bluuebunny/crossref_metadata_2025 huggingface dataset:
