that the mutant CMV2b(1-76 expressing the 2b dsRNA-binding domain exhibited the same virulence as wild-type CMV in infection with either wild-type Arabidopsis or rdr1/6 plants with RDR1- and RDR6-deficient mutations. However, remarkably reduced viral RNA levels and increased virus (vsiRNAs were detected in CMV2b(1-76-infected Arabidopsis in comparison to CMV infection, which demonstrated that the 2b(1-76 deleted AGO-binding domain failed to suppress the RDR1/RDR6-dependent degradation of viral RNAs. The mutant CMV2b(8-111 expressing mutant 2b, in which the N-terminal 7 amino acid (aa was deleted, exhibited slightly reduced virulence, but not viral RNA levels, in both wild-type and rdr1/6 plants, which indicated that 2b retained the AGO-binding activity acquired the counter-RDRs degradation of viral RNAs. The deletion of the N-terminal 7 aa of 2b affected virulence due to the reduced affinity for long dsRNA. The mutant CMV2b(18-111 expressing mutant 2b lacked the N-terminal 17 aa but retained its AGO-binding activity greatly reduced virulence and viral RNA level. Together with the instability of both 2b(18-111-EGFP and RFP-AGO4 proteins when co-expressed in Nicotiana benthamiana leaves, our data demonstrates that the effect of 2b-AGO interaction on counter-RDRs antiviral defense required the presence of 2b dsRNA-binding activity. Taken together, our findings demonstrate that the dsRNA-binding activity of the

  2. Effects of thermal annealing on the magnetic interactions in nanogranular Fe-Ag thin films

    Energy Technology Data Exchange (ETDEWEB)

    Alonso, J.; Fdez-Gubieda, M.L.; Svalov, A. [Departamento de Electricidad y Electronica, Universidad del Pais Vasco (UPV/EHU), Campus de Leioa, 48940 Leioa (Spain); Meneghini, C. [Dipartimento di Fisica ' E. Amaldi' , Universita degli Studi Roma Tre, 00146 Roma (Italy); Orue, I. [SGIker, Universidad del Pais Vasco (UPV/EHU), Campus de Leioa, 48940 Leioa (Spain)

    2012-09-25

    Highlights: Black-Right-Pointing-Pointer Fe{sub x}Ag{sub 100-x} granular thin films with competing interactions (25 {<=} x{<=} 35). Black-Right-Pointing-Pointer Annealing up to 200 Degree-Sign C mainly modifies the interface of Fe nanoparticles. Black-Right-Pointing-Pointer Annealing reduces RKKY interactions in Fe{sub 25}Ag{sub 75}. Black-Right-Pointing-Pointer Annealing favors exchange interactions and ferromagnetic order in Fe{sub 35}Ag{sub 65}. - Abstract: In this paper we have studied, by analysing the evolution of the magnetic behaviour during thermal treatment, the role of the interparticle magnetic interactions in Fe{sub x}Ag{sub 100-x} granular thin films prepared by sputtering deposition technique. Two compositions have been selected: x = 25 and 35, below and around the magnetic percolation of the system, respectively, according to our previous works. The structure of these thin films has been studied by X-ray diffraction (XRD) and X-ray absorption spectroscopy (XAS) measurements. To analyse the magnetic behaviour, DC magnetic measurements have been carried out after progressively annealing the samples at different temperatures (0 {<=} T{sub ann} {<=} 200 Degree-Sign C). These measurements have revealed that, upon thermal treatment, the frustrated state at low temperatures (T < 80 K) for the x = 25 sample tends to disappear, probably due to the weakening of RKKY interactions after the segregation of soluted Fe atoms in the Ag matrix. However, dipolar interactions are not affected by the annealing. On the contrary, at x = 35, around the magnetic percolation, the annealing gives rise to an increasingly ordered interface, thereby enhancing the transfer of the direct exchange interactions.

  3. Gauge angle dependence in TDHFB calculations of ${}^{20}$O + ${}^{20}$O head-on collisions with the Gogny interaction

    CERN Document Server

    Hashimoto, Yukio

    2016-01-01

    A numerical method to solve the TDHFB equations by using a hybrid basis of the two-dimensional harmonic oscillator eigenfunctions and one-dimensional Lagrange mesh with the Gogny effective interaction is applied to the head-on collisions of the superfluid nuclei ${}^{20}$O's. Taking the energies around the barrier top energy, the trajectories, pairing energies, and numbers of transferred nucleons are displayed. Their dependence on the relative gauge angle at the initial time is studied by taking typical sample points of the gauge angle. It turned out that the functional form of the flux of the neutrons across a section plane is proportional to the sine of the two times of the gauge angle.

  4. Stability and anomalous compressibility of Bose gases near resonance: The scale-dependent interactions and thermal effects

    Science.gov (United States)

    Jiang, Shao-Jian; Zhou, Fei

    2015-07-01

    The stability of Bose gases near resonance has been a puzzling problem in recent years. In this article, we demonstrate that in addition to generating thermal pressure, thermal atoms enhance the repulsiveness of the scale-dependent interactions between condensed atoms due to a renormalization effect and further stabilize the Bose gases. Consequently, we find that, as a precursor of instability, the compressibility develops an anomalous structure as a function of scattering length and is drastically reduced compared with the mean-field value. Furthermore, the density profile of a Bose gas in a harmonic trap is found to develop a flat top near the center. This is due to the anomalous behavior of compressibility and can be a potential smoking gun for probing such an effect.

  5. Strong-field ionization rates of linear polyenes simulated with time-dependent configuration interaction with an absorbing potential

    Science.gov (United States)

    Krause, Pascal; Schlegel, H. Bernhard

    2014-11-01

    The strong field ionization rates for ethylene, trans 1,3-butadiene, and trans,trans 1,3,5-hexatriene have been calculated using time-dependent configuration interaction with single excitations and a complex absorbing potential (TDCIS-CAP). The calculations used the aug-cc-pVTZ basis set with a large set of diffuse functions (3 s, 2 p, 3 d, and 1 f) on each atom. The absorbing boundary was placed 3.5 times the van der Waals radius from each atom. The simulations employed a seven-cycle cosine squared pulse with a wavelength of 800 nm. Ionization rates were calculated for intensities ranging from 0.3 × 1014 W/cm2 to 3.5 × 1014 W/cm2. Ionization rates along the molecular axis increased markedly with increasing conjugation length. By contrast, ionization rates perpendicular to the molecular axis were almost independent of the conjugation length.

  6. A three-dimensional time-dependent theory for helix traveling wave tubes in beam-wave interaction

    Institute of Scientific and Technical Information of China (English)

    Peng Wei-Feng; Hu Yu-Lu; Yang Zhong-Hai; Li Jian-Qing; Lu Qi-Ru; Li Bin

    2011-01-01

    This paper presents a three-dimensional time-dependent nonlinear theory of helix traveling wave tubes for beam-wave interaction. The radio frequency electromagnetic fields are represented as the superposition of azimuthally symmetric Waves in a vacuum sheath helix. Coupling impedance is introduced to the electromagnetic field equations' stimulating sources, which makes the theory easier and more flexible to realize. The space charge fields are calculated by electron beam space-charge waves expressed as the superposition solutions of Helmholtz equations. The focusing forces due to either a solenoidal field or a periodic permanent magnetic field is also included. The dynamical equations of electrons are Lorentz equations associating with electromagnetic fields, focusing fields and space-charge fields. The numerically simulated results of a tube are presented.

  7. Interaction between O{sub 2} and ZnO films probed by time-dependent second-harmonic generation

    Energy Technology Data Exchange (ETDEWEB)

    Andersen, S. V., E-mail: sva@nano.aau.dk [Department of Applied Physics, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven (Netherlands); Department of Physics and Nanotechnology, Aalborg University, Skjernvej 4A, DK-9220 Aalborg Øst (Denmark); Vandalon, V.; Bosch, R. H. E. C.; Loo, B. W. H. van de; Kessels, W. M. M., E-mail: w.m.m.kessels@tue.nl [Department of Applied Physics, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven (Netherlands); Pedersen, K. [Department of Physics and Nanotechnology, Aalborg University, Skjernvej 4A, DK-9220 Aalborg Øst (Denmark)

    2014-02-03

    The interaction between O{sub 2} and ZnO thin films prepared by atomic layer deposition has been investigated by time-dependent second-harmonic generation, by probing the electric field induced by adsorbed oxygen molecules on the surface. The second-harmonic generated signal decays upon laser exposure due to two-photon assisted desorption of O{sub 2}. Blocking and unblocking the laser beam for different time intervals reveals the adsorption rate of O{sub 2} onto ZnO. The results demonstrate that electric field induced second-harmonic generation provides a versatile non-contact probe of the adsorption kinetics of molecules on ZnO thin films.

  8. p16(INK4A) enhances the transcriptional and the apoptotic functions of p53 through DNA-dependent interaction.

    Science.gov (United States)

    Al-Khalaf, Huda H; Nallar, Shreeram C; Kalvakolanu, Dhananjaya V; Aboussekhra, Abdelilah

    2017-02-20

    p16(INK4A) and p53 are two important tumor suppressor proteins that play essential roles during cell proliferation and aging through regulating the expression of several genes. Here, we report that p16(INK4A) and p53 co-regulate a plethora of transcripts. Furthermore, both proteins colocalize in the nucleus of human primary skin fibroblasts and breast luminal cells, and form a heteromer whose level increases in response to genotoxic stress as well as aging of human fibroblasts and various mouse organs. CDK4 is also present in this heteromeric complex, which is formed only in the presence of DNA both in vitro using pure recombinant proteins and in vivo. We have also shown that p16(INK4A) enhances the binding efficiency of p53 to its cognate sequence presents in the CDKN1A promoter in vitro, and both proteins are present at the promoters of CDKN1A and BAX in vivo. Importantly, the fourth ankyrin repeat of p16(INK4A) and the C-terminal domain of p53 were necessary for the physical association between these two proteins. The physiologic importance of this association was revealed by the inability of cancer-associated p16(INK4A) mutants to interact with p53 and to transactivate the expression of its major targets CDKN1A and BAX in the p16-defective U2OS cells expressing either wild-type or mutated p16(INK4A) . Furthermore, the association between p16(INK4A) and p53 was capital for their nuclear colocalization, the X-ray-dependent induction of p21 and Bax proteins as well as the induction of apoptosis in various types of cells. Together, these results show DNA-dependent physical interaction between p16(INK4A) and p53.

  9. Interactions between growth-dependent changes in cell size, nutrient supply and cellular elemental stoichiometry of marine Synechococcus.

    Science.gov (United States)

    Garcia, Nathan S; Bonachela, Juan A; Martiny, Adam C

    2016-11-01

    The factors that control elemental ratios within phytoplankton, like carbon:nitrogen:phosphorus (C:N:P), are key to biogeochemical cycles. Previous studies have identified relationships between nutrient-limited growth and elemental ratios in large eukaryotes, but little is known about these interactions in small marine phytoplankton like the globally important Cyanobacteria. To improve our understanding of these interactions in picophytoplankton, we asked how cellular elemental stoichiometry varies as a function of steady-state, N- and P-limited growth in laboratory chemostat cultures of Synechococcus WH8102. By combining empirical data and theoretical modeling, we identified a previously unrecognized factor (growth-dependent variability in cell size) that controls the relationship between nutrient-limited growth and cellular elemental stoichiometry. To predict the cellular elemental stoichiometry of phytoplankton, previous theoretical models rely on the traditional Droop model, which purports that the acquisition of a single limiting nutrient suffices to explain the relationship between a cellular nutrient quota and growth rate. Our study, however, indicates that growth-dependent changes in cell size have an important role in regulating cell nutrient quotas. This key ingredient, along with nutrient-uptake protein regulation, enables our model to predict the cellular elemental stoichiometry of Synechococcus across a range of nutrient-limited conditions. Our analysis also adds to the growth rate hypothesis, suggesting that P-rich biomolecules other than nucleic acids are important drivers of stoichiometric variability in Synechococcus. Lastly, by comparing our data with field observations, our study has important ecological relevance as it provides a framework for understanding and predicting elemental ratios in ocean regions where small phytoplankton like Synechococcus dominates.

  10. Continuous flow atomic force microscopy imaging reveals fluidity and time-dependent interactions of antimicrobial dendrimer with model lipid membranes.

    Science.gov (United States)

    Lind, Tania Kjellerup; Zielińska, Paulina; Wacklin, Hanna Pauliina; Urbańczyk-Lipkowska, Zofia; Cárdenas, Marité

    2014-01-28

    In this paper, an amphiphilic peptide dendrimer with potential applications against multi-resistant bacteria such as Staphylococcus aureus was synthesized and studied on model cell membranes. The combination of quartz crystal microbalance and atomic force microscopy imaging during continuous flow allowed for in situ monitoring of the very initial interaction processes and membrane transformations on longer time scales. We used three different membrane compositions of low and high melting temperature phospholipids to vary the membrane properties from a single fluid phase to a pure gel phase, while crossing the phase coexistence boundaries at room temperature. The interaction mechanism of the dendrimer was found to be time-dependent and to vary remarkably with the fluidity and coexistence of liquid-solid phases in the membrane. Spherical micelle-like dendrimer-lipid aggregates were formed in the fluid-phase bilayer and led to partial solubilization of the membrane, while in gel-phase membranes, the dendrimers caused areas of local depressions followed by redeposition of flexible lipid patches. Domain coexistence led to a sequence of events initiated by the formation of a ribbon-like network and followed by membrane solubilization via spherical aggregates from the edges of bilayer patches. Our results show that the dendrimer molecules were able to destroy the membrane integrity through different mechanisms depending on the lipid phase and morphology and shed light on their antimicrobial activity. These findings could have an impact on the efficacy of the dendrimers since lipid membranes in certain bacteria have transition temperatures very close to the host body temperature.

  11. Testing the distance-dependence of the van der Waals interaction between an atom and a surface through spectroscopy in a vapor nanocell

    CERN Document Server

    Laliotis, A; Todorov, P; Hamdi, I; Dutier, G; Yarovitski, A; Saltiel, S; Gorza, M P; Fichet, M; Ducloy, M; Bloch, D; Laliotis, Athanasdios; Maurin, Isabelle; Todorov, Petko; Hamdi, Ismah\\`{e}ne; Dutier, Gabriel; Yarovitski, Alexander; Saltiel, Solomon; Gorza, Marie-Pascale; Fichet, Mich\\`{e}le; Ducloy, Martial; Bloch, Daniel

    2007-01-01

    This paper presents our current measurements in a vapor nanocell aiming at a test of the distance-dependence of the atom-surface interaction, when simple asymptotic descriptions may turn to be not valid. A state-of-the-art of atom-surface interaction measurements is provided as an introduction, along with the comparison with the theory of the van der Waals (or Casimir-Polder) interaction; it is followed by a presentation of the most salient features of nanocell spectroscopy

  12. Structural Basis of the Interaction of Cyclin-Dependent Kinase 2 with Roscovitine and Its Analogues Having Bioisosteric Central Heterocycles.

    Science.gov (United States)

    Nekardová, Michaela; Vymětalová, Ladislava; Khirsariya, Prashant; Kováčová, Silvia; Hylsová, Michaela; Jorda, Radek; Kryštof, Vladimír; Fanfrlík, Jindřich; Hobza, Pavel; Paruch, Kamil

    2017-04-05

    The structural basis for the interaction of roscovitine and analogues containing 13 different bioisosteric central heterocycles with the enzyme cyclin-dependent kinase 2 (CDK2) is elucidated. Although all the central scaffolds are very similar to the purine core of roscovitine, the experimentally determined IC50 values of the inhibitors span three orders of magnitude. By using an extensive computational chemistry approach, the affinities of the inhibitors to CDK2 are determined as calculated binding scores of complexes of the inhibitors with the protein. The interactions of the inhibitors with CDK2 are computationally described by using a hybrid quantum mechanics/semi-empirical quantum mechanics method (QM/SQM), which combines the DFT-D method for the QM part and the PM6-D3H4X method for the SQM part. The solvent effect is described by the COSMO implicit solvation model at the SQM level for the whole system. The contributions of the scaffolds and the individual substituents, quantified and evaluated in relation to conformations of optimized protein-inhibitor complexes, are found not to be simply additive. The inhibitory activity of the selected candidates, including two newly prepared compounds, is tested against CDK2. The results of the calculations are in close agreement with the experimental data. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Constraints on short-range spin-dependent interactions from scalar spin-spin coupling in deuterated molecular hydrogen

    CERN Document Server

    Ledbetter, Micah; Jackson-Kimball, Derek

    2012-01-01

    A comparison between existing measurements and calculations of the scalar spin-spin interaction (J-coupling) in deuterated molecular hydrogen (HD) yields stringent constraints on anomalous spin-dependent potentials between nucleons at the atomic scale (${\\rm \\sim 1 \\AA}$). The dimensionless coupling constant $g_P^pg_P^{N}/4\\pi$ associated with exchange of pseudoscalar (axion-like) bosons between nucleons is constrained to be less than $5\\times 10^{-7}$ for boson masses in the range of $5 {\\rm keV}$. This represents improvement by a factor of about 100 over constraints placed by measurements of the dipole-dipole interaction in molecular ${\\rm H_2}$. The dimensionless coupling constant $g_A^pg_A^N/4 \\pi$ associated with exchange of a heretofore undiscovered axial-vector boson between nucleons is constrained to be $g_A^pg_A^N/4 \\pi < 2 \\times 10^{-19}$ for bosons of mass $\\lesssim 1000 {\\rm eV}$, improving constraints at this distance scale by a factor of 100 for proton-proton couplings and more than 8 orders...

  14. Temperature Dependence of the Stability of Ion Pair Interactions, and its Implications on the Thermostability of Proteins from Thermophiles

    Indian Academy of Sciences (India)

    SWETHA BIKKINA; AGASTYA P BHATI; SILADITYA PADHI; U DEVA PRIYAKUMAR

    2017-03-01

    An understanding of the determinants of the thermal stability of thermostable proteins is expected to enable design of enzymes that can be employed in industrial biocatalytic processes carried out at high temperatures. A major factor that has been proposed to stabilize thermostable proteins is the high occurrenceof salt bridges. The current study employs free energy calculations to elucidate the thermodynamics of the formation of salt bridge interactions and the temperature dependence, using acetate and methylguanidium ionsas model systems. Three different orientations of the methylguanidinium approaching the carboxylate grouphave been considered for obtaining the free energy profiles. The association of the two ions becomes more favorable with an increase in temperature. The desolvation penalty corresponding to the association of the ionpair is the lowest at high temperatures. The occurrence of bridging water molecules between the ions ensures that the ions are not fully desolvated, and this could provide an explanation for the existence of internal watermolecules in thermostable proteins reported recently. The findings provide a detailed picture of the interactions that make ion pair association at high temperatures a favorable process, and reaffirm the importance of saltbridges in the design of thermostable proteins.

