bluuebunny/crossref_metadata_2025 huggingface dataset:
Determination of the effective transport coefficients of pore networks from transient immiscible and miscible displacement experiments
Authors: Tsakiroglou C. D. , Theodoropoulou M. A. , Karoutsos V. , Papanicolaou D.
Published: February 2005

Transient immiscible and miscible displacement experiments performed on artificial glass‐etched pore networks are used to determine the capillary and relative permeability curves as well as the hydrodynamic dispersion coefficients. The transient responses of the total and axial distribution of the wetting phase (WP) saturation and the pressure drop across the pore network are introduced into an inverse modeling scheme to estimate the imbibition capillary pressure and relative permeability curves of pore networks by varying the capillary number, the contact angle, and the shear‐thinning rheology of the nonwetting phase (NWP). The temporal evolution of the spatial distribution of the solute concentration profiles over selected areas of the pore network is fitted to analytical one‐dimensional solute dispersion models to estimate the longitudinal dispersion coefficient as a function of the Peclet number, in single‐ and dual‐pore networks. Under an unfavorable viscosity ratio the growth pattern is a two‐dimensional fractal object, its description with the one‐dimensional macroscopic two‐phase flow equations is questionable, a high uncertainty is introduced into the capillary pressure curve, whereas “average” relative permeability functions are estimated. The relative permeability of the NWP may be a decreasing or increasing function of the capillary number over the viscous or capillary fingering pattern, respectively. The relative permeability of the WP is an increasing function of the capillary number and increases weakly with the NWP shear‐thinning rheology strengthening. The longitudinal dispersion coefficient varies nonlinearly with Peclet number following power laws with exponents ranging from 1 to 2 and depending on the relative contribution fraction of the macrodispersion (associated with the spatial variation of pore sizes) and Taylor dispersion (associated with the flow channeling) to the entire process.
Prediction of a N2++ layer in the upper atmosphere of Titan
Authors: Lilensten J. , Witasse O. , Simon C. , Soldi‐Lose H. , Dutuit O. , Thissen R. , Alcaraz C.
Published: February 2005

Calculations of dication N2++ density in the atmosphere of Titan is performed for the first time. The metastable lifetime of this species is 3 seconds in its ground state. The density of the N2++ layer centred around 1100–1200 km altitude can reach 104 m−3. The ions are produced by both the double photoionisation and the photoelectron impact of N2. They are lost by dissociative recombination with the thermal electrons and chemical reactions with N2 and CH4. The most recent chemical reaction rate constants, given by laboratory experiments, were used in this study. Finally, we explore the possible detection of this ion layer by a spectrophotometer and show that the UVIS instrument onboard CASSINI could be capable to observe it.
The sub‐Parker spiral structure of the heliospheric magnetic field
Authors: Schwadron N. A. , McComas D. J.
Published: February 2005

Recent studies have shown that the heliospheric magnetic field can be much more radial than the standard Parker spiral in the rarefactions of co‐rotation interaction regions (CIRs). This effect can be explained by the motion of open magnetic field foot points at the Sun across the coronal hole boundary. Such motion causes magnetic field lines to be connected and stretched across the CIR's fast‐slow wind transition, creating a less transverse, “sub‐Parker” magnetic field spiral. Here we include foot point motion at the Sun in a steady‐state magneto‐hydrodynamic (MHD) model to quantify the formation and evolution of such sub‐Parker spirals out to 5 AU. We compare these results with Ulysses CIR observations during its first polar orbit, and find that sub‐Parker spirals consistent with our model are almost always present in CIR rarefactions. Thus, we explain the existence and frequent occurrence of the sub‐Parker spiral structure of heliospheric magnetic field.
The role of land‐sea distribution in the formation of the Asian summer monsoon
Authors: Liang Xiaoyun , Liu Yimin , Wu Guoxiong
Published: February 2005

The role of land‐sea distribution in the formation of the Asian summer monsoon is examined through a series of idealized numerical experiments. Results show that the existence and geometric shape of land‐sea distribution crucially affect the Asian summer monsoon. In an aqua‐planet case, no monsoon is observed. In an experiment in which only the subtropical Eurasian landmass exists, there is a weak summer monsoon over its southeastern corner, but there is no tropical summer monsoon. The existence of tropical lands induces cross‐equatorial flows and strong low‐level southwesterlies over the tropical regions, leading to the formation of the Asian summer monsoon over India, the Bay of Bengal (BOB), and the South China Sea (SCS). The extension of the subtropical continent into the tropics greatly enhances the “East Asian monsoon”.
Hockey sticks, principal components, and spurious significance
Authors: McIntyre Stephen , McKitrick Ross
Published: February 2005

The “hockey stick” shaped temperature reconstruction of Mann et al. (1998, 1999) has been widely applied. However it has not been previously noted in print that, prior to their principal components (PCs) analysis on tree ring networks, they carried out an unusual data transformation which strongly affects the resulting PCs. Their method, when tested on persistent red noise, nearly always produces a hockey stick shaped first principal component (PC1) and overstates the first eigenvalue. In the controversial 15th century period, the MBH98 method effectively selects only one species (bristlecone pine) into the critical North American PC1, making it implausible to describe it as the “dominant pattern of variance”. Through Monte Carlo analysis, we show that MBH98 benchmarks for significance of the Reduction of Error (RE) statistic are substantially under‐stated and, using a range of cross‐validation statistics, we show that the MBH98 15th century reconstruction lacks statistical significance.
Observed electric fields associated with lightning initiation
Authors: Marshall T. C. , Stolzenburg M. , Maggio C. R. , Coleman L. M. , Krehbiel P. R. , Hamlin T. , Thomas R. J. , Rison W.
Published: February 2005

