bluuebunny/crossref_metadata_2025 huggingface dataset:
Asymmetry at the molecular level in biology
Authors: JOHNSON LOUISE N.
Published: August 2005

Naturally occurring biological molecules are made of homochiral building blocks. Proteins are composed of L-amino acids (and not D-amino acids); nucleic acids such as DNA have D-ribose sugars (and not L-ribose sugars). It is not clear why nature selected a particular chirality. Selection could have occurred by chance or as a consequence of basic physical chemistry. Possible proposals, including the contribution of the parity violating the weak nuclear force, are discussed together with the mechanisms by which this very small contribution might be amplified. Homochirality of the amino acids has consequences for protein structure. Helices are right handed and beta sheets have a left-hand twist. When incorporated into the tertiary structure of a protein these chiralities limit the topologies of connections between helices and sheets. Polypeptides comprised of D-amino acids can be synthesized chemically and have been shown to adopt stable structures that are the mirror image of the naturally occurring L-amino acid polypeptides. Chirality is important in drug design. Three examples are discussed: penicillin; the CD4 antagonistic peptides; and thalidomide. The absolute hand of a biological structure can only be established by X-ray crystallographic methods using the technique of anomalous scattering.
Development of the asymmetric human
Authors: WOLPERT LEWIS
Published: August 2005

Symmetry across the midline is present in many animals, together with the left/right asymmetry of several organs, such as the heart in vertebrates. The development of such asymmetries during embryonic development requires first the specification of the midline and then specification of left/right. One model proposes the transfer of molecular asymmetry to the multicellular level. Nodal expression on the left side in mammals and chicks is a key event, and is due to the release of calcium on the left possibly involving an ion pump and the Notch pathway
Spatial and temporal analysis of water chemistry records (1958–2000) in the Huanghe (Yellow River) basin
Authors: Chen Jingsheng , Wang Feiyue , Meybeck Michel , He Dawei , Xia Xinghui , Zhang Litian
Published: August 2005

The chemistry of major dissolved ions (Ca2+, Mg2+, Na+ + K+, HCO3−, SO42−, Cl−) and dissolved silica (SiO2) in the river water of the Huanghe (Yellow River), China, was studied from historical records at 100 stations in the drainage basin for the period 1958–2000 (not all the parameters were continuously monitored during the entire period). This river system (750,000 km2) presents an exceptional temporal and spatial water chemistry variability compared to other major rivers. The total dissolved solid (TDS) concentration of the Huanghe varied over 2 to 3 orders of magnitude throughout the basin, with a median TDS concentration of 452 mg/L, which is about 4 times the world spatial median value (WSM). In particular, the concentrations of Na+ + K+, SO42−, and Cl− were 10–20 times higher than in other major world rivers. Similar to the Changjiang (Yangtze River) and many other Himalayan rivers, the TDS at a given station is seasonally variable and inversely related to river runoff with a variation factor less than 2.0, despite a water dilution of fourfold to fivefold in the summer flood season. In addition to chemical weathering of sedimentary rocks, evaporation and fractional crystallization were found to be the major natural process controlling the major element chemistry of the Huanghe, owing to the abundance of loess and clastic rocks under arid and semiarid climates. A persistent increasing trend from year to year has been observed in the concentrations of TDS and all the salts except for HCO3− at all main‐channel stations except for the uppermost Lanzhou. The rate of increase in the TDS concentration was the highest in the middle reaches (10.52 mg/L yr−1 at Toudaoguai) and remained to be unusually high in the lower reaches (5.5 mg/L yr−1 at Stations Luokou and Lijin). The increasing trend coincided with a significant decrease in water discharge at most of the main‐channel stations in the past 40 years, and is attributed to increasing regulations of reservoirs and intensive water withdrawal for irrigation and diversions, as well as many other anthropogenic processes. Despite the increasing trend in TDS concentrations, the seaward TDS flux to the sea by the Huanghe has decreased dramatically from more than 20 × 109 kg/yr in the 1960s to less than 10 × 109 kg/yr at present, due to the sharp decrease in water discharge (sometimes completely dried up) in the lower reaches of the river. The significant decreases in sea‐ward fluxes of water and dissolved salts are expected to have profound physical, ecological, and socio‐economic impacts on the lower reaches of the river, the coastal areas and the Bohai Sea.
The winter Arctic Oscillation, the timing of spring, and carbon fluxes in the Northern Hemisphere
Authors: Schaefer Kevin , Denning A. Scott , Leonard Owen
Published: August 2005

Various observations show trends toward warmer and earlier springs in the Northern Hemisphere. We hypothesize that the positive trend in the winter Arctic Oscillation (AO) has led to higher winter temperatures, advanced spring, and increased seasonal amplitudes in atmospheric CO2. To test this hypothesis, we modeled leaf‐out and terrestrial carbon fluxes using the Simple Biosphere model, Version 2 (SiB2) and the National Centers for Environmental Prediction (NCEP) reanalysis for 1958–2002. We found that our modeled leaf‐out trends were consistent with observed phenology and that the winter AO trend can statistically explain 20–70% of the modeled leaf‐out trends in the eastern United States and northern Europe. We also found that warmer winter temperatures associated with the positive trend in the winter AO increased winter respiration. At the same time, these warmer winter temperatures advanced the date of leaf‐out, increasing the total spring uptake of atmospheric CO2 by plants. These seasonally asymmetric trends toward increased respiration in winter and increased photosynthesis in spring can help explain the trend toward increased seasonal amplitudes in observed atmospheric CO2 concentration.
Dissolved inorganic phosphorus export to the coastal zone: Results from a spatially explicit, global model
Authors: Harrison John A. , Seitzinger Sybil P. , Bouwman A. F. , Caraco Nina F. , Beusen Arthur H. W. , Vörösmarty Charles J.
Published: August 2005

