bluuebunny/crossref_metadata_2025 huggingface dataset:
Nucleation and growth of GaN nanorods on Si (111) surfaces by plasma-assisted molecular beam epitaxy - The influence of Si- and Mg-doping
Authors: Furtmayr Florian , Vielemeyer Martin , Stutzmann Martin , Arbiol Jordi , Estradé Sònia , Peirò Francesca , Morante Joan Ramon , Eickhoff Martin
Published: August 2008

The self-assembled growth of GaN nanorods on Si (111) substrates by plasma-assisted molecular beam epitaxy under nitrogen-rich conditions is investigated. An amorphous silicon nitride layer is formed in the initial stage of growth that prevents the formation of a GaN wetting layer. The nucleation time was found to be strongly influenced by the substrate temperature and was more than 30 min for the applied growth conditions. The observed tapering and reduced length of silicon-doped nanorods is explained by enhanced nucleation on nonpolar facets and proves Ga-adatom diffusion on nanorod sidewalls as one contribution to the axial growth. The presence of Mg leads to an increased radial growth rate with a simultaneous decrease of the nanorod length and reduces the nucleation time for high Mg concentrations.
The vortex merger rate in freely decaying, two-dimensional turbulence
Authors: LaCasce J. H.
Published: August 2008

New numerical simulations of decaying two-dimensional turbulence are examined, with a focus on the statistics of the coherent vortices. The number of vortices decays as a power law, as in previous studies, but the rate varies between experiments. While the rate is not significantly affected by changes in the initial conditions, it does depend on the choice of small scale dissipation. In contrast, the vortex dispersion rate is approximately the same in all the experiments. Assuming energy conservation, the decay rate can be determined from the dispersion rate. The prediction agrees well with the rate observed in the least dissipative experiments. In the more dissipative experiments, the decay rate is greater because the dissipation increases lateral extent of the vortices and hence their collision cross section. In such cases, the density decay rate can be predicted from a scaling relation involving the collision time, given the observed growth rate of the mean vortex area.
Landau automorphic functions on Cn of magnitude ν
Authors: Ghanmi A. , Intissar A.
Published: August 2008

We investigate the spectral theory of the invariant Landau Hamiltonian, Lν=−1/2{4∑j=1n∂2/∂zj∂z¯j+2ν∑j=1n(zj∂/∂zj−z¯j∂/∂z¯j)−ν2|z|2}, acting on the space FΓ,χν of (Γ,χ)-automorphic functions on Cn, constituted of C∞ functions satisfying the functional equation f(z+γ)=χ(γ)eiνIm⟨z,γ⟩f(z);  z∊Cn,γ∊Γ, for given real number ν>0, lattice Γ of Cn and a map χ:Γ→U(1) such that the triplet (ν,Γ,χ) satisfies a Riemann–Dirac quantization-type condition. More precisely, we show that the eigenspace EΓ,χν(λ)={f∊FΓ,χν; Lνf=ν(2λ+n)f}; λ∊C, is nontrivial if and only if λ=l=0,1,2,…,. In such case, EΓ,χν(l) is a finite dimensional vector space whose the dimension is given explicitly by dim EΓ,χν(l)=(n+l−1l)(ν/π)nvol(Cn/Γ). Furthermore, we show that the eigenspace EΓ,χν(0) associated with the lowest Landau level of Lν is isomorphic to the space, OΓ,χν(Cn), of holomorphic functions on Cn satisfying g(z+γ)=χ(γ)eν/2|γ|2+ν⟨z,γ⟩g(z), (∗) that we can realize also as the null space of the differential operator, ∑j=1n(−∂2/∂zj∂z¯j+νz¯j∂/∂z¯j) acting on C∞ functions on Cn satisfying (∗).
A gradient-directed Monte Carlo approach to molecular design
Authors: Hu Xiangqian , Beratan David N. , Yang Weitao
Published: August 2008

The recently developed linear combination of atomic potentials (LCAP) approach [M. Wang et al., J. Am. Chem. Soc. 128, 3228 (2006)] allows continuous optimization in a discrete chemical space, and thus is useful in the design of molecules for targeted properties. To address further challenges arising from the rugged, continuous property surfaces in the LCAP approach, we develop a gradient-directed Monte Carlo (GDMC) strategy as an augmentation to the original LCAP optimization method. The GDMC method retains the power of exploring molecular space by utilizing local gradient information computed from the LCAP approach to jump between discrete molecular structures. It also allows random MC moves to overcome barriers between local optima on property surfaces. The combined GDMC–LCAP approach is demonstrated here for optimizing nonlinear optical properties in a class of donor-acceptor substituted benzene and porphyrin frameworks. Specifically, one molecule with four nitrogen atoms in the porphyrin ring was found to have a larger first hyperpolarizability than structures with the conventional porphyrin motif.
Cytoskeleton mediated effective elastic properties of model red blood cell membranes
Authors: Zhang Rui , Brown Frank L. H.
Published: August 2008

The plasma membrane of human red blood cells consists of a lipid bilayer attached to a regular network of underlying cytoskeletal polymers. We model this system at a dynamic coarse-grained level, treating the bilayer as an elastic sheet and the cytoskeletal network as a series of phantom entropic springs. In contrast to prior simulation efforts, we explicitly account for dynamics of the cytoskeletal network, both via motion of the protein anchors that attach the cytoskeleton to the bilayer and through breaking and reconnection of individual cytoskeletal filaments. Simulation results are explained in the context of a simple mean field percolation model and comparison is made to experimental measurements of red blood cell fluctuation amplitudes.
Reappraisal of cis effect in 1,2-dihaloethenes: An improved virtual orbital multireference approach
Authors: Chaudhuri Rajat K. , Hammond Jeff R. , Freed Karl F. , Chattopadhyay Sudip , Mahapatra Uttam Sinha
Published: August 2008