  15. Material dependence of Casimir interaction between a sphere and a plate: First analytic correction beyond proximity force approximation

    CERN Document Server

    Teo, L P

    2013-01-01

    We derive analytically the asymptotic behavior of the Casimir interaction between a sphere and a plate when the distance between them, $d$, is much smaller than the radius of the sphere, $R$. The leading order and next-to-leading order terms are derived from the exact formula for the Casimir interaction energy. They are found to depend nontrivially on the dielectric functions of the objects. As expected, the leading order term coincides with that derived using the proximity force approximation. The result on the next-to-leading order term complements that found by Bimonte, Emig and Kardar [Appl. Phys. Lett. \\textbf{100}, 074110 (2012)] using derivative expansion. Numerical results are presented when the dielectric functions are given by the plasma model or the Drude model, with the plasma frequency (for plasma and Drude models) and relaxation frequency (for Drude model) given respectively by 9eV and 0.035eV, the conventional values used for gold metal. It is found that if plasma model is used instead of Drude...

  16. Task-dependent interaction between parietal and contralateral primary motor cortex during explicit versus implicit motor imagery.

    Directory of Open Access Journals (Sweden)

    Florent Lebon

    Full Text Available Both mental rotation (MR and motor imagery (MI involve an internalization of movement within motor and parietal cortex. Transcranial magnetic stimulation (TMS techniques allow for a task-dependent investigation of the interhemispheric interaction between these areas. We used image-guided dual-coil TMS to investigate interactions between right inferior parietal lobe (rIPL and left primary motor cortex (M1 in 11 healthy participants. They performed MI (right index-thumb pinching in time with a 1 Hz metronome or hand MR tasks, while motor evoked potentials (MEPs were recorded from right first dorsal interosseous. At rest, rIPL conditioning 6 ms prior to M1 stimulation facilitated MEPs in all participants, whereas this facilitation was abolished during MR. While rIPL conditioning 12 ms prior to M1 stimulation had no effect on MEPs at rest, it suppressed corticomotor excitability during MI. These results support the idea that rIPL forms part of a distinct inhibitory network that may prevent unwanted movement during imagery tasks.

  17. Diffusion and partitioning of macromolecules in casein microgels: evidence for size-dependent attractive interactions in a dense protein system.

    Science.gov (United States)

    Peixoto, Paulo D S; Bouchoux, Antoine; Huet, Sébastien; Madec, Marie-Noëlle; Thomas, Daniel; Floury, Juliane; Gésan-Guiziou, Geneviève

    2015-02-10

    Understanding the mechanisms that determine the diffusion and interaction of macromolecules (such as proteins and polysaccharides) that disperse through dense media is an important fundamental issue in the development of innovative technological and medical applications. In the current work, the partitioning and diffusion of macromolecules of different sizes (from 4 to 10 nm in diameter) and shapes (linear or spherical) within dispersions of casein micelles (a protein microgel) is studied. The coefficients for diffusion and partition are measured using FRAP (fluorescence recovery after photobleaching) and analyzed with respect to the structural characteristics of the microgel determined by the use of TEM (transmission electron microscopy) tomography. The results show that the casein microgel displays a nonspecific attractive interaction for all macromolecules studied. When the macromolecular probes are spherical, this affinity is clearly size-dependent, with stronger attraction for the larger probes. The current data show that electrostatic effects cannot account for such an attraction. Rather, nonspecific hydration molecular forces appear to explain these results. These findings show how weak nonspecific forces affect the diffusion and partitioning of proteins and polysaccharides in a dense protein environment. These results could be useful to better understand the mechanisms of diffusion and partitioning in other media such as cells and tissues. Furthermore, there arises the possibility of using the casein micelle as a size-selective molecular device.

  18. Structural Dynamics of Actin during Active Interaction with Myosin Depends on the Isoform of the Essential Light Chain

    Science.gov (United States)

    Prochniewicz, Ewa; Guhathakurta, Piyali; Thomas, David D.

    2013-01-01

    We have used time-resolved phosphorescence anisotropy (TPA) to investigate the effects of essential light chain (ELC) isoforms (A1 and A2) on the interaction of skeletal muscle myosin with actin, in order to relate structural dynamics to previously reported functional effects. Actin was labeled with a phosphorescent probe at C374, and the myosin head (S1) was separated into isoenzymes S1A1 and S1A2 by ion-exchange chromatography. As previously reported, S1A1 exhibited substantially lower ATPase activity at saturating actin but substantially higher apparent actin affinity, resulting in higher catalytic efficiency. In the absence of ATP, each isoenzyme increased actin’s final anisotropy cooperatively and to a similar extent, indicating similar restriction of the amplitude of intrafilament rotational motions in the strong-binding (S) state of actomyosin. In contrast, in the presence of saturating ATP, S1A1 increased actin anisotropy much more than S1A2 and with greater cooperativity, indicating that S1A1 was more effective in restricting actin dynamics during the active interaction of actin and myosin. We conclude that during the active interaction of actin and ATP with myosin, S1A1 is more effective at stabilizing the S state (probably the force-generating state) of actomyosin, while S1A2 tends to stabilize the weak-binding (non-force-generating) W state. When a mixture of isoenzymes is present, S1A1 is dominant in its effects on actin dynamics. We conclude that ELC of skeletal muscle myosin modulates strong-to-weak structural transitions during the actomyosin ATPase cycle in an isoform-dependent manner, with significant implications for the contractile function of actomyosin. PMID:23339370

  19. Solvent dependency of the UV-Vis spectrum of indenoisoquinolines: role of keto-oxygens as polarity interaction probes.

    Directory of Open Access Journals (Sweden)

    Andrea Coletta

    Full Text Available Indenoisoquinolines are the most promising non-campthotecins topoisomerase IB inhibitors. We present an integrated experimental/computational investigation of the UV-Vis spectra of the IQNs parental compound (NSC314622 and two of its derivatives (NSC724998 and NSC725776 currently undergoing Phase I clinical trials. In all the three compounds a similar dependence of the relative absorption intensities at 270 nm and 290 nm on solvent polarity is found. The keto-oxygens in positions 5 and 11 of the molecular scaffold of the molecule are the principal chromophores involved in this dependence. Protic interactions on these sites are also found to give rise to absorptions at wavelength <250 nm observed in water solution, due to the stabilization of highly polarized tautomers of the molecule. These results suggest that the keto-oxygens are important polarizable groups that can act as useful interactors with the molecular receptor, providing at the same time an useful fingerprint for the monitoring of the drug binding to topoisomerase IB.

  20. Time-dependent generalized-active-space configuration-interaction approach to photoionization dynamics of atoms and molecules

    CERN Document Server

    Bauch, Sebastian; Madsen, Lars Bojer

    2014-01-01

    We present a wave-function based method to solve the time-dependent many-electron Schr\\"odinger equation (TDSE) with special emphasis on strong-field ionization phenomena. The theory builds on the configuration-interaction (CI) approach supplemented by the generalized-active-space (GAS) concept from quantum chemistry. The latter allows for a controllable reduction in the number of configurations in the CI expansion by imposing restrictions on the active orbital space. The method is similar to the recently formulated time-dependent restricted-active-space (TD-RAS) CI method [D. Hochstuhl, and M. Bonitz, Phys. Rev. A 86, 053424 (2012)]. We present details of our implementation and address convergence properties with respect to the active spaces and the associated account of electron correlation in both ground state and excitation scenarios. We apply the TD-GASCI theory to strong-field ionization of polar diatomic molecules and illustrate how the method allows us to uncover a strong correlation-induced shift of ...

  1. Effects of viscous heating and wall-fluid interaction energy on rate-dependent slip behavior of simple fluids

    Science.gov (United States)

    Bao, Luyao; Priezjev, Nikolai V.; Hu, Haibao; Luo, Kai

    2017-09-01

    Molecular dynamics simulations are used to investigate the rate and temperature dependence of the slip length in thin liquid films confined by smooth, thermal substrates. In our setup, the heat generated in a force-driven flow is removed by the thermostat applied on several wall layers away from liquid-solid interfaces. We found that for both high and low wall-fluid interaction (WFI) energies, the temperature of the fluid phase rises significantly as the shear rate increases. Surprisingly, with increasing shear rate, the slip length approaches a constant value from above for high WFI energies and from below for low WFI energies. The two distinct trends of the rate-dependent slip length are rationalized by examining S ( G1) , the height of the main peak of the in-plane structure factor of the first fluid layer (FFL) together with DWF, which is the average distance between the wall and FFL. The results of numerical simulations demonstrate that reduced values of the structure factor, S ( G1) , correlate with the enhanced slip, while smaller distances DWF indicate that fluid atoms penetrate deeper into the surface potential leading to larger friction and smaller slip. Interestingly, at the lowest WFI energy, the combined effect of the increase of S ( G1) and decrease of DWF with increasing shear rate results in a dramatic reduction of the slip length.

  2. Superovulatory responses in cynomolgus monkeys (Macaca fascicularis) depend on the interaction between donor status and superovulation method used

    Science.gov (United States)

    KIM, Ji-Su; YOON, Seung-Bin; JEONG, Kang-Jin; SIM, Bo-Woong; CHOI, Seon-A; LEE, Sang-Il; JIN, Yeung Bae; SONG, Bong-Seok; LEE, Sang-Rae; KIM, Sun-Uk; CHANG, Kyu-Tae

    2017-01-01

    The current study was performed to investigate the effect of oocyte donor status, including age and body weight, on metaphase II (MII) oocyte recovery using two superovulation methods in cynomolgus monkeys. The use of Method A [recombinant gonadotrophin (75 IU/kg, 3 ×, 3-day intervals) and human chorionic gonadotropin (hCG)] led to great increases in ovary size and the mean number of MII oocytes retrieved in age- and body-weight-dependent manner; in contrast, both the parameters were similar in Method B [recombinant gonadotrophin (60 IU, twice daily, 6 days), recombinant gonadotropin and recombinant human luteinizing hormone (rhLH) (60 IU, twice daily, 3 days), and hCG]. Importantly, Method A showed maximal MII oocyte recovery rate in > 60-month-old or 4.5–5.0-kg female monkeys, whereas Method B was equally effective regardless of the donor age and body weight. These results indicate that superovulatory responses depend on the interaction between oocyte donor status and the superovulation method used in cynomolgus monkeys. PMID:28070055

  3. Toxoplasma DJ-1 Regulates Organelle Secretion by a Direct Interaction with Calcium-Dependent Protein Kinase 1

    Directory of Open Access Journals (Sweden)

    Matthew A. Child

    2017-02-01

    Full Text Available Human DJ-1 is a highly conserved and yet functionally enigmatic protein associated with a heritable form of Parkinson’s disease. It has been suggested to be a redox-dependent regulatory scaffold, binding to proteins to modulate their function. Here we present the X-ray crystal structure of the Toxoplasma orthologue Toxoplasma gondii DJ-1 (TgDJ-1 at 2.1-Å resolution and show that it directly associates with calcium-dependent protein kinase 1 (CDPK1. The TgDJ-1 structure identifies an orthologously conserved arginine dyad that acts as a phospho-gatekeeper motif to control complex formation. We determined that the binding of TgDJ-1 to CDPK1 is sensitive to oxidation and calcium, and that this interaction potentiates CDPK1 kinase activity. Finally, we show that genetic deletion of TgDJ-1 results in upregulation of CDPK1 expression and that disruption of the CDPK1/TgDJ-1 complex in vivo prevents normal exocytosis of parasite virulence-associated organelles called micronemes. Overall, our data suggest that TgDJ-1 functions as a noncanonical kinase-regulatory scaffold that integrates multiple intracellular signals to tune microneme exocytosis in T. gondii.

  4. Glycol-Water Interactions and co-existing phases and Temperature Dependent Solubility. An Example Of Carbon-Hydrogen Chemistry In Water

    CERN Document Server

    Michael, Fredrick

    2010-01-01

    Recently there has been great interest in Glycol-Water chemistry and solubility and temperature dependent phase dynamics. The Glycol-Water biochemistry of interactions is present in plant biology and chemistry, is of great interest to chemical engineers and biochemists as it is a paradigm of Carbon-Hydrogen Water organic chemistry. There is an interest moreover in formulating a simpler theory and computation model for the Glycol-Water interaction and phase dynamics, that is not fully quantum mechanical yet has the high accuracy available from a fully quantum mechanical theory of phase transitions of fluids and Fermi systems. Along these lines of research interest we have derived a Lennard-Jones -like theory of interacting molecules-Water in a dissolved adducts of Glycol-Water system interacting by Hydrogen bonds whose validity is supported at the scale of interactions by other independent molecular dynamics investigations that utilize force fields dependent on their experimental fittings to the Lennard-Jones ...

  5. INTERACT

    DEFF Research Database (Denmark)

    Jochum, Elizabeth; Borggreen, Gunhild; Murphey, TD

    This paper considers the impact of visual art and performance on robotics and human-computer interaction and outlines a research project that combines puppetry and live performance with robotics. Kinesics—communication through movement—is the foundation of many theatre and performance traditions...... interaction between a human operator and an artificial actor or agent. We can apply insights from puppetry to develop culturally-aware robots. Here we describe the development of a robotic marionette theatre wherein robotic controllers assume the role of human puppeteers. The system has been built, tested...

  6. Magnetism and exchange interaction of small rare-earth clusters; Tb as a representative

    CERN Document Server

    Peters, Lars; Sanyal, Biplab; van Dijk, Chris; Bowlan, John; de Heer, Walt; Delin, Anna; Di Marco, Igor; Eriksson, Olle; Katsnelson, Mikhail I; Johansson, Börje; Kirilyuk, Andrei

    2016-01-01

    Here we follow, both experimentally and theoretically, the development of magnetism in Tb clusters from the atomic limit, adding one atom at a time. The exchange interaction is, surprisingly, observed to drastically increase compared to that of bulk, and to exhibit irregular oscillations as a function of the interatomic distance. From electronic structure theory we find that the theoretical magnetic moments oscillate with cluster size in exact agreement with experimental data. Unlike the bulk, the oscillation is not caused by the RKKY mechanism. Instead, the inter-atomic exchange is shown to be driven by a competition between wave-function overlap of the 5d shell and the on-site exchange interaction, which leads to a competition between ferromagnetic double-exchange and antiferromagnetic super-exchange. This understanding opens up new ways to tune the magnetic properties of rare-earth based magnets with nano-sized building blocks.

  7. Mutational Analysis Reveals a Noncontractile but Interactive Role of Actin and Profilin in Viral RNA-Dependent RNA Synthesis▿

    Science.gov (United States)

    Harpen, Mary; Barik, Tiasha; Musiyenko, Alla; Barik, Sailen

    2009-01-01

    As obligatory parasites, viruses co-opt a variety of cellular functions for robust replication. The expression of the nonsegmented negative-strand RNA genome of respiratory syncytial virus (RSV), a significant pediatric pathogen, absolutely requires actin and is stimulated by the actin-regulatory protein profilin. As actin is a major contractile protein, it was important to determine whether the known functional domains of actin and profilin were important for their ability to activate RSV transcription. Analyses of recombinant mutants in a reconstituted RSV transcription system suggested that the divalent-cation-binding domain of actin is critically needed for binding to the RSV genome template and for the activation of viral RNA synthesis. In contrast, the nucleotide-binding domain and the N-terminal acidic domain were needed neither for template binding nor for transcription. Specific surface residues of actin, required for actin-actin contact during filamentation, were also nonessential for viral transcription. Unlike actin, profilin did not directly bind to the viral template but was recruited by actin. Mutation of the interactive residues of actin or profilin, resulting in the loss of actin-profilin binding, also abolished profilin's ability to stimulate viral transcription. Together, these results suggest that actin acts as a classical transcription factor for the virus by divalent-cation-dependent binding to the viral template and that profilin acts as a transcriptional cofactor, in part by associating with actin. This essential viral role of actin is independent of its contractile cellular role. PMID:19710142

  8. Spin-dependent thermoelectric effect and spin battery mechanism in triple quantum dots with Rashba spin-orbital interaction

    Science.gov (United States)

    Xu, Wei-Ping; Zhang, Yu-Ying; Wang, Qiang; Nie, Yi-Hang

    2016-11-01

    We have studied spin-dependent thermoelectric transport through parallel triple quantum dots with Rashba spin-orbital interaction (RSOI) embedded in an Aharonov-Bohm interferometer connected symmetrically to leads using nonequilibrium Green’s function method in the linear response regime. Under the appropriate configuration of magnetic flux phase and RSOI phase, the spin figure of merit can be enhanced and is even larger than the charge figure of merit. In particular, the charge and spin thermopowers as functions of both the magnetic flux phase and the RSOI phase present quadruple-peak structures in the contour graphs. For some specific configuration of the two phases, the device can provide a mechanism that converts heat into a spin voltage when the charge thermopower vanishes while the spin thermopower is not zero, which is useful in realizing the thermal spin battery and inducing a pure spin current in the device. Project supported by the National Natural Science Foundation of China (Grant Nos. 11274208 and 11447170).

  9. Cytoplasmic utilization of human immunodeficiency virus type 1 genomic RNA is not dependent on a nuclear interaction with gag.

    Science.gov (United States)

    Grewe, Bastian; Hoffmann, Bianca; Ohs, Inga; Blissenbach, Maik; Brandt, Sabine; Tippler, Bettina; Grunwald, Thomas; Uberla, Klaus

    2012-03-01

    In some retroviruses, such as Rous sarcoma virus and prototype foamy virus, Gag proteins are known to shuttle between the nucleus and the cytoplasm and are implicated in nuclear export of the viral genomic unspliced RNA (gRNA) for subsequent encapsidation. A similar function has been proposed for human immunodeficiency virus type 1 (HIV-1) Gag based on the identification of nuclear localization and export signals. However, the ability of HIV-1 Gag to transit through the nucleus has never been confirmed. In addition, the lentiviral Rev protein promotes efficient nuclear gRNA export, and previous reports indicate a cytoplasmic interaction between Gag and gRNA. Therefore, functional effects of HIV-1 Gag on gRNA and its usage were explored. Expression of gag in the absence of Rev was not able to increase cytoplasmic gRNA levels of subgenomic, proviral, or lentiviral vector constructs, and gene expression from genomic reporter plasmids could not be induced by Gag provided in trans. Furthermore, Gag lacking the reported nuclear localization and export signals was still able to mediate an efficient packaging process. Although small amounts of Gag were detectable in the nuclei of transfected cells, a Crm1-dependent nuclear export signal in Gag could not be confirmed. Thus, our study does not provide any evidence for a nuclear function of HIV-1 Gag. The encapsidation process of HIV-1 therefore clearly differs from that of Rous sarcoma virus and prototype foamy virus.

  10. Time-dependent quantum transport through an interacting quantum dot beyond sequential tunneling: second-order quantum rate equations.

    Science.gov (United States)

    Dong, B; Ding, G H; Lei, X L

    2015-05-27

    A general theoretical formulation for the effect of a strong on-site Coulomb interaction on the time-dependent electron transport through a quantum dot under the influence of arbitrary time-varying bias voltages and/or external fields is presented, based on slave bosons and the Keldysh nonequilibrium Green's function (GF) techniques. To avoid the difficulties of computing double-time GFs, we generalize the propagation scheme recently developed by Croy and Saalmann to combine the auxiliary-mode expansion with the celebrated Lacroix's decoupling approximation in dealing with the second-order correlated GFs and then establish a closed set of coupled equations of motion, called second-order quantum rate equations (SOQREs), for an exact description of transient dynamics of electron correlated tunneling. We verify that the stationary solution of our SOQREs is able to correctly describe the Kondo effect on a qualitative level. Moreover, a comparison with other methods, such as the second-order von Neumann approach and Hubbard-I approximation, is performed. As illustrations, we investigate the transient current behaviors in response to a step voltage pulse and a harmonic driving voltage, and linear admittance as well, in the cotunneling regime.

  11. Strong-field ionization rates of linear polyenes simulated with time-dependent configuration interaction with an absorbing potential

    Energy Technology Data Exchange (ETDEWEB)

    Krause, Pascal; Schlegel, H. Bernhard [Department of Chemistry, Wayne State University, Detroit, Michigan 48202-3489 (United States)

    2014-11-07

    The strong field ionization rates for ethylene, trans 1,3-butadiene, and trans,trans 1,3,5-hexatriene have been calculated using time-dependent configuration interaction with single excitations and a complex absorbing potential (TDCIS-CAP). The calculations used the aug-cc-pVTZ basis set with a large set of diffuse functions (3 s, 2 p, 3 d, and 1 f) on each atom. The absorbing boundary was placed 3.5 times the van der Waals radius from each atom. The simulations employed a seven-cycle cosine squared pulse with a wavelength of 800 nm. Ionization rates were calculated for intensities ranging from 0.3 × 10{sup 14} W/cm{sup 2} to 3.5 × 10{sup 14} W/cm{sup 2}. Ionization rates along the molecular axis increased markedly with increasing conjugation length. By contrast, ionization rates perpendicular to the molecular axis were almost independent of the conjugation length.

  12. Analytic derivative couplings for spin-flip configuration interaction singles and spin-flip time-dependent density functional theory.

    Science.gov (United States)

    Zhang, Xing; Herbert, John M

    2014-08-14

    We revisit the calculation of analytic derivative couplings for configuration interaction singles (CIS), and derive and implement these couplings for its spin-flip variant for the first time. Our algorithm is closely related to the CIS analytic energy gradient algorithm and should be straightforward to implement in any quantum chemistry code that has CIS analytic energy gradients. The additional cost of evaluating the derivative couplings is small in comparison to the cost of evaluating the gradients for the two electronic states in question. Incorporation of an exchange-correlation term provides an ad hoc extension of this formalism to time-dependent density functional theory within the Tamm-Dancoff approximation, without the need to invoke quadratic response theory or evaluate third derivatives of the exchange-correlation functional. Application to several different conical intersections in ethylene demonstrates that minimum-energy crossing points along conical seams can be located at substantially reduced cost when analytic derivative couplings are employed, as compared to use of a branching-plane updating algorithm that does not require these couplings. Application to H3 near its D(3h) geometry demonstrates that correct topology is obtained in the vicinity of a conical intersection involving a degenerate ground state.

  13. Microplastic interactions with freshwater microalgae: Hetero-aggregation and changes in plastic density appear strongly dependent on polymer type.

    Science.gov (United States)

    Lagarde, Fabienne; Olivier, Ophélie; Zanella, Marie; Daniel, Philippe; Hiard, Sophie; Caruso, Aurore

    2016-08-01

    In this study, the interactions between microplastics, chosen among the most widely used in industry such as polypropylene (PP) and high-density polyethylene (HDPE), and a model freshwater microalgae, Chlamydomas reinhardtii, were investigated. It was shown that the presence of high concentrations of microplastics with size >400 μm did not directly impact the growth of microalgae in the first days of contact and that the expression of three genes involved in the stress response was not modified after 78 days. In parallel, a similar colonization was observed for the two polymers. However, after 20 days of contact, in the case of PP only, hetero-aggregates constituted of microalgae, microplastics and exopolysaccharides were formed. An estimation of the hetero-aggregates composition was approximately 50% of PP fragments and 50% of microalgae, which led to a final density close to 1.2. Such hetero-aggregates appear as an important pathway for the vertical transport of PP microplastics from the water surface to sediment. Moreover, after more than 70 days of contact with microplastics, the microalgae genes involved in the sugar biosynthesis pathways were strongly over-expressed compared to control conditions. The levels of over-expression were higher in the case of HDPE than in PP condition. This work presents the first evidence that depending on their chemical nature, microplastics will follow different fates in the environment. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. A growth-dependent transcription initiation factor (TIF-IA) interacting with RNA polymerase I regulates mouse ribosomal RNA synthesis.

    Science.gov (United States)

    Schnapp, A; Pfleiderer, C; Rosenbauer, H; Grummt, I

    1990-09-01

    Control of mouse ribosomal RNA synthesis in response to extracellular signals is mediated by TIF-IA, a regulatory factor whose amount or activity correlates with cell proliferation. Factor TIF-IA interacts with RNA polymerase I (pol I), thus converting it into a transcriptionally active holoenzyme, which is able to initiate specifically at the rDNA promoter in the presence of the other auxiliary transcription initiation factors, designated TIF-IB, TIF-IC and UBF. With regard to several criteria, the growth-dependent factor TIF-IA behaves like a bacterial sigma factor: (i) it associates physically with pol I, (ii) it is required for initiation of transcription, (iii) it is present in limiting amounts and (iv) under certain salt conditions, it is chromatographically separable from the polymerase. In addition, evidence is presented that dephosphorylation of pol I abolishes in vitro transcription initiation from the ribosomal gene promoter without significantly affecting the polymerizing activity of the enzyme at nonspecific templates. The involvement of both a regulatory factor and post-translational modification of the transcribing enzyme provides an efficient and versatile mechanism of rDNA transcription regulation which enables the cell to adapt ribosome synthesis rapidly to a variety of extracellular signals.

  15. Ribosome-dependent ATPase interacts with conserved membrane protein in Escherichia coli to modulate protein synthesis and oxidative phosphorylation.

    Directory of Open Access Journals (Sweden)

    Mohan Babu

    Full Text Available Elongation factor RbbA is required for ATP-dependent deacyl-tRNA release presumably after each peptide bond formation; however, there is no information about the cellular role. Proteomic analysis in Escherichia coli revealed that RbbA reciprocally co-purified with a conserved inner membrane protein of unknown function, YhjD. Both proteins are also physically associated with the 30S ribosome and with members of the lipopolysaccharide transport machinery. Genome-wide genetic screens of rbbA and yhjD deletion mutants revealed aggravating genetic interactions with mutants deficient in the electron transport chain. Cells lacking both rbbA and yhjD exhibited reduced cell division, respiration and global protein synthesis as well as increased sensitivity to antibiotics targeting the ETC and the accuracy of protein synthesis. Our results suggest that RbbA appears to function together with YhjD as part of a regulatory network that impacts bacterial oxidative phosphorylation and translation efficiency.

  16. Size-Dependent Protein-Nanoparticle Interactions in Citrate-Stabilized Gold Nanoparticles: The Emergence of the Protein Corona.

    Science.gov (United States)

    Piella, Jordi; Bastús, Neus G; Puntes, Víctor

    2017-01-18

    Surface modifications of highly monodisperse citrate-stabilized gold nanoparticles (AuNPs) with sizes ranging from 3.5 to 150 nm after their exposure to cell culture media supplemented with fetal bovine serum were studied and characterized by the combined use of UV-vis spectroscopy, dynamic light scattering, and zeta potential measurements. In all the tested AuNPs, a dynamic process of protein adsorption was observed, evolving toward the formation of an irreversible hard protein coating known as Protein Corona. Interestingly, the thickness and density of this protein coating were strongly dependent on the particle size, making it possible to identify different transition regimes as the size of the particles increased: (i) NP-protein complexes (or incomplete corona), (ii) the formation of a near-single dense protein corona layer, and (iii) the formation of a multilayer corona. In addition, the different temporal patterns in the evolution of the protein coating came about more quickly for small particles than for the larger ones, further revealing the significant role that size plays in the kinetics of this process. Since the biological identity of the NPs is ultimately determined by the protein corona and different NP-biological interactions take place at different time scales, these results are relevant to biological and toxicological studies.

  17. Effect of super-exchange interaction on ground state magnetic properties of spin-dependent Falicov-Kimball model on a triangular lattice

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, Sant, E-mail: santkumar1210@gmail.com; Maitra, Tulika; Singh, Ishwar [Department of Physics, Indian Institute of Technology Roorkee, Roorkee-247667, Uttarakhand (India); Yadav, Umesh K. [Center for Condensed Matter Theory, Indian Institute of Science, Bangalore-560012 (India)

    2015-06-24

    Ground state magnetic properties are studied by incorporating the super-exchange interaction (J{sub se}) in the spin-dependent Falicov-Kimball model (FKM) between localized (f-) electrons on a triangular lattice for half filled case. Numerical diagonalization and Monte-Carlo simulation are used to study the ground state magnetic properties. We have found that the magnetic moment of (d-) and (f-) electrons strongly depend on the value of Hund’s exchange (J), super-exchange interaction (J{sub se}) and also depends on the number of (d-) electrons (N{sub d}). The ground state changes from antiferromagnetic (AFM) to ferromagnetic (FM) state as we decrease (N{sub d}). Also the density of d electrons at each site depends on the value of J and J{sub se}.

  18. Effect of super-exchange interaction on ground state magnetic properties of spin-dependent Falicov-Kimball model on a triangular lattice

    Science.gov (United States)

    Kumar, Sant; Yadav, Umesh K.; Maitra, Tulika; Singh, Ishwar

    2015-06-01

    Ground state magnetic properties are studied by incorporating the super-exchange interaction (Jse) in the spin-dependent Falicov-Kimball model (FKM) between localized (f-) electrons on a triangular lattice for half filled case. Numerical diagonalization and Monte-Carlo simulation are used to study the ground state magnetic properties. We have found that the magnetic moment of (d-) and (f-) electrons strongly depend on the value of Hund's exchange (J), super-exchange interaction (Jse) and also depends on the number of (d-) electrons (Nd). The ground state changes from antiferromagnetic (AFM) to ferromagnetic (FM) state as we decrease (Nd). Also the density of d electrons at each site depends on the value of J and Jse.

  19. Interactions

    DEFF Research Database (Denmark)

    The main theme of this anthology is the unique interaction between mathematics, physics and philosophy during the beginning of the 20th century. Seminal theories of modern physics and new fundamental mathematical structures were discovered or formed in this period. Significant physicists...... such as Lorentz and Einstein as well as mathematicians such as Poincare, Minkowski, Hilbert and Weyl contributed to this development. They created the new physical theories and the mathematical disciplines that play such paramount roles in their mathematical formulations. These physicists and mathematicians were...

  20. Scale-Dependent Fracture-Matrix Interactions and Their Impact on Radionuclide Transport: Development of efficient particle-tracking methods

    Energy Technology Data Exchange (ETDEWEB)

    Rajaram, Harihar [University of Colorado, Boulder; Brutz, Michael [University of Colorado, Boulder; Klein, Dylan R [University of Colorado, Boulder; Mallikamas, Wasin [University of Colorado, Boulder

    2014-09-18

    Matrix Diffusion and Adsorption within a rock matrix are important mechanisms for retarding transport of radionuclides in fractured rock. Due to computational limitations and difficulties in characterizing complex subsurface systems, diffusive exchange between a fracture network and surrounding rock matrix is often modeled using simplified conceptual representations. There is significant uncertainty in “effective” parameters used in these models, such as the “effective matrix diffusivity”. Often, these parameters are estimated by fitting sparse breakthrough data, and estimated values fall outside meaningful ranges, because simplified interpretive models do not consider complex three-dimensional flow. There is limited understanding of the relationship between the effective parameters and rock mass characteristics including network structure and matrix properties. There is also evidence for an apparent scale-dependence in “effective matrix diffusion” coefficients. These observations raise questions on whether fracture-matrix interaction parameters estimated from small-scale tracer tests can be used for predicting radionuclide fate and transport at the scale of DOE field sites. High-resolution three-dimensional Discrete-Fracture-Network-Matrix (DFNM) models based on well-defined local scale transport equations can help to address some of these questions. Due to tremendous advances in computational technology over the last 10 years, DFNM modeling in relatively large domains is now feasible. The overarching objective of our research is to use DFNM modeling to improve fundamental understanding of how effective parameters in conceptual models are related to fracture network structure and matrix properties. An advanced three-dimensional DFNM model is being developed, which combines upscaled particle-tracking algorithms for fracture-matrix interaction and a parallel fracture-network flow simulator. The particle-tracking algorithms allow complexity in flow fields

  1. Computer modeling reveals that modifications of the histone tail charges define salt-dependent interaction of the nucleosome core particles.

    Science.gov (United States)

    Yang, Ye; Lyubartsev, Alexander P; Korolev, Nikolay; Nordenskiöld, Lars

    2009-03-18

    Coarse-grained Langevin molecular dynamics computer simulations were conducted for systems that mimic solutions of nucleosome core particles (NCPs). The NCP was modeled as a negatively charged spherical particle representing the complex of DNA and the globular part of the histones combined with attached strings of connected charged beads modeling the histone tails. The size, charge, and distribution of the tails relative to the core were built to match real NCPs. Three models of NCPs were constructed to represent different extents of covalent modification on the histone tails: (nonmodified) recombinant (rNCP), acetylated (aNCP), and acetylated and phosphorylated (paNCP). The simulation cell contained 10 NCPs in a dielectric continuum with explicit mobile counterions and added salt. The NCP-NCP interaction is decisively dependent on the modification state of the histone tails and on salt conditions. Increasing the monovalent salt concentration (KCl) from salt-free to physiological concentration leads to NCP aggregation in solution for rNCP, whereas NCP associates are observed only occasionally in the system of aNCPs. In the presence of divalent salt (Mg(2+)), rNCPs form dense stable aggregates, whereas aNCPs form aggregates less frequently. Aggregates are formed via histone-tail bridging and accumulation of counterions in the regions of NCP-NCP contacts. The paNCPs do not show NCP-NCP interaction upon addition of KCl or in the presence of Mg(2+). Simulations for systems with a gradual substitution of K(+) for Mg(2+), to mimic the Mg(2+) titration of an NCP solution, were performed. The rNCP system showed stronger aggregation that occurred at lower concentrations of added Mg(2+), compared to the aNCP system. Additional molecular dynamics simulations performed with a single NCP in the simulation cell showed that detachment of the tails from the NCP core was modest under a wide range of salt concentrations. This implies that salt-induced tail dissociation of the

  2. Surface Structure Dependence of SO 2 Interaction with Ceria Nanocrystals with Well-Defined Surface Facets

    Energy Technology Data Exchange (ETDEWEB)

    Tumuluri, Uma; Li, Meijun; Cook, Brandon G.; Sumpter, Bobby; Dai, Sheng; Wu, Zili

    2015-12-31

    The effects of the surface structure of ceria (CeO2) on the nature, strength, and amount of species resulting from SO2 adsorption were studied using in situ IR and Raman spectroscopies coupled with mass spectrometry, along with first-principles calculations based on density functional theory (DFT). CeO2 nanocrystals with different morphologies, namely, rods (representing a defective structure), cubes (100 facet), and octahedra (111 facet), were used to represent different CeO2 surface structures. IR and Raman spectroscopic studies showed that the structure and binding strength of adsorbed species from SO2 depend on the shape of the CeO2 nanocrystals. SO2 adsorbs mainly as surface sulfites and sulfates at room temperature on CeO2 rods, cubes, and octahedra that were either oxidatively or reductively pretreated. The formation of sulfites is more evident on CeO2 octahedra, whereas surface sulfates are more prominent on CeO2 rods and cubes. This is explained by the increasing reducibility of the surface oxygen in the order octahedra < cubes < rods. Bulk sulfites are also formed during SO2 adsorption on reduced CeO2 rods. The formation of surface sulfites and sulfates on CeO2 cubes is in good agreement with our DFT results of SO2 interactions with the CeO2(100) surface. CeO2 rods desorb SO2 at higher temperatures than cubes and octahedra nanocrystals, but bulk sulfates are formed on CeO2 rods and cubes after high-temperature desorption whereas only some surface sulfates/sulfites are left on octahedra. This difference is rationalized by the fact that CeO2 rods have the highest surface basicity and largest amount of defects among the three nanocrystals, so they bind and react with SO2 strongly and are the most degraded after SO2 adsorption cycles. The fundamental understanding obtained in this work on the effects of the surface structure and defects on the interaction of SO2 with CeO2 provides insights for the design of more sulfur-resistant CeO2-based catalysts.

  3. On the existence of weak solution to the coupled fluid-structure interaction problem for non-Newtonian shear-dependent fluid

    OpenAIRE

    Hundertmark-Zaušková, A.; Lukáčová-Medviďová, M.; Nečasová, Š. (Šárka)

    2016-01-01

    We study the existence of weak solution for unsteady fluid-structure interaction problem for shear-thickening flow. The time dependent domain has at one part a flexible elastic wall. The evolution of fluid domain is governed by the generalized string equation with action of the fluid forces. The power-law viscosity model is applied to describe shear-dependent non-Newtonian fluids.

  4. Lithium enhances CRTC oligomer formation and the interaction between the CREB coactivators CRTC and CBP--implications for CREB-dependent gene transcription.

    Science.gov (United States)

    Heinrich, Annette; von der Heyde, Anne Sophie; Böer, Ulrike; Phu, Do Thanh; Tzvetkov, Mladen; Oetjen, Elke

    2013-01-01

    Lithium salts are important drugs to treat bipolar disorder. Previous work showed that lithium by enforcing the interaction between the transcription factor CREB and its coactivator CRTC1 enhanced cAMP-stimulated CREB-dependent gene transcription. Both CREB and CRTC have been implicated in neuronal adaptation, which might underlie lithium's therapeutic action. In the present study the mechanisms of lithium action on cAMP-induced CREB-dependent gene transcription were further elucidated. Transient transfection assays revealed that all three CRTC isoforms conferred lithium responsiveness to CREB whereas their intrinsic transcriptional activities remained unchanged by lithium, suggesting a conformational change of CREB or CRTC by lithium. In in vitro protein-protein interaction assays lithium enhanced the interaction between CREB and both coactivators CRTC and CBP. Furthermore, lithium enforced the oligomerization of CRTC, a prerequisite for CREB interaction. For further evaluation it was investigated whether lithium competes with magnesium, which coordinates the conformation of the CREB basic region leucine zipper (bZip). Mutational analysis of the magnesium coordinating lysine-290 within the bZip, in vitro and intracellular interaction assays and luciferase reporter-gene assays revealed that the effect of lithium on the CREB-CRTC interaction or on the transcriptional activity, respectively, was not affected by the mutation, thus excluding a magnesium-lithium competition. However, the CREB-CRTC interaction was strongly increased in lysine-290-mutants thereby extending the CRTC-CREB interaction domain. Taken together the results exclude a competition between lithium and magnesium at the bZip, but suggest that lithium by enforcing the CRTC-oligomer formation and the interaction of CREB-CBP-CRTC enhances cAMP-induced CREB-dependent gene transcription.