Here we describe, test, and apply a spatially explicit, global model of river‐borne dissolved inorganic phosphorus (DIP) export called NEWS‐DIP. Among the innovations in NEWS‐DIP are increased spatial resolution (0.5 × 0.5°), explicit treatment of sewage, fertilizer, manure, and weathering P sources, and inclusion of reservoir retention and consumptive water use terms. The NEWS‐DIP model performed better than pre‐existing global models in predicting DIP yield for both calibration and validation basins (r2 = 0.72 and 0.56, respectively). NEWS‐DIP predicts that of the 34 Tg of P yr−1 loaded on watersheds by human activity globally, approximately 3% reaches river mouths as DIP; anthropogenic sources account for 65% (0.71 Tg yr−1) of the DIP exported to the coastal zone, with the remainder (0.38 Tg yr−1) attributable to natural weathering processes; DIP yields range over 5 orders of magnitude, from less than 0.01 to 1153 kg P km−2 yr−1 with highest predicted DIP yields clustering in East Asia, Europe, and Indonesia; human sewage is the largest anthropogenic source of DIP to the coastal zone on all continents and to all ocean basins. NEWS‐DIP also suggests that despite regional variability, at the global scale, non‐point sources of DIP such as inorganic P fertilizer and manure are much less important in determining coastal export of DIP than point sources and natural weathering processes.
Seasonal and bleaching‐induced changes in coral reef metabolism and CO2 flux
Authors: Kayanne Hajime , Hata Hiroshi , Kudo Setsuko , Yamano Hiroya , Watanabe Atsushi , Ikeda Yutaka , Nozaki Ken , Kato Ken , Negishi Akira , Saito Hiroshi
Published: August 2005

Monitoring seawater CO2 for a full year with seasonal observations of community metabolism in Ishigaki Island, Japan, revealed seasonal variation and anomalous values owing to the bleaching event in 1998. The daily average pCO2 showed a seasonal pattern on an annual scale, 280 to 320 μatm in winter and 360 to 400 μatm in summer, which was determined primarily by the seasonal change in seawater temperature. By contrast, the range in the diel variation in pCO2, 400 to 500 μatm in summer 200 to 300 μatm in winter, was attributed to the seasonal variation in community metabolism: Gross primary production (Pg) and respiration (R) were high in summer and low in winter. During the 1998 bleaching event, although Pg and R increased, community excess organic production (E) decreased by three quarters compared with the same month in 1999, when the coral community showed high recovery. This change in metabolism led to large diel range and increased average value of pCO2 levels in the seawater on the reef flat. The decrease in the range and increase in the average value of pCO2 were observed by monitoring the Palau barrier reef flat, where overall mortality of corals occurred after the bleaching. All the metabolic parameters, Pg, R, E and calcification (G) were reduced by half after the bleaching, which increased the average pCO2 value by 10 μatm and decreased its diel range from 200–400 μatm to 100–200 μatm. Bleaching and resultant mortality of coral reefs led to degradation of their metabolic performance, and thus resulted in the loss of their active interaction with the carbon cycle.
Ionospheric Weather Forecasting on the Horizon
Authors: Schunk Robert , Scherliess Ludger , Sojka Jan J. , Thompson Donald C. , Zhu Lie
Published: August 2005

In an effort to mitigate the adverse effects of the ionosphere on military and civilian operations, specification and forecast models are being developed that employ state‐of‐the‐art data assimilation techniques. Utah State University has recently developed two data assimilation models for the ionosphere as part of the USU Global Assimilation of Ionospheric Measurements (USU GAIM) program. One of these models is currently being implemented at the Air Force Weather Agency for operational use. The USU‐GAIM models are also being used for scientific studies, and this should lead to a dramatic advance in our understanding of ionospheric physics similar to what occurred in meteorology and oceanography after the introduction of data assimilation models in those fields.
From ductile to brittle: Evolution and localization of deformation below a crustal detachment (Tinos, Cyclades, Greece)
Authors: Mehl C. , Jolivet L. , Lacombe O.
Published: August 2005

The Cycladic Oligo‐Miocene detachment of Tinos island is an example of a flat‐lying extensional shear zone evolving into a low‐angle brittle detachment. A clear continuum of extensional strain from ductile to brittle regime is observed in the footwall. The main brittle structures marking extension are shallow‐ and steeply dipping normal faults associated with subvertical extensional joints and veins. The earliest brittle structures are low‐angle normal faults which commonly superimpose on, and reactivate, earlier (precursory) ductile shear bands, but newly formed low‐angle normal faults could also be observed. Low‐angle normal faults are cut by late steeply dipping normal faults. The inversion of fault slip data collected within, and away from, the main detachment zone shows that the direction of the minimum stress axis is strictly parallel to the NE‐SW stretching lineation and that the maximum principal stress axis remained subvertical during the whole brittle evolution, in agreement with the subvertical attitude of veins throughout the island. The high angle of σ1 to the main detachment suggests that the detachment was weak. This observation, together with the presence of a thick layer of cataclasites below the main detachment and the kinematic continuum from ductile to brittle, leads us to propose a kinematic model for the formation of the detachment. Boudinage at the crustal scale induces formation, near the brittle‐ductile transition, of ductile shear zones near the edges of boudins. Shear zones are progressively exhumed and replaced by shallow‐dipping cataclastic shear zones when they reached the brittle field. Most of the displacement is achieved through cataclastic flow in the upper crust and only the last increment of strain gives rise to the formation of brittle faults. The formation of the low‐angle brittle detachment is thus “prepared” by the ductile shear zone and the cataclasites and favored by the circulation of surface‐derived fluids in the shear zone.
Modeling storm events to investigate the influence of the stream‐catchment interface zone on stream biogeochemistry
Authors: Butturini Andrea , Bernal Susana , Sabater Francesc
Published: August 2005

We formulate a new mixing model to explore hydrological and chemical conditions under which the interface between the stream and catchment interface (SCI) influences the release of reactive solutes into stream water during storms. Physically, the SCI corresponds to the hyporheic/riparian sediments. In the new model this interface is coupled through a bidirectional water exchange to the conventional two components mixing model. Simulations show that the influence of the SCI on stream solute dynamics during storms is detectable when the runoff event is dominated by the infiltrated groundwater component that flows through the SCI before entering the stream and when the flux of solutes released from SCI sediments is similar to, or higher than, the solute flux carried by the groundwater. Dissolved organic carbon (DOC) and nitrate data from two small Mediterranean streams obtained during storms are compared to results from simulations using the new model to discern the circumstances under which the SCI is likely to control the dynamics of reactive solutes in streams. The simulations and the comparisons with empirical data suggest that the new mixing model may be especially appropriate for streams in which the periodic, or persistent, abrupt changes in the level of riparian groundwater exert hydrologic control on flux of biologically reactive fluxes between the riparian/hyporheic compartment and the stream water.
Variable solar irradiance as a plausible agent for multidecadal variations in the Arctic‐wide surface air temperature record of the past 130 years
Authors: Soon Willie W.‐H.
Published: August 2005

This letter offers new evidence motivating a more serious consideration of the potential Arctic temperature responses as a consequence of the decadal, multidecadal and longer‐term persistent forcing by the ever‐changing solar irradiance both in terms of total solar irradiance (TSI, i.e., integrated over all wavelengths) and the related UV irradiance. The support for such a solar modulator can be minimally derived from the large (>75%) explained variance for the decadally‐smoothed Arctic surface air temperatures (SATs) by TSI and from the time‐frequency structures of the TSI and Arctic SAT variability as examined by wavelet analyses. The reconstructed Arctic SAT time series based on the inverse wavelet transform, which includes decadal (5–15 years) and multidecadal (40–80 years) variations and a longer‐term trend, contains nonstationary but persistent features that are highly correlated with the Sun's intrinsic magnetic variability especially on multidecadal time scales.
Detecting atmospheric perturbations produced by Venus quakes
Authors: Garcia Raphaël , Lognonné Philippe , Bonnin Xavier
Published: August 2005

The possibility to detect seismic activity on Venus by using the mechanical coupling of the solid‐atmosphere system is investigated. First, the atmospheric attenuation of infrasonic waves produced by quakes is theoretically determined from a pure CO2 atmospheric model, demonstrating that frequencies below 0.1 Hz are amplified by a factor of 10 000 above 120 km altitude. With a simple quake model, an upper limit of infrasonic adiabatic temperature and density perturbations above the source is estimated. Then, we demonstrate that the temperature increase due to high altitude acoustic energy dissipation above a quake is large enough to be measured by remote sensing methods. Finally, the expected post‐seismic effects are analyzed in the framework of the VIRTIS instrument on board the ESA Venus Express mission.
River discharge into the Bay of Bengal in an inverse ocean model
Authors: Yaremchuk M. , Yu Z. , McCreary J.
Published: August 2005

The seasonal cycle of river runoff in the Bay of Bengal is estimated by assimilating climatological salinity/temperature and precipitation data into an ocean model of intermediate complexity. The resulting optimized river‐transport field fits independent land‐based observations within their error bars. Six precipitation products are discussed for their ability to reproduce the observed salinity field within the Bay.
An obliquely propagating electromagnetic drift instability in the lower hybrid frequency range
Authors: Ji Hantao , Kulsrud Russell , Fox William , Yamada Masaaki
Published: August 2005

By employing a local two‐fluid theory, we investigate an obliquely propagating electromagnetic instability in the lower hybrid frequency range driven by cross‐field current or relative drifts between electrons and ions. The theory self‐consistently takes into account local cross‐field current and accompanying pressure gradients. It is found that the instability is caused by reactive coupling between the backward propagating whistler (fast) wave in the electron frame and the forward propagating sound (slow) wave in the ion frame when the relative drifts are large. The unstable waves we consider propagate obliquely to the unperturbed magnetic field and have mixed polarization with significant electromagnetic components. A physical picture of the instability emerges in the limit of a large wave number characteristic of the local approximation. The primary positive feedback mechanism is based on reinforcement of initial electron density perturbations by compression of electron fluid via induced Lorentz force. The resultant waves are qualitatively consistent with the measured electromagnetic fluctuations in reconnecting current sheet in a laboratory plasma.
Tropical instability waves at 0°N, 23°W in the Atlantic: A case study using Pilot Research Moored Array in the Tropical Atlantic (PIRATA) mooring data
Authors: Grodsky Semyon A. , Carton James A. , Provost Christine , Servain Jacques , Lorenzzetti Joao A. , McPhaden Michael J.
Published: August 2005

Temperature, salinity, velocity, and wind from a mooring at 0°N, 23°W are used along with satellite data for sea surface temperature and sea level to examine the contribution of tropical instability waves (TIWs) to the energy and heat balance of the equatorial Atlantic mixed layer. The TIWs appear as periodic 20–30 day fluctuations of currents, temperature, and salinity, which intensify beginning in June and peak in late boreal summer. The intensification occurs in phase with strengthening of the southeasterly trade winds and the seasonal appearance of the equatorial tongue of cold mixed layer temperatures. In 2002 these waves, which warm the mixed layer by 0.35°C during summer months, are maintained by both barotropic and baroclinic conversions that are of comparable size. Salinity fluctuations, previously neglected, increase the magnitude of baroclinic energy conversion.
Major Leader of U.S. Space Weather Forecasting Retires
Authors: Simpson Sarah
Published: August 2005

The U.S. space weather community took a hit in early August when Ernest Hildner retired as director of NOAA's Space Environment Center (SEC). For nearly two decades, Hildner steered the world's premier forecasting agency with a passionate devotion cited by scientists and administrators alike.
Flow structure in a model of aircraft trailing vortices
Authors: Faddy J. M. , Pullin D. I.
Published: August 2005

We consider a model of incompressible trailing vortices consisting of an array of counter-rotating structures in a doubly periodic domain, infinite in the vertical direction. The two-dimensional vortex array of Mallier and Maslowe is combined with an axial velocity profile chosen proportional to the initial axial vorticity to provide an initial condition for the vortex wake. This base flow is a weak solution of the steady Euler equations with three velocity components that are functions of two spatial coordinates, thus allowing its linear stability properties to be investigated. These are used to interpret several stages in the development of vortex structure observed in fully three-dimensional direct numerical simulation (DNS) at Reynolds numbers Γ∕(2πν)=O(1000). For sufficiently high axial velocity, its effect can be seen, in that each vortex in the linear array first develops helical structures before undergoing a period of relaminarization. At later times the more slowly growing cooperative elliptical instabilities become apparent, but the helical structure persists and the observed vortical structures remain coherent for longer periods than in the absence of axial velocity. Using the stretched-vortex subgrid model, large-eddy simulation runs are performed at large Reynolds numbers and a mixing transition identified at about Re=1−2×104. Similar phenomena are observed in these simulations as are seen in the DNS.
A two-color infrared-vacuum ultraviolet laser pulsed field ionization photoelectron study of NH3
Authors: Bahng Mi-Kyung , Xing Xi , Baek Sun Jong , Ng C. Y.
Published: August 2005

We have observed fully rotationally resolved transitions of the photoelectron vibrational bands 24, 25, 1121, and 1123 for ammonia cation (NH3+) by two-color infrared (IR)-vacuum ultraviolet (VUV)- pulsed field-ionization photoelectron (PFI-PE) measurements. By preparing an intermediate rovibrational state of neutral NH3 with a known parity by IR excitation followed by VUV-PFI-PE measurements, we show that the photoelectron parity can be determined unambiguously. The IR-VUV-PFI-PE measurement of the 24 band clearly reveals the formation of both even and odd l states for the photoelectrons, where l is the orbital angular momentum quantum number. This observation is consistent with the conclusion that the lack of inversion symmetry for NH3 and NH3+ allows odd/even l mixings, rendering the production of both odd and even l states for the photoelectrons. Evidence is also found, indicating that the photoionization transitions with ΔK=0 are strongly favored compared to that with ΔK=3. For the 25, 1121, and 1123 bands, only ΔK=0 transitions for the production of even l photoelectron states from the JK′′=20 rotational level of NH3(ν1=1) are observed. The preferential formation of even l photoelectron states for these vibrational bands is attributed to the fact that the ΔK=0 transitions for the formation of odd l photoelectron states from the 20 rotational level of NH3(ν1=1) are suppressed by the constraint of nuclear-spin statistics. In addition to information obtained on the photoionization dynamics of NH3, this experiment also provides a more precise value of 3232±10cm−1 for the ν1+ (N–H stretch) vibrational frequency of NH3+.
Spin-conserving and spin-flipping equation-of-motion coupled-cluster method with triple excitations
Authors: Slipchenko Lyudmila V. , Krylov Anna I.
Published: August 2005

We report the implementation of the spin-conserving and spin-flipping variants of the equation-of-motion (EOM) coupled-cluster (CC) model, which includes single and double excitations in the CC part and single, double, and triple excitations in the EOM part, i.e., EOM-CC(2,3) [Hirata, Nooijen, Bartlett, Chem. Phys. Lett. 326, 255 (2000)] for closed- and open-shell references. Inclusion of triples significantly improves the accuracy of EOM-CCSD for excitation energies (EOM-EE-CCSD) and its spin-flip (SF) counterpart, EOM-SF-CCSD, especially when the reference wave function is strongly spin-contaminated. A less computationally demanding active space variant with semi-internal triples has also been implemented. The capabilities of full and active space EOM-CC(2,3) are demonstrated by applications to CO+ and CH radicals as well as to the methylene and trimethylenemethane diradicals and the dehydro-m-xylylene triradical.
Ionization energies of argon clusters: A combined experimental and theoretical study
Authors: Echt O. , Fiegele T. , Rümmele M. , Probst M. , Matt-Leubner S. , Urban J. , Mach P. , Leszczynski J. , Scheier P. , Märk T. D.
Published: August 2005

We have measured appearance energies of Arn+,n⩽30, by electron impact of gas phase clusters. Quantum-chemical calculations have been performed to determine the adiabatic and vertical ionization energies of argon clusters up to n=4 and 6, respectively. The experimental appearance energy of the dimer ion approaches, under suitable cluster source conditions, the adiabatic ionization energy. The agreement with values obtained by photoionization and threshold photoelectron-photoion coincidence (TPEPICO) spectra demonstrates that autoionizing Rydberg states are accessible by electron impact. Appearance energies of larger clusters, though, exceed the TPEPICO values by about 0.5 eV.
Dynamical effects on vibrational and electronic spectra of hydroperoxyl radical water clusters
Authors: Iyengar Srinivasan S.
Published: August 2005

We have carried out ab initio molecular-dynamics studies on hydroperoxyl water clusters. Our studies are complemented by optimization, frequency, and excited-state calculations. The three main results we obtained are (a) the dynamically averaged energy gap between the highest-occupied molecular orbital and the lowest-unoccupied molecular orbital monotonically decreases as the number of water molecules is increased in a hydroperoxyl water cluster system, (b) the dynamical averaging of the potential-energy surface at finite temperature broadens the electronic excitation spectrum and changes the infrared spectrum in nontrivial ways, and (c) the structural analysis of our dynamics simulation indicates that the oxygen-oxygen distance in a solvated hydroperoxyl-water cluster is very similar to that found in protonated water clusters (Zundel: H5O2+) inspite of the fact that the latter possesses a positive charge and the hydroperoxyl-water cluster does not. Dynamical charge analysis and the weak acidity of HO2 are used to justify this result.
Density-functional description of water condensation in proximity of nanoscale asperity
Authors: Paramonov Pavel B. , Lyuksyutov Sergei F.
Published: August 2005

We apply nonlocal density-functional formalism to describe an equilibrium distribution of the waterlike fluid in the asymmetric nanoscale junction presenting an atomic force microscope tip dwelling above an arbitrary surface. The hydrogen bonding dominating in intermolecular attraction is modeled as a square-well potential with two adjustable parameters (energy and length) characterizing well’s depth and width. A liquid meniscus formed inside the nanoscale junction is explicitly described for different humidity. Furthermore, we suggest a simple approach using polymolecular adsorption isotherms for the evaluation of an energetic parameter characterizing fluid (water) attraction to substrate. This model can be easily generalized for more complex geometries and effective intermolecular potentials. Our study establishes a framework for the density-functional description of fluid with orientational anisotropy induced by nonuniform external electric field.
Photoinduced intramolecular charge separation in a polymer solid below the glass transition temperature
Authors: Benten Hiroaki , Ohkita Hideo , Ito Shinzaburo , Yamamoto Masahide , Tohda Yasuo , Tani Keita
Published: August 2005

Photoinduced intramolecular charge separation (CS) in a polar polymer glass, cyanoethylated pullulan (CN-PUL), was studied below the glass transition temperature (Tg=395K). A series of three carbazole (Cz: donor)-cyclohexane (S: spacer)-acceptor (A: acceptor) molecules (Cz-S-A) was used as intramolecular donor-acceptor dyads. The photoinduced CS rate was evaluated by the fluorescence decay measurement at temperatures from 100 to 400 K. The CS rate (kCS) increased above 200 K even far below Tg where micro-Brownian motions of the whole polymer chain are frozen. Below 200 K, on the other hand, kCS showed weak dependence on temperature. The temperature dependence of kCS is discussed in terms of the dielectric relaxation time of the polymer matrix. Consequently, CS below Tg was well explained by a thermally nonequilibrium electron transfer (ET) formula above 200 K and by a two-mode quantum-mechanical ET formula below 200 K. The increase in kCS above 200 K is mainly caused by a thermally activated low-frequency matrix mode originating from the side-chain relaxation of polar cyano groups. The weak temperature dependence of kCS can be explained by a nuclear-tunneling effect caused by a high-frequency matrix mode (ℏωH=250cm−1) and an intramolecular vibrational mode (ℏωQ=1300cm−1). The high-frequency mode of the polymer matrix was attributed to a vibrational or librational motion of polar groups in the CN-PUL glassy solid.
Ab initioEhrenfest dynamics
Authors: Li Xiaosong , Tully John C. , Schlegel H. Bernhard , Frisch Michael J.
Published: August 2005

We present an ab initio direct Ehrenfest dynamics scheme using a three time-step integrator. The three different time steps are implemented with nuclear velocity Verlet, nuclear-position-coupled midpoint Fock integrator, and time-dependent Hartree-Fock with a modified midpoint and unitary transformation algorithm. The computational cost of the ab initio direct Ehrenfest dynamics presented here is found to be only a factor of 2–4 larger than that of Born-Oppenheimer (BO) dynamics. As an example, we compute the vibration of the NaCl molecule and the intramolecular torsional motion of H2CNH2+ by Ehrenfest dynamics compared with BO dynamics. For the vibration of NaCl with an initial kinetic energy of 1.16 eV, Ehrenfest dynamics converges to BO dynamics with the same vibrational frequency. The intramolecular rotation of H2CNH2+ produces significant electronic excitation in the Ehrenfest trajectory. The amount of nonadiabaticity, suggested by the amplitude of the coherent progression of the excited and ground electronic states, is observed to be directly related to the strength of the electron-nuclear coupling. Such nonadiabaticity is seen to have a significant effect on the dynamics compared with the adiabatic approximation.
“Locally homogeneous turbulence”: Is it an inconsistent framework?
Authors: Frisch Uriel , Bec Jérémie , Aurell Erik
Published: August 2005

In his first 1941 paper Kolmogorov assumed that the velocity has increments that are homogeneous and independent of the velocity at a suitable reference point. This assumption of local homogeneity is consistent with the nonlinear dynamics only in an asymptotic sense when the reference point is far away. This inconsistency is illustrated numerically using the Burgers equation. Kolmogorov’s derivation of the four-fifths law for the third-order structure function and its anisotropic generalization are actually valid only for homogeneous turbulence, but a local version due to Duchon and Robert still holds. A Kolmogorov-Landau approach is proposed to handle the effect of fluctuations in the large-scale velocity on small-scale statistical properties; it is only a mild extension of the 1941 theory and does not incorporate intermittency effects.
A quasinormal scale elimination model of turbulent flows with stable stratification
Authors: Sukoriansky Semion , Galperin Boris , Staroselsky Ilya
Published: August 2005

A new spectral model for turbulent flows with stable stratification is presented. The model is based on a quasi-Gaussian mapping of the velocity and temperature fields using the Langevin equations and employs a recursive procedure of small-scale mode elimination that results in a coupled system of differential equations for effective, horizontal and vertical, viscosities and diffusivities. With increasing stratification, the vertical viscosity and diffusivity are suppressed while their horizontal counterparts are enhanced thus explicitly accounting for the anisotropy introduced by stable stratification. The new model is used to derive various spectral characteristics of stably stratified turbulent flows. It accounts for energy accumulation in the horizontal components at the expense of the energy reduction in the vertical component. The scale elimination algorithm explicitly accounts for the combined effect of turbulence and internal waves. A modified dispersion relation for internal waves, a relationship for internal wave frequency shift, and a threshold criterion for internal wave generation in the presence of turbulent scrambling are derived. It is shown how the model can be utilized to derive parameters needed for Reynolds-averaged Navier-Stokes modeling. Implemented in the K-ϵ format, the new model produces results that agree very well with the observational data on stably stratified atmospheric boundary layers and that are difficult to obtain using traditional two-equation turbulence modeling.
The maximum hardness principle implies the hard/soft acid/base rule
Authors: Chattaraj Pratim K. , Ayers Paul W.
Published: August 2005

A recent paper [P. W. Ayers, J. Chem. Phys122, 141102 (2005)] considered the hard/soft acid/base exchange reaction, showing that the products associated with the hard/soft acid/base rule (in which the hard acid and hard base are bound, as are the soft acid and soft base) have lower energy than the alternative (in which the hard acid and soft base would have been bound and similarly the soft acid and hard base). Here we show that the maximum hardness principle also predicts this result. Unlike the previous derivation, we do not need to make any assumptions about the relative strength of the acids and bases.
Pore water convection within carbonaceous chondrite parent bodies: Temperature-dependent viscosity and flow structure
Authors: Zhang Keke , Liao Xinhao , Schubert Gerald
Published: August 2005

Thermal convection of pore water within a permeable, internally heated spherical body is investigated. Account is taken of the strong temperature dependence of the viscosity of water. With application to hydrothermal circulation in carbonaceous chondrite parent bodies in mind, the variation of gravity with radius in the body is also accounted for. The critical Rayleigh number for the onset of hydrothermal convection in a spherical porous body is determined as a function of the central temperature. It is found that the basic motionless state always becomes unstable with respect to an infinitesimal disturbance characterized by spherical harmonic degree l=2. The order of the spherical harmonics m, and hence the three-dimensional structure of the convective flow, cannot be determined by the stability analysis because of the degeneracy of the linear solution. The three-dimensional structure of the convective flow is determined by removing the degeneracy through the nonlinear effect of the temperature-dependent water viscosity. Three different convection solutions are found. However, the three-dimensional structures of these solutions are exactly the same and axisymmetric after an appropriate rotational transformation. The stability criterion is most effectively viewed as a requirement that the product of permeability and square of planetesimal radius exceed a quantity mainly dependent on central temperature. In this way, the criterion applies to planetesimals independent of the specific identification of the short-lived radionuclide responsible for early heating or its concentration. Evaluation of the criterion in this form leads to the conclusion that hydrothermal convection is likely in carbonaceous chondrite parent bodies heated sufficiently to melt the ice and raise the water temperature by tens to a hundred degrees Celsius. Weakly nonlinear convection in the planetesimals has two regions of hot upwelling water providing significant volumes of hydrothermally altered rock.
A note on the stability of slip channel flows
Authors: Lauga Eric , Cossu Carlo
Published: August 2005