Computed relative stabilities for isomers of 1,2-difluoroethene and 1,2-dichloroethene isomers are compared with predictions based on chemical hardness (η) and electrophilicity (ω) using the principles of maximum hardness and minimum electrophilicity. The chemical hardness and electrophilicity deduced either from improved virtual orbital (IVO) energies or from correlated treatments correctly predict that cis 1,2-difluoroethene and 1,2-dichloroethene are energetically more stable than the corresponding trans isomers, and the ground state energies from multireference perturbation theory with IVO orbitals agree with these predictions. However, when the same quantities are computed using Hartree–Fock orbitals, serious inconsistencies between the two approaches emerge in predicting the stability of the isomers of the 1,2-dihaloethenes. The present study clearly demonstrates that the IVO energies are appropriate for the computation of hardness related parameters, notably the chemical hardness and electrophilicity. Moreover, the IVO methods also provide smooth potential energy curves for the cis-trans isomerization of the two 1,2-dihaloethenes.
Nitroxide spin exchange due to re-encounter collisions in a series of n-alkanes
Authors: Kurban Mark R. , Peric Miroslav , Bales Barney L.
Published: August 2008

Bimolecular collisions between perdeuterated 2,2,6,6-tetramethyl-4-oxopiperidine-l-oxyl molecules in three alkanes have been studied by measuring the electron paramagnetic resonance (EPR) spectral changes induced by spin exchange. We define an “encounter” to be a first-time collision followed by a series of re-encounters prior to the diffusing pair’s escaping each other’s presence. The present work stems from a recent proposal [B. L. Bales et al., J. Phys. Chem. A 107, 9086 (2003)] that an unexpected linear dependence of the spin-exchange-induced EPR line shifts on spin-exchange frequency can be explained by re-encounters of the same probe pair during one encounter. By employing nonlinear least-squares fitting, full use of the information available from the spectral changes allows us to study encounters and re-encounters separately. The encounter rate constants appear to be dominated by hydrodynamic forces, forming a common curve for hexane, decane, and hexadecane when plotted against T∕η, where η is the shear viscosity. Unexpectedly, encounters are not dependent on the ratio μ=a∕as, where a and as are the van der Waals radii of the nitroxide probe and the solvent, respectively. It is argued that the near coincidence of the resulting encounter rate constant with the hydrodynamic prediction is likely due to a near cancellation of terms in the general diffusion coefficient. Thus, the semblance of hydrodynamic behavior is coincidental rather than intrinsic. In contrast, the mean times between re-encounters do depend on the relative sizes of probe and solvent. For hexane at lower temperatures, the Stokes–Einstein equation apparently describes re-encounters well; however, at higher temperatures and for decane and hexadecane, departures from the hydrodynamic prediction become larger as μ becomes smaller. This is in qualitative agreement with the theory of microscopic diffusion of Hynes et al. [J. Chem. Phys. 70, 1456 (1979)]. These departures are well correlated with the free volume available in the solvent; thus, the mean times between re-encounters form a common curve when plotted versus the free volume. Because free volume is manifested macroscopically by the isothermal compressibility, it is expected and observed that the re-encounter rate also forms a common curve across all three solvents when plotted with respect to compressibility. The existence of a common curve for alkanes raises the prospect of using EPR to determine the compressibility of substances such as fossil fuels and biological membranes.
On the Fermi level pinning in as-grown GaInNAs(Sb)/GaAs quantum wells with indium content of 8%–32%
Authors: Kudrawiec R. , Yuen H. B. , Bank S. R. , Bae H. P. , Wistey M. A. , Harris James S. , Motyka M. , Misiewicz J.
Published: August 2008

Modified van Hoof structures containing GaInNAs(Sb) quantum wells (QWs) with indium content varying from 8% to 32% have been investigated using contactless electroreflectance (CER) spectroscopy. In CER spectra, both the QW transitions and GaAs-related Franz–Keldysh oscillations (FKOs) have been clearly observed. The band gap discontinuity at the GaInNAs(Sb)/GaAs interface has been determined by analyzing the QW transitions. The built-in electric field in the GaAs cap layer has been extracted from the FKO periodicity. The Fermi level position in the GaInNAs(Sb) QW has been determined through knowledge of the electric field in the GaAs cap layer and band gap discontinuity in the GaInNAs(Sb)/GaAs QW. It has been found that the Fermi level is pinned for all samples at the same energy, ∼4.7 eV below the vacuum level. The Fermi level is located very close to the Fermi level stabilization energy, ∼4.9 eV below the vacuum level. A high concentration of native point defects in the as-grown material is the reason for the Fermi level pinning at this energy.
Optimized nonadiabatic nanofocusing of plasmons by tapered metal rods
Authors: Gramotnev Dmitri K. , Vogel Michael W. , Stockman Mark I.
Published: August 2008

