bluuebunny/crossref_metadata_2025 huggingface dataset:
Pressure induced phase transitions in hydroquinone
Authors: Rao Rekha , Sakuntala T. , Arora Akhilesh K. , Deb S. K.
Published: October 2004

High pressure behavior of α-hydroquinone (1,4-dihydroxybenzene) has been studied using Raman spectroscopy up to pressures of 19 GPa. Evolution of Raman spectra suggests two transitions around 3.3 and 12.0 GPa. The first transition appears to be associated with the lowering of crystal symmetry. Above 12.0 GPa, Raman bands in the internal modes region exhibit continuous broadening suggesting that the system is progressively evolving into a disordered state. This disorder is understood as arising due to distortion of the hydrogen-bonded cage across the second transition around 12 GPa.
Hydrophobic effect in the pressure-temperature plane
Authors: Koga Kenichiro
Published: October 2004

The free energy of the hydrophobic hydration and the strength of the solvent-mediated attraction between hydrophobic solute molecules are calculated in the pressure-temperature plane. This is done in the framework of an exactly soluble model that is an extension of the lattice model proposed by Kolomeisky and Widom [A. B. Kolomeisky and B. Widom, Faraday Discuss. 112, 81 (1999)]. The model takes into account both the mechanism of the hydrophobic effect dominant at low temperatures and the opposite mechanism of solvation appearing at high temperatures and has the pressure as a second thermodynamic variable. With this model, two boundaries are identified in the pressure-temperature plane: the first one within which the solubility, or the Ostwald absorption coefficient, decreases with increasing temperature at fixed pressure and the second one within which the strength of solvent-mediated attraction increases with increasing temperature. The two are nearly linear and parallel to each other, and the second boundary lies in the low-temperature and low-pressure side of the first boundary. It is found that a single, near-linear relation between the hydration free energy and the strength of the hydrophobic attraction holds over the entire area within the second boundary in the pressure-temperature plane.
Interatomic Lennard-Jones potentials of linear and branched alkanes calibrated by Gibbs ensemble simulations for vapor-liquid equilibria
Authors: Chang Jaeeon , Sandler Stanley I.
Published: October 2004

We propose Lennard-Jones potential parameters for interatomic interactions of linear and branched alkanes based on matching the results of Gibbs ensemble simulations of vapor-liquid equilibria to experimental data. The alkane model is similar as in the OPLS-AA [W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives, J. Am. Chem. Soc. 118, 11225 (1996)], but multiple atom types for carbon based on the number of covalently bonded hydrogen atoms are necessary to accurately reproduce liquid densities and enthalpies of vaporization with the errors of 2.1% and 3.3%, respectively, for hydrocarbons of various chain lengths and structures. We find that the attraction energies of the carbon atoms are almost proportional to the number of covalent hydrogen atoms with each increasing the carbon energy parameter by ≈0.033 kcal/mol. Though the present force field outperforms the OPLS-AA force field for alkanes we studied, systematic deviations for vapor pressures are still observed with errors of 15%–30%, and critical temperatures are slightly underestimated. We think that these shortcomings are probably due to the inadequacy of the two-parameter Lennard-Jones potential, and especially its behavior at short distances.
NMR polarization echoes in a nematic liquid crystal
Authors: Levstein Patricia R. , Chattah Ana K. , Pastawski Horacio M. , Raya Jésus , Hirschinger Jérôme
Published: October 2004

We have modified the polarization echo (PE) sequence through the incorporation of Lee-Goldburg cross polarization steps to quench the H1-H1H dipolar dynamics. In this way, the C13 becomes an ideal local probe to inject and detect polarization in the proton system. This improvement made possible the observation of the local polarization P00(t) and polarization echoes in the interphenyl proton of the liquid crystal N-(4-methoxybenzylidene)-4-butylaniline. The decay of P00(t) was well fitted to an exponential law with a characteristic time τC≈310 μs. The hierarchy of the intramolecular dipolar couplings determines a dynamical bottleneck that justifies the use of the Fermi Golden Rule to obtain a spectral density consistent with the structural parameters. The time evolution of P00(t) was reversed by the PE sequence generating echoes at the time expected by the scaling of the dipolar Hamiltonian. This indicates that the reversible H1-H1 dipolar interaction is the main contribution to the local polarization decrease and that the exponential decay for P00(t) does not imply irreversibility. The attenuation of the echoes follows a Gaussian law with a characteristic time τφ≈527 μs. The shape and magnitude of the characteristic time of the PE decay suggest that it is dominated by the unperturbed homonuclear dipolar Hamiltonian. This means that τφ is an intrinsic property of the dipolar coupled network and not of other degrees of freedom. In this case, one cannot unambiguously identify the mechanism that produces the decoherence of the dipolar order. This is because even weak interactions are able to break the fragile multiple coherences originated on the dipolar evolution, hindering its reversal. Other schemes to investigate these underlying mechanisms are proposed.
The dynamics of the Cl+n-C4H10→HCl (v′,j′)+C4H9 reaction at 0.32 eV
Authors: Bass M. J. , Brouard M. , Vallance C. , Kitsopoulos T. N. , Samartzis P. C. , Toomes R. L.
Published: October 2004