  5. BioC-compatible full-text passage detection for protein-protein interactions using extended dependency graph.

    Science.gov (United States)

    Peng, Yifan; Arighi, Cecilia; Wu, Cathy H; Vijay-Shanker, K

    2016-01-01

    There has been a large growth in the number of biomedical publications that report experimental results. Many of these results concern detection of protein-protein interactions (PPI). In BioCreative V, we participated in the BioC task and developed a PPI system to detect text passages with PPIs in the full-text articles. By adopting the BioC format, the output of the system can be seamlessly added to the biocuration pipeline with little effort required for the system integration. A distinctive feature of our PPI system is that it utilizes extended dependency graph, an intermediate level of representation that attempts to abstract away syntactic variations in text. As a result, we are able to use only a limited set of rules to extract PPI pairs in the sentences, and additional rules to detect additional passages for PPI pairs. For evaluation, we used the 95 articles that were provided for the BioC annotation task. We retrieved the unique PPIs from the BioGRID database for these articles and show that our system achieves a recall of 83.5%. In order to evaluate the detection of passages with PPIs, we further annotated Abstract and Results sections of 20 documents from the dataset and show that an f-value of 80.5% was obtained. To evaluate the generalizability of the system, we also conducted experiments on AIMed, a well-known PPI corpus. We achieved an f-value of 76.1% for sentence detection and an f-value of 64.7% for unique PPI detection.Database URL: http://proteininformationresource.org/iprolink/corpora.

  6. Thermoperiodic control of hypocotyl elongation depends on auxin-induced ethylene signaling that controls downstream PHYTOCHROME INTERACTING FACTOR3 activity.

    Science.gov (United States)

    Bours, Ralph; Kohlen, Wouter; Bouwmeester, Harro J; van der Krol, Alexander

    2015-02-01

    We show that antiphase light-temperature cycles (negative day-night temperature difference [-DIF]) inhibit hypocotyl growth in Arabidopsis (Arabidopsis thaliana). This is caused by reduced cell elongation during the cold photoperiod. Cell elongation in the basal part of the hypocotyl under -DIF was restored by both 1-aminocyclopropane-1-carboxylic acid (ACC; ethylene precursor) and auxin, indicating limited auxin and ethylene signaling under -DIF. Both auxin biosynthesis and auxin signaling were reduced during -DIF. In addition, expression of several ACC Synthase was reduced under -DIF but could be restored by auxin application. In contrast, the reduced hypocotyl elongation of ethylene biosynthesis and signaling mutants could not be complemented by auxin, indicating that auxin functions upstream of ethylene. The PHYTOCHROME INTERACTING FACTORS (PIFs) PIF3, PIF4, and PIF5 were previously shown to be important regulators of hypocotyl elongation. We now show that, in contrast to pif4 and pif5 mutants, the reduced hypocotyl length in pif3 cannot be rescued by either ACC or auxin. In line with this, treatment with ethylene or auxin inhibitors reduced hypocotyl elongation in PIF4 overexpressor (PIF4ox) and PIF5ox but not PIF3ox plants. PIF3 promoter activity was strongly reduced under -DIF but could be restored by auxin application in an ACC Synthase-dependent manner. Combined, these results show that PIF3 regulates hypocotyl length downstream, whereas PIF4 and PIF5 regulate hypocotyl length upstream of an auxin and ethylene cascade. We show that, under -DIF, lower auxin biosynthesis activity limits the signaling in this pathway, resulting in low activity of PIF3 and short hypocotyls.

  7. Interactions between colon cancer cells and tumor-infiltrated macrophages depending on cancer cell-derived colony stimulating factor 1.

    Science.gov (United States)

    Wang, Huayang; Shao, Qianqian; Sun, Jintang; Ma, Chao; Gao, Wenjuan; Wang, Qingjie; Zhao, Lei; Qu, Xun

    2016-04-01

    Tumor-infiltrated macrophages were potential targets of the immune therapy for patients with colon cancer. Colony stimulating factor 1 (CSF1) is a primary chemoattractant and functional regulator for macrophages, and therefore would be a feasible intervention for the macrophage-targeting therapeutics. However, the expression of CSF1 in colon cancer microenvironment and its roles in cancer development is largely unknown. In the present study, we found that CSF1 was over-expressed exclusively in colon cancer cells and was correlated with macrophages infiltration. The high CSF1 expression and macrophages infiltration were related to the tumor-node-metastasis (TNM) stage of colon cancer, and suggested to be positively associated with survival of colon cancer patients. In the in vitro studies based on an indirect Transwell system, we found that co-culture with macrophage promoted CSF1 production in colon cancer cells. Further investigation on regulatory mechanisms suggested that CSF1 production in colon cancer cells was dependent on PKC pathway, which was activated by IL-8, mainly produced by macrophages. Moreover, colon cancer cell-derived CSF1 drove the recruitment of macrophages and re-educated their secretion profile, including the augment of IL-8 production. The mice tumor xenografts study also found that over-expression of CSF1 in colon cancer cells promoted intratumoral infiltration of macrophages, and partially suppressed tumor growth. In all, our results demonstrated that CSF1 was an important factor in the colon cancer microenvironment, involving in the interactions between colon cancer cells and tumor-infiltrated macrophages.

  8. DNA interactions with a Methylene Blue redox indicator depend on the DNA length and are sequence specific.

    Science.gov (United States)

    Farjami, Elaheh; Clima, Lilia; Gothelf, Kurt V; Ferapontova, Elena E

    2010-06-01

    A DNA molecular beacon approach was used for the analysis of interactions between DNA and Methylene Blue (MB) as a redox indicator of a hybridization event. DNA hairpin structures of different length and guanine (G) content were immobilized onto gold electrodes in their folded states through the alkanethiol linker at the 5'-end. Binding of MB to the folded hairpin DNA was electrochemically studied and compared with binding to the duplex structure formed by hybridization of the hairpin DNA to a complementary DNA strand. Variation of the electrochemical signal from the DNA-MB complex was shown to depend primarily on the DNA length and sequence used: the G-C base pairs were the preferential sites of MB binding in the duplex. For short 20 nts long DNA sequences, the increased electrochemical response from MB bound to the duplex structure was consistent with the increased amount of bound and electrochemically readable MB molecules (i.e. MB molecules that are available for the electron transfer (ET) reaction with the electrode). With longer DNA sequences, the balance between the amounts of the electrochemically readable MB molecules bound to the hairpin DNA and to the hybrid was opposite: a part of the MB molecules bound to the long-sequence DNA duplex seem to be electrochemically mute due to long ET distance. The increasing electrochemical response from MB bound to the short-length DNA hybrid contrasts with the decreasing signal from MB bound to the long-length DNA hybrid and allows an "off"-"on" genosensor development.

  9. Specific interaction between EF-G and RRF and its implication for GTP-dependent ribosome splitting into subunits

    Science.gov (United States)

    Gao, Ning; Zavialov, Andrey V.; Ehrenberg, Måns; Frank, Joachim

    2008-01-01

    Summary After termination of protein synthesis, the bacterial ribosome is split into its 30S and 50S subunits by the action of ribosome recycling factor (RRF) and elongation factor G (EF-G) in a GTP-hydrolysis dependent manner. Based on a previous cryo-electron microscopy (cryo-EM) study of ribosomal complexes, we have proposed that the binding of EF-G to an RRF containing post-termination ribosome triggers an inter-domain rotation of RRF, which destabilizes two strong intersubunit bridges (B2a and B3) and, ultimately, separates the two subunits. Here, we present a 9 Å (FSC at 0.5 cutoff) cryo-EM map of a 50S EFG GDPNP RRF complex and a quasi-atomic model derived from it, showing the interaction between EF-G and RRF on the 50S subunit in the presence of the non-cleavable GTP analogue GDPNP. The detailed information in this model and a comparative analysis of EF-G structures in various nucleotide- and ribosome-bound states show how rotation of the RRF head domain may be triggered by various domains of EF-G. For validation of our structural model, all known mutations in EF-G and RRF that relate to ribosome recycling have been taken into account. More importantly, our results indicate a substantial conformational change in the Switch I region of EF-G, suggesting that a conformational signal transduction mechanism, similar to that employed in tRNA translocation on the ribosome by EF-G, translates a large-scale movement of EF-G’s domain IV, induced by GTP hydrolysis, into the domain rotation of RRF that eventually splits the ribosome into subunits. PMID:17996252

  10. Design of spin-forbidden transitions for polypyridyl metal complexes by time-dependent density functional theory including spin-orbit interaction.

    Science.gov (United States)

    Kanno, Shohei; Imamura, Yutaka; Hada, Masahiko

    2016-05-25

    We explore spin-forbidden transitions for a Ru dye with an N3 skeleton and an Fe dye with a DX1 skeleton by time-dependent density functional theory with spin-orbit interaction. The modified N3-based Ru dye with iodine anions has an absorption edge in the long wavelength region which is not observed in the original N3 dye. The long wavelength absorption edge originates from the spin-orbit interaction with iodine. Although the Fe dye has a small spin-orbit interaction, because of less spin-orbit interaction from the light metal, spin-forbidden transitions also occur for DX1-based Fe dye systems with iodine anions. This result indicates that the introduction of iodine can strengthen the spin-orbit interaction for a dye sensitizer and offers a new approach for designing spin-forbidden transitions.

  11. The concentration-dependent nature of in vitro amphotericin B-itraconazole interaction against Aspergillus fumigatus: isobolographic and response surface analysis of complex pharmacodynamic interactions.

    NARCIS (Netherlands)

    Meletiadis, J.; Dorsthorst, D.T.A. te; Verweij, P.E.

    2006-01-01

    The interaction between polyenes and azoles is not well understood. We therefore explored the in vitro combination of amphotericin B with itraconazole against 14 clinical Aspergillus fumigatus isolates (9 itraconazole susceptible and 5 itraconazole resistant) with a colorimetric broth microdilution

  12. Exact Solutions of the Mass-Dependent Klein-Gordon Equation with the Vector Quark-Antiquark Interaction and Harmonic Oscillator Potential

    Directory of Open Access Journals (Sweden)

    M. K. Bahar

    2013-01-01

    Full Text Available Using the asymptotic iteration and wave function ansatz method, we present exact solutions of the Klein-Gordon equation for the quark-antiquark interaction and harmonic oscillator potential in the case of the position-dependent mass.

  13. Efficient Interaction between Arenavirus Nucleoprotein (NP) and RNA-Dependent RNA Polymerase (L) Is Mediated by the Virus Nucleocapsid (NP-RNA) Template.

    Science.gov (United States)

    Iwasaki, Masaharu; Ngo, Nhi; Cubitt, Beatrice; de la Torre, Juan C

    2015-05-01

    In this study, we document that efficient interaction between arenavirus nucleoprotein (NP) and RNA-dependent RNA polymerase (L protein), the two trans-acting viral factors required for both virus RNA replication and gene transcription, requires the presence of virus-specific RNA sequences located within the untranslated 5' and 3' termini of the viral genome.

  14. Order Effects of Learning with Modeling and Simulation Software on Field-Dependent and Field-Independent Children's Cognitive Performance: An Interaction Effect

    Science.gov (United States)

    Angeli, Charoula; Valanides, Nicos; Polemitou, Eirini; Fraggoulidou, Elena

    2014-01-01

    The study examined the interaction between field dependence-independence (FD/I) and learning with modeling software and simulations, and their effect on children's performance. Participants were randomly assigned into two groups. Group A first learned with a modeling tool and then with simulations. Group B learned first with simulations and then…

  15. Spin-Dependent Weakly-Interacting-Massive-Particle-Nucleon Cross Section Limits from First Data of PandaX-II Experiment

    Science.gov (United States)

    Fu, Changbo; Cui, Xiangyi; Zhou, Xiaopeng; Chen, Xun; Chen, Yunhua; Fang, Deqing; Giboni, Karl; Giuliani, Franco; Han, Ke; Huang, Xingtao; Ji, Xiangdong; Ju, Yonglin; Lei, Siao; Li, Shaoli; Liu, Huaxuan; Liu, Jianglai; Ma, Yugang; Mao, Yajun; Ren, Xiangxiang; Tan, Andi; Wang, Hongwei; Wang, Jiming; Wang, Meng; Wang, Qiuhong; Wang, Siguang; Wang, Xuming; Wang, Zhou; Wu, Shiyong; Xiao, Mengjiao; Xie, Pengwei; Yan, Binbin; Yang, Yong; Yue, Jianfeng; Zhang, Hongguang; Zhang, Tao; Zhao, Li; Zhou, Ning; PandaX-II Collaboration

    2017-02-01

    New constraints are presented on the spin-dependent weakly-interacting-massive-particle- (WIMP-)nucleon interaction from the PandaX-II experiment, using a data set corresponding to a total exposure of 3.3 ×104 kg day . Assuming a standard axial-vector spin-dependent WIMP interaction with Xe 129 and Xe 131 nuclei, the most stringent upper limits on WIMP-neutron cross sections for WIMPs with masses above 10 GeV /c2 are set in all dark matter direct detection experiments. The minimum upper limit of 4.1 ×10-41 cm2 at 90% confidence level is obtained for a WIMP mass of 40 GeV /c2 . This represents more than a factor of 2 improvement on the best available limits at this and higher masses. These improved cross-section limits provide more stringent constraints on the effective WIMP-proton and WIMP-neutron couplings.

  16. Quantum equations of motion for multimode laser generation with a spatial dependence of the atom interaction with the field taken into account

    Science.gov (United States)

    Kozlovskii, A. V.

    2011-04-01

    We derive equations of motion for the electromagnetic field operators a{q'/ + }aq″ for a three-level multimode laser with a spatial dependence of the interaction of atoms with the field of a standing wave in a cavity taken into account. We calculate and analyze the dynamics of means of photon numbers in the field modes and of the correlation function of field modes. We explore the effect of intermode correlations on the dynamics of establishing stationary laser generation. We find that taking the spatial dependence of the interaction of atoms with the field and the intermode correlation into account in investigating the means of photon numbers leads to revealing new properties of laser generation, such as saturation of the laser radiation intensity in a single-mode regime and generation of short light pulses of side below-threshold modes with the amplitudes depending on the initial state of the field in a cavity.

  17. TP53INP1, a tumor suppressor, interacts with LC3 and ATG8-family proteins through the LC3-interacting region (LIR) and promotes autophagy-dependent cell death.

    Science.gov (United States)

    Seillier, M; Peuget, S; Gayet, O; Gauthier, C; N'Guessan, P; Monte, M; Carrier, A; Iovanna, J L; Dusetti, N J

    2012-09-01

    TP53INP1 (tumor protein 53-induced nuclear protein 1) is a tumor suppressor, whose expression is downregulated in cancers from different organs. It was described as a p53 target gene involved in cell death, cell-cycle arrest and cellular migration. In this work, we show that TP53INP1 is also able to interact with ATG8-family proteins and to induce autophagy-dependent cell death. In agreement with this finding, we observe that TP53INP1, which is mainly nuclear, relocalizes in autophagosomes during autophagy where it is eventually degraded. TP53INP1-LC3 interaction occurs via a functional LC3-interacting region (LIR). Inactivating mutations of this sequence abolish TP53INP1-LC3 interaction, relocalize TP53INP1 in autophagosomes and decrease TP53INP1 ability to trigger cell death. Interestingly, TP53INP1 binds to ATG8-family proteins with higher affinity than p62, suggesting that it could partially displace p62 from autophagosomes, modifying thereby their composition. Moreover, silencing the expression of autophagy related genes (ATG5 or Beclin-1) or inhibiting caspase activity significantly decreases cell death induced by TP53INP1. These data indicate that cell death observed after TP53INP1-LC3 interaction depends on both autophagy and caspase activity. We conclude that TP53INP1 could act as a tumor suppressor by inducing cell death by caspase-dependent autophagy.

  18. Immobilization of copper by biochar in Cu-enriched agricultural soils depends on interactions with soil organic carbon

    Science.gov (United States)

    Mlinkov, Slađana; Zehetner, Franz; Rosner, Franz; Dersch, Georg; Soja, Gerhard

    2017-04-01

    The appearance of downy mildew (Plasmopara viticola) in European vineyards of the 19th century was the starting point for the search of effective fungicides to avoid severe yield losses. Copper has been found as an important ingredient for several fungicides that have been used in agriculture and horticulture. For organic viticulture, several diseases can only be antagonized with Cu-containing fungicides as the application of organic fungicides is not permitted. This long-lasting dependence on Cu-fungicides has led to a gradual Cu enrichment of vineyard soils in traditional wine-growing areas, locally exceeding 300 mg/kg. Although these concentrations do not affect the vines or wine quality, they may impair soil microbiological functions in the top soil layer or the root growth of green cover plants. Therefore, measures are demanded that reduce the bioavailability of copper, thereby reducing the ecotoxicological effects. The use of biochar and compost as soil amendment has been suggested as a strategy to immobilize Cu and reduce the exchangeable fractions. In our study we have tested the hypothesis that biochar immobilizes the bioavailability of Cu for soil cover crops and reduces soil pore water concentrations. This study had the objective to test the interactions of compost and biochar with respect to Cu immobilization in vineyard soils. A Cu-enriched vineyard soil (250 mg Cu kg-1) was analyzed both in greenhouse and field experiments. In both experiments, soil with or without biochar and/or compost and mixtures of the two components were used. In the greenhouse experiments, was used as test plant Lolium multiflorum for Cu uptake; in the field, Lolium perenne and Trifolium repens were analyzed. Greenhouse experiment: Soil pore water concentrations showed clearer differences in Cu concentration than Lolium multiflorum shoots. Compost increased dissolved organic carbon (DOC) and Cu in soil pore water and biochar reduced it significantly. The mixtures of compost and

  19. pH dependent salinity-boron interactions impact yield, biomass, evapotranspiration and boron uptake in broccoli (Brassica oleracea L.)

    Science.gov (United States)

    Soil pH is known to influence many important biochemical processes in plants and soils, however its role in salinity - boron interactions affecting plant growth and ion relations has not been examined. The purpose of this research was to evaluate the interactive effects of salinity, boron and soil ...

  20. Electrons, muons and hadrons in extensive air showers and how do they depend on nuclear interaction model, part 1

    Science.gov (United States)

    Wrotniak, J. A.; Yodh, G. B.

    1985-01-01

    Monte Carlo simulations of extensive air showers were performed using a couple of different nuclear interaction models and obtaining a variety of shower characteristics. The discussion of these shows that the sensitivity of observables to the primary mass spectrum is significantly stronger than to the interaction model, the latter being quite weak.

  1. Pursuing Financial Stability: A Resource Dependence Perspective on Interactions between Pro-Vice Chancellors in a Network of Universities

    Science.gov (United States)

    Pilbeam, Colin

    2012-01-01

    In resource-constrained environments universities increasingly must interact collaboratively and competitively to ensure financial stability. Such interactions are supported by the actions of senior university managers. This study investigated the extent and purpose of the interconnections between members of two groups of pro-vice chancellors…

  2. Predicting Vocational Rehabilitation Outcomes for People with Alcohol Abuse/Dependence: An Application of Chi-Squared Automatic Interaction Detector

    Science.gov (United States)

    Brickham, Dana M.

    2012-01-01

    People with alcohol abuse/dependence disabilities are often faced with a complex recovery process due to the exacerbating and chronic aspects of their condition. Vocational rehabilitation for people with alcohol abuse/dependence can help individuals access and maintain employment, and through employment can enhance physical and psychological…

  3. Human I-mfa domain proteins specifically interact with KSHV LANA and affect its regulation of Wnt signaling-dependent transcription.

    Science.gov (United States)

    Kusano, Shuichi; Eizuru, Yoshito

    2010-06-04

    Kaposi's sarcoma-associated herpes virus (KSHV)-encoded latency-associated nuclear antigen (LANA) protein has been reported to interact with glycogen synthase kinase 3beta (GSK-3beta) and to negatively regulate its activity, leading to stimulation of GSK-3beta-dependent beta-catenin degradation. We show here that the I-mfa domain proteins, HIC (human I-mfa domain-containing protein) and I-mfa (inhibitor of MyoD family a), interacted in vivo with LANA through their C-terminal I-mfa domains. This interaction affected the intracellular localization of HIC, inhibited the LANA-dependent transactivation of a beta-catenin-regulated reporter construct, and decreased the level of the LANA.GSK-3beta complex. These data reveal for the first time that I-mfa domain proteins interact with LANA and negatively regulate LANA-mediated activation of Wnt signaling-dependent transcription by inhibiting the formation of the LANA.GSK-3beta complex.

  4. Human I-mfa domain proteins specifically interact with KSHV LANA and affect its regulation of Wnt signaling-dependent transcription

    Energy Technology Data Exchange (ETDEWEB)

    Kusano, Shuichi, E-mail: skusano@m2.kufm.kagoshima-u.ac.jp [Division of Persistent and Oncogenic Viruses, Center for Chronic Viral Diseases, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima 890-8544 (Japan); Eizuru, Yoshito [Division of Persistent and Oncogenic Viruses, Center for Chronic Viral Diseases, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima 890-8544 (Japan)

    2010-06-04

    Kaposi's sarcoma-associated herpes virus (KSHV)-encoded latency-associated nuclear antigen (LANA) protein has been reported to interact with glycogen synthase kinase 3{beta} (GSK-3{beta}) and to negatively regulate its activity, leading to stimulation of GSK-3{beta}-dependent {beta}-catenin degradation. We show here that the I-mfa domain proteins, HIC (human I-mfa domain-containing protein) and I-mfa (inhibitor of MyoD family a), interacted in vivo with LANA through their C-terminal I-mfa domains. This interaction affected the intracellular localization of HIC, inhibited the LANA-dependent transactivation of a {beta}-catenin-regulated reporter construct, and decreased the level of the LANA.GSK-3{beta} complex. These data reveal for the first time that I-mfa domain proteins interact with LANA and negatively regulate LANA-mediated activation of Wnt signaling-dependent transcription by inhibiting the formation of the LANA.GSK-3{beta} complex.

  5. PIP₂-dependent coupling is prominent in Kv7.1 due to weakened interactions between S4-S5 and S6.

    Science.gov (United States)

    Kasimova, Marina A; Zaydman, Mark A; Cui, Jianmin; Tarek, Mounir

    2015-01-06

    Among critical aspects of voltage-gated potassium (Kv) channels' functioning is the effective communication between their two composing domains, the voltage sensor (VSD) and the pore. This communication, called coupling, might be transmitted directly through interactions between these domains and, as recently proposed, indirectly through interactions with phosphatidylinositol-4,5-bisphosphate (PIP₂), a minor lipid of the inner plasma membrane leaflet. Here, we show how the two components of coupling, mediated by protein-protein or protein-lipid interactions, both contribute in the Kv7.1 functioning. On the one hand, using molecular dynamics simulations, we identified a Kv7.1 PIP₂ binding site that involves residues playing a key role in PIP₂-dependent coupling. On the other hand, combined theoretical and experimental approaches have shown that the direct interaction between the segments of the VSD (S4-S5) and the pore (S6) is weakened by electrostatic repulsion. Finally, we conclude that due to weakened protein-protein interactions, the PIP2-dependent coupling is especially prominent in Kv7.1.

  6. PIP2-dependent coupling is prominent in Kv7.1 due to weakened interactions between S4-S5 and S6

    Science.gov (United States)

    Kasimova, Marina A.; Zaydman, Mark A.; Cui, Jianmin; Tarek, Mounir

    2015-01-01

    Among critical aspects of voltage-gated potassium (Kv) channels' functioning is the effective communication between their two composing domains, the voltage sensor (VSD) and the pore. This communication, called coupling, might be transmitted directly through interactions between these domains and, as recently proposed, indirectly through interactions with phosphatidylinositol-4,5-bisphosphate (PIP2), a minor lipid of the inner plasma membrane leaflet. Here, we show how the two components of coupling, mediated by protein-protein or protein-lipid interactions, both contribute in the Kv7.1 functioning. On the one hand, using molecular dynamics simulations, we identified a Kv7.1 PIP2 binding site that involves residues playing a key role in PIP2-dependent coupling. On the other hand, combined theoretical and experimental approaches have shown that the direct interaction between the segments of the VSD (S4-S5) and the pore (S6) is weakened by electrostatic repulsion. Finally, we conclude that due to weakened protein-protein interactions, the PIP2-dependent coupling is especially prominent in Kv7.1.

  7. Regulation of Nucleocytoplasmic Shuttling of Bruton's Tyrosine Kinase (Btk) through a Novel SH3-Dependent Interaction with Ankyrin Repeat Domain 54 (ANKRD54)

    Science.gov (United States)

    Hussain, Alamdar; Mohammad, Dara K.; Mohamed, Abdalla J.; Nguyen, Vivian; Metalnikov, Pavel; Colwill, Karen; Pawson, Tony; Nore, Beston F.

    2012-01-01

    Bruton's tyrosine kinase (Btk), belonging to the Tec family of tyrosine kinases (TFKs), is essential for B-lymphocyte development. Abrogation of Btk signaling causes human X-linked agammaglobulinemia (XLA) and murine X-linked immunodeficiency (Xid). We employed affinity purification of Flag-tagged Btk, combined with tandem mass spectrometry, to capture and identify novel interacting proteins. We here characterize the interaction with ankryin repeat domain 54 protein (ANKRD54), also known as Lyn-interacting ankyrin repeat protein (Liar). While Btk is a nucleocytoplasmic protein, the Liar pool was found to shuttle at a higher rate than Btk. Importantly, our results suggest that Liar mediates nuclear export of both Btk and another TFK, Txk/Rlk. Liar-mediated Btk shuttling was enriched for activation loop, nonphosphorylated Btk and entirely dependent on Btk's SH3 domain. Liar also showed reduced binding to an aspartic acid phosphomimetic SH3 mutant. Three other investigated nucleus-located proteins, Abl, estrogen receptor β (ERβ), and transcription factor T-bet, were all unaffected by Liar. We mapped the interaction site to the C terminus of the Btk SH3 domain. A biotinylated, synthetic Btk peptide, ARDKNGQEGYIPSNYVTEAEDS, was sufficient for this interaction. Liar is the first protein identified that specifically influences the nucleocytoplasmic shuttling of Btk and Txk and belongs to a rare group of known proteins carrying out this activity in a Crm1-dependent manner. PMID:22527282

  8. Interactions between plant traits and sediment characteristics influencing species establishment and scale-dependent feedbacks in salt marsh ecosystems

    NARCIS (Netherlands)

    Schwarz, C.; Bouma, T.J.; Zhang, L.Q.; Temmerman, S.; Ysebaert, T.; Herman, P.M.J.

    2015-01-01

    The importance of ecosystem engineering and biogeomorphic processes in shaping many aquatic and semi-aquatic landscapes is increasingly acknowledged. Ecosystem engineering and biogeomorphic landscape formation involves two critical processes: (1) species establishment, and (2) scale-dependent

  9. Interactions between plant traits and sediment characteristics influencing species establishment and scale-dependent feedbacks in salt marsh ecosystems

    NARCIS (Netherlands)

    Schwarz, C.; Bouma, T.J.; Zhang, L.Q.; Temmerman, S.; Ysebaert, T.; Herman, P.M.J.

    2015-01-01

    The importance of ecosystem engineering and biogeomorphic processes in shaping many aquatic and semi-aquatic landscapes is increasingly acknowledged. Ecosystem engineering and biogeomorphic landscape formation involves two critical processes: (1) species establishment, and (2) scale-dependent

  10. Interaction of the mu-opioid receptor with GPR177 (Wntless) inhibits Wnt secretion: potential implications for opioid dependence

    OpenAIRE

    Stagljar Igor; Van Bockstaele Elisabeth J; Reyes Beverly AS; Wong Victoria; Kittanakom Saranya; Jin Jay; Berrettini Wade; Levenson Robert

    2010-01-01

    Abstract Background Opioid agonist drugs produce analgesia. However, long-term exposure to opioid agonists may lead to opioid dependence. The analgesic and addictive properties of opioid agonist drugs are mediated primarily via the mu-opioid receptor (MOR). Opioid agonists appear to alter neuronal morphology in key brain regions implicated in the development of opioid dependence. However, the precise role of the MOR in the development of these neuronal alterations remains elusive. We hypothes...

  11. No simple dependence between protein evolution rate and the number of protein-protein interactions: only the most prolific interactors tend to evolve slowly

    Directory of Open Access Journals (Sweden)

    Koonin Eugene V

    2003-01-01

    support the hypothesis that the evolutionary rates of the majority of proteins substantially depend on the number of protein-protein interactions they are involved in. However, a small fraction of yeast proteins with the largest number of interactions (the hubs of the interaction network tend to evolve slower than the bulk of the proteins.

  12. The dependence of Ig class-switching on the nuclear export sequence of AID likely reflects interaction with factors additional to Crm1 exportin

    Science.gov (United States)

    Ellyard, Julia I; Benk, Amelie S; Taylor, Benjamin; Rada, Cristina; Neuberger, Michael S

    2011-01-01

    Activation-induced deaminase (AID) is a B lymphocyte-specific DNA deaminase that triggers Ig class-switch recombination (CSR) and somatic hypermutation. It shuttles between cytoplasm and nucleus, containing a nuclear export sequence (NES) at its carboxyterminus. Intriguingly, the precise nature of this NES is critical to AID's function in CSR, though not in somatic hypermutation. Many alterations to the NES, while preserving its nuclear export function, destroy CSR ability. We have previously speculated that AID's ability to potentiate CSR may critically depend on the affinity of interaction between its NES and Crm1 exportin. Here, however, by comparing multiple AID NES mutants, we find that – beyond a requirement for threshold Crm1 binding – there is little correlation between CSR and Crm1 binding affinity. The results suggest that CSR, as well as the stabilisation of AID, depend on an interaction between the AID C-terminal decapeptide and factor(s) additional to Crm1. PMID:21268017

  13. The dependence of Ig class-switching on the nuclear export sequence of AID likely reflects interaction with factors additional to Crm1 exportin.

    Science.gov (United States)

    Ellyard, Julia I; Benk, Amelie S; Taylor, Benjamin; Rada, Cristina; Neuberger, Michael S

    2011-02-01

    Activation-induced deaminase (AID) is a B lymphocyte-specific DNA deaminase that triggers Ig class-switch recombination (CSR) and somatic hypermutation. It shuttles between cytoplasm and nucleus, containing a nuclear export sequence (NES) at its carboxyterminus. Intriguingly, the precise nature of this NES is critical to AID's function in CSR, though not in somatic hypermutation. Many alterations to the NES, while preserving its nuclear export function, destroy CSR ability. We have previously speculated that AID's ability to potentiate CSR may critically depend on the affinity of interaction between its NES and Crm1 exportin. Here, however, by comparing multiple AID NES mutants, we find that - beyond a requirement for threshold Crm1 binding - there is little correlation between CSR and Crm1 binding affinity. The results suggest that CSR, as well as the stabilisation of AID, depend on an interaction between the AID C-terminal decapeptide and factor(s) additional to Crm1.

  14. Strategic Sexual Signals: Women's Display versus Avoidance of the Color Red Depends on the Attractiveness of an Anticipated Interaction Partner.

    Directory of Open Access Journals (Sweden)

    Daniela Niesta Kayser

    Full Text Available The color red has special meaning in mating-relevant contexts. Wearing red can enhance perceptions of women's attractiveness and desirability as a potential romantic partner. Building on recent findings, the present study examined whether women's (N = 74 choice to display the color red is influenced by the attractiveness of an expected opposite-sex interaction partner. Results indicated that female participants who expected to interact with an attractive man displayed red (on clothing, accessories, and/or makeup more often than a baseline consisting of women in a natural environment with no induced expectation. In contrast, when women expected to interact with an unattractive man, they eschewed red, displaying it less often than in the baseline condition. Findings are discussed with respect to evolutionary and cultural perspectives on mate evaluation and selection.

  15. Hydrogenation induced deviation of temperature and concentration dependences of polymer-solvent interactions in poly(vinyl chloride) and a new eco-friendly plasticizer

    Science.gov (United States)

    Liu, Yang; Zhang, Rongchun; Wang, Xiaoliang; Sun, Pingchuan; Chen, Wei; Shen, Jianyi; Xue, Gi

    2015-06-01

    As a substitute for di-2-ethylhexyl phthalate (DOP), a new eco-friendly plasticizer, di(2-ethylhexyl) cyclohexane-1,2-dicarboxylate (DEHHP), was systematically studied in this work, mainly focusing on its interaction with poly(vinyl chloride) (PVC). The temperature and concentration dependences of polymer-solvent interactions in PVC/DEHHP were systematically investigated by rheology, low-field NMR and molecular dynamics simulations, and the results were quite different from those in PVC/DOP. With temperature increasing or PVC concentration decreasing, rheology experiments revealed that polymer-solvent interactions in PVC/DEHHP were weaker than that in PVC/DOP. Low-field 1H NMR results showed that the number of polymer-solvent complexes decreased as temperature increased. A faster decreasing rate of this number made the polymer-solvent interactions weaker in PVC/DEHHP than in PVC/DOP. Molecular dynamics simulations were further performed to study the role of polymer-solvent hydrogen bonding interactions in the systems. The radial distribution function showed that heating and dilution both resulted in faster molecular motions, and disassociation of the hydrogen bonds in the simplex hydrogen bonding system. Therefore, heating and dilution had an equivalent effect on the polymer-solvent interactions.

  16. DNA Mismatch Repair Interacts with CAF-1- and ASF1A-H3-H4-dependent Histone (H3-H4)2 Tetramer Deposition.

    Science.gov (United States)

    Rodriges Blanko, Elena; Kadyrova, Lyudmila Y; Kadyrov, Farid A

    2016-04-22

    DNA mismatch repair (MMR) is required for the maintenance of genome stability and protection of humans from several types of cancer. Human MMR occurs in the chromatin environment, but little is known about the interactions between MMR and the chromatin environment. Previous research has suggested that MMR coincides with replication-coupled assembly of the newly synthesized DNA into nucleosomes. The first step in replication-coupled nucleosome assembly is CAF-1-dependent histone (H3-H4)2 tetramer deposition, a process that involves ASF1A-H3-H4 complex. In this work we used reconstituted human systems to investigate interactions between MMR and CAF-1- and ASF1A-H3-H4-dependent histone (H3-H4)2 tetramer deposition. We have found that MutSα inhibits CAF-1- and ASF1A-H3-H4-dependent packaging of a DNA mismatch into a tetrasome. This finding supports the idea that MMR occurs before the DNA mismatch is packaged into the tetrasome. Our experiments have also revealed that CAF-1- and ASF1A-H3-H4-dependent deposition of the histone (H3-H4)2 tetramers does not interfere with MMR reactions. In addition, we have established that unnecessary degradation of the discontinuous strand that takes place in both DNA polymerase δ (Pol δ)- and DNA polymerase ϵ (Pol ϵ)-dependent MMR reactions is suppressed by CAF-1- and ASF1A-H3-H4-dependent deposition of the histone (H3-H4)2 tetramers. These data suggest that CAF-1- and ASF1A-H3-H4-dependent deposition of the histone (H3-H4)2 tetramers is compatible with MMR and protects the discontinuous daughter strand from unnecessary degradation by MMR machinery.

  17. Phase-dependent inversionless gain in a four-level atomic system with a closed interaction loop

    Institute of Scientific and Technical Information of China (English)

    Xu Wei-Hua; Wu Jin-Hui; Gao Jin-Yue

    2007-01-01

    A four-level atomic system with a closed interaction loop connected by two coherent driving fields and a microwave field is investigated. The results show that inversionless gain can be achieved on a higher frequency transition outside the closed interaction loop, and the gain behaviour can be modulated by the phase of the closed loop as well as the amplitude of the microwave field. The phase sensitivity property in such a scheme is similar to that in an analogous configuration with spontaneously generated coherence, but it is beyond the rigorous condition of near-degenerate levels with non-orthogonal dipole moments. Therefore this scheme is much more convenient in experimental realization.

  18. Intramolecular bond length dependence of the anisotropic dispersion coefficients for interactions of rare gas atoms with N2, CO, Cl2, HCl and HBr

    Science.gov (United States)

    Hettema, Hinne; Wormer, Paul E. S.; Thakkar, Ajit J.

    Ab initio many body perturbation theory is used to calculate the imaginary frequency multipole polarizabilities of N2, Cl2, CO, HCl and HBr as a function of bond length. These are combined with previously calculated dynamic polarizabilities for rare gas atoms to obtain the intramolecular bond length dependence of the anisotropic dispersion and induction coefficients through R-8 for AB-X (AB = N2, Cl2, CO, HCl, HBr and X = He, Ne, Ar, Kr, Xe) interactions.

  19. Experimental and theoretical investigations of the gain dependence at two-wave interaction on the thickness and orientation angle of the Bi12GeO20 crystal

    Science.gov (United States)

    Shepelevich, V. V.; Makarevich, A. V.; Shandarov, S. M.

    2017-06-01

    Experimental studies of the dependence of object wave gain at two-wave interaction on the effective thickness of cubic photorefractive optically active crystal Bi12GeO20 were performed using only one (\\bar 1\\bar 10) -cut crystal sample. It is shown that the obtained experimental results can be satisfactorily theoretically interpreted taking into account the inverse piezoelectric and the photo-elastic effects in addition to the traditionally considered electro-optical one.

  20. Recent development of self-interaction-free time-dependent density-functional theory for nonperturbative treatment of atomic and molecular multiphoton processes in intense laser fields.

    Science.gov (United States)

    Chu, Shih-I

    2005-08-08

    In this paper, we present a short account of some recent developments of self-interaction-free density-functional theory (DFT) and time-dependent density-functional theory (TDDFT) for accurate and efficient treatment of the electronic structure, and time-dependent quantum dynamics of many-electron atomic and molecular systems. The conventional DFT calculations using approximate and explicit exchange-correlation energy functional contain spurious self-interaction energy and improper long-range asymptotic potential, preventing reliable treatment of the excited, resonance, and continuum states. We survey some recent developments of DFT/TDDFT with optimized effective potential (OEP) and self-interaction correction (SIC) for both atomic and molecular systems for overcoming some of the above mentioned difficulties. These DFT (TDDFT)/OEP-SIC approaches allow the use of orbital-independent single-particle local potential which is self-interaction free. In addition we discuss several numerical techniques recently developed for efficient and high-precision treatment of the self-interaction-free DFT/TDDFT equations. The usefulness of these procedures is illustrated by a few case studies of atomic, molecular, and condensed matter processes of current interests, including (a) autoionizing resonances, (b) relativistic OEP-SIC treatment of atomic structure (Z=2-106), (c) shell-filling electronic structure in quantum dots, (d) atomic and molecular processes in intense laser fields, including multiphoton ionization, and very-high-order harmonic generation, etc. For the time-dependent processes, an alternative Floquet formulation of TDDFT is introduced for time-independent treatment of multiphoton processes in intense periodic or quasiperiodic fields. We conclude this paper with some open questions and perspectives of TDDFT.

  1. Temperature-dependent exchange interaction in molecular magnets Cu(hfac)2L(R) studied by EPR: methodology and interpretations.

    Science.gov (United States)

    Veber, Sergey L; Fedin, Matvey V; Maryunina, Ksenia Yu; Potapov, Alexey; Goldfarb, Daniella; Reijerse, Edward; Lubitz, Wolfgang; Sagdeev, Renad Z; Ovcharenko, Victor I; Bagryanskaya, Elena G

    2011-10-17

    Exchange-coupled spin triads nitroxide-copper(II)-nitroxide are the key building blocks of molecular magnets Cu(hfac)(2)L(R). These compounds exhibit thermally induced structural rearrangements and spin transitions, where the exchange interaction between spins of copper(II) ion and nitroxide radicals changes typically by 1 order of magnitude. We have shown previously that electron paramagnetic resonance (EPR) spectroscopy is sensitive to the observed magnetic anomalies and provides information on both inter- and intracluster exchange interactions. The value of intracluster exchange interaction is temperature-dependent (J(T)), that can be accessed by monitoring the effective g-factor of the spin triad as a function of temperature (g(eff)(T)). This paper describes approaches for studying the g(eff)(T) and J(T) dependences and establishes correlations between them. The experimentally obtained g(eff)(T) dependences are interpreted using three different models for the mechanism of structural rearrangements on the molecular level leading to different meanings of the J(T) function. The contributions from these mechanisms and their manifestations in X-ray, magnetic susceptibility and EPR data are discussed.

  2. FGF1-mediated cardiomyocyte cell cycle reentry depends on the interaction of FGFR-1 and Fn14.

    Science.gov (United States)

    Novoyatleva, Tatyana; Sajjad, Amna; Pogoryelov, Denys; Patra, Chinmoy; Schermuly, Ralph T; Engel, Felix B

    2014-06-01

    Fibroblast growth factors (FGFs) signal through FGF receptors (FGFRs) mediating a broad range of cellular functions during embryonic development, as well as disease and regeneration during adulthood. Thus, it is important to understand the underlying molecular mechanisms that modulate this system. Here, we show that FGFR-1 can interact with the TNF receptor superfamily member fibroblast growth factor-inducible molecule 14 (Fn14) resulting in cardiomyocyte cell cycle reentry. FGF1-induced cell cycle reentry in neonatal cardiomyocytes could be blocked by Fn14 inhibition, while TWEAK-induced cell cycle activation was inhibited by blocking FGFR-1 signaling. In addition, costimulation experiments revealed a synergistic effect of FGF1 and TWEAK in regard to cardiomyocyte cell cycle induction via PI3K/Akt signaling. Overexpression of Fn14 with either FGFR-1 long [FGFR-1(L)] or FGFR-1 short [FGFR-1(S)] isoforms resulted after FGF1/TWEAK stimulation in cell cycle reentry of >40% adult cardiomyocytes. Finally, coimmunoprecipitation and proximity ligation assays indicated that endogenous FGFR-1 and Fn14 interact with each other in cardiomyocytes. This interaction was strongly enhanced in the presence of their corresponding ligands, FGF1 and TWEAK. Taken together, our data suggest that FGFR-1/Fn14 interaction may represent a novel endogenous mechanism to modulate the action of these receptors and their ligands and to control cardiomyocyte cell cycle reentry.

  3. Noxa controls Mule-dependent Mcl-1 ubiquitination through the regulation of the Mcl-1/USP9X interaction.

    Science.gov (United States)

    Gomez-Bougie, Patricia; Ménoret, Emmanuelle; Juin, Philippe; Dousset, Christelle; Pellat-Deceunynck, Catherine; Amiot, Martine

    2011-09-30

    The level of the Mcl-1 pro-survival protein is highly regulated, and the down-regulation of Mcl-1 expression favors the apoptotic process. Mcl-1 physically interacts with different BH3-only proteins; particularly, Noxa is involved in the modulation of Mcl-1 expression. In this study, we demonstrated that Noxa triggers the degradation of Mcl-1 at the mitochondria according to the exclusive location of Noxa at this compartment. The Noxa-induced degradation of Mcl-1 required the E3 ligase Mule, which is responsible for the polyubiquitination of Mcl-1. Because the USP9X deubiquitinase was recently demonstrated to be involved in Mcl-1 protein turnover by preventing its degradation through the removal of conjugated ubiquitin, we investigated whether Noxa affected the deubiquitination process. Interestingly, Noxa over-expression caused a decrease in the USP9X/Mcl-1 interaction associated with an increase in the Mcl-1 polyubiquitinated forms. Additionally, Noxa over-expression triggered an increase in the Mule/Mcl-1 interaction in parallel with the decrease in Mule/USP9X complex formation. Taken together, these modifications result in the degradation of Mcl-1 by the proteasome machinery. The implication of Noxa in the regulation of Mcl-1 proteasomal degradation adds complexity to this process, which is governed by multiple interactions.

  4. Glutathione-dependent interaction of heavy metal compounds with multidrug resistance proteins MRP1 and MRP2

    NARCIS (Netherlands)

    Wortelboer, H.M.; Balvers, M.G.J.; Usta, M.; Bladeren, P.J. van; Cnubben, N.H.P.

    2008-01-01

    The interactions of three heavy metal-containing compounds, cisplatin (CDDP), arsenic trioxide (As2O3), and mercury dichloride (HgCl2), with the multidrug resistance transporters MRP1 and MRP2 and the involvement of glutathione (GSH)-related processes herein were investigated. In Madin-Darby canine

  5. Glutathione-dependent interaction of heavy metal compounds with multidrug resistance proteins MRP1 and MRP2

    NARCIS (Netherlands)

    Wortelboer, H.M.; Balvers, M.G.J.; Usta, M.; Bladeren, van P.J.; Cnubben, N.H.P.

    2008-01-01

    The interactions of three heavy metal-containing compounds, cisplatin (CDDP), arsenic trioxide (AS(2)O(3)), and mercury dichloride (HgCl2), with the multidrug resistance transporters MRP1 and MRP2 and the involvement of glutathione (GSH)-related processes herein were investigated. In Madin-Darby can

  6. Chain conformation-dependent thermal conductivity of amorphous polymer blends: the impact of inter- and intra-chain interactions.

    Science.gov (United States)

    Wei, Xingfei; Zhang, Teng; Luo, Tengfei

    2016-11-30

    Polymers with high thermal conductivities are of great interest for both scientific research and industrial applications. In this study, model amorphous polymer blends are studied using molecular dynamics simulations. We have examined the effects of inter- and intra-chain interactions on the molecular-level conformations of the blends, which in turn impact their thermal conductivity. It is found that the thermal conductivity of polymer blends is strongly related to the molecular conformation, especially the spatial extent of the molecular chains indicated by their radius of gyration. Tuning the intra-chain van der Waals (vdW) interaction leads to different molecular structures of the minor component in the binary blend, but the thermal conductivity is not changed. However, increasing the inter-chain vdW interactions between the major and the minor components will increase the thermal conductivity of the blend, which is due to the conformation change in the major component that leads to enhanced thermal transport along the chain backbone through the intra-chain bonding interactions. The fundamental structure-property relationship from this study may provide useful guidance for designing and synthesizing polymer blends with desirable thermal conductivity.

  7. Role of MINOS in Mitochondrial Membrane Architecture : Cristae Morphology and Outer Membrane Interactions Differentially Depend on Mitofilin Domains

    NARCIS (Netherlands)

    Zerbes, Ralf M.; Bohnert, Maria; Stroud, David A.; von der Malsburg, Karina; Kram, Anita; Oeljeklaus, Silke; Warscheid, Bettina; Becker, Thomas; Wiedemann, Nils; Veenhuis, Marten; van der Klei, Ida J.; Pfanner, Nikolaus; van der Laan, Martin

    2012-01-01

    The mitochondrial inner membrane contains a large protein complex crucial for membrane architecture, the mitochondrial inner membrane organizing system (MINOS). MINOS is required for keeping cristae membranes attached to the inner boundary membrane via crista junctions and interacts with protein com

  8. Human amniotic membrane-derived stromal cells (hAMSC) interact depending on breast cancer cell type through secreted molecules.

    Science.gov (United States)

    Kim, Sun-Hee; Bang, So Hee; Kang, So Yeong; Park, Ki Dae; Eom, Jun Ho; Oh, Il Ung; Yoo, Si Hyung; Kim, Chan-Wha; Baek, Sun Young

    2015-02-01

    Human amniotic membrane-derived stromal cells (hAMSC) are candidates for cell-based therapies. We examined the characteristics of hAMSC including the interaction between hAMSC and breast cancer cells, MCF-7, and MDA-MB-231. Human amniotic membrane-derived stromal cells showed typical MSC properties, including fibroblast-like morphology, surface antigen expression, and mesodermal differentiation. To investigate cell-cell interaction via secreted molecules, we cultured breast cancer cells in hAMSC-conditioned medium (hAMSC-CM) and analyzed their proliferation, migration, and secretome profiles. MCF-7 and MDA-MB-231 cells exposed to hAMSC-CM showed increased proliferation and migration. However, in hAMSC-CM, MCF-7 cells proliferated significantly faster than MDA-MB-231 cells. When cultured in hAMSC-CM, MCF-7 cells migrated faster than MDA-MB-231 cells. Two cell types showed different profiles of secreted factors. MCF-7 cells expressed much amounts of IL-8, GRO, and MCP-1 in hAMSC-CM. Human amniotic membrane-derived stromal cells interact with breast cancer cells through secreted molecules. Factors secreted by hAMSCs promote the proliferation and migration of MCF-7 breast cancer cells. For much safe cell-based therapies using hAMSC, it is necessary to study carefully about interaction between hAMSC and cancer cells.

  9. Hepatitis C Virus RNA-Dependent RNA Polymerase Interacts with the Akt/PKB Kinase and Induces Its Subcellular Relocalization.

    Science.gov (United States)

    Valero, María Llanos; Sabariegos, Rosario; Cimas, Francisco J; Perales, Celia; Domingo, Esteban; Sánchez-Prieto, Ricardo; Mas, Antonio

    2016-06-01

    Hepatitis C virus (HCV) interacts with cellular components and modulates their activities for its own benefit. These interactions have been postulated as a target for antiviral treatment, and some candidate molecules are currently in clinical trials. The multifunctional cellular kinase Akt/protein kinase B (PKB) must be activated to increase the efficacy of HCV entry but is rapidly inactivated as the viral replication cycle progresses. Viral components have been postulated to be responsible for Akt/PKB inactivation, but the underlying mechanism remained elusive. In this study, we show that HCV polymerase NS5B interacts with Akt/PKB. In the presence of transiently expressed NS5B or in replicon- or virus-infected cells, NS5B changes the cellular localization of Akt/PKB from the cytoplasm to the perinuclear region. Sequestration of Akt/PKB by NS5B could explain its exclusion from its participation in early Akt/PKB inactivation. The NS5B-Akt/PKB interaction represents a new regulatory step in the HCV infection cycle, opening possibilities for new therapeutic options.

  10. INTERACTION OF CLATHRIN WITH LARGE UNILAMELLAR PHOSPHOLIPID-VESICLES AT NEUTRAL PH - LIPID DEPENDENCE AND PROTEIN PENETRATION

    NARCIS (Netherlands)

    SEPPEN, J; RAMALHOSANTOS, J; DECARVALHO, AP; TERBEEST, M; KOK, JW; DELIMA, MCP; HOEKSTRA, D

    1992-01-01

    The interaction of clathrin with large unilamellar vesicles of various lipid compositions has been examined at neutral pH. Clathrin induces leakage of contents of vesicles that contain the acidic phospholipid phosphatidylserine. Leakage is greatly enhanced by the presence of a relatively minor

  11. Deformed epidermal autoregulatory factor-1 (DEAF1 interacts with the Ku70 subunit of the DNA-dependent protein kinase complex.

    Directory of Open Access Journals (Sweden)

    Philip J Jensik

    Full Text Available Deformed Epidermal Autoregulatory Factor 1 (DEAF1 is a transcription factor linked to suicide, cancer, autoimmune disorders and neural tube defects. To better understand the role of DEAF1 in protein interaction networks, a GST-DEAF1 fusion protein was used to isolate interacting proteins in mammalian cell lysates, and the XRCC6 (Ku70 and the XRCC5 (Ku80 subunits of DNA dependent protein kinase (DNA-PK complex were identified by mass spectrometry, and the DNA-PK catalytic subunit was identified by immunoblotting. Interaction of DEAF1 with Ku70 and Ku80 was confirmed to occur within cells by co-immunoprecipitation of epitope-tagged proteins, and was mediated through interaction with the Ku70 subunit. Using in vitro GST-pulldowns, interaction between DEAF1 and the Ku70 subunit was mapped to the DEAF1 DNA binding domain and the C-terminal Bax-binding region of Ku70. In transfected cells, DEAF1 and Ku70 colocalized to the nucleus, but Ku70 could not relocalize a mutant cytoplasmic form of DEAF1 to the nucleus. Using an in vitro kinase assay, DEAF1 was phosphorylated by DNA-PK in a DNA-independent manner. Electrophoretic mobility shift assays showed that DEAF1 or Ku70/Ku80 did not interfere with the DNA binding of each other, but DNA containing DEAF1 binding sites inhibited the DEAF1-Ku70 interaction. The data demonstrates that DEAF1 can interact with the DNA-PK complex through interactions of its DNA binding domain with the carboxy-terminal region of Ku70 that contains the Bax binding domain, and that DEAF1 is a potential substrate for DNA-PK.

  12. Mapping temporal dynamics in social interactions with unified structural equation modeling: A description and demonstration revealing time-dependent sex differences in play behavior.

    Science.gov (United States)

    Beltz, Adriene M; Beekman, Charles; Molenaar, Peter C M; Buss, Kristin A

    2013-07-01

    Developmental science is rich with observations of social interactions, but few available methodological and statistical approaches take full advantage of the information provided by these data. The authors propose implementation of the unified structural equation model (uSEM), a network analysis technique, for observational data coded repeatedly across time; uSEM captures the temporal dynamics underlying changes in behavior at the individual level by revealing the ways in which a single person influences - concurrently and in the future - other people. To demonstrate the utility of uSEM, the authors applied it to ratings of positive affect and vigor of activity during children's unstructured laboratory play with unfamiliar, same-sex peers. Results revealed the time-dependent nature of sex differences in play behavior. For girls more than boys, positive affect was dependent upon peers' prior positive affect. For boys more than girls, vigor of activity was dependent upon peers' current vigor of activity.

  13. Sign of the Casimir-Polder interaction between atoms and oil-water interfaces: Subtle dependence on dielectric properties

    CERN Document Server

    Boström, Mathias; Brevik, Iver; Parsons, Drew F; Sernelius, Bo E

    2012-01-01

    We demonstrate that Casimir-Polder energies between noble gas atoms (dissolved in water) and oil-water interfaces are highly surface specific. Both repulsion (e.g. hexane) and attraction (e.g. glycerol and cyclodecane) is found with different oils. For several intermediate oils (e.g. hexadecane, decane, and cyclohexane) both attraction and repulsion can be found in the same system. Near these oil-water interfaces the interaction is repulsive in the non-retarded limit and turns attractive at larger distances as retardation becomes important. These highly surface specific interactions may have a role to play in biological systems where the surface may be more or less accessible to dissolved atoms.

  14. Emission switching in carbon dots coated CdTe quantum dots driving by pH dependent hetero-interactions

    Energy Technology Data Exchange (ETDEWEB)

    Dai, Xiao; Wang, Hao; Yi, Qinghua; Wang, Yun; Cong, Shan; Zhao, Jie; Sun, Yinghui; Zou, Guifu, E-mail: zouguifu@suda.edu.cn, E-mail: jiexiong@uestc.edu.cn [College of Physics, Optoelectronics and Energy and Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou 215006 (China); Qian, Zhicheng [School of Electronic and Information Engineering, Xi' an Jiaotong University, Xi' an 710049 (China); Huang, Jianwen; Xiong, Jie, E-mail: zouguifu@suda.edu.cn, E-mail: jiexiong@uestc.edu.cn [State Key Laboratory of Electronic Thin Films and Integrated Devices, University of Electronic Science and Technology of China, Chengdu 610054 (China); Luo, Hongmei [Department of Chemical and Materials Engineering, New Mexico State University, Las Cruces, New Mexico 88003 (United States)

    2015-11-16

    Due to the different emission mechanism between fluorescent carbon dots and semiconductor quantum dots (QDs), it is of interest to explore the potential emission in hetero-structured carbon dots/semiconducting QDs. Herein, we design carbon dots coated CdTe QDs (CDQDs) and investigate their inherent emission. We demonstrate switchable emission for the hetero-interactions of the CDQDs. Optical analyses indicate electron transfer between the carbon dots and the CdTe QDs. A heterojunction electron process is proposed as the driving mechanism based on N atom protonation of the carbon dots. This work advances our understanding of the interaction mechanism of the heterostructured CDQDs and benefits the future development of optoelectronic nanodevices with new functionalities.

  15. Composition and size dependence of hydrogen interaction with carbon supported bulk-immiscible Pd-Rh nanoalloys.

    Science.gov (United States)

    Oumellal, Yassine; Provost, Karine; Ghimbeu, Camelia Matei; de Yuso, Alicia Martinez; Zlotea, Claudia

    2016-11-18

    In-depth clarification of hydrogen interaction with noble metal nanoparticles and nanoalloys is essential for further development and design of efficient catalysts and hydrogen storage nanomaterials. This issue becomes even more challenging for nanoalloys of bulk-immiscible metals. The hydrogen interaction with bulk-immiscible Pd-Rh nanoalloys (3-6 nm) supported on mesoporous carbon is studied by both laboratory and large scale facility techniques. X-ray diffraction (XRD) reveals a single phase fcc structure for all nanoparticles confirming the formation of nanoalloys in the whole composition range. In situ extended x-ray absorption fine structure (EXAFS) experiments suggest segregated local structures into Pd-rich surface and Rh-rich core coexisting within the nanoparticles. Hydrogen sorption can be tuned by chemical composition: Pd-rich nanoparticles form a hydride phase, whereas Rh-rich phases do not absorb hydrogen under ambient temperature and pressure conditions. The thermodynamics of hydride formation can be tailored by the composition without affecting hydrogen capacity at full hydrogenation. Furthermore, for hydrogen absorbing nanoalloys, in situ EXAFS reveals a preferential occupation of hydrogen for the interstitial sites around Pd atoms. To our knowledge, this is the first study providing insights into the hydrogen interaction mechanism with Pd-Rh nanoalloys that can guide the design of catalysts for hydrogenation reactions and the development of nanomaterials for hydrogen storage.

  16. The adrenal specific toxicant mitotane directly interacts with lipid membranes and alters membrane properties depending on lipid composition.

    Science.gov (United States)

    Scheidt, Holger A; Haralampiev, Ivan; Theisgen, Stephan; Schirbel, Andreas; Sbiera, Silviu; Huster, Daniel; Kroiss, Matthias; Müller, Peter

    2016-06-15

    Mitotane (o,p'.-DDD) is an orphan drug approved for the treatment of adrenocortical carcinoma. The mechanisms, which are responsible for this activity of the drug, are not completely understood. It can be hypothesized that an impact of mitotane is mediated by the interaction with cellular membranes. However, an interaction of mitotane with (lipid) membranes has not yet been investigated in detail. Here, we characterized the interaction of mitotane and its main metabolite o,p'-dichlorodiphenyldichloroacetic acid (o,p'-DDA) with lipid membranes by applying a variety of biophysical approaches of nuclear magnetic resonance, electron spin resonance, and fluorescence spectroscopy. We found that mitotane and o,p'-DDA bind to lipid membranes by inserting into the lipid-water interface of the bilayer. Mitotane but not o,p'-DDA directly causes a disturbance of bilayer structure leading to an increased permeability of the membrane for polar molecules. Mitotane induced alterations of the membrane integrity required the presence of phosphatidylethanolamine and/or cholesterol. Collectively, our data for the first time characterize the impact of mitotane on the lipid membrane structure and dynamics, which may contribute to a better understanding of specific mitotane effects and side effects.

  17. The chaperonin CCT inhibits assembly of α-synuclein amyloid fibrils by a specific, conformation-dependent interaction

    Science.gov (United States)

    Sot, Begoña; Rubio-Muñoz, Alejandra; Leal-Quintero, Ahudrey; Martínez-Sabando, Javier; Marcilla, Miguel; Roodveldt, Cintia; Valpuesta, José M.

    2017-01-01

    The eukaryotic chaperonin CCT (chaperonin containing TCP-1) uses cavities built into its double-ring structure to encapsulate and to assist folding of a large subset of proteins. CCT can inhibit amyloid fibre assembly and toxicity of the polyQ extended mutant of huntingtin, the protein responsible for Huntington’s disease. This raises the possibility that CCT modulates other amyloidopathies, a still-unaddressed question. We show here that CCT inhibits amyloid fibre assembly of α-synuclein A53T, one of the mutants responsible for Parkinson’s disease. We evaluated fibrillation blockade in α-synuclein A53T deletion mutants and CCT interactions of full-length A53T in distinct oligomeric states to define an inhibition mechanism specific for α-synuclein. CCT interferes with fibre assembly by interaction of its CCTζ and CCTγ subunits with the A53T central hydrophobic region (NAC). This interaction is specific to NAC conformation, as it is produced once soluble α-synuclein A53T oligomers form and blocks the reaction before fibres begin to grow. Finally, we show that this association inhibits α-synuclein A53T oligomer toxicity in neuroblastoma cells. In summary, our results and those for huntingtin suggest that CCT is a general modulator of amyloidogenesis via a specific mechanism. PMID:28102321

  18. Composition and size dependence of hydrogen interaction with carbon supported bulk-immiscible Pd-Rh nanoalloys

    Science.gov (United States)

    Oumellal, Yassine; Provost, Karine; Matei Ghimbeu, Camelia; Martinez de Yuso, Alicia; Zlotea, Claudia

    2016-11-01

    In-depth clarification of hydrogen interaction with noble metal nanoparticles and nanoalloys is essential for further development and design of efficient catalysts and hydrogen storage nanomaterials. This issue becomes even more challenging for nanoalloys of bulk-immiscible metals. The hydrogen interaction with bulk-immiscible Pd-Rh nanoalloys (3-6 nm) supported on mesoporous carbon is studied by both laboratory and large scale facility techniques. X-ray diffraction (XRD) reveals a single phase fcc structure for all nanoparticles confirming the formation of nanoalloys in the whole composition range. In situ extended x-ray absorption fine structure (EXAFS) experiments suggest segregated local structures into Pd-rich surface and Rh-rich core coexisting within the nanoparticles. Hydrogen sorption can be tuned by chemical composition: Pd-rich nanoparticles form a hydride phase, whereas Rh-rich phases do not absorb hydrogen under ambient temperature and pressure conditions. The thermodynamics of hydride formation can be tailored by the composition without affecting hydrogen capacity at full hydrogenation. Furthermore, for hydrogen absorbing nanoalloys, in situ EXAFS reveals a preferential occupation of hydrogen for the interstitial sites around Pd atoms. To our knowledge, this is the first study providing insights into the hydrogen interaction mechanism with Pd-Rh nanoalloys that can guide the design of catalysts for hydrogenation reactions and the development of nanomaterials for hydrogen storage.

  19. Pathways to decoding the clinical potential of stress response FOXO-interaction networks for Huntington’s disease: of gene prioritization and context dependence

    Directory of Open Access Journals (Sweden)

    Frederic eParmentier

    2013-06-01

    Full Text Available The FOXO family of transcription factors is central to the regulation of organismal longevity and cellular survival. Several studies have indicated that FOXO factors lie at the center of a complex network of upstream pathways, cofactors and downstream targets (FOXO-interaction networks, which may have developmental and post-developmental roles in the regulation of chronic-stress response in normal and diseased cells. Noticeably, FOXO factors are important for the regulation of proteotoxicity and neuron survival in several models of neurodegenerative disease, suggesting that FOXO-interaction networks may have therapeutic potential. However, the status of FOXO-interaction networks in neurodegenerative disease remains largely unknown. Systems modeling is anticipated to provide a comprehensive assessment of this question. In particular, interrogating the context-dependent variability of FOXO-interaction networks could predict the clinical potential of cellular-stress response genes and aging regulators for tackling brain and peripheral pathology in neurodegenerative disease. Using published transcriptomic data obtained from murine models of Huntington’s disease and post-mortem brains, blood samples and induced-pluripotent-stem cells from Huntington’s disease carriers as a case example, this review briefly highlights how the biological status and clinical potential of FOXO-interaction networks for Huntington’s disease may be decoded by developing network and entropy based feature selection across heterogeneous datasets.

  20. S phase-dependent interaction with DNMT1 dictates the role of UHRF1 but not UHRF2 in DNA methylation maintenance

    Institute of Scientific and Technical Information of China (English)

    Jiqin Zhang; Jiemin Wong; Qinqin Gao; Pishun Li; Xiaoli Liu; Yuanhui Jia; Weicheng Wu; Jiwen Li; Shuo Dong; Haruhiko Koseki

    2011-01-01

    Recent studies demonstrate that UHRF1 is required for DNA methylation maintenance by targeting DNMT1 to DNA replication loci,presumably through its unique hemi-methylated DNA-binding activity and interaction with DNMT1.UHRF2,another member of the UHRF family proteins,is highly similar to UHRF1 in both sequence and structure,raising questions about its role in DNA methylation.In this study,we demonstrate that,like UHRF1,UHRF2 also binds preferentially to methylated histone H3 lysine 9 (H3K9) through its conserved tudor domain and hemi-methylated DNA through the SET and Ring associated domain.Like UHRF1,UHRF2 is enriched in pericentric heterochromatin.The heterochromatin localization depends to large extent on its methylated H3K9-binding activity and to less extent on its methylated DNA-binding activity.Coimmunoprecipitation experiments demonstrate that both UHRF1 and UHRF2 interact with DNMT1,DNMT3a,DNMT3b and G9a.Despite all these conserved functions,we find that UHRF2 is not able to rescue the DNA methylation defect in Uhrf1 null mouse embryonic stem cells.This can be attributed to the inability for UHRF2 to recruit DNMT1 to replication foci during S phase of the cell cycle.Indeed,we find that while UHRF1 interacts with DNMT1 in an S phase-dependent manner in cells,UHRF2 does not.Thus,our study demonstrates that UHRF2 and UHRF1 are not functionally redundant in DNA methylation maintenance and reveals the cell-cycle-dependent interaction between UHRF1 and DNMT1 as a key regulatory mechanism targeting DNMT1 for DNA methylation.

  1. Rab3 interacting molecule 3 mutations associated with autism alter regulation of voltage-dependent Ca²⁺ channels.

    Science.gov (United States)

    Takada, Yoshinori; Hirano, Mitsuru; Kiyonaka, Shigeki; Ueda, Yoshifumi; Yamaguchi, Kazuma; Nakahara, Keiko; Mori, Masayuki X; Mori, Yasuo

    2015-09-01

    Autism is a neurodevelopmental psychiatric disorder characterized by impaired reciprocal social interaction, disrupted communication, and restricted and stereotyped patterns of interests. Autism is known to have a strong genetic component. Although mutations in several genes account for only a small proportion of individuals with autism, they provide insight into potential biological mechanisms that underlie autism, such as dysfunction in Ca(2+) signaling, synaptic dysfunction, and abnormal brain connectivity. In autism patients, two mutations have been reported in the Rab3 interacting molecule 3 (RIM3) gene. We have previously demonstrated that RIM3 physically and functionally interacts with voltage-dependent Ca(2+) channels (VDCCs) expressed in neurons via the β subunits, and increases neurotransmitter release. Here, by introducing corresponding autism-associated mutations that replace glutamic acid residue 176 with alanine (E176A) and methionine residue 259 with valine (M259V) into the C2B domain of mouse RIM3, we demonstrate that both mutations partly cancel the suppressive RIM3 effect on voltage-dependent inactivation of Ba(2+) currents through P/Q-type CaV2.1 recombinantly expressed in HEK293 cells. In recombinant N-type CaV2.2 VDCCs, the attenuation of the suppressive RIM3 effect on voltage-dependent inactivation is conserved for M259V but not E176A. Slowing of activation speed of P/Q-type CaV2.1 currents by RIM3 is abolished in E176A, while the physical interaction between RIM3 and β subunits is significantly attenuated in M259V. Moreover, increases by RIM3 in depolarization-induced Ca(2+) influx and acetylcholine release are significantly attenuated by E176A in rat pheochromocytoma PC12 cells. Thus, our data raise the interesting possibility that autism phenotypes are elicited by synaptic dysfunction via altered regulation of presynaptic VDCC function and neurotransmitter release.

  2. Non-Instrumental Movement Inhibition (NIMI differentially suppresses head and thigh movements during screenic engagement: dependence on interaction

    Directory of Open Access Journals (Sweden)

    Harry J Witchel

    2016-02-01

    Full Text Available Background: Estimating engagement levels from postural micromovements has been summarized by some researchers as: increased proximity to the screen is a marker for engagement, while increased postural movement is a signal for disengagement or negative affect. However, these findings are inconclusive: the movement hypothesis challenges other findings of dyadic interaction in humans, and experiments on the positional hypothesis diverge from it.Hypotheses: 1 Under controlled conditions, adding a relevant visual stimulus to an auditory stimulus will preferentially result in Non-Instrumental Movement Inhibition (NIMI of the head. 2 When instrumental movements are eliminated and computer-interaction rate is held constant, for two identically-structured stimuli, cognitive engagement (i.e. interest will result in measurable NIMI of the body generally. Methods: Twenty-seven healthy participants were seated in front of a computer monitor and speakers. Discrete three-minute stimuli were presented with interactions mediated via a handheld trackball without any keyboard, to minimize instrumental movements of the participant's body. Music videos and audio-only music were used to test hypothesis 1. Time-sensitive, highly interactive stimuli were used to test hypothesis 2. Subjective responses were assessed via visual analogue scales. The computer users' movements were quantified using video motion tracking from the lateral aspect. Repeated measures ANOVAs with Tukey post hoc comparisons were performed.Results: For two equivalently-engaging music videos, eliminating the visual content elicited significantly increased non-instrumental movements of the head (while also decreasing subjective engagement; a highly engaging user-selected piece of favorite music led to further increased non-instrumental movement. For two comparable reading tasks, the more engaging reading significantly inhibited (42% movement of the head and thigh; however, when a highly engaging

  3. Effect of lactoperoxidase-catalyzed iodination on the Ca sub 2+ -dependent interactions of human C anti 1 s. Location of the iodination sites

    Energy Technology Data Exchange (ETDEWEB)

    Illy, C.; Thielens, N.M.; Gagnon, J.; Arlaud, G.J. (Centre d' Etudes Nucleaires de Grenoble (France))

    1991-07-23

    C{anti 1}s, one of the two serine proteases of C{anti 1}, the first component of complement has the ability to mediate heterologous (C{anti 1}r-C{anti 1}s) as well as homologous (C{anti 1}s-C{anti 1}s) Ca{sup 2+}-dependent interactions, both involving the NH{sub 2}-terminal {alpha} region of its A chain. Lactoperoxidase-catalyzed iodination of C{anti 1}s in its monomeric form was found to abolish its ability to form Ca{sup 2+}-dependent homodimers, without impairing its ability to mediate C{anti 1}r-C{anti 1}s heteroassociation. C{anti 1}s iodinated in its dimeric form in contrast, fully retained the ability to self-associate. With a view to identify the tyrosine residues iodinated in each case, C{anti 1}s was radioiodinated in its monomeric and dimeric forms, and comparative tryptic mapping was performed on the resulting {sup 125}I-labeled A chains. Most of the tyrosine residues either were not iodinated or were equivalently iodinated in both monomeric and dimeric C{anti 1}s. In contrast, Tyr-33 and Tyr-38 were iodinated in the monomer but not in the dimer. Conversely, Try-52 and Tyr-147 were iodinated only in the dimer. These results provide further evidence that the structural determinants of C{anti 1}s required for Ca{sup 2+} binding and Ca{sup 2+}-dependent protein-protein interactions are contributed by both the NH{sub 2}-terminal motif 1 (positions 1-110) and the epidermal growth factor like motif 2 (positions 111-159) of the {alpha} region. On the basis of available information, tentative models of the C{anti 1}s-C{anti 1}S and C{anti 1}r-C{anti 1}s Ca{sup 2+}-dependent interactions are proposed.

  4. Time and dose-dependent risk of pneumococcal pneumonia following influenza: a model for within-host interaction between influenza and Streptococcus pneumoniae.

    Science.gov (United States)

    Shrestha, Sourya; Foxman, Betsy; Dawid, Suzanne; Aiello, Allison E; Davis, Brian M; Berus, Joshua; Rohani, Pejman

    2013-09-06

    A significant fraction of seasonal and in particular pandemic influenza deaths are attributed to secondary bacterial infections. In animal models, influenza virus predisposes hosts to severe infection with both Streptococcus pneumoniae and Staphylococcus aureus. Despite its importance, the mechanistic nature of the interaction between influenza and pneumococci, its dependence on the timing and sequence of infections as well as the clinical and epidemiological consequences remain unclear. We explore an immune-mediated model of the viral-bacterial interaction that quantifies the timing and the intensity of the interaction. Taking advantage of the wealth of knowledge gained from animal models, and the quantitative understanding of the kinetics of pathogen-specific immunological dynamics, we formulate a mathematical model for immune-mediated interaction between influenza virus and S. pneumoniae in the lungs. We use the model to examine the pathogenic effect of inoculum size and timing of pneumococcal invasion relative to influenza infection, as well as the efficacy of antivirals in preventing severe pneumococcal disease. We find that our model is able to capture the key features of the interaction observed in animal experiments. The model predicts that introduction of pneumococcal bacteria during a 4-6 day window following influenza infection results in invasive pneumonia at significantly lower inoculum size than in hosts not infected with influenza. Furthermore, we find that antiviral treatment administered later than 4 days after influenza infection was not able to prevent invasive pneumococcal disease. This work provides a quantitative framework to study interactions between influenza and pneumococci and has the potential to accurately quantify the interactions. Such quantitative understanding can form a basis for effective clinical care, public health policies and pandemic preparedness.

  5. Characteristic interpersonal behavior in dependent and avoidant personality disorder can be observed within very short interaction sequences.

    Science.gov (United States)

    Leising, Daniel; Sporberg, Doreen; Rehbein, Diana

    2006-08-01

    We present a behavior observation study of interpersonal behavior in 96 female subjects, who had been screened for the presence of dependent, avoidant, narcissistic and histrionic personality disorder features. Each subject took part in three short role-plays, taken from assertiveness training. Afterwards, both the subject and her role-play partner judged, how assertive the subject had been. Although observation time was very short, dependent and avoidant subjects could be easily identified from their overly submissive behavior in the role-plays. Histrionic and narcissistic subjects did not show distinctive interpersonal behavior. Contrary to a common belief, higher scores on some personality disorder (PD) scales were positively related to cross-situational variability of behavior. Results are discussed with regard to their implications for clinical diagnostics, therapy and the methodology of personality disorder research in general.

  6. Apolipoprotein E – Low Density Lipoprotein Receptor Interaction Affects Spatial Memory Retention and Brain ApoE Levels in an Isoform-Dependent Manner

    Science.gov (United States)

    Johnson, Lance A.; Olsen, Reid H.J.; Merkens, Louise S.; DeBarber, Andrea; Steiner, Robert D.; Sullivan, Patrick M.; Maeda, Nobuyo; Raber, Jacob

    2014-01-01

    Human apolipoprotein E (apoE) exists in three isoforms: apoE2, apoE3 and apoE4. APOE ε4 (E4) is a major genetic risk factor for cardiovascular disease (CVD) and Alzheimer's disease (AD). ApoE mediates cholesterol metabolism by binding various receptors. The low-density lipoprotein receptor (LDLR) has a high affinity for apoE, and is the only member of its receptor family to demonstrate an apoE isoform specific binding affinity (E4>E3>>E2). Evidence suggests that a functional interaction between apoE and LDLR influences the risk of CVD and AD. We hypothesize that the differential cognitive effects of the apoE isoforms are a direct result of their varying interactions with LDLR. To test this hypothesis, we have employed transgenic mice that express human apoE2, apoE3, or apoE4, and either human LDLR (hLDLR) or no LDLR (LDLR−/−). Our results show that plasma and brain apoE levels, cortical cholesterol, and spatial memory are all regulated by isoform-dependent interactions between apoE and LDLR. Conversely, both anxiety-like behavior and cued associative memory are strongly influenced by APOE genotype, but these processes appear to occur via an LDLR-independent mechanism. Both the lack of LDLR and the interaction between E4 and the LDLR were associated with significant impairments in the retention of long term spatial memory. Finally, levels of hippocampal apoE correlate with long term spatial memory retention in mice with human LDLR. In summary, we demonstrate that the apoE-LDLR interaction affects regional brain apoE levels, brain cholesterol, and cognitive function in an apoE isoform-dependent manner. PMID:24412220

  7. Apolipoprotein E-low density lipoprotein receptor interaction affects spatial memory retention and brain ApoE levels in an isoform-dependent manner.

    Science.gov (United States)

    Johnson, Lance A; Olsen, Reid H J; Merkens, Louise S; DeBarber, Andrea; Steiner, Robert D; Sullivan, Patrick M; Maeda, Nobuyo; Raber, Jacob

    2014-04-01

    Human apolipoprotein E (apoE) exists in three isoforms: apoE2, apoE3 and apoE4. APOE ε4 is a major genetic risk factor for cardiovascular disease (CVD) and Alzheimer's disease (AD). ApoE mediates cholesterol metabolism by binding various receptors. The low-density lipoprotein receptor (LDLR) has a high affinity for apoE, and is the only member of its receptor family to demonstrate an apoE isoform specific binding affinity (E4>E3>E2). Evidence suggests that a functional interaction between apoE and LDLR influences the risk of CVD and AD. We hypothesize that the differential cognitive effects of the apoE isoforms are a direct result of their varying interactions with LDLR. To test this hypothesis, we have employed transgenic mice that express human apoE2, apoE3, or apoE4, and either human LDLR (hLDLR) or no LDLR (LDLR(-/-)). Our results show that plasma and brain apoE levels, cortical cholesterol, and spatial memory are all regulated by isoform-dependent interactions between apoE and LDLR. Conversely, both anxiety-like behavior and cued associative memory are strongly influenced by APOE genotype, but these processes appear to occur via an LDLR-independent mechanism. Both the lack of LDLR and the interaction between E4 and the LDLR were associated with significant impairments in the retention of long term spatial memory. Finally, levels of hippocampal apoE correlate with long term spatial memory retention in mice with human LDLR. In summary, we demonstrate that the apoE-LDLR interaction affects regional brain apoE levels, brain cholesterol, and cognitive function in an apoE isoform-dependent manner. Copyright © 2014 Elsevier Inc. All rights reserved.

  8. Turning-off Signaling by Siglecs, Selectins and Galectins: Chemical Inhibition of Glycan-dependent Interactions in Cancer

    Directory of Open Access Journals (Sweden)

    Alejandro Javier Cagnoni

    2016-05-01

    Full Text Available Aberrant glycosylation, a common feature associated with malignancy, has been implicated in important events during cancer progression. Our understanding of the role of glycans in cancer has grown exponentially in the last few years, concurrent with important advances in glycomics and glycoproteomic technologies, paving the way for the validation of a number of glycan structures as potential glycobiomarkers. However, the molecular bases underlying cancer-associated glycan modifications are still far from understood. Glycans exhibit a natural heterogeneity, crucial for their diverse functional roles as specific carriers of biologically-relevant information. This information is decoded by families of proteins named lectins, including siglecs, C-type lectin receptors (CLRs and galectins. Siglecs, sialic-acid binding transmembrane lectins, are primarily expressed on the surface of immune cells and differentially control innate and adaptive immune responses. Among CLRs, selectins are a family of cell adhesion molecules that mediate interactions between cancer cells and platelets, leukocytes and endothelial cells, thus facilitating tumor cell invasion and metastasis. Galectins, a family of soluble proteins that bind β-galactoside-containing glycans, have been implicated in diverse events associated with cancer biology such as apoptosis, homotypic cell aggregation, angiogenesis, cell migration and tumor-immune escape. Consequently, individual members of these lectin families have become promising targets for the design of novel anticancer therapies. During the past decade a number of inhibitors of lectin-glycan interactions have been developed including small-molecule inhibitors, multivalent saccharide ligands, and more recently peptides and peptidomimetics have offered alternatives for tackling tumor progression. In this article, we review the current status of the discovery and development of chemical lectin inhibitors and discuss novel strategies

  9. Electrons, muons and hadrons in extensive air showers and how do they depend on nuclear interaction model, part 2

    Science.gov (United States)

    Wrotniak, J. A.; Yodh, G. B.

    1985-01-01

    Some of the results of Monte Carlo simulations of extensive air showers for nuclear interactions models are presented. The most significant part of scaling violation effect is generated by the inclusion of rising cross-section. Among the models considered the lowest value for Eo/N(max) is obtained when rapidly rising cross-section and charge exchange are both included (model R-F01). The value is still 1.38 GeV/electron. Except at the highest energies, the sensitivity to atomic mass of the primary is greater than to specific assumptions about multiple production.

  10. Laser spectroscopy with nanometric gas cells distance dependence of atom-surface interaction and collisions under confinement

    CERN Document Server

    Hamdi, I; Yarovitski, A; Dutier, G; Maurin, I; Saltiel, S; Li, Y; Lezama, A; Vartapetyan, T; Sarkisyan, D; Gorza, M P; Fichet, M; Bloch, D; Ducloy, M; Hamdi, Ismah\\`{e}ne; Todorov, Petko; Yarovitski, Alexander; Dutier, Gabriel; Maurin, Isabelle; Saltiel, Solomon; Li, Yuanyuan; Lezama, Arturo; Varzhapetyan, Tigran; Sarkisyan, David; Gorza, Marie-Pascale; Fichet, Mich\\`{e}le; Bloch, Daniel; Ducloy, Martial

    2005-01-01

    The high sensitivity of Laser Spectroscopy has made possible the exploration of atomic resonances in newly designed "nanometric" gas cells, whose local thickness varies from 20nm to more than 1000 nm. Following the initial observation of the optical analogous of the coherent Dicke microwave narrowing, the newest prospects include the exploration of long-range atom surface van der Waals interaction with spatial resolution in an unprecedented range of distances, modification of atom dielectric resonant coupling under the influence of the coupling between the two neighbouring dielectric media, and even the possible modification of interatomic collisions processes under the effect of confinement.

  11. Social interaction rescues memory deficit in an animal model of Alzheimer's disease by increasing BDNF-dependent hippocampal neurogenesis.

    Science.gov (United States)

    Hsiao, Ya-Hsin; Hung, Hui-Chi; Chen, Shun-Hua; Gean, Po-Wu

    2014-12-03

    It has been recognized that the risk of cognitive decline during aging can be reduced if one maintains strong social connections, yet the neural events underlying this beneficial effect have not been rigorously studied. Here, we show that amyloid precursor protein (APP) and presenilin 1 (PS1) double-transgenic (APP/PS1) mice demonstrate improvement in memory after they are cohoused with wild-type mice. The improvement was associated with increased protein and mRNA levels of BDNF in the hippocampus. Concomitantly, the number of BrdU(+)/NeuN(+) cells in the hippocampal dentate gyrus was significantly elevated after cohousing. Methylazoxymethanol acetate, a cell proliferation blocker, markedly reduced BrdU(+) and BrdU/NeuN(+) cells and abolished the effect of social interaction. Selective ablation of mitotic neurons using diphtheria toxin (DT) and a retrovirus vector encoding DT receptor abolished the beneficial effect of cohousing. Knockdown of BDNF by shRNA transfection blocked, whereas overexpression of BDNF mimicked the memory-improving effect. A tropomyosin-related kinase B agonist, 7,8-dihydroxyflavone, occluded the effect of social interaction. These results demonstrate that increased BDNF expression and neurogenesis in the hippocampus after cohousing underlie the reversal of memory deficit in APP/PS1 mice. Copyright © 2014 the authors 0270-6474/14/3416207-13$15.00/0.

  12. On-Beads Digestion in Conjunction with Data-Dependent Mass Spectrometry: A Shortcut to Quantitative and Dynamic Interaction Proteomics

    Directory of Open Access Journals (Sweden)

    Benedetta Turriziani

    2014-04-01

    Full Text Available With the advent of the “-omics” era, biological research has shifted from functionally analyzing single proteins to understanding how entire protein networks connect and adapt to environmental cues. Frequently, pathological processes are initiated by a malfunctioning protein network rather than a single protein. It is therefore crucial to investigate the regulation of proteins in the context of a pathway first and signaling network second. In this study, we demonstrate that a quantitative interaction proteomic approach, combining immunoprecipitation, in-solution digestion and label-free quantification mass spectrometry, provides data of high accuracy and depth. This protocol is applicable, both to tagged, exogenous and untagged, endogenous proteins. Furthermore, it is fast, reliable and, due to a label-free quantitation approach, allows the comparison of multiple conditions. We further show that we are able to generate data in a medium throughput fashion and that we can quantify dynamic interaction changes in signaling pathways in response to mitogenic stimuli, making our approach a suitable method to generate data for system biology approaches.

  13. Population effects of growth hormone transgenic coho salmon depend on food availability and genotype by environment interactions.

    Science.gov (United States)

    Devlin, Robert H; D'Andrade, Mark; Uh, Mitchell; Biagi, Carlo A

    2004-06-22

    Environmental risk assessment of genetically modified organisms requires determination of their fitness and invasiveness relative to conspecifics and other ecosystem members. Cultured growth hormone transgenic coho salmon (Oncorhynchus kisutch) have enhanced feeding capacity and growth, which can result in large enhancements in body size (>7-fold) relative to nontransgenic salmon, but in nature, the ability to compete for available food is a key factor determining survival fitness and invasiveness of a genotype. When transgenic and nontransgenic salmon were cohabitated and competed for different levels of food, transgenic salmon consistently outgrew nontransgenic fish and could affect the growth of nontransgenic cohorts except when food availability was high. When food abundance was low, dominant individuals emerged, invariably transgenic, that directed strong agonistic and cannibalistic behavior to cohorts and dominated the acquisition of limited food resources. When food availability was low, all groups containing transgenic salmon experienced population crashes or complete extinctions, whereas groups containing only nontransgenic salmon had good (72.0 +/- 4.3% SE) survival, and their population biomass continued to increase. Thus, effects of growth hormone transgenic salmon on experimental populations were primarily mediated by an interaction between food availability and population structure. These data, while indicative of forces which may act on natural populations, also underscore the importance of genotype by environment interactions in influencing risk assessment data for genetically modified organisms and suggest that, for species such as salmon which are derived from large complex ecosystems, considerable caution is warranted in applying data from individual studies.

  14. Fluorescence probe study of Ca2+-dependent interactions of calmodulin with calmodulin-binding peptides of the ryanodine receptor.

    Science.gov (United States)

    Gangopadhyay, Jaya Pal; Grabarek, Zenon; Ikemoto, Noriaki

    2004-10-22

    We have used a highly environment-sensitive fluorescent probe 6-bromoacetyl-2-dimethylaminonaphthalene (badan) to study the interaction between calmodulin (CaM) and a CaM-binding peptide of the ryanodine receptor (CaMBP) and its sub-fragments F1 and F4. Badan was attached to the Thr34Cys mutant of CaM (CaM-badan). Ca(2+) increase in a physiological range of Ca(2+) (0.1-2 microM) produced about 40 times increase in the badan fluorescence. Upon binding to CaMBP, the badan fluorescence of apo-CaM showed a small increase at a slow rate; whereas that of Ca-CaM showed a large decrease at a very fast rate. Upon binding of CaM to the badan-labeled CaMBP, the badan fluorescence showed a small and slow increase at low Ca(2+), and a large and fast increase at high Ca(2+). Thus, the badan probe attached to CaM Cys(34) can be used to monitor conformational changes occurring not only in CaM, but also those in the CaM-CaMBP interface. Based on our results we propose that both the interaction interface and the global conformation of the CaM-CaMBP complex are altered by calcium.

  15. Monte-Carlo Analysis of the Composition Dependence of the Flory-Huggins Interaction Parameter in PE-dPE Blends

    Science.gov (United States)

    Russell, Travis; Edwards, Brian; Khomami, Bamin

    2012-02-01

    Experimental SANS research displays a significant concentration dependence of the Flory-Huggins (χ) interaction parameter in isotopic polymer blends. At the extremes of the deuterated polymer concentration (φD 0.8), χ is shown to exhibit a greater than fourfold increase over its value at φD = 0.5. However, despite numerous attempts to theoretically describe the nature of this phenomenon, consensus is still lacking regarding the mechanisms at work in this system. This study uses free-space, spatially discretized Monte Carlo simulations to investigate the χ composition dependence of PE-dPE blends. Initial simulations are run on simple Lennard-Jones fluids to display the capability of the simulation method to track local concentration and energy across the discretized space as well as to investigate the concentration dependence of the radial distribution function, g(r), and structure factor, S(k). After which, MC simulations are performed on the PE-dPE system with varying φD. Both local and average system energies are tracked in addition to g(r) and S(k). The Flory-Huggins interaction parameter is then calculated using the Random Phase Approximation.

  16. Role of the chemical bonding for the time-dependent electron transport through an interacting quantum dot

    KAUST Repository

    Goker, Ali

    2011-06-01

    A combination of ab initio and many-body calculations is utilized to determine the effects of the bonding in Au electrodes on the time dependent current through a quantum dot suddenly shifted into the Kondo regime by a gate voltage. For an asymmetrically coupled system the instantaneous conductance exhibits fluctuations. The frequencies of the fluctuations turn out to be proportional to the energetic separation between the dominating peaks in the density of states and the Fermi level. The chemical bonding in the electrodes, thus, drastically alters the transient current, which can be accessed by ultrafast pump-probe techniques. © 2011 Elsevier B.V. All rights reserved.

  17. State-dependent electrostatic interactions of S4 arginines with E1 in S2 during Kv7.1 activation.

    Science.gov (United States)

    Wu, Dick; Delaloye, Kelli; Zaydman, Mark A; Nekouzadeh, Ali; Rudy, Yoram; Cui, Jianmin

    2010-06-01

    The voltage-sensing domain of voltage-gated channels is comprised of four transmembrane helices (S1-S4), with conserved positively charged residues in S4 moving across the membrane in response to changes in transmembrane voltage. Although it has been shown that positive charges in S4 interact with negative countercharges in S2 and S3 to facilitate protein maturation, how these electrostatic interactions participate in channel gating remains unclear. We studied a mutation in Kv7.1 (also known as KCNQ1 or KvLQT1) channels associated with long QT syndrome (E1K in S2) and found that reversal of the charge at E1 eliminates macroscopic current without inhibiting protein trafficking to the membrane. Pairing E1R with individual charge reversal mutations of arginines in S4 (R1-R4) can restore current, demonstrating that R1-R4 interact with E1. After mutating E1 to cysteine, we probed E1C with charged methanethiosulfonate (MTS) reagents. MTS reagents could not modify E1C in the absence of KCNE1. With KCNE1, (2-sulfonatoethyl) MTS (MTSES)(-) could modify E1C, but [2-(trimethylammonium)ethyl] MTS (MTSET)(+) could not, confirming the presence of a positively charged environment around E1C that allows approach by MTSES(-) but repels MTSET(+). We could change the local electrostatic environment of E1C by making charge reversal and/or neutralization mutations of R1 and R4, such that MTSET(+) modified these constructs depending on activation states of the voltage sensor. Our results confirm the interaction between E1 and the fourth arginine in S4 (R4) predicted from open-state crystal structures of Kv channels and reveal an E1-R1 interaction in the resting state. Thus, E1 engages in electrostatic interactions with arginines in S4 sequentially during the gating movement of S4. These electrostatic interactions contribute energetically to voltage-dependent gating and are important in setting the limits for S4 movement.

  18. Size dependent gold nanoparticle interaction at nano-micro interface using both monolayer and multilayer (tissue-like) cell models

    Science.gov (United States)

    Yohan, Darren; Yang, Celina; Lu, Xiaofeng; Chithrani, Devika B.

    2016-03-01

    Gold nanoparticles (GNPs) can be used as a model NP system to improve the interface between nanotechnology and medicine since their size and surface properties can be tailored easily. GNPs are being used as radiation dose enhancers and as drug carriers in cancer research. Hence, it is important to know the optimum NP size for uptake not only at monolayer level but also at tissue level. Once GNPs leave tumor vasculature, they enter the tumor tissue. Success of any therapeutic technique using NPs depends on how well NPs penetrate the tumor tissue and reach individual tumor cells. In this work, multicellular layers (MCLs) were grown to model the post-vascular tumor environment. GNPs of 20 nm and 50 nm diameters were used to elucidate the effects of size on the GNP penetration and distribution dynamics. Larger NPs (50 nm) were better at monolayer level, but smaller NPs (20 nm) were at tissue level. The MCLs exhibited a much more extensive extracellular matrix (ECM) than monolayer cell cultures. This increased ECM created a barrier for NP transport and ECM was also dependent on the tumor cell lines. Smaller NPs penetrated better compared to larger NPs. Transport of NPs was better in MDA-MB231 vs MCF-7. This MCL model tissue structures are better tools to optimize NP transport through tissue before using them in animal models. Based on our study, we believe that smaller NPs are better for improved outcome in future cancer therapeutics.

  19. Modeling the light- and redox-dependent interaction of PpsR/AppA in Rhodobacter sphaeroides.

    Science.gov (United States)

    Pandey, Rakesh; Flockerzi, Dietrich; Hauser, Marcus J B; Straube, Ronny

    2011-05-18

    Facultative photosynthetic bacteria switch their energy generation mechanism from respiration to photosynthesis depending on oxygen tension and light. Part of this transition is mediated by the aerobic transcriptional repressor PpsR. In Rhodobacter sphaeroides, the repressive action of PpsR is antagonized by the redox- and blue-light-sensitive flavoprotein AppA which results in a unique phenotype: the repression of photosynthesis genes at intermediate oxygen levels and high light intensity, which is believed to reduce the risk of photooxidative stress. To analyze the underlying mechanism we developed a simple mathematical model based on the AppA-dependent reduction of a disulfide bond in PpsR and the light-sensitive complex formation between the reduced forms of AppA and PpsR. A steady-state analysis shows that high light repression can indeed occur at intermediate oxygen levels if PpsR is reduced on a faster timescale than AppA and if the electron transfer from AppA to PpsR is effectively irreversible. The model further predicts that if AppA copy numbers exceed those of PpsR by at least a factor of two, the transition from aerobic to anaerobic growth mode can occur via a bistable regime. We provide necessary conditions for the emergence of bistability and discuss possible experimental verifications.

  20. Collaboration and nested environmental governance: Scale dependency, scale framing, and cross-scale interactions in collaborative conservation.

    Science.gov (United States)

    Wyborn, Carina; Bixler, R Patrick

    2013-07-15

    The problem of fit between social institutions and ecological systems is an enduring challenge in natural resource management and conservation. Developments in the science of conservation biology encourage the management of landscapes at increasingly larger scales. In contrast, sociological approaches to conservation emphasize the importance of ownership, collaboration and stewardship at scales relevant to the individual or local community. Despite the proliferation of initiatives seeking to work with local communities to undertake conservation across large landscapes, there is an inherent tension between these scales of operation. Consequently, questions about the changing nature of effective conservation across scales abound. Through an analysis of three nested cases working in a semiautonomous fashion in the Northern Rocky Mountains in North America, this paper makes an empirical contribution to the literature on nested governance, collaboration and communication across scales. Despite different scales of operation, constituencies and scale frames, we demonstrate a surprising similarity in organizational structure and an implicit dependency between these initiatives. This paper examines the different capacities and capabilities of collaborative conservation from the local to regional to supra regional. We draw on the underexplored concept of 'scale-dependent comparative advantage' (Cash and Moser, 2000), to gain insight into what activities take place at which scale and what those activities contribute to nested governance and collaborative conservation. The comparison of these semiautonomous cases provides fruitful territory to draw lessons for understanding the roles and relationships of organizations operating at different scales in more connected networks of nested governance.