Using rigorous numerical methods of analysis, this paper investigates nonadiabatic nanofocusing in tapered nanorods with the major emphasis on structural optimization for achieving maximal possible local field enhancement. Simple analytical equations for the determination of the optimal length of the tapered rod are presented and discussed. It is also shown that for the considered structures, optimal taper angle and optimal length of the rod only very weakly depend on the radius of curvature of the rounded tip of the rod. Contrary to this, enhancement of the local electric field at the rounded tip strongly increases with decreasing radius of the tip. Comparison of the numerical results with the adiabatic theory of nanofocusing results in accurate verification of the applicability conditions for adiabatic approximation in tapered nanorods.
Hardening-softening transition in Fe-doped Pb(Zr,Ti)O3 ceramics and evolution of the third harmonic of the polarization response
Authors: Morozov Maxim I. , Damjanovic Dragan
Published: August 2008

It is shown that the phase angle of the third harmonic of polarization response (δ3) is very sensitive to the aging state of hard, Fe-doped lead zirconate titanate [Pb(Zr,Ti)O3 or PZT] ceramics and may thus provide rich information on processes responsible for aging in hard ferroelectrics. When hard PZT ceramics experience hardening (aged state)-softening (deaged state) transition, δ3 changes by about 90° at subswitching fields and by about 180° at switching conditions. Evolution of δ3 with time, temperature and electric field amplitude during deaging suggests that at least two mechanisms of charge migration, one short-range and one long-range, may participate in the deaging process.
Extending the class of solvable potentials. I. The infinite potential well with a sinusoidal bottom
Authors: Alhaidari A. D. , Bahlouli H.
Published: August 2008

This is the first in a series of papers where we succeed in enlarging the class of exactly solvable potentials in one and three dimensions by obtaining solutions for new relativistic and nonrelativistic problems. This is accomplished by constructing a matrix representation of the wave operator in a complete square integrable basis that makes it tridiagonal. Expanding the wave function in this basis makes the wave equation equivalent to a three-term recursion relation for the expansion coefficients. Consequently, finding solutions of the recursion relation is equivalent to solving the original problem. Doing so results in a larger class of solvable potentials. The usual diagonal representation constraint results in a reduction from the larger class to the conventional class of solvable potentials, giving the well-known energy spectra and the corresponding wave functions. Moreover, some of the new solvable problems show evidence of a Klauder-like phenomenon. In the present work, we give an exact solution for the infinite potential well with a bottom that has a sinusoidal shape.
Dielectric dispersion behavior of Ba(ZrxTi1−x)O3 solid solutions with a quasiferroelectric state
Authors: Ke Shanming , Fan Huiqing , Huang Haitao , Chan Helen L. W. , Yu Shuhui
Published: August 2008

The temperature dependence of dielectric permittivity was investigated for the barium zirconium titanate solid solution system [BZT, Ba(ZrxTi1−x)O3 0.25≤x≤0.5]. The dielectric relaxation behavior was observed in these ferroelectrics with diffused phase transition. In contrast to the canonical relaxors such as Pb(Mg1/3Nb2/3)O3, the diffused phase transition of BZT could not be well described by the popular modified Curie–Weiss law. Quasiferroelectric state theory was introduced to explain the dielectric results of the BZT relaxors.
The vector potential of a circular cylindrical antenna in terms of a toroidal harmonic expansion
Authors: Selvaggi Jerry , Salon Sheppard , Chari M. V. K.
Published: August 2008

A toroidal harmonic expansion is developed which is used to represent the vector potential due to a circular cylindrical antenna with a rectangular cross section at any arbitrary point in space. The singular part of the antenna kernel is represented by an associated toroidal harmonic expansion and the analytic part of the kernel is represented by a binomial expansion. A simple example is given to illustrate the application of the toroidal expansion.
Application of slanted finger interdigital transducer surface acoustic wave devices to ultraviolet array photodetectors
Authors: Ma Chein-Ching , Huang Tsai-Ju , Yu Jhih-Ming
Published: August 2008

An ultraviolet array photodetector is developed by the application of a LiNbO3-based slanted finger interdigital transducer (SFIT) and several ZnO optically active areas. This array photodetector can obtain ultraviolet light intensities within a single measurement. In this analysis, the acoustoelectric interaction between the photogenerated carriers in several active areas and a SFIT surface acoustic wave device is simulated. In the experiment, the photodetector with one to three optically active areas are fabricated. Ultraviolet light with a wavelength of 380 nm and an intensity of 65 μW cm−2 is detectable from the photodetector developed in this study. The minimum size of the optically active areas is 0.04 mm2 that can provide good spatial resolution. The ultraviolet array photodetector is capable of measuring a distributed light field.
The spin-flip extended single excitation configuration interaction method
Authors: Casanova David , Head-Gordon Martin
Published: August 2008

An extension of the spin-flip single excitation configuration interaction (SF-CIS) method is introduced. The extension, abbreviated as SF-XCIS, includes all configurations in which no more than one virtual level of the high spin triplet reference becomes occupied and no more than one doubly occupied level becomes vacant. The number of such configurations is quadratic with molecule size, and the method is implemented in a direct algorithm whose cost scales in the same way with molecule size as CIS itself, thus permitting applications to large systems. Starting from a spin restricted triplet determinant, SF-XCIS yields spin-pure singlet, triplet, and quintet states, and treats both half-occupied reference orbitals in a fully balanced way to allow application to strongly correlated problems. Tests on bond dissociation in the HF molecule, the torsional potential of ethylene, and excited states of polyenes show encouraging improvements using SF-XCIS compared to SF-CIS and a previously suggested extension, the spin-complete CIS model.
Ideal magnetohydrodynamics stability spectrum with a resistive wall
Authors: Smith S. P. , Jardin S. C.
Published: August 2008

The eigenvalue equations describing a cylindrical ideal magnetohydrodynamics plasma interacting with a thin resistive wall are presented in the standard mathematical form, A⋅x=λB⋅x, without discretizing the vacuum regions surrounding the plasma. This is accomplished by using a finite-element basis for the plasma perturbations, and by coupling the plasma surface perturbations to the perturbed electrical current in the wall using a Green’s-function approach. The perturbed wall current introduces a single additional degree of freedom into the system, which, together with an auxiliary variable, u=ωξ, allows the system to take the standard linear form. The standard form allows the use of linear eigenvalue solvers, without additional iterations, to compute the complete spectrum of plasma modes in the presence of a surrounding resistive wall at arbitrary separation. Standard results are recovered in the limits of (i) an infinitely resistive wall (no wall), and (ii) a zero resistance wall (ideal wall).
Ab initio and direct dynamics study of the reaction of Cl atoms with HOCO
Authors: Yu Hua-Gen , Francisco Joseph S. , Muckerman James T.
Published: August 2008

The reaction of Cl with HOCO has been examined using the coupled-cluster method to locate and optimize the critical points on the ground-state potential energy surface. The results show that the reaction produces the HCl and CO2 products as experimentally observed. The reaction occurs via a HOC(O)Cl intermediate with an estimated heat of formation of −97.8±2.0 kcal/mol. A direct ab initio dynamics method has been used to provide insight into the reaction mechanisms and to determine the thermal rate coefficients in the temperature range of 200–600 K. At room temperature, the thermal rate coefficient is predicted to be 3.0×10−11 cm3 molecule−1 s−1 with an activation energy of −0.2 kcal/mol. Two kinds of reactive trajectories are found. One kind proceeds through short-lived HOC(O)Cl complexes with a lifetime of 310 fs while the other kind occurs via longer-lived intermediates with a lifetime of 1.9 ps.
Monte Carlo configuration interaction predictions for the electronic spectra of Ne, CH2, C2, N2, and H2O compared to full configuration interaction calculations
Authors: Győrffy W. , Bartlett R. J. , Greer J. C.
Published: August 2008

Singlet and triplet electronic excitation energies have been calculated for Ne, CH2, C2, N2, and H2O using the Monte Carlo configuration interaction (CI) method. We find that excitation energies can be predicted to within a few tens of meV of full CI (FCI) results using expansions consisting of only a few thousand configuration state functions as compared to the O(108) configurations occurring in the corresponding FCI expansions. The method provides a consistently accurate and balanced description of electronic excitations with accuracy for small molecular systems comparable to the equation-of-motion coupled cluster method with full triples.
Transient hydroxyl formation from water on oxygen-covered Au(111)
Authors: Quiller R. G. , Baker T. A. , Deng X. , Colling M. E. , Min B. K. , Friend C. M.
Published: August 2008

We present evidence for the formation of transient hydroxyls from the reaction of water with atomic oxygen on Au(111) and investigate the effect of adsorbed oxygen on the hydrogen bonding of water. Water is evolved in peaks at 175 and 195 K in temperature programed reaction experiments following adsorption of water on oxygen-covered Au(111). The peak at 175 K is ascribed to sublimation of multilayers of water, whereas the peak at 195 K is associated with oxygen-stabilized water or a water-hydroxyl surface complex. Infrared reflection absorption spectra are consistent with the presence of molecular water over the entire range of coverages studied, indicating that isolated stable hydroxyls are not formed. Isotopic exchange of adsorbed O16 with H2O18 following adsorption and subsequent temperature programed reaction, however, indicates that transient OH species are formed. The extent of oxygen exchange was considerable—up to 70%. The degree of oxygen exchange depends on the initial coverage of oxygen, the surface temperature when preparing oxygen adatoms, and the H2O18 coverage. The hydroxyls are short-lived, forming and disproportionating multiple times before water desorption during temperature programed reaction. It was also found that chemisorbed oxygen is critical in the formation of hydroxyls and stabilizing water, whereas gold oxide does not contribute to these effects. These results identify transient hydroxyls as species that could play a critical role in oxidative chemical reactions on gold, especially in ambient water vapor. The crystallinity of adsorbed water also depended on the degree of surface ordering and chemical modification based on scanning tunneling microscopy and infrared spectra. These results demonstrate that oxidation of interfaces has a major impact on their interaction with water.
Dielectric process of space-charge polarization for an electrolytic cell with blocking electrodes
Authors: Sawada Atsushi
Published: August 2008

The dielectric process of space-charge polarization for an electrolytic cell with blocking electrodes is simulated considering bound charges externally supplied to the electrodes. A numerical calculation is performed to determine the distribution of mobile charges under an ac field satisfying Poisson’s equation in which the dielectric constant varies with frequency. An exact frequency-dependent curve of the complex dielectric constant is obtained by including the contribution of bound charges induced by the space-charge polarization itself in Poisson’s equation at every frequency. The present model of the space-charge polarization enables one to correctly understand the experimental results on the complex dielectric constant of electrolytic cells in low-frequency regions.
Phase-separation transition in liquid mixtures near curved charged objects
Authors: Marcus Gilad , Samin Sela , Tsori Yoav
Published: August 2008

We study the thermodynamic behavior of nonpolar liquid mixtures in the vicinity of curved charged objects, such as electrodes or charged colloids. There is a critical value of charge (or potential), above which a phase-separation transition occurs, and the interface between high- and low-dielectric constant components becomes sharp. Analytical and numerical composition profiles are given, and the equilibrium front location as a function of charge or voltage is found. We further employ a simple Cahn–Hilliard type equation to study the dynamics of phase separation in spatially nonuniform electric fields. We find an exponential temporal relaxation of the demixing front location. We give the dependence of the steady-state location and characteristic time on the charge, mixture composition and ambient temperature.
Electrical and magnetic properties of multiferroic BiFeO3/CoFe2O4 heterostructure
Authors: Zheng R. Y. , Wang J. , Ramakrishna S.
Published: August 2008

To realize a magnetoelectric heterostructure with desired ferroelectric and magnetic properties, a heterostructure consisting of BiFeO3 (BFO)/CoFe2O4 (CFO) layers has been grown on SrRuO3 buffered Pt/TiO2/SiO2/Si substrate by rf sputtering. X-ray diffraction shows that the BFO and CFO phases have been successfully retained in the heterostructure. Grain growth of the CFO phase was enhanced on top of the BFO layer. The heterostructure exhibits both ferroelectric and magnetic behaviors at room temperature. Its remanent polarization (2Pr) is measured to be ∼146 μC/cm2 and the coercive field (2Ec) is ∼1803 kV/cm, while the saturation magnetization (2Ms) is 140 emu/cm3 and the coercive field (2Hc) is ∼2.7 kOe. The leakage current behavior of the heterostructure is consistent with space charge limited conduction mechanism. While the heterostructure is promising for multiferroic behavior, it would be necessary to control the structural defects such that the leakage is minimized.
Time evolution of ion-acoustic double layers in an unmagnetized plasma
Authors: Bharuthram R. , Momoniat E. , Mahomed F. , Singh S. V. , Islam M. K.
Published: August 2008

Ion-acoustic double layers are examined in an unmagnetized, three-component plasma consisting of cold ions and two temperature electrons. Both of the electrons are considered to be Boltzmann distributed and the ions follow the usual fluid dynamical equations. Using the method of characteristics, a time-dependent solution for ion-acoustic double layers is obtained. Results of the findings may have important consequences for the real time satellite observations in the space environment.
Atomic assembly of Cu/Ta multilayers: Surface roughness, grain structure, misfit dislocations, and amorphization
Authors: Francis M. F. , Neurock M. N. , Zhou X. W. , Quan J. J. , Wadley H. N. G. , Webb Edmund B.
Published: August 2008

Molecular dynamics simulations and selected experiments have been carried out to study the growth of Cu films on (010) bcc Ta and the deposition of CuxTa1−x alloy films on (111) fcc Cu. They indicate that fcc Cu films with a (111) texture are always formed when Cu is deposited on Ta surfaces. These films are polycrystalline even when the Ta substrate is single crystalline. The grains have one of two different orientations and are separated by either orientational or misfit dislocations. Periodic misfit dislocations and stacking faults develop within these grains to release structure difference induced misfit strain energy. The Cu film surface roughness was found to decrease with increase in the adatom energy for deposition. When CuxTa1−x is deposited on Ta, the films always have a higher Cu composition than that of the vapor mixture. This arises from a surface segregation phenomenon. When the Cu and Ta fractions in the films are comparable, amorphous structures form. The fundamental origins for the segregation and amorphization phenomena are discussed.
Tyr130 phosphorylation triggers Syk release from antigen receptor by long-distance conformational uncoupling
Authors: Zhang Yajie , Oh Hyunju , Burton Robert A. , Burgner John W. , Geahlen Robert L. , Post Carol Beth
Published: August 2008

The Syk protein-tyrosine kinase plays a major role in signaling through the B cell receptor for antigen (BCR). Syk binds the receptor via its tandem pair of SH2 domains interacting with a doubly phosphorylated immunoreceptor tyrosine-based activation motif (dp-ITAM) of the BCR complex. Upon phosphorylation of Tyr-130, which lies between the two SH2 domains distant to the phosphotyrosine binding sites, Syk dissociates from the receptor. To understand the structural basis for this dissociation, we investigated the structural and dynamic characteristics of the wild type tandem SH2 region (tSH2) and a variant tandem SH2 region (tSH2pm) with Tyr-130 substituted by Glu to permanently introduce a negative charge at this position. NMR heteronuclear relaxation experiments, residual dipolar coupling measurements and analytical ultracentrifugation revealed substantial differences in the hydrodynamic behavior of tSH2 and tSH2pm. Although the two SH2 domains in tSH2 are tightly associated, the two domains in tSH2pmare partly uncoupled and tumble in solution with a faster correlation time. In addition, the equilibrium dissociation constant for the binding of tSH2pmto dp-ITAM (1.8 μM) is significantly higher than that for the interaction between dp-ITAM and tSH2 but is close to that for a singly tyrosine-phosphorylated peptide binding to a single SH2 domain. Experimental data and hydrodynamic calculations both suggest a loss of domain-domain contacts and change in relative orientation upon the introduction of a negative charge on residue 130. A long-distance structural mechanism by which the phosphorylation of Y130 negatively regulates the interaction of Syk with immune receptors is proposed.
Cooperative capture of large prey solves scaling challenge faced by spider societies
Authors: Yip Eric C. , Powers Kimberly S. , Avilés Leticia
Published: August 2008

A decrease in the surface area per unit volume is a well known constraint setting limits to the size of organisms at both the cellular and whole-organismal levels. Similar constraints may apply to social groups as they grow in size. The communal three-dimensional webs that social spiders build function ecologically as single units that intercept prey through their surface and should thus be subject to this constraint. Accordingly, we show that web prey capture area per spider, and thus number of insects captured per capita, decreases with colony size in a neotropical social spider. Prey biomass intake per capita, however, peaks at intermediate colony sizes because the spiders forage cooperatively and larger colonies capture increasingly large insects. A peaked prey biomass intake function would explain not only why these spiders live in groups and cooperate but also why they disperse only at large colony sizes, thus addressing both sociality and colony size range in this social spider. These findings may also explain the conspicuous absence of social spiders from higher latitudes and higher elevations, areas that we have previously shown to harbor considerably fewer insects of the largest size classes than the lowland tropical rainforests where social spiders thrive. Our findings thus illustrate the relevance of scaling laws to the size and functioning of levels of organization above the individual.
Synergistic control of T cell development and tumor suppression by diacylglycerol kinase α and ζ
Authors: Guo Rishu , Wan Chi-Keung , Carpenter Jeffery H. , Mousallem Talal , Boustany Rose-Mary N. , Kuan Chien-Tsun , Burks A. Wesley , Zhong Xiao-Ping
Published: August 2008

Diacylglycerol (DAG) kinases (DGKs) are a family of enzymes that convert DAG to phosphatidic acid (PA), the physiologic functions of which have been poorly defined. We report here that DGK α and ζ synergistically promote T cell maturation in the thymus. Absence of both DGKα and ζ (DGKα
−/−
ζ
−/−
) results in a severe decrease in the number of CD4
+
CD8
−
and CD4
−
CD8
+
single-positive thymocytes correlating with increased DAG-mediated signaling. Positive selection, but not negative selection, is impaired in DGKα
−/−
ζ
−/−
mice. The developmental blockage in DGKα
−/−
ζ
−/−
mice can be partially overcome by treatment with PA. Furthermore, decreased DGK activity also promotes thymic lymphomagenesis accompanying elevated Ras and Erk1/2 activation. Our data demonstrate a synergistic and critical role of DGK isoforms in T cell development and tumor suppression, and indicate that DGKs not only terminate DAG signaling but also initiate PA signaling in thymocytes to promote positive selection.
Closely related antibody receptors exploit fundamentally different strategies for steroid recognition
Authors: Verdino Petra , Aldag Caroline , Hilvert Donald , Wilson Ian A.
Published: August 2008

Molecular recognition by the adaptive immune system relies on specific high-affinity antibody receptors that are generated from a restricted set of starting sequences through homologous recombination and somatic mutation. The steroid binding antibody DB3 and the catalytic Diels–Alderase antibody 1E9 derive from the same germ line sequences but exhibit very distinct specificities and functions. However, mutation of only two of the 36 sequence differences in the variable domains, Leu
H47
Trp and Arg
H100
Trp, converts 1E9 into a high-affinity steroid receptor with a ligand recognition profile similar to DB3. To understand how these changes switch binding specificity and function, we determined the crystal structures of the 1E9 Leu
H47
Trp/Arg
H100
Trp double mutant (1E9dm) as an unliganded Fab at 2.05 Å resolution and in complex with two configurationally distinct steroids at 2.40 and 2.85 Å. Surprisingly, despite the functional mimicry of DB3, 1E9dm employs a distinct steroid binding mechanism. Extensive structural rearrangements occur in the combining site, where residue H47 acts as a specificity switch and H100 adapts to different ligands. Unlike DB3, 1E9dm does not use alternative binding pockets or different sets of hydrogen-bonding interactions to bind configurationally distinct steroids. Rather, the different steroids are inserted more deeply into the 1E9dm combining site, creating more hydrophobic contacts that energetically compensate for the lack of hydrogen bonds. These findings demonstrate how subtle mutations within an existing molecular scaffold can dramatically modulate the function of immune receptors by inducing unanticipated, but compensating, mechanisms of ligand interaction.
Hierarchical coding for sequential task events in the monkey prefrontal cortex
Authors: Sigala Natasha , Kusunoki Makoto , Nimmo-Smith Ian , Gaffan David , Duncan John
Published: August 2008

The frontal lobes play a key role in sequential organization of behavior. Little is known, however, of the way frontal neurons code successive phases of a structured task plan. Using correlational analysis, we asked how a population of frontal cells represents the multiple events of a complex sequential task. Monkeys performed a conventional cue–target association task, with distinct cue, delay, and target phases. Across the population of recorded cells, we examined patterns of activity for different task phases, and in the same phase, for different stimulus objects. The results show hierarchical representation of task events. For different task phases, there were different, approximately orthogonal patterns of activity across the population of neurons. Modulations of each basic pattern encoded stimulus information within each phase. By orthogonal coding, the frontal lobe may control transitions between the discrete steps of a mental program; by correlated coding within each step, similar operations may be applied to different stimulus content.
Patch–clamp coordinated spectroscopy shows P2X
2
receptor permeability dynamics require cytosolic domain rearrangements but not Panx-1 channels
Authors: Chaumont Severine , Khakh Baljit S.
Published: August 2008