Rotational state resolved center-of-mass angular scattering and kinetic energy release distributions have been determined for the HCl (v′=0, j′=0–6) products of the reaction of chlorine with n-butane using the photon-initiated reaction technique, coupled with velocity-map ion imaging. The angular and kinetic energy release distributions derived from the ion images are very similar to those obtained previously for the Cl plus ethane reaction. The angular distributions are found to shift from forward scattering to more isotropic scattering with increasing HCl rotational excitation. The kinetic energy release distributions indicate that around 30% of the available energy is channeled into internal excitation of the butyl radical products. The data analysis also suggests that H-atom abstraction takes place from both primary and secondary carbon atom sites, with the primary site producing rotationally cold, forward scattered HCl (v′=0) products, and the secondary site yielding more isotropically scattered HCl (v′=0) possessing higher rotational excitation. The mechanisms leading to these two product channels are discussed in the light of the present findings, and in comparison with studies of other Cl plus alkane reactions.
Ambiguities in the semiclassical assignment of the asymmetric rotor rotational quantum numbers
Authors: Faure Alexandre , Wiesenfeld Laurent
Published: October 2004

The semiclassical quantization of the rigid asymmetric rotor is revisited in the context of classical inelastic collisions. It is shown that the standard bin histogram method, widely used in quasiclassical trajectory calculations involving linear target molecules, cannot be generalized to the case of asymmetric top molecules owing to ambiguities in the assignment of the final classical action to a particular rotational quantum state. These ambiguities result from pairs of states which are indistinguishable within the bin histogram approach at all the common levels of semiclassical theory. A single value of the classical action can thus correspond to two different quantum states, preventing the distinction between these states in the calculation of rotational cross sections. Our results are illustrated for the rotational states J=1–4 of the water molecule at its equilibrium geometry.
Physical properties of sulfur near the polymerization transition
Authors: Kozhevnikov V. F. , Payne W. B. , Olson J. K. , McDonald C. L. , Inglefield C. E.
Published: October 2004

Acoustical measurements, electron spin resonance, and Raman spectroscopy have been employed to probe sulfur over the temperature range 80–180 °C, which includes the polymerization transition and the supercooled liquid state. Acoustical properties (sound velocity, absorption, and impedance) have been studied with both longitudinal and transverse waves at frequencies between 500 kHz and 22 MHz. The results confirm that polymeric sulfur is a solution of long chain molecules in monomeric solvent, and that the polymerization transition is not a second-order phase transition, as was proposed theoretically. Sulfur is a viscous liquid, but not viscoelastic, both below and above the polymerization transition temperature. It is shown that the classical Navier-Stokes theory is not applicable to the sound absorption in liquid sulfur in the highly viscous state.
Computation of the properties of liquid neon, methane, and gas helium at low temperature by the Feynman-Hibbs approach
Authors: Tchouar N. , Ould-Kaddour F. , Levesque D.
Published: October 2004

The properties of liquid methane, liquid neon, and gas helium are calculated at low temperatures over a large range of pressure from the classical molecular-dynamics simulations. The molecular interactions are represented by the Lennard-Jones pair potentials supplemented by quantum corrections following the Feynman-Hibbs approach. The equations of state, diffusion, and shear viscosity coefficients are determined for neon at 45 K, helium at 80 K, and methane at 110 K. A comparison is made with the existing experimental data and for thermodynamical quantities, with results computed from quantum numerical simulations when they are available. The theoretical variation of the viscosity coefficient with pressure is in good agreement with the experimental data when the quantum corrections are taken into account, thus reducing considerably the 60% discrepancy between the simulations and experiments in the absence of these corrections.
Experimental and theoretical study of the infrared spectra of BrHI− and BrDI−
Authors: Nee M. J. , Osterwalder A. , Neumark D. M. , Kaposta C. , Cibrián Uhalte C. , Xie T. , Kaledin A. , Bowman J. M. , Carter S. , Asmis K. R.
Published: October 2004

Gas phase vibrational spectra of BrHI− and BrDI− have been measured from 6 to 17 μm (590–1666 cm−1) using tunable infrared radiation from the free electron laser for infrared experiments in order to characterize the strong hydrogen bond in these species. BrHI−⋅Ar and BrDI−⋅Ar complexes were produced and mass selected, and the depletion of their signal due to vibrational predissociation was monitored as a function of photon energy. Additionally, BrHI− and BrDI− were dissociated into HBr (DBr) and I− via resonant infrared multiphoton dissociation. The spectra show numerous transitions, which had not been observed by previous matrix studies. New ab initio calculations of the potential-energy surface and the dipole moment are presented and are used in variational ro-vibrational calculations to assign the spectral features. These calculations highlight the importance of basis set in the simulation of heavy atoms such as iodine. Further, they demonstrate extensive mode mixing between the bend and the H-atom stretch modes in BrHI− and BrDI− due to Fermi resonances. These interactions result in major deviations from simple harmonic estimates of the vibrational energies. As a result of this new analysis, previous matrix-isolation spectra assignments are reevaluated.
Measurement of Br photofragment orientation and alignment from HBr photodissociation: Production of highly spin-polarized hydrogen atoms
Authors: Rakitzis T. Peter , Samartzis P. C. , Toomes R. L. , Kitsopoulos Theofanis N.
Published: October 2004

The orientation and alignment of the P23/2 and P21/2 Br photofragments from the photodissociation of HBr is measured at 193 nm in terms of aq(k)(p) parameters, using slice imaging. The A 1Π state is excited almost exclusively, and the measured aq(k)(p) parameters and the spin-orbit branching ratio show that the dissociation proceeds predominantly via nonadiabatic transitions to the a 3Π and 1 3Σ+ states. Conservation of angular momentum shows that the electrons of the nascent H atom cofragments (recoiling parallel to the photolysis polarization) are highly spin polarized: about 100% for the Br(2P1/2) channel, and 86% for the Br(2P3/2) channel. A similar analysis is demonstrated for the photodissociation of HCl.
Equation of state for hard-sphere fluid in restricted geometry
Authors: Kamenetskiy I. E. , Mon K. K. , Percus J. K.
Published: October 2004

Many practical applications require the knowledge of the equation of state of fluids in restricted geometry. We study a hard-sphere fluid at equilibrium in a narrow cylindrical pore with hard walls for pore radii R<(3+2)/4 (in units of the hard sphere diameter). In this case each particle can interact only with its nearest neighbors, which makes possible the use of analytical methods to study the thermodynamics of the system. Using a transfer operator formalism and expanding in low- and high-pressure regions, we can obtain a simple analytical equation of state for almost all ranges of pressure. The results agree with Monte Carlo simulations. Additionally, it is shown that a convenient analytical representation can be chosen to accurately describe the equation of state within the error of the Monte Carlo simulation.
Interpretation of Hund’s multiplicity rule for the carbon atom
Authors: Hongo Kenta , Maezono Ryo , Kawazoe Yoshiyuki , Yasuhara Hiroshi , Towler M. D. , Needs R. J.
Published: October 2004

Hund’s multiplicity rule is investigated for the carbon atom using quantum Monte Carlo methods. Our calculations give an accurate account of electronic correlation and obey the virial theorem to high accuracy. This allows us to obtain accurate values for each of the energy terms and therefore to give a convincing explanation of the mechanism by which Hund’s rule operates in carbon. We find that the energy gain in the triplet with respect to the singlet state is due to the greater electron-nucleus attraction in the higher spin state, in accordance with Hartree-Fock calculations and studies including correlation. The method used here can easily be extended to heavier atoms.
Dynamics of Rydberg electron transfer to CH3CN: Velocity dependent studies
Authors: Suess L. , Liu Y. , Parthasarathy R. , Dunning F. B.
Published: October 2004

The dynamics of free-ion production through electron transfer in K(np)/CH3CN collisions are examined through measurements using velocity-selected Rydberg atoms. The data show that Rydberg electron transfer leads to the creation of two groups of dipole-bound CH3CN− ions, one long lived (τ>85 μs), the other short lived (τ<1 μs). The velocity dependences associated with the production of both groups of ions are similar, the ion formation rate decreasing markedly with decreasing Rydberg atom velocity, principally as a consequence of postattachment electrostatic interactions between the product ions. The results are in reasonable accord with the predictions of a Monte Carlo collision model that considers the effect of crossings between the diabatic potential curves for the covalent K(np)/CH3CN system and the K+/CH3CN− ion pair. This model also accounts for the relatively small reaction rate constants, ∼0.5–1.0×10−8 cm3 s−1, associated with the formation of long-lived CH3CN− ions. No velocity dependence in the lifetime of the CH3CN− ions is observed.
On the Adam-Gibbs-Kirkpatrick-Thirumalai-Wolynes scenario for the viscosity increase in glasses
Authors: Bouchaud Jean-Philippe , Biroli Giulio
Published: October 2004

We reformulate the interpretation of the mean-field glass transition scenario for finite dimensional systems, proposed by Kirkpatrick, Thirumalai, and Wolynes (KTW) [Phys. Rev. A 40 (1989) 1045]. This allows us to establish clearly a temperature dependent length ξ* above which the mean-field glass transition picture has to be modified. We argue in favor of the mosaic state introduced by KTW, which leads to the Adam-Gibbs relation between the viscosity and configurational entropy of glass forming liquids. Our argument is a mixture of thermodynamics and kinetics, partly inspired by the random energy model: small clusters of particles are thermodynamically frozen in low energy states, whereas large clusters are kinetically frozen by large activation energies. The relevant relaxation time is that of the smallest “liquid” clusters. Some physical consequences are discussed.
Dielectric study of the α and β processes in supercooled ethylene glycol oligomer–water mixtures
Authors: Sudo Seiichi , Tsubotani Sosuke , Shimomura Mayumi , Shinyashiki Naoki , Yagihara Shin
Published: October 2004

Broadband dielectric measurements for 65 wt % ethylene glycol oligomer (EGO)–water mixtures with one to six repeat units of EGO molecules were performed in the frequency range of 10 μHz–10 GHz and the temperature range of 128–298 K. In the case of the water-EGO mixtures with one and two repeat units of the EGO molecule (small EGO), the shape of the dielectric loss peak of the primary process is asymmetrical about the logarithm of the frequency of maximum loss above the crossover temperature, TC. The asymmetric process continues to the α process at a low frequency, and an additional β process appears in the frequency range higher than that of the α process below TC. In contrast, the water-EGO mixtures with three or more repeat units of the EGO molecule (large EGO) show a broad and symmetrical loss peak of the primary process above TC. The symmetric process continues to the β process, and an additional α process appears in the frequency range lower than that of the β process below TC. These different scenarios of the α-β separation related to the shape of the loss peak above TC are a result of the difference in the cooperative motion of water and solute molecules. The solute and water molecules move cooperatively in the small EGO-water mixtures above TC, and this cooperative motion leads to the asymmetric loss peak above TC and the α process below TC. For the large EGO-water mixtures, the spatially restricted motion of water confined by solute molecules leads to the symmetric loss peak above TC and the β process below TC.
A first-principles potential energy surface and vibrational states for hydrogen on Cu(100)
Authors: Lai Wenzhen , Xie Daiqian , Yang Jinlong , Zhang Dong Hui
Published: October 2004