In situ electric field (E) measurements and inferred lightning initiation locations of three cloud‐to‐ground flashes are used to identify a thunderstorm region in which the preflash E exceeded the threshold for runaway breakdown. The maximum measured E in the region was 186 kV m−1 at 5.77 km altitude, which for runaway electrons is equivalent to 370 kV m−1 at sea level; this E value is ∼130% of the estimated threshold for an avalanche of runaway electrons. In addition, the volume where E exceeded the runaway threshold was estimated to be 1–4 km3, with a vertical depth of about 1000 m. At least within part of this volume the characteristic scale height for exponential growth of runaway electrons was 100 m or less. Thus for these three flashes the electric field conditions necessary for runaway breakdown existed, and runaway breakdown could have initiated the flashes.
Iceland as a heat island
Authors: Douglass D. H. , Patel V. , Knox R. S.
Published: February 2005

Iceland is a strong localized source of non‐eruptive volcanic warming and cooling. Temperature trend maps show that this phenomenon is localized to an area of about twice that of Iceland. With altitude the area remains constant but the phenomenon weakens and changes sign upon passing through the tropopause. The effect's magnitude implies a large positive feedback, according to a conventional climate forcing estimate. This phenomenon is unique in that it is not observed for the other major volcanic islands.
On the sampling timescale required to reliably monitor interannual variability in the Antarctic circumpolar transport
Authors: Meredith Michael P. , Hughes Chris W.
Published: February 2005

Numerous field programs have been conducted with the intention of monitoring the transport variability of the Antarctic Circumpolar Current (ACC). Some programs are ongoing, with further efforts planned. Here we address, for the first time, the sampling frequency required for reliable monitoring of the ACC at interannual periods. We find that, for all practical purposes, sampling with a frequency significantly higher than weekly is required to obtain reliable annual means; coarser sampling leads to serious aliasing and degradation of the true temporal progression of transport. Monitoring changes in the seasonality of the ACC requires even more rapid sampling. In practice, hydrographic sections, repeat XBT sections and even altimetry along a single repeat groundtrack will fail to capture the true interannual variability; instead, in situ instrumentation (fixed gauges, moorings or bottom lander‐based equipment) is required. Combinations of techniques may be useful, if they include data from fixed in situ sources.
Nightside detached auroras due to precipitating protons/ions during intense magnetic storms
Authors: Zhang Y. , Paxton L. J. , Morrison D. , Wolven B. , Kil H. , Wing S.
Published: February 2005

Nightside detached auroras (NDA) during intense magnetic storms are studied by using FUV image data from Thermosphere‐Ionosphere‐Mesosphere Energetics and Dynamics (TIMED)/Global Ultraviolet Imager (GUVI), Imager for Magnetopause‐to‐Aurora Global Exploration (IMAGE)/FUV, and particle data from DMSP/SSJ/4 instruments. We found that NDA are caused by proton/ion precipitation only. Thin arc‐shaped NDA are very likely due to soft (<1 keV) proton/ion precipitation. Thick or patch‐shaped NDA are caused by energetic (∼10 keV) proton/ion precipitation. All the cases indicate that the NDA were observed when Dst was less −130 nT. More specifically, the NDA occurred during recovery or the lowest Dst period for each intense storm. The magnetic latitudes of the NDA are between 45° and 55° (L shell: 2.0–3.0). We found that the latitude location of the NDA is quasi‐linearly correlated with Dst. The magnetic local time (MLT) of the NDA ranges from 1930 to 0300. All the facts indicate that the source of the NDA is the trapped protons/ions in the ring current. Precipitation of the trapped protons/ions is caused by an interaction between the perpendicularly heated ring current particles and the cold/dense plasma at the plasmapause.
Diamagnetic solar wind ions changing the MHD conditions at the heliospheric termination shock
Authors: Fahr Hans J. , Scherer Klaus
Published: February 2005

With the two Voyager spacecraft presently flying at solar distances larger than 80 AU, it not only becomes very interesting to study the changing particle environments but also to study the behavior of the distant magnetic fields which are swept out with the solar wind. It is especially challenging to look for the predicted shock features of the magnetic fields which are expected at the solar wind termination shock. While classical MHD theories clearly predict a strong abrupt increase in the magnetic field magnitude at perpendicular MHD shocks, Voyager‐1 either has recently not crossed the termination shock, as claimed by Krimigis et al. [2003], or it did not see the predicted field increase, as stated by Burlaga et al. [2003]. To perhaps clarify on these open points, we here investigate the role of diamagnetism of the solar wind ions approaching the termination shock when becoming shocked there. As we shall show, the magnetic field induction is influenced by the magnetic moments of the gyrating solar wind ions. The magnetic moment per unit volume thereby is determined by the ion pressure and influences the effective magnetic fields. On the basis of that we here derive new MHD shock relations which show that deviating from classical MHD shock expectations the magnetic field compression ratio for a perpendicular shock is different from the density compression ratio and actually is determined by the preshock Alfvénic and sonic solar wind Mach numbers. If these data are carefully taken into account, it may become explainable why Voyager‐1 in fact did cross the termination shock without seeing the expected magnetic field increase. Energetic neutral atoms (ENAs) originating from decharged pick‐up ions beyond the termination shock, by their spectra could serve as messengers of these new features of the shock [see Fahr and Scherer, 2004a].
Modeling the age of Baltic Seawater masses: Quantification and steady state sensitivity experiments
Authors: Meier H. E. Markus
Published: February 2005