ATP-gated P2X receptors display ion permeability increases within seconds of receptor activation as the channels enter the I
2
state, which is permeable to organic cations and dye molecules. The mechanisms underlying this important behavior are not completely understood. In one model, the I
2
state is thought to be due to opening of Pannexin-1 (Panx-1) channels, and, in the second, it is thought to be an intrinsic P2X property. We tested both models by measuring ion and dye permeability and used a patch–clamp coordinated spectroscopy approach to measure conformational changes. Our data show that Panx-1 channels make no detectable contribution to the P2X
2
receptor I
2
state. However, P2X
2
receptors display permeability dynamics, which are correlated with conformational changes in the cytosolic domain remote from the selectivity filter itself. Finally, the data illustrate the utility of a new approach, using tetracysteine tags and biarsenical fluorophores to measure site-specific conformational changes in membrane proteins.
Dynamic changes in accumbens dopamine correlate with learning during intracranial self-stimulation
Authors: Owesson-White Catarina A. , Cheer Joseph F. , Beyene Manna , Carelli Regina M. , Wightman R. Mark
Published: August 2008

Dopamine in the nucleus accumbens (NAc) is an important neurotransmitter for reward-seeking behaviors such as intracranial self-stimulation (ICSS), although its precise role remains unclear. Here, dynamic fluctuations in extracellular dopamine were measured during ICSS in the rat NAc shell with fast-scan cyclic voltammetry at carbon-fiber microelectrodes. Rats were trained to press a lever to deliver electrical stimulation to the substantia nigra (SNc)/ventral tegmental area (VTA) after the random onset of a cue that predicted reward availability. Latency to respond after cue onset significantly declined across trials, indicative of learning. Dopamine release was evoked by the stimulation but also developed across trials in a time-locked fashion to the cue. Once established, the cue-evoked dopamine transients continued to grow in amplitude, although they were variable from trial to trial. The emergence of cue-evoked dopamine correlated with a decline in electrically evoked dopamine release. Extinction of ICSS resulted in a significant decline in goal-directed behavior coupled to a significant decrease in cue-evoked phasic dopamine across trials. Subsequent reinstatement of ICSS was correlated with a return to preextinction transient amplitudes in response to the cue and reestablishment of ICSS behavior. The results show the dynamic nature of chemical signaling in the NAc during ICSS and provide new insight into the role of NAc dopamine in reward-related behaviors.
Glycan microarray of Globo H and related structures for quantitative analysis of breast cancer
Authors: Wang Cheng-Chi , Huang Yen-Lin , Ren Chien-Tai , Lin Chin-Wei , Hung Jung-Tung , Yu Jyh-Cherng , Yu Alice L. , Wu Chung-Yi , Wong Chi-Huey
Published: August 2008

Cancer-associated carbohydrate antigens are often found on the surface of cancer cells. Understanding their roles in cancer progression will lead to the development of new therapeutics and high-sensitivity diagnostics for cancers. Globo H is a member of this family, which is highly expressed on breast cancer cells. Here, we report the development of a glycan microarray of Globo H and its analogs for measurement of the dissociation constants on surface (
K
D,surf
) with three different monoclonal antibodies (VK-9, Mbr1, and anti-SSEA-3), to deduce their binding specificity. The glycan microarray was also used to detect the amount of antibodies present in the plasma of breast cancer patients and normal blood donors. It was shown that the amount of antibodies against Globo H from breast cancer patients were significantly higher than normal blood donors, providing a new tool for possible breast cancer diagnosis. Compared with the traditional ELISA method, this array method required only atto-mole amounts of materials and is more effective and more sensitive (5 orders of magnitude). The glycan microarray thus provides a new platform for use to monitor the immune response to carbohydrate epitopes after vaccine therapy or during the course of cancer progression.
Abrogation of T cell quiescence characterizes patients at high risk for multiple sclerosis after the initial neurological event
Authors: Corvol Jean-Christophe , Pelletier Daniel , Henry Roland G. , Caillier Stacy J. , Wang Joanne , Pappas Derek , Casazza Simona , Okuda Darin T. , Hauser Stephen L. , Oksenberg Jorge R. , Baranzini Sergio E.
Published: August 2008

Clinically isolated syndrome (CIS) refers to the earliest clinical manifestation of multiple sclerosis (MS). Currently there are no prognostic biological markers that accurately predict conversion of CIS to clinically definite MS (CDMS). Furthermore, the earliest molecular events in MS are still unknown. We used microarrays to study gene expression in naïve CD4+T cells from 37 CIS patients at time of diagnosis and after 1 year. Supervised machine-learning methods were used to build predictive models of disease conversion. We identified 975 genes whose expression segregated CIS patients into four distinct subgroups. A subset of 108 genes further discriminated patients in one of these (group 1) from other CIS patients. Remarkably, 92% of patients in group 1 converted to CDMS within 9 months. Consistent down-regulation ofTOB1, a critical regulator of cell proliferation, was characteristic of group 1 patients. DecreasedTOB1expression at the RNA and protein levels also was confirmed in experimental autoimmune encephalomyelitis. Finally, a genetic association was observed betweenTOB1variation and MS progression in an independent cohort. These results indicate that CIS patients at high risk of conversion have impaired regulation of T cell quiescence, possibly resulting in earlier activation of pathogenic CD4+cells.
The role of ATP signaling in the migration of intermediate neuronal progenitors to the neocortical subventricular zone
Authors: Liu Xiuxin , Hashimoto-Torii Kazue , Torii Masaaki , Haydar Tarik F. , Rakic Pasko
Published: August 2008