Density-functional theory calculations based on plane-wave expansion and pseudopotential treatment were carried out for atomic hydrogen on a rigid Cu(100) surface. A global potential energy surface was then obtained by using a three-dimensional spline interpolation. It is found that the minimum of the potential is located at the fourfold hollow site with a diffusion barrier of 88 meV at the bridge site. The vibrational states of atomic hydrogen and deuterium on the Cu(100) surface were calculated on the potential surface. Our calculations show that the vibrational states A10, A11, E1, and B21 of H/Cu(100) exhibit strong localized character and very narrow band widths, whereas other excited vibrational states have considerable delocalized character and broad band widths. The vibrational frequency of 71.2 (51.5) meV for H(D) in the perpendicular direction obtained in this study is in good agreement with the experimentally observed value of 70 (52) meV [Surf. Sci. 248, 35 (1991)].
Molecular dynamics simulation on devitrification: Isothermal devitrification and thermodynamics of PbF2 glasses
Authors: Silva Maurı́cio A. P. , Rino José Pedro , Monteil André , Ribeiro Sidney J. L. , Messaddeq Younès
Published: October 2004

The vitrification and devitrification features of lead fluoride are investigated by means of molecular dynamic simulations. The influence of heating rate on the devitrification temperature as well as the dependence of the glass properties on its thermal history, i.e., the cooling rate employed, is identified. As expected, different glasses are obtained when the cooling rates differ. Diffusion coefficient analysis during heating of glass and crystal, indicates that the presence of defects on the glassy matrix favors the transition processes from the ionic to a superionic state, with high mobility of fluorine atoms, responsible for the high anionic conduction of lead fluoride. Nonisothermal and isothermal devitrification processes are simulated in glasses obtained at different cooling rates and structural organizations occurring during the heat treatments are clearly observed. When a fast cooling rate is employed during the glass formation, the devitrification of a single crystal (limited by the cell dimensions) is observed, while the glass obtained with slower cooling rate, allowing relaxations and organization of various regions on the glass bulk during the cooling process, devitrifies in more than one crystalline plane.
Polyhedral ground states in clusters of asymmetric hard sphere ions
Authors: Wootton Adam , Harrowell Peter
Published: October 2004

Clusters of hard sphere ions with sufficient size asymmetry to stabilize a tetrahedral structure in the bulk are found to exhibit trivalent polyhedral ground states in clusters of up to roughly 200 ions. The map of cluster ground state structures over the space of cluster size and ion asymmetry is presented.
Interdiffusion of solvent into glassy polymer films: A molecular dynamics study
Authors: Tsige Mesfin , Grest Gary S.
Published: October 2004

Large scale molecular dynamics and grand canonical Monte Carlo simulation techniques are used to study the behavior of the interdiffusion of a solvent into an entangled polymer matrix as the state of the polymer changes from a melt to a glass. The weight gain by the polymer increases with time t as t1/2 in agreement with Fickian diffusion for all cases studied, although the diffusivity is found to be strongly concentration dependent especially as one approaches the glass transition temperature of the polymer. The diffusivity as a function of solvent concentration determined using the one-dimensional Fick’s model of the diffusion equation is compared to the diffusivity calculated using the Darken equation from simulations of equilibrated solvent-polymer solutions. The diffusivity calculated using these two different approaches are in good agreement. The behavior of the diffusivity strongly depends on the state of the polymer and is related to the shape of the solvent concentration profile.
Saddles and softness in simple model liquids
Authors: Angelani L. , De Michele C. , Ruocco G. , Sciortino F.
Published: October 2004

We report a numerical study of saddles properties of the potential energy landscape for soft spheres with different softness, i.e., different power n of the interparticle repulsive potential. We find that saddle-based quantities rescale into master curves once energies and temperatures are scaled by mode-coupling temperature TMCT, confirming and generalizing previous findings obtained for Lennard-Jones-like models.
Evidence of dissociative collision induced diatomic and triatomic hydrogen ion formation from hydrocarbon ion interaction with silicon surface
Authors: Shoji Fumiya
Published: October 2004

A singly charged hydrocarbon ion CHx+ (x=0,1,2,3,4) was extracted from an electron bombardment type ion source using methane as the reagent gas and irradiated onto the Si(100) surface at glancing angle. Scattered ion spectrometry using an electrostatic energy analyzer revealed that H+, H2+, and H3+ ions were clearly formed at the scattering angle of 15°, associated with dissociative collisions of hydrocarbon ion species of incidence energy of 1000 eV. The formation of H3+ was tentatively interpreted as resulting from combination of excited atomic hydrogen produced by dissociative collisions of CH4+ ions with Si(100) surface.
Rovibrational product state distribution for inelastic H+D2 collisions
Authors: Pomerantz Andrew E. , Ausfelder Florian , Zare Richard N. , Juanes-Marcos Juan Carlos , Althorpe Stuart C. , Sáez Rábanos V. , Aoiz F. J. , Bañares L. , Castillo J. F.
Published: October 2004

Experimental measurements of rovibrational product state distributions for the inelastic scattering process H+D2(ν=0,j)→H+D2(ν′=1,2,j′) are presented and compared with the results of quasiclassical and quantum mechanical calculations. Agreement between theory and experiment is almost quantitative. Two subtle trends are found: the relative amount of energy in product rotational excitation decreases slightly with increasing collision energy and increases slightly with increasing product vibrational excitation. These trends are the reverse of what has been found for reactive scattering in which the opposite trends are much more pronounced.
Sigma-1 receptors at galactosylceramide-enriched lipid microdomains regulate oligodendrocyte differentiation
Authors: Hayashi Teruo , Su Tsung-Ping
Published: October 2004

In the brain, myelin is important in regulating nerve conduction and neurotransmitter release by providing insulation at axons. Myelin is a specialized yet continuous sheet structure of differentiated oligodendrocytes (OLs) that is enriched in lipids, specifically galactosylceramides (GalCer) originated at the endoplasmic reticulum (ER). GalCer are known to affect OL differentiation. However, the mechanism whereby GalCer affect OL differentiation is not well understood. Sigma-1 receptors (Sig-1Rs), shown by us to exist in detergent-insoluble lipid microdomains at lipid-enriched loci of ER in NG108 cells, are important in the compartmentalization/transport of ER-synthesized lipids and in cellular differentiation. In this study, we used rat primary hippocampal cultures and found that Sig-1Rs form GalCer-enriched lipid rafts at ER lipid droplet-like structures in the entire myelin sheet of mature OLs. In rat OL progenitors (CG-4 cells), levels of lipid raft-residing Sig-1Rs and GalCer increase as cells differentiate. Sig-1Rs also increase in OLs and myelin of developing rat brains. Sig-1R, GalCer, and cholesterol are colocalized and are resistant to the Triton X-100 solubilization. Treating cells with a Sig-1R agonist or targeting Sig-1Rs at lipid rafts by overexpression of Sig-1Rs in CG-4 cells enhances differentiation, whereas reducing Sig-1Rs at lipid rafts by transfection of functionally dominant-negative Sig-1Rs attenuates differentiation. Furthermore, Sig-1R siRNA inhibits differentiation. Our findings indicate that, in the brain, Sig-1Rs targeting GalCer-containing lipid microdomains are important for OL differentiation and that Sig-1Rs may play an important role in the pathogenesis of certain demyelinating diseases.
Dynamical transition and proteinquake in photoactive yellow protein
Authors: Itoh Kazuhito , Sasai Masaki
Published: October 2004

Conformational dynamics in protein functioning covers a wide range of time scales from nanosecond fluctuations around a conformation to the large-amplitude conformational changes of milliseconds or longer. We illustrate a picture of cooperative coupling among such motions of different time scales in a model protein, photoactive yellow protein, by proposing a model that can consistently explain the experimental results on the photocycle of photoactive yellow protein. The model provides a scenario in which the global collective motion induced by the unfolding of the N-terminal domain promotes the loosening of the atomistic packing around the chromophore, which produces the favorable molecular environment for the photoexcited chromophore, thereby stabilizing the partially unfolded intermediate in the photocycle. The proteinquake, the large conformational change triggered by the local structural disturbance, plays a decisive role in controlling the kinetics of functioning.
Identification of inhibitors of auxin transcriptional activation by means of chemical genetics in
Arabidopsis
Authors: Armstrong Joshua I. , Yuan Shiaulou , Dale Joseph M. , Tanner Vanessa N. , Theologis Athanasios
Published: October 2004

Auxin modulates diverse plant developmental pathways through direct transcriptional regulation and cooperative signaling with other plant hormones. Genetic and biochemical approaches have clarified several aspects of the auxin-regulated networks; however, the mechanisms of perception and subsequent signaling events remain largely uncharacterized. To elucidate unidentified intermediates, we have developed a high-throughput screen for identifying small molecule inhibitors of auxin signaling in
Arabidopsis
. Analysis of 10,000 compounds revealed several potent lead structures that abrogate transcription of an auxin-inducible reporter gene. Three compounds were found to interfere with auxin-regulated proteolysis of an auxin/indole-3-acetic acid transcription factor, and two impart phenotypes indicative of an altered auxin response, including impaired root development. Microarray analysis was used to demonstrate the mechanistic similarities of the two most potent molecules. This strategy promises to yield powerful tools for the discovery of unidentified components of the auxin-signaling networks and the study of auxin's participation in various stages of plant development.
Divergence of T2R chemosensory receptor families in humans, bonobos, and chimpanzees
Authors: Parry Christopher M. , Erkner Alfrun , le Coutre Johannes
Published: October 2004

T2R (Tas2R) genes encode a family of G protein-coupled gustatory receptors, several involved in bitter taste perception. So far, few ligands for these receptors have been identified, and the specificity of most T2Rs is unclear. Differences between individual T2Rs result in altered taste perception in either specificity or sensitivity. All 33 human T2Rs are characterized by significant sequence homology. However, with a total of eight pseudogenes and >83 coding region single-nucleotide polymorphisms, the family displays broad diversity. The underlying variability of individual T2Rs might be the source for personalized taste perception. To test this hypothesis and also to identify T2Rs that possibly function beyond bitter taste, we compared all human T2R genes with those of the closely related primate species
Pan paniscus
(bonobo) and
Pan troglodytes
(chimpanzee). The differences identified range from large sequence alterations to nonsynonymous and synonymous changes of single base pairs. In contrast to olfactory receptors, no human-specific loss of the amount of functional genes was observed. Taken together, the results indicate ongoing evolutionary diversification of T2R receptors and a role for T2Rs in dietary adaptation and personalized food uptake.
Astrocytes generate Na
+
-mediated metabolic waves
Authors: Bernardinelli Yann , Magistretti Pierre J. , Chatton Jean-Yves
Published: October 2004

Glutamate-evoked Na
+
increase in astrocytes has been identified as a signal coupling synaptic activity to glucose consumption. Astrocytes participate in multicellular signaling by transmitting intercellular Ca
2+
waves. Here we show that intercellular Na
+
waves are also evoked by activation of single cultured cortical mouse astrocytes in parallel with Ca
2+
waves; however, there are spatial and temporal differences. Indeed, maneuvers that inhibit Ca
2+
waves also inhibit Na
+
waves; however, inhibition of the Na
+
/glutamate cotransporters or enzymatic degradation of extracellular glutamate selectively inhibit the Na
+
wave. Thus, glutamate released by a Ca
2+
wave-dependent mechanism is taken up by the Na
+
/glutamate cotransporters, resulting in a regenerative propagation of cytosolic Na
+
increases. The Na
+
wave gives rise to a spatially correlated increase in glucose uptake, which is prevented by glutamate transporter inhibition. Therefore, astrocytes appear to function as a network for concerted neurometabolic coupling through the generation of intercellular Na
+
and metabolic waves.
Hidden complexity of free energy surfaces for peptide (protein) folding
Authors: Krivov Sergei V. , Karplus Martin
Published: October 2004

An understanding of the thermodynamics and kinetics of protein folding requires a knowledge of the free energy surface governing the motion of the polypeptide chain. Because of the many degrees of freedom involved, surfaces projected on only one or two progress variables are generally used in descriptions of the folding reaction. Such projections result in relatively smooth surfaces, but they could mask the complexity of the unprojected surface. Here we introduce an approach to determine the actual (unprojected) free energy surface and apply it to the second β-hairpin of protein G, which has been used as a model system for protein folding. The surface is represented by a disconnectivity graph calculated from a long equilibrium folding-unfolding trajectory. The denatured state is found to have multiple low free energy basins. Nevertheless, the peptide shows exponential kinetics in folding to the native basin. Projected surfaces obtained from the present analysis have a simple form in agreement with other studies of the β-hairpin. The hidden complexity found for the β-hairpin surface suggests that the standard funnel picture of protein folding should be revisited.
The complete genomic sequence of
Nocardia farcinica
IFM 10152
Authors: Ishikawa Jun , Yamashita Atsushi , Mikami Yuzuru , Hoshino Yasutaka , Kurita Haruyo , Hotta Kunimoto , Shiba Tadayoshi , Hattori Masahira
Published: October 2004

We determined the genomic sequence of
Nocardia farcinica
IFM 10152, a clinical isolate, and revealed the molecular basis of its versatility. The genome consists of a single circular chromosome of 6,021,225 bp with an average G+C content of 70.8% and two plasmids of 184,027 (pNF1) and 87,093 (pNF2) bp with average G+C contents of 67.2% and 68.4%, respectively. The chromosome encoded 5,674 putative protein-coding sequences, including many candidate genes for virulence and multidrug resistance as well as secondary metabolism. Analyses of paralogous protein families suggest that gene duplications have resulted in a bacterium that can survive not only in soil environments but also in animal tissues, resulting in disease.
The Deconcentration of Poverty in Chicago: 1990-2000
Authors: McDonald John F.
Published: October 2004

This paper documents the fact that the concentration of poverty in the inner city of Chicago declined appreciably during the 1990s. Exploratory data analysis suggests that the decline in family poverty is strongly associated with an increase in the employment of females who reside in those areas. The decade of the 1990s is notable for its strong economy, the large expansion of the Earned Income Tax Credit and dramatic change in the public assistance programme.
The Meaning of Words in Urban Conflicts: Language, Argumentation Patterns and Local Politics in Israel
Authors: Alfasi Nurit
Published: October 2004

Urban development is frequently accompanied by planning disputes. Such disputes are often the battleground for a variety of opposing views and interests, in relation to specific urban and environmental assets and lifestyles. Analysis of three disputes that took place in Israel recently reveals a similarity in the patterns of argumentation that form the foundations of such debates. These patterns are valid, in spite of considerable differences between the contexts and actors involved in the three disputes. The claims made by disagreeing actors have their roots in common images of the built environment, the conflicting situation and the general politics of the conflict. In addition, in all three disputes, the same symmetrical structure of argumentation emerged, as each statement was countered with an opposite assertion.
The Interplay of Three Established-Outsider Figurations in a Deprived Inner-city Neighbourhood
Authors: May David M.
Published: October 2004

This article discusses Norbert Elias' theory of established-outsider figurations and applies it to the case of one deprived inner-city neighbourhood in Germany, Dortmund Nordstadt. According to this theory, the social cohesion of the established together with the stigmatisation of outsiders leads to status and power differentials that exclude the outsiders. In Nordstadt, three levels of established-outsider figurations overlap and influence each other. At the societal level, the legal system assigns to immigrants the position of outsiders. At the city level, Nordstadt is stigmatised as a neighbourhood for workers and immigrants. At the neighbourhood level, immigrants can, thanks to their greater internal cohesion, establish themselves to some degree, while the Germans attempt to implement the established-outsider figuration of the societal level. By way of conclusion, this article discusses the relevance of Elias' theory both for social theory and for urban studies.
Cohort Effects, Differential Accumulation and Hong Kong's Volatile Housing Market
Authors: Forrest Ray , Lee James
Published: October 2004

As in much of east Asia, the past few decades have seen extraordinary rates of house price inflation in Hong Kong. After a relatively modest downturn in the early 1980s, prices rose rapidly until the Asian financial crisis in 1997. Since then, and despite increased government efforts to stimulate the stagnant property market, prices have continued to fall and negative equity remains pervasive. Given the centrality of property investment and speculation historically for households, financial institutions and for wider government economic strategies, the state of the residential market remains of central political and policy concern. Against this background of Hong Kong's apparently declining economic fortunes and major shifts in housing policy, this paper explores aspects of wealth accumulation in the home-ownership sector. Linking to a well-established set of debates in the academic literature, the paper explores the impact of policy change and house price trajectories on different cohorts of households. For example, those cohorts who entered home-ownership in the late 1980s generally saw rapid increases in their property values fuelled by generous state-assisted home-ownership schemes and a buoyant economy. By contrast, those entering in the late 1990s have experienced a much less favourable policy and economic environment. The paper also explores the extent to which price trajectories have varied in different sectors.
The Contradictions in Enabling Private Developers of Affordable Housing: A Cautionary Case from Ahmedabad, India
Authors: Mukhija Vinit
Published: October 2004

Through a case study of a private developer of housing in India, this paper critically examines the policy advice of enabling markets and market-based actors to provide affordable housing in developing countries. In this case, after receiving public sector help, the developer stopped constructing housing for low-income groups. The paper argues for a more cautious, circumspect and varied approach because enabling strategies focused on market actors can produce highly uncertain outcomes. In addition, it emphasises that policy-makers need a better understanding of how the informal and formal sectors can overlap. Enabling informal developers can be even trickier because public support can reduce their flexibility and incentives, as well as impacting on the expectations and opportunities of the home-buyers.
MARK/PAR1 kinase is a regulator of microtubule-dependent transport in axons
Authors: Mandelkow Eva-Maria , Thies Edda , Trinczek Bernhard , Biernat Jacek , Mandelkow Eckard
Published: October 2004

Microtubule-dependent transport of vesicles and organelles appears saltatory because particles switch between periods of rest, random Brownian motion, and active transport. The transport can be regulated through motor proteins, cargo adaptors, or microtubule tracks. We report here a mechanism whereby microtubule associated proteins (MAPs) represent obstacles to motors which can be regulated by microtubule affinity regulating kinase (MARK)/Par-1, a family of kinases that is known for its involvement in establishing cell polarity and in phosphorylating tau protein during Alzheimer neurodegeneration. Expression of MARK causes the phosphorylation of MAPs at their KXGS motifs, thereby detaching MAPs from the microtubules and thus facilitating the transport of particles. This occurs without impairing the intrinsic activity of motors because the velocity during active movement remains unchanged. In primary retinal ganglion cells, transfection with tau leads to the inhibition of axonal transport of mitochondria, APP vesicles, and other cell components which leads to starvation of axons and vulnerability against stress. This transport inhibition can be rescued by phosphorylating tau with MARK.
Disruption of LTBP-4 function reduces TGF-β activation and enhances BMP-4 signaling in the lung
Authors: Koli Katri , Wempe Frank , Sterner-Kock Anja , Kantola Anna , Komor Martina , Hofmann Wolf-K. , von Melchner Harald , Keski-Oja Jorma
Published: October 2004

Disruption of latent TGF-β binding protein (LTBP)–4 expression in the mouse leads to abnormal lung development and colorectal cancer. Lung fibroblasts from these mice produced decreased amounts of active TGF-β, whereas secretion of latent TGF-β was significantly increased. Expression and secretion of TGF-β2 and -β3 increased considerably. These results suggested that TGF-β activation but not secretion would be severely impaired in LTBP-4 −/− fibroblasts. Microarrays revealed increased expression of bone morphogenic protein (BMP)–4 and decreased expression of its inhibitor gremlin. This finding was accompanied by enhanced expression of BMP-4 target genes, inhibitors of differentiation 1 and 2, and increased deposition of fibronectin-rich extracellular matrix. Accordingly, increased expression of BMP-4 and decreased expression of gremlin were observed in mouse lung. Transfection of LTBP-4 rescued the −/− fibroblast phenotype, while LTBP-1 was inefficient. Treatment with active TGF-β1 rescued BMP-4 and gremlin expression to wild-type levels. Our results indicate that the lack of LTBP-4–mediated targeting and activation of TGF-β1 leads to enhanced BMP-4 signaling in mouse lung.
Sec1p directly stimulates SNARE-mediated membrane fusion in vitro
Authors: Scott Brenton L. , Van Komen Jeffrey S. , Irshad Hassan , Liu Song , Wilson Kirilee A. , McNew James A.
Published: October 2004

Sec1 proteins are critical players in membrane trafficking, yet their precise role remains unknown. We have examined the role of Sec1p in the regulation of post-Golgi secretion in Saccharomyces cerevisiae. Indirect immunofluorescence shows that endogenous Sec1p is found primarily at the bud neck in newly budded cells and in patches broadly distributed within the plasma membrane in unbudded cells. Recombinant Sec1p binds strongly to the t-SNARE complex (Sso1p/Sec9c) as well as to the fully assembled ternary SNARE complex (Sso1p/Sec9c;Snc2p), but also binds weakly to free Sso1p. We used recombinant Sec1p to test Sec1p function using a well-characterized SNARE-mediated membrane fusion assay. The addition of Sec1p to a traditional in vitro fusion assay moderately stimulates fusion; however, when Sec1p is allowed to bind to SNAREs before reconstitution, significantly more Sec1p binding is detected and fusion is stimulated in a concentration-dependent manner. These data strongly argue that Sec1p directly stimulates SNARE-mediated membrane fusion.
Molecular barcodes detect redundancy and contamination in hairpin-bisulfite PCR
Authors: Miner Brooks E. , Stöger Reinhard J. , Burden Alice F. , Laird Charles D. , Hansen R. Scott
Published: October 2004

PCR amplification of limited amounts of DNA template carries an increased risk of product redundancy and contamination. We use molecular barcoding to label each genomic DNA template with an individual sequence tag prior to PCR amplification. In addition, we include molecular ‘batch-stamps’ that effectively label each genomic template with a sample ID and analysis date. This highly sensitive method identifies redundant and contaminant sequences and serves as a reliable method for positive identification of desired sequences; we can therefore capture accurately the genomic template diversity in the sample analyzed. Although our application described here involves the use of hairpin-bisulfite PCR for amplification of double-stranded DNA, the method can readily be adapted to single-strand PCR. Useful applications will include analyses of limited template DNA for biomedical, ancient DNA and forensic purposes.
(2,2′-Bipyridyl-κ2
N,N′)bis(salicylato-κ2
O,O′)zinc(II)
Authors: Lemoine Pascale , Bendada Karima , Viossat Bernard
Published: October 2004

The asymmetric unit of the title compound, [Zn(C7H5O3)2(C10H8N2)], contains one monomeric zinc complex. The Zn atom is coordinated to one 2,2′-bipyridyl ligand via both N atoms and to two salicylate anions (Hsal−) in a bidentate chelating manner involving carboxylate O-atom coordination. The complex exhibits a distorted octahedral geometry about the ZnII atom, with the `apical' positions occupied by one of the two N atoms of the bipyridyl ligand and an O atom from one Hsal− ligand; the Zn atom is 0.168 (1) Å out of the `basal' plane. Two intramolecular six-membered hydrogen-bonded rings are present, generated from interactions between the carboxyl and hydroxyl groups of the salicylate ligands. The crystal packing is governed by weak C—H...O and C—H...π interactions.
Transition metal complexes with pyrazole-based ligands. XIX. Diaquabis(3,5-dimethyl-1H-pyrazole-1-carboxamidine-κ2
N,N′)metal(II) dinitrate, with metal = Co and Ni
Authors: Jaćimović Željko K. , Leovac Vukadin , Mészáros Szécsényi Katalin , Howard Judith A. K. , Radosavljević Evans Ivana
Published: October 2004

The two title isostructural and isomorphous complexes, [M(C6H10N4)2(H2O)2](NO3)2 (M is Co or Ni), contain the transition metal in a distorted octahedral geometry, coordinated by four N atoms of two neutral bidentate organic ligands in the equatorial plane and two water O atoms molecules in the axial positions. The cation is centrosymmetric, with the transition metal located on an inversion centre. The structures are stabilized by a three-dimensional network of hydrogen bonding.
Hydantoin and hydrogen-bonding patterns in hydantoin derivatives
Authors: Yu Fang-Lei , Schwalbe Carl H. , Watkin David J.
Published: October 2004

The structure of hydantoin (imidazolidine-2,4-dione), C3H4N2O2, has been determined from a twinned crystal. The two carbonyl bond lengths are nearly equal, even though one of them adjoins electron-donating NH groups to either side while the other is adjacent to only one. Ab initio molecular-orbital calculations yield more negative Löwdin charge on the former than the latter. Hydantoin molecules form two chains linked by N—H...O hydrogen bonds, from which inversion centres create a `chain of rings'. Out of 50 hydantoin moieties in 49 independent molecules of hydantoin derivatives in the Cambridge Structural Database [Version 5.25; Allen (2002). Acta Cryst. B58, 380–388], five show this arrangement, six are a variant using the same O atom twice, five form a chain of edge-fused 12-membered hydrogen-bonded rings, and all but three of the remainder have one eight-membered ring and/or one chain connecting their hydantoin rings.
Two N,N-dimethylbiguanidium salts displaying double hydrogen bonds to the counter-ions
Authors: Lu Li-Ping , Zhang Hong-Mei , Feng Si-Si , Zhu Miao-Li
Published: October 2004

The crystal structures of N,N-dimethylbiguanidium oxalate monohydrate, C4H13N5
2+·C2O4
2−·H2O, (I), and N,N-dimethylbiguanidium sulfate monohydrate, C4H13N5
2+·SO4
2−·H2O, (II), show that both compounds contain the same N,N-dimethylbiguanidium dication. In (I), two independent oxalate ions lie about inversion centres. Strong double hydrogen bonds, with D...A distances of 2.658 (2) and 2.830 (3) Å in (I), and 2.722 (3) and 2.815 (3) Å in (II), are present between N atoms of the N,N-dimethylbiguanidium moieties and either the carboxylate group of the oxalate anion or the sulfate anion.