Ages of Baltic Seawater masses for the period 1903–1998 were quantified using a three‐dimensional (3‐D) coupled ice‐ocean model. Therefore an additional Eulerian tracer for the age of seawater was embedded. The age is the time elapsed since a water particle left the sea surface. Median ages of the bottom water between 1 year in the Bornholm Basin and 7 years in the northwestern Gotland Basin were found. During 1903–1998 the oldest bottom water of about 11 years appeared at Landsort Deep. In the halocline of the deeper basins a secondary age maximum was calculated. In the eastern Gotland Basin 3 stagnation periods (in the 1920/1930s, 1950/1960s, and 1980/1990s) with ages exceeding 8 years were found. Further, the sensitivities of modeled salinity and age on freshwater supply, wind speed, and amplitude of the sea level in Kattegat were investigated. In steady state the average salinity of the Baltic is most sensitive to perturbations of freshwater inflow. Increased freshwater inflow and wind speed result both in decreased salinity whereas increased amplitude of the Kattegat sea level results in increased salinity. The average age is most sensitive to perturbations of the wind speed. Especially, decreased wind speed causes significantly increased age of the deep water. On the other hand, the impact of changing freshwater or sea level in Kattegat on the average age is comparatively small, suggesting invariance of stability and ventilation in steady state approximately. A simple conceptual model for the Baltic deep water ventilation was applied to explain the 3‐D model results.
Inferring black carbon content and specific absorption from Aerosol Robotic Network (AERONET) aerosol retrievals
Authors: Schuster Gregory L. , Dubovik Oleg , Holben Brent N. , Clothiaux Eugene E.
Published: February 2005

Black carbon is ubiquitous in the atmosphere and is the main anthropogenic absorbing particulate. Absorption by black carbon is thought to be comparable to the cooling associated with sulfate aerosols, although present‐day satellites are incapable of obtaining this measurement, and model estimates are highly uncertain. More measurements of black carbon concentration are necessary for improving and validating transport and general circulation models. The Aerosol Robotics Network (AERONET) of 180 worldwide radiometers offers an opportunity to obtain these measurements. We use the Maxwell Garnett effective medium approximation to infer the column‐averaged black carbon concentration and specific absorption of AERONET retrievals at 46 locations. The yearly averaged black carbon column concentrations exhibit the expected regional dependence, with remote island locations having values about an order of magnitude lower than the continental biomass burning locations. The yearly averaged black carbon specific absorption cross section is consistent with other measured values, 9.9 m2 g−1 for 19,591 retrievals, but varies from 7.7 to 12.5 m2 g−1. We attribute this variability to the details of the size distributions and the fraction of black carbon contained in the aerosol mixture. We also used the Maxwell Garnett equations to parameterize the imaginary refractive index with respect to the black carbon volume fraction, enabling simple but accurate absorption estimates for aerosol mixtures when the black carbon fraction and size distribution is known. The black carbon concentrations that we derive from AERONET measurements correctly describe the radiance field and represent an alternative to absorption optical thickness in the link between models and AERONET measurements.
Size‐resolved fine and ultrafine particle composition in Baltimore, Maryland
Authors: Tolocka Michael P. , Lake Derek A. , Johnston Murray V. , Wexler Anthony S.
Published: February 2005

The third‐generation real‐time single‐particle mass spectrometer (RSMS‐3) was deployed from March to December 2002 in Baltimore, Maryland, as part of the Baltimore Particulate Matter Supersite. The site was located to the east of the downtown area and northwest of many local industrial emission sites. RSMS‐3 actively sampled and analyzed over 380,000 individual particles within the 48–770 nm size range. The resulting positive and negative ion spectra for each particle were classified using a neural network algorithm, adaptive resonance theory ART 2‐a. A subset of these data, particles analyzed between 1 April and 30 November 2003, is presented here. Over 99% of these particles could be described by 10 major composition types. Ambient number concentrations were determined for each type and correlated with particle size, wind direction, and time of day/year. On the basis of this information, local and regional sources of different composition classes are postulated. Almost 40% of all particles in the Baltimore aerosol are internally mixed, consisting primarily of organic carbon, ammonium nitrate, and ammonium sulfate. Most of these particles are likely derived from regional sources. The remaining particles appear to be derived mainly from local sources and processes and include elemental carbon (almost 30%), ammonium nitrate (over 10%), and various metals (over 20%). The particle composition types found in Baltimore aerosol are compared to previous measurements in Houston and Atlanta.
Stochastic modeling of colloid‐contaminant transport in physically and geochemically heterogeneous porous media
Authors: Bekhit Hesham M. , Hassan Ahmed E.
Published: February 2005

A two‐dimensional model is used to describe contaminant transport in the presence of colloids for heterogeneous porous media. The model accounts for both spatially varying conductivity (physical heterogeneity) and the spatially varying distribution coefficient and colloid attachment coefficient (chemical heterogeneity). The model is tested against experimental data, and the results are favorable. The model is implemented in a stochastic Monte Carlo fashion, and both absolute and relative dispersion frameworks are used for the analysis. One finding in this study indicates that the presence of colloids reduces variability in mass arrival times to a downstream control plane. The study also indicates that the effect of geochemical heterogeneity is important only if it is correlated to physical heterogeneity. Spatial variability of the contaminant distribution coefficient or colloid attachment coefficient (i.e., geochemical heterogeneity) is not important in determining the mean plume shape and concentration values when it is not correlated to the hydraulic conductivity variability. Moreover, the comparison between absolute and relative dispersion shows that including the plume meandering in the overall ensemble (absolute mean) would reduce the peak concentration 20–30%. It is also found that the positive correlation structure of geochemical parameters and hydraulic conductivity reduces the difference between absolute and relative dispersion results.
Iron monoxide photodissociation
Authors: Chestakov D. A. , Parker D. H. , Baklanov A. V.
Published: February 2005

The photodissociation of Fe56O was studied by means of the velocity map imaging technique. A molecular beam of iron atoms and iron monoxide molecules was created using an electrical discharge with an iron electrode in a supersonic expansion of molecular oxygen. The ground state iron atom Fe(D45) and FeO concentrations in the molecular beam have been estimated. The dissociation energy of the FeO XΔ5 ground electronic state was found to be D00(FeO)=4.18±0.01eV. The effective absorption cross section of FeO at 252.39nm (vac), leading to the Fe(D45)+O(P3) dissociation channel, is ∼1.2×10−18cm2. A (1+1) resonantly enhanced multiphoton ionization spectrum of Fe56O in the region 39550–39580cm−1 with rotational structure has been observed, but not assigned. Angular distributions of Fe(D45) and Fe(D35) products for the channel FeO→Fe(D4,35)+O(P3) have been measured at several points in the 210–260nm laser light wavelength region. The anisotropy parameter varies strongly with wavelength for both channels.
Electrophoresis of ionic microgel particles: From charged hard spheres to polyelectrolyte-like behavior
Authors: Fernández-Nieves A. , Márquez M.
Published: February 2005

We perform electrophoretic mobility measurements of ionic microgel particles in the deswollen and swollen phases. The results show that microgels behave as charged hard spheres in the first case and as free-draining spherical polyelectrolytes in the latter. A unified theory for the electrophoresis of polyelectrolyte-coated particles [H. Ohshima, Adv. Colloid Interface Sci. 62, 189 (1995)] is shown to contain the essential physics for describing the experiments, upon adequate consideration of the particles swelling behavior and network-solvent friction variations.
A study of 173nm light emission from discharge cells in plasma display panel
Authors: Uhm Han S. , Choi Eun H. , Jung Kyu B.
Published: February 2005

Emission properties of the 173nm lights from the electrical discharge cells of the plasma display panel are investigated. The dimer formation and a theoretical model of 173nm emission are presented. It is shown that the diffusion loss of the excited xenon atoms in the metastable level is one of the most important population depreciation factor of excited xenon atoms. The decay time τd of excited atom number increases from zero, reaches its peak, and then decreases to zero, as the gas pressure p increases from zero, agreeing well with experimental data. A simple analytical expression Y of the total emission intensity is described in terms of the diffusion loss df, the three-body collision η, the gas pressure p, and the xenon mole fraction χ. The emission intensity Y of 173nm photon decreases with an increasing value of parameter df. Moreover, the emission intensity Y increases drastically with an increasing value of the gas pressure p and the xenon mole fraction χ. Results from the theoretical model agree remarkably well with experimental data.
Collective natural orbital occupancies of harmonium
Authors: Cioslowski Jerzy , Buchowiecki Marcin
Published: February 2005

In the harmonium atom, the collective occupancies {nl} of natural orbitals with different angular momenta l can be rigorously studied for those values of the confinement strength ω that lead to ground-state wave functions with correlation factors given by polynomials of kth order. Analysis of two such cases, with ω equal to 1∕2(k=1) and 1∕10(k=2), uncovers some interesting properties of {nl}, which turn out to be given by rational functions of π1∕2 with simple coefficients. In particular, contrary to naive expectations, the collective occupancies for l>2 actually decrease upon strengthening of correlation. The explicit formulas for l-matrices and {nl} can be readily utilized in testing, calibration, and benchmarking of approximate implementations of the density matrix functional theory (DMFT).
Stoichiometric polyelectrolyte complexes as comb copolymers
Authors: Kramarenko E. Yu. , Pevnaya O. S. , Khokhlov A. R.
Published: February 2005

The collapse behavior of a single comblike copolymer chain has been studied by Monte Carlo simulations. It has been supposed that the solvent is good for the side chains but the solvent quality for the backbone chain changes. It has been shown that depending on the structural parameters of the comb copolymer (the lengths of the backbone and side chains, grafting density of the side chains) various thermodynamically stable morphologies of the collapsed backbone chain can be realized. In addition to ordinary spherical globule we have observed elongated structures as well as necklacelike conformations. The proposed model can be used to describe conformational behavior of stoichiometric complexes between block copolymers with a polyelectrolyte short block and oppositely charged linear homopolymers.
Angular distribution of different vibrational components of the X and B states reached after resonant Auger decay of core-excited H2O: Experiment and theory
Authors: Hjelte I. , Karlsson L. , Svensson S. , De Fanis A. , Carravetta V. , Saito N. , Kitajima M. , Tanaka H. , Yoshida H. , Hiraya A. , Koyano I. , Ueda K. , Piancastelli M. N.
Published: February 2005

Vibrationally resolved spectra have been obtained for the lowest-lying cationic states XB12,AA12, and BB22 of the water molecule reached after participator resonant Auger decay of core-excited states. The angular distribution has been measured of the first four vibrational components of the X state in the photon energy regions including the O 1s→4a1 and the O 1s→2b2 core excitations, and for different portions of the vibrational envelope of the B state in the photon energy region including the O 1s→2b2 core excitation. For the X state, a large relative spread in β values of the different vibrational components is observed across both resonances. For the B state, a very different trend is observed for the high binding energy side and the low binding energy side of the related spectral feature as a function of photon energy. A theoretical method based on the scattering K matrix has been used to calculate both the photoabsorption spectrum and the β values, by taking both interference between direct and resonant photoemission and vibrational/lifetime interference into account. The numerical results show qualitative agreement with the trends detected in the experimental values and explain the conspicuous variations of the β values primarily in terms of coupling between direct and resonant photoemission by interaction terms of different sign for different final vibrational states.
Ballooning mode stability in the Hall-magnetohydrodynamics model
Authors: Torasso R. , Hameiri Eliezer
Published: February 2005

The governing equations of the ballooning modes are derived within the Hall-magneto-hydrodynamics (HMHD) model and given a standard Hamiltonian form, which is then used to derive sufficient conditions for stability. In most cases, ideal magnetohydrodynamics (MHD) stability implies HMHD stability, as is the case for tokamak configurations if the pressure is a monotone increasing function of density and the entropy is monotone decreasing. The same result holds for general MHD plasmas with constant entropy and for incompressible plasmas. However, in the case of (compressible) closed-line systems such as the field-reversed configuration, or in a typical magnetospheric magnetic field, MHD ballooning stability does not guarantee HMHD stability. For the explicitly solvable configuration of the Z pinch it is in fact shown that the plasma can be MHD stable but HMHD unstable.
The size of a polymer in a symmetric solvent
Authors: Lowe C. P. , Dreischor M. W.
Published: February 2005

Using a simple thermodynamic model, we derive an expression for the excluded volume parameter v of a polymer chain in a symmetric solvent (solvated by its own monomers). For a chain with a given segment length and number of monomers, this parameter determines whether the chain is collapsed or expanded. For the latter it determines the degree of expansion. Using a simple off-lattice version of Flory’s model [P. J. Flory, Principles of Polymer Chemistry (Cornell University Press, Ithaca, 1953)] and relaxing the assumption of incompressibility, we obtain the result v=(1−κ)∕ρ0, where κ is the dimensionless compressibility and ρ0 the number density of solvent. In the incompressible limit (in the sense that κ→0) the chain is expanded and the inverse of the solvent number density determines the degree of expansion of the chain. Using the van der Waals equation of state to estimate κ (allowing for nonzero compressibility in a system that can undergo a gas-liquid phase transition), the model predicts that upon raising the temperature at constant pressure there is both a lower (coil to globule) and upper (globule to coil) Flory temperature. This is in quantitative agreement with experiment and computer simulations.
Abnormal enhancement of interface trap generation under dynamic oxide field stress at MHz region
Authors: Zhu Shiyang , Nakajima Anri , Ohashi Takuo , Miyake Hideharu
Published: February 2005

By stressing metal-oxide-semiconductor field-effect transistors with ultrathin silicon dioxide or oxynitride gate dielectrics under square wave form voltage at the MHz region, an abnormal enhancement of interface trap generation in the midchannel region has been observed at some special frequencies. A hypothesis, including self-accelerating interface trap generation originated from the positive feedback of a charge pumping current to be contributed by the stress-induced near-interface oxide traps and a resonant tunneling via the near interface oxide trap states at those frequencies, is proposed to explain the observed phenomenon.
A nonequilibrium molecular dynamics method for thermal conductivities based on thermal noise
Authors: Terao Takamichi , Müller-Plathe Florian
Published: February 2005

We developed a nonequilibrium molecular dynamics (NEMD) method for calculating thermal conductivities. In contrast to other NEMD algorithms, here only the heat sink is localized, whereas the heat source can be uniformly distributed throughout the system. The noise due to cutting off the pair forces or to integration errors is such a uniform heat source. In traditional NEMD methods it is normally considered a nuisance factor. The new algorithm accounts for it and uses it. The algorithm is easy to derive, analyse and implement. Moreover, it circumvents the need to calculate energy fluxes. It is tested on the enhanced simple-point charge model for liquid water and reproduces the known thermal conductivity of this model liquid of 0.81Wm−1K−1. It can be generalized to situations, where the thermal noise is replaced by another uniform heat source, or to the inverse situation, where the heat source is localized but the heat sink extends over the entire system.
Elastic modulus of shape-memory NiTi from in situ neutron diffraction during macroscopic loading, instrumented indentation, and extensometry
Authors: Rajagopalan S. , Little A. L. , Bourke M. A. M. , Vaidyanathan R.
Published: February 2005

The elastic modulus of B19’ shape-memory NiTi was determined using three techniques; from the response of lattice planes measured using in situ neutron diffraction during loading, instrumented indentation using a spherical indenter and macroscopic extensometry. The macroscopic measurements resulted in a modulus of 68 GPa, significantly less than the 101 GPa from indentation and the lattice plane average of 109 GPa from neutron diffraction. Evidence from the neutron measurements suggests that the disparity derives from the onset of small amounts of twinning at stresses less that 40 MPa, which might otherwise be considered elastic from a macroscopic view point.
Influence of elastic strains on the mask ratio in glassy polymer nanoimprint
Authors: Cross Graham L. W. , O’Connell Barry S. , Pethica John B.
Published: February 2005

During glassy polymer nanoimprint, a supported film is extruded from protruding (punch) to recessed (cavity) regions of a patterned stamp. The completeness of this extrusion determines the mask ratio for lithographic applications. We show that, for a given punch contact size, there is a residual layer of unextruded material with a mean thickness that is independent of initial film thickness, stamping time, or applied maximum load. Depth sensing indentation enables us to monitor deformation during the imprinting as well as after, and so understand the deformation process involved. It is found that both the geometry and mean thickness of the residual layer are influenced by the overall elastic properties of the stamping system.
Single-layer multiband infrared metallodielectric photonic crystals designed by genetic algorithm optimization
Authors: Drupp Robert P. , Bossard Jeremy A. , Werner Douglas H. , Mayer Theresa S.
Published: February 2005

Metallodielectric photonic crystals (MDPCs) consisting of a planar periodic array of metallic patch elements designed by genetic algorithm (GA) optimization were patterned on flexible dielectric substrates and exhibit strong mid- and far-infrared (IR) dual-band response. The GA uses biological principles of natural selection to evolve nonintuitive geometries by optimizing the MDPC scattering response based on a user-defined fitness function. The transmission spectra measured on two different MDPCs optimized for optically thin and thick substrates have two strong stop bands with attenuation greater than 10dB, which agree well with those predicted by full-wave periodic method of moments (PMM) modeling. This versatile GA optimization approach will facilitate design of scaled mid- and near-IR MDPCs with user-defined scattering response.
High-Q optical resonators in silicon-on-insulator-based slot waveguides
Authors: Baehr-Jones Tom , Hochberg Michael , Walker Chris , Scherer Axel
Published: February 2005

This letter describes the design, fabrication and characterization of high-Q oval resonators based on slot waveguide geometries in thin silicon-on-insulator material. Optical quality factors of up to 27 000 were measured in such filters, and we estimate losses of −10 dB/cm in the slotted waveguides on the basis of our resonator measurements. Such waveguides enable the concentration of light to very high optical fields within nanoscale dimensions, and show promise for the confinement of light in low-index material with potential applications for optical modulation, nonlinear optics and optical sensing.
Mouse Na+/K+-ATPase β1-subunit has a K+-dependent cell adhesion activity for β-GlcNAc-terminating glycans
Authors: Kitamura Noriaki , Ikekita Masahiko , Sato Takeshi , Akimoto Yoshihiro , Hatanaka Yasumaru , Kawakami Hayato , Inomata Mitsushi , Furukawa Kiyoshi
Published: February 2005

A 48-kDa β-N-acetylglucosamine (GlcNAc)-binding protein was isolated from mouse brain by GlcNAc-agarose column chromatography. The N-terminal amino acid residues showed the protein to be a mouse Na+/K+-ATPase β1-subunit. When the recombinant FLAG-β1-subunit expressed in Sf-9 cells was applied to a GlcNAc-agarose column, only the glycosylated 38- and 40-kDa proteins bound to the column. In the absence of KCl, little of the proteins bound to a GlcNAc-agarose column, but the 38- and 40-kDa proteins bound in the presence of KCl at concentrations above 1 mM. Immunohistochemical study showed that the β1-subunit and GlcNAc-terminating oligosaccharides are at the cell contact sites. Inclusion of anti-β1-subunit antibody or chitobiose in cell aggregation assays using mouse neural cells resulted in inhibition of cell aggregation. These results indicate that the Na+/K+-ATPase β1-subunit is a potassium-dependent lectin that binds to GlcNAc-terminating oligosaccharides: it may be involved in neural cell interactions.
Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping
Authors: Roh Tae-Young , Cuddapah Suresh , Zhao Keji
Published: February 2005

The identity and developmental potential of a human cell is specified by its epigenome that is largely defined by patterns of chromatin modifications including histone acetylation. Here we report high-resolution genome-wide mapping of diacetylation of histone H3 at Lys 9 and Lys 14 in resting and activated human T cells by genome-wide mapping technique (GMAT). Our data show that high levels of the H3 acetylation are detected in gene-rich regions. The chromatin accessibility and gene expression of a genetic domain is correlated with hyperacetylation of promoters and other regulatory elements but not with generally elevated acetylation of the entire domain. Islands of acetylation are identified in the intergenic and transcribed regions. The locations of the 46,813 acetylation islands identified in this study are significantly correlated with conserved noncoding sequences (CNSs) and many of them are colocalized with known regulatory elements in T cells. TCR signaling induces 4045 new acetylation loci that may mediate the global chromatin remodeling and gene activation. We propose that the acetylation islands are epigenetic marks that allow prediction of functional regulatory elements.
Solution Structure of an Arabidopsis WRKY DNA Binding Domain
Authors: Yamasaki Kazuhiko , Kigawa Takanori , Inoue Makoto , Tateno Masaru , Yamasaki Tomoko , Yabuki Takashi , Aoki Masaaki , Seki Eiko , Matsuda Takayoshi , Tomo Yasuko , Hayami Nobuhiro , Terada Takaho , Shirouzu Mikako , Tanaka Akiko , Seki Motoaki , Shinozaki Kazuo , Yokoyama Shigeyuki
Published: February 2005

The WRKY proteins comprise a major family of transcription factors that are essential in pathogen and salicylic acid responses of higher plants as well as a variety of plant-specific reactions. They share a DNA binding domain, designated as the WRKY domain, which contains an invariant WRKYGQK sequence and a CX4–5CX22–23HXH zinc binding motif. Herein, we report the NMR solution structure of the C-terminal WRKY domain of the Arabidopsis thaliana WRKY4 protein. The structure consists of a four-stranded β-sheet, with a zinc binding pocket formed by the conserved Cys/His residues located at one end of the β-sheet, revealing a novel zinc and DNA binding structure. The WRKYGQK residues correspond to the most N-terminal β-strand, kinked in the middle of the sequence by the Gly residue, which enables extensive hydrophobic interactions involving the Trp residue and contributes to the structural stability of the β-sheet. Based on a profile of NMR chemical shift perturbations, we propose that the same strand enters the DNA groove and forms contacts with the DNA bases.
The Rice Nuclear Genome Continuously Integrates, Shuffles, and Eliminates the Chloroplast Genome to Cause Chloroplast–Nuclear DNA Flux
Authors: Matsuo Mitsuhiro , Ito Yuki , Yamauchi Ryo , Obokata Junichi
Published: February 2005

Plastid DNA fragments are often found in the plant nuclear genome, and DNA transfer from plastids to the nucleus is ongoing. However, successful gene transfer is rare. What happens to compensate for this? To address this question, we analyzed nuclear-localized plastid DNA (nupDNA) fragments throughout the rice (Oryza sativa ssp japonica) genome, with respect to their age, size, structure, and integration sites on chromosomes. The divergence of nupDNA sequences from the sequence of the present plastid genome strongly suggests that plastid DNA has been transferred repeatedly to the nucleus in rice. Age distribution profiles of the nupDNA population, together with the size and structural characteristics of each fragment, revealed that once plastid DNAs are integrated into the nuclear genome, they are rapidly fragmented and vigorously shuffled, and surprisingly, 80% of them are eliminated from the nuclear genome within a million years. Large nupDNA fragments preferentially localize to the pericentromeric region of the chromosomes, where integration and elimination frequencies are markedly higher. These data indicate that the plant nuclear genome is in equilibrium between frequent integration and rapid elimination of the chloroplast genome and that the pericentromeric regions play a significant role in facilitating the chloroplast–nuclear DNA flux.
Spatial patterns of the biological traits of freshwater fish communities in south‐west France
Authors: Santoul F. , Cayrou J. , Mastrorillo S. , Céréghino R.
Published: February 2005

Spatial patterns in the combinations of biological traits of fish communities were studied in the Garonne River system (57 000 km2, south‐west France). Fish species assemblages were recorded at 554 sampling sites, and the biological traits of species were described using a fuzzy‐coding method. A co‐inertia analysis of species distributions and biological traits identified some spatial patterns of species trait combinations. Fish species richness progressively increased from up‐ to downstream sections, and the longitudinal patterns of fish assemblages partitioned the river into clear biogeographic areas, such as the brown trout Salmo trutta(headwater streams), the grayling Thymallus thymallus, the barbel Barbus barbus and the bream Abramis brama zones (most downstream sections), which fitted with Huet's well‐known zonation for western European rivers. Only a few biological traits, chiefly related to life‐history attributes, significantly influenced the observed fish distributions. Fecundity, potential size, maximum age and reproductive factor increased from headwater to plain reaches. As a theoretical framework for assessing and predicting the functional organization of stream fish communities, spatial variations in species traits can be related to habitat conditions, thus providing explicit spatial schemes that may be useful to the design of both scientific studies and river management.
Long‐term changes in the feeding of Pollachius virens on the Scotian Shelf: responses to a dynamic ecosystem
Authors: Carruthers E. H. , Neilson J. D. , Waters C. , Perley P.
Published: February 2005

The diet and feeding ecology of pollock Pollachius virens from the Scotian Shelf and Bay of Fundy in the north‐west Atlantic changed over the last few decades, which was associated with decreases in euphausiid abundance. Stomach contents data for 2078 pollock collected during the 1958–1967 period and for 1230 pollock collected during the 1996–2002 period indicated that pollock diet contained fewer euphausiids and feeding activity decreased. During the early period, euphausiids were present in 65% of the pollock stomachs that contained food and only 9% of these stomachs in the recent period. The decrease of euphausiids was not wholly offset by an increase in piscivory, since there was little increase in the frequency of fish prey in the diet or in the fullness index for this prey type. Empty stomachs were significantly more common in the recent period during both the winter and summer. The decreased occurrence of euphausiids in stomach samples coincided with a significantly decreased abundance of this prey, suggesting that the near‐absence of euphausiids in recently collected pollock stomachs reflected prey abundance. Concurrent with changes in diet and feeding intensity, the condition or ‘plumpness’ of pollock significantly declined from the early to the late sampling periods.
Movements of Macquaria ambigua, in the Murray River, south‐eastern Australia
Authors: O'Connor J. P. , O'Mahony D. J. , O'Mahony J. M.
Published: February 2005

A 2 year (2000–2001) radio‐tagging study was undertaken to investigate the movements of 51 golden perch Macquaria ambigua in the Murray River at Nyah in north‐western Victoria, Australia. During the winter of both years, golden perch did not undertake movements >5 km and displayed strong home range fidelity. In the first year of the study there was an increase in the distance of golden perch movement during late spring which coincided with increasing water temperature and river discharge. Nineteen golden perch were tracked during this period, of which 10 travelled downstream between 11 and 290 km. Seven of these fish moved to an area below the junction of the Murray and Wakool Rivers. Five golden perch travelled upstream between 13 and 35 km, four of which travelled to an area around the junction of the Murray River and Speewa Creek. The remaining four golden perch undertook localized movements of <5 km. Many of the long distance movements undertaken in spring 2000 were rapid and 53% of these golden perch returned to within 3 km of their release locations, indicating homing behaviour. Given that the rapid movements of golden perch in spring coincided with the known spawning season of this species, these long distance movements may be associated with reproductive strategy.
The first record of Misgurnus anguillicaudatus in Germany
Authors: Freyhof J. , Korte E.
Published: February 2005

Oriental weatherfish Misgurnus anguillicaudatus, from southern China, have been imported to Germany in large numbers for the garden pond trade. The first record of M. anguillicaudatus from Central Europe, a population that has been established for at least 14 years in a small nature reserve in Germany, is detailed.
Discovery of a normal hermaphroditic chondrichthyan species: Apristurus longicephalus
Authors: Iglésias S. P. , Sellos D. Y. , Nakaya K.
Published: February 2005

Examination of the internal genital apparatus of Apristurus longicephalus, a small, deep‐water bottom‐dwelling catshark (Scyliorhinidae) from the western Pacific and Indian Oceans has revealed that it is a hermaphroditic species. It possesses both the developed genital apparatus of one sex and the undeveloped genital apparatus of the opposite sex in the same individual. Apristurus longicephalus is the first case of normal hermaphroditism to be recorded in cartilaginous fishes and this has been further classified as rudimentary hermaphroditism.
The angle of attack of the body of common bream while swimming at different speeds in a flume tank
Authors: Svendsen J. C. , Koed A. , Lucas M. C.
Published: February 2005

The body attack angle of common bream Abramis brama varied with swimming speed and was best described by θ = −3·32 (±0·24) − 9·23 (±0·54)e−u(r2 = 0·56, P < 0·0001; ±1s.e. given in parentheses), where θ is the body attack angle and u is swimming speed. The hypothesis that neutrally buoyant fishes may swim with body attack angles deviating increasingly from 0° as the swimming speed decreases is supported.
Spatial and temporal changes in the nekton of the Terminos Lagoon, Campeche, Mexico
Authors: Ramos‐Miranda J. , Quiniou L. , Flores‐Hernandez D. , Do‐Chi T. , Ayala‐Perez L. , Sosa‐Lopez A.
Published: February 2005

This study describes the current state of the nektonic communities in Terminos Lagoon in relation to the main environmental factors, and documents variations in number of fish species, dominance and abundance, compared to studies performed in 1980. Information on several environmental factors (temperature, salinity, oxygen, pH and transparency) in the Terminos Lagoon between October 1997 and March 1999 allowed the classification of the lagoon into five zones or subsystems. The hydrological characteristics of these subsystems showed spatial differences compared with studies carried out during the 1980s. During the study period, the number of fish species was 105, compared with 154 species reported in the 1980s. Five fish assemblages were identified and appeared to be associated with the five zones or subsystems. Five fish species considered important based on their abundance in the lagoon during the 1980s declined in numbers: pig fish Orthopristis chrysoptera, Atlantic croaker Micropogonias undulates, striped burrfish Chilomycterus schoepfi, spotted seatrout Cynoscion nebulosus and Gulf toadfish Opsanus beta. Six fish species, previously of minor importance, however, were very abundant: star drum Stellifer lanceolatus, Atlantic anchoveta Cetengraulis edentulus, gafftopsail catfish Bagre marinus, sand seatrout Cynoscion arenarius, striped mojarra Eugerres plumieri and ground croaker Bairdiella ronchus. Among the dominant species, the silver croaker Bairdiella chrysoura and the sea bream Archosargus rhomboidalis experienced significant changes in average abundance and distribution patterns. These changes were probably related to the impact of human activities in the Terminos Lagoon and natural variability.