We consider the influence of slip boundary conditions on the modal and nonmodal stability of pressure-driven channel flows. In accordance with previous results by Gersting [“Hydrodynamic stability of plane porous slip flow,” Phys. Fluids 17, 2126 (1974)] but in contradiction with the recent investigation of Chu [“Instability of Navier slip flow of liquids,” C. R. Mec. 332, 895 (2004)], we show that the slip increases significantly the value of the critical Reynolds number for linear instability. The nonmodal stability analysis, however, reveals that slip has a very weak influence on the maximum transient energy growth of perturbations at subcritical Reynolds numbers. Slip boundary conditions are therefore not likely to have a significant effect on the transition to turbulence in channel flows.
Onset of convection in anisotropic porous media subject to a rapid change in boundary conditions
Authors: Ennis-King Jonathan , Preston Ian , Paterson Lincoln
Published: August 2005

Previous studies of fluid convection in porous media have considered the onset of convection in isotropic systems and the steady convection in anisotropic systems. This paper bridges between these and develops new results for the onset of convection in anisotropic porous media subject to a rapid change in boundary conditions. These results are relevant to sedimentary formations where the average vertical permeability is some fraction γ of the average horizontal permeability. Linear and global stability analyses are used to define the critical time tc at which the instability occurs as a function of γ and the dimensionless Rayleigh-Darcy number Ra* for both thermal and solute-driven convection in an infinite horizontal slab. Numerical results and approximate analytical solutions are obtained for both a slab of finite thickness and the limit of large slab thickness. For a thick slab, the increase in tc as γ decreases is approximately given by (1+γ)4∕(16γ2). One important application is to the geological storage of carbon dioxide where it is shown that the use of an effective vertical permeability in estimating the critical time is only valid for low permeabilities. The time scale for the onset of convection in geological storage can range from less than a year (for high-permeability formations) to decades or centuries (for low-permeability ones).
Miniaturized injection-locked laser using microelectromechanical systems technology
Authors: Liu A. Q. , Zhang X. M. , Cai H. , Tang D. Y. , Lu C.
Published: August 2005

This letter reports a miniaturized injection-locked laser (ILL) using the microelectromechanical systems (MEMS) technology. The device is formed by the integration of a MEMS grated-tuned laser and a Fabry–Perot multimode laser within dimensions of 3mm×2mm×0.6mm. A movable prism serves for both active alignment and optical isolation. Single injection and multiple injections to the slave laser are both tested, it has achieved a side mode suppression ratio of 55dB, a range of fully locked state of 0.16nm and a rate of all optical switching at 100MHz. Some observed phenomena such as the wave mixing and detuning hysteresis are explained qualitatively. The miniaturization may help pave the way for the ILLs to the emerging applications such as all optical networks, coherent communications and portable atomic clocks.
Faster H recovery in Pd nanoparticle layer based Gd switchable mirrors: Size-induced geometric and electronic effects
Authors: Aruna I. , Mehta B. R. , Malhotra L. K.
Published: August 2005

An investigation of the effect of the nanoparticle size in the Pd overlayer on the hydrogen-induced changes in the Gd switchable mirrors is reported in the present study. Deposition of a 10nm thick Pd overlayer consisting of nanoparticles of 9nm size results in a large increase in optical and electrical contrast and a substantial decrease in response and recovery time in Gd switchable mirrors. This study shows that a uniformly-deposited nanoparticle catalytic layer is important for improving H recovery. These results have been explained in terms of the size-induced increase in surface area, lattice contraction, and shift of Pd d-band centroid. The results of the present study, specifically the observation of decrease in recovery time has important implications for hydrogen sensor, storage, and switching applications.
Optical nonlinearity induced by exciton-biexciton coherent effects in InGaAs quantum dots
Authors: Gotoh Hideki , Kamada Hidehiko , Nakano Hidetoshi , Saitoh Tadashi , Ando Hiroaki , Temmyo Jiro
Published: August 2005

We report on large optical nonlinear effects induced by coherent interactions between excitons and biexcitons in quantum dots. The absorption spectra in an exciton–biexciton system are measured in InGaAs quantum dots by using single dot spectroscopy. The spectra exhibit unusual shapes that have a transparent region under a strong excitation condition. A pump–probe measurement ensures that the exciton state is erased by a quantum interference effect with exciton and biexciton photoabsorption processes. These results suggest that optical functions such as electromagnetically induced transparency are feasible with excitons and biexcitons in quantum dots.
Tailoring Fe∕Ag superparamagnetic composites by multilayer deposition
Authors: Balogh J. , Kaptás D. , Kiss L. F. , Pusztai T. , Szilágyi E. , Tunyogi Á. , Swerts J. , Vandezande S. , Temst K. , Van Haesendonck C.
Published: August 2005