Most neurons of the cerebral cortex are generated in the germinal zones near the embryonic cerebral ventricle and migrate radially to the overlying cortical plate. Initially, all dividing cells are attached to the surface of the embryonic ventricle (ventricular zone) until a subset of dividing cells (basal or intermediate neuronal progenitors, INPs), recognized by their immunoreactivity to Tbr2, detach from the ventricular surface and migrate a short distance to establish a secondary proliferative compartment (the subventricular zone). The mechanism that regulates migration of the Tbr2
+
INPs from the ventricular to the subventricular zones is unknown. Here, we show that INPs, unlike the postmitotic neurons that tend to lose the ATP response, continue to express the purinergic P2Y1 receptor. Furthermore, blocking ATP signaling by the P2Y1 blockers, MRS2176, suramin, and apyrase, reduces Ca
2+
transients and retards INP migration to the subventricular zone. In addition, genetic knockdown of the P2Y1 receptor by
in vivo
application of short hairpin RNA selectively impairs the migration of INPs to the subventricular zone. Together, these results suggest that intercellular ATP signaling is essential for the migration of INPs and the proper formation of the subventricular zone. Interference of ATP signaling or abnormal Ca
2+
fluctuations in INPs may play a significant role in variety of genetic or acquired cortical malformations.
Membrane curvature induced by Arf1-GTP is essential for vesicle formation
Authors: Beck Rainer , Sun Zhe , Adolf Frank , Rutz Chistoph , Bassler Jochen , Wild Klemens , Sinning Irmgard , Hurt Ed , Brügger Britta , Béthune Julien , Wieland Felix
Published: August 2008

The GTPase Arf1 is considered as a molecular switch that regulates binding and release of coat proteins that polymerize on membranes to form transport vesicles. Here, we show that Arf1-GTP induces positive membrane curvature and find that the small GTPase can dimerize dependent on GTP. Investigating a possible link between Arf dimerization and curvature formation, we isolated an Arf1 mutant that cannot dimerize. Although it was capable of exerting the classical role of Arf1 as a coat receptor, it could not mediate the formation of COPI vesicles from Golgi-membranes and was lethal when expressed in yeast. Strikingly, this mutant was not able to deform membranes, suggesting that GTP-induced dimerization of Arf1 is a critical step inducing membrane curvature during the formation of coated vesicles.
The basic nonuniformity of the cerebral cortex
Authors: Herculano-Houzel Suzana , Collins Christine E. , Wong Peiyan , Kaas Jon H. , Lent Roberto
Published: August 2008

Evolutionary changes in the size of the cerebral cortex, a columnar structure, often occur through the addition or subtraction of columnar modules with the same number of neurons underneath a unit area of cortical surface. This view is based on the work of Rockel
et al.
[Rockel AJ, Hiorns RW, Powell TP (1980) The basic uniformity in structure of the neocortex.
Brain
103:221–244], who found a steady number of approximately 110 neurons underneath a surface area of 750 μm
2
(147,000 underneath 1 mm
2
) of the cerebral cortex of five species from different mammalian orders. These results have since been either corroborated or disputed by different groups. Here, we show that the number of neurons underneath 1 mm
2
of the cerebral cortical surface of nine primate species and the closely related
Tupaia
sp. is not constant and varies by three times across species. We found that cortical thickness is not inversely proportional to neuronal density across species and that total cortical surface area increases more slowly than, rather than linearly with, the number of neurons underneath it. The number of neurons beneath a unit area of cortical surface varies linearly with neuronal density, a parameter that is neither related to cortical size nor total number of neurons. Our finding of a variable number of neurons underneath a unit area of the cerebral cortex across primate species indicates that models of cortical organization cannot assume that cortical columns in different primates consist of invariant numbers of neurons.
Acquisition of classical CTX prophage from
Vibrio cholerae
O141 by El Tor strains aided by lytic phages and chitin-induced competence
Authors: Udden S. M. Nashir , Zahid M. Shamim Hasan , Biswas Kuntal , Ahmad Qazi Shafi , Cravioto Alejandro , Nair G. Balakrish , Mekalanos John J. , Faruque Shah M.
Published: August 2008

The El Tor biotype of
Vibrio cholerae
O1, causing the current seventh pandemic of cholera, has replaced the classical biotype, which caused the sixth pandemic. The CTX prophages encoding cholera toxin in the two biotypes have distinct repressor (
rstR
) genes. Recently, new variants of El Tor strains that carry the classical type (CTX
class
) prophage have emerged. These “hybrid” strains apparently originate through lateral gene transfer and recombination events. To explore possible donors of the CTX
class
prophage and its mode of transfer, we tested environmental
V. cholerae
isolates for the presence of CTX
class
prophage and mobility of the phage genome. Of the 272 environmental
V. cholerae
isolates tested, 6 were found to carry the CTX
class
prophage; all of these belonged to the O141 serogroup. These O141 strains were unable to produce infectious CTX
class
phage or to transmit the prophage to recipient strains in the mouse model of infection; however, the CTX
class
prophage was acquired by El Tor strains when cultured with the O141 strains in microcosms composed of filtered environmental water, a chitin substrate, and a
V. cholerae
O141-specific bacteriophage. The CTX
class
prophage either coexisted with or replaced the resident CTX
ET
prophage, resulting in El Tor strains with CTX genotypes similar to those of the naturally occurring hybrid strains. Our results support a model involving phages and natural chitin substrate in the emergence of new variants of pathogenic
V. cholerae
. Furthermore, the O141 strains apparently represent an alternative reservoir of the CTX
class
phage genome, because the classical
V. cholerae
O1 strains are possibly extinct.