Fe ∕ Ag granular multilayers were examined by magnetization and Mössbauer spectroscopy measurements. Very-thin (0.2 nm) discontinuous Fe layers show superparamagnetic properties that can be tailored by the thickness of both the magnetic and the spacer layers. Novel heterostructures, superparamagnetic and ferromagnetic layers stacked in different sequences, were prepared and the specific contribution of the ferromagnetic layers to the low-field magnetic susceptibility was identified.
Evanescent light scattering with magnetic colloids
Authors: Blickle V. , Babič D. , Bechinger C.
Published: August 2005

We measure magnetic interactions between paramagnetic colloidal beads and an external magnetic field by using total internal reflection microscopy (TIRM). Our results demonstrate that TIRM can be applied to absorptive paramagnetic probe particles and thus extends the range of interaction types which can be addressed with this method. With our setup, we can detect magnetic forces on single superparamagnetic particle ranging from about 10 to 600 fN.
Precise determination of band offsets and chemical states in SiN∕Si studied by photoemission spectroscopy and x-ray absorption spectroscopy
Authors: Toyoda S. , Okabayashi J. , Kumigashira H. , Oshima M. , Liu G. L. , Liu Z. , Ikeda K. , Usuda K.
Published: August 2005

We have investigated chemical states and band offsets in SiN∕Si by photoemission spectroscopy and x-ray absorption spectroscopy. N1s photoemission spectra in SiN for three kinds of layer-thickness films are fitted by a single component, suggesting that a nitrogen atom is surrounded by three silicon and nine nitrogen atoms for the first and the second nearest neighbor, respectively. Valence-band offsets between SiN and the Si substrates are determined to be 1.6 eV using valence-band spectra by subtracting the contribution from Si substrates. Band gap of SiN is estimated to be 5.6–5.7 eV from valence-band, N1s core level, and NK-edge-absorption spectra. Furthermore, time-dependent measurements of N1s photoemission spectra reveal that the x-ray irradiation time is a significant factor to determine the precise valence-band offsets excluding the differential charging effects.
High-quality planar high-Tc Josephson junctions
Authors: Bergeal N. , Grison X. , Lesueur J. , Faini G. , Aprili M. , Contour J. P.
Published: August 2005

Reproducible high-Tc Josephson junctions have been made in a rather simple two-step process using ion irradiation. A microbridge (1 to 5μm wide) is firstly designed by ion irradiating a c-axis-oriented YBa2Cu3O7−δ film through a gold mask such as the nonprotected part becomes insulating. A lower Tc part is then defined within the bridge by irradiating with a much lower fluence through a narrow slit (20 nm) opened in a standard electronic photoresist. These planar junctions, whose settings can be finely tuned, exhibit reproducible and nearly ideal Josephson characteristics. This process can be used to produce complex Josephson circuits.
Growth process of close-packed aligned carbon nanotubes on SiC
Authors: Kusunoki M. , Honjo C. , Suzuki T. , Hirayama T.
Published: August 2005

Densely aligned carbon nanotubes (CNTs) by surface decomposition of SiC (0001¯) C-face in vacuum were observed by plan-view transmission electron microscopy. It was found that the wall number of CNTs was directly proportional to the diameter of CNTs. Comparing with the theoretical calculation, it was revealed that all of the carbon atoms remained on the surface after the selective evaporation of Si atoms by decomposition of each monolayer of SiC (0001¯), and then constructed the CNT walls with the minimum diffusion distance at the interface.
Enhanced second- and third-harmonic generation and induced photoluminescence in a two-dimensional GaN photonic crystal
Authors: Coquillat Dominique , Vecchi Gabriele , Comaschi Carlo , Malvezzi Andrea Marco , Torres Jérémi , Le Vassor d’Yerville Marine
Published: August 2005

We observed visible second-harmonic and ultraviolet third-harmonic fields generated in reflection from the surface of a two-dimensional triangular GaN/sapphire photonic crystal. When the pump radiation resonates with a photonic mode, enhancement factors as high as 250 and 3500 occurred for the second- and third-harmonic signals, respectively, as compared to the unpatterned GaN slab. The very large increase of third-harmonic field, with a photon energy exceeding that of the electronic band gap, was used as an efficient mechanism to induce GaN photoluminescence.
Low-temperature high-resolution magnetic force microscopy using a quartz tuning fork
Authors: Seo Yongho , Cadden-Zimansky Paul , Chandrasekhar Venkat
Published: August 2005

We have developed a low-temperature high resolution magnetic force microscope (MFM) using a quartz tuning fork that can operate in a magnetic field. A tuning fork with a spring constant of 1300N∕m mounted with a commercial MFM cantilever tip was used. We have obtained high-resolution images of the stray magnetic fields exerted from grains with a spatial resolution of 15 nm and force resolution of 2 pN at 4.2 K. Tuning fork-based magnetic force microscopes have the potential to be used at millikelvin temperatures due to their low power dissipation and high force sensitivity.
Mode-selecting acoustic filter by using resonant tunneling of two-dimensional double phononic crystals
Authors: Qiu Chunyin , Liu Zhengyou , Mei Jun , Shi Jing
Published: August 2005

In this letter, we investigated the resonant tunneling of elastic waves through double phononic potential barriers formed by two slabs of two-dimensional phononic crystals consisting of pure solid components. It is found that the resonant tunneling longitudinal waves can be distinguished easily from the resonant tunneling transverse waves. Thus, such double-barrier structures can be served as a mode-selecting acoustic filter, used to pick out the single longitudinal wave component or transverse wave component at a certain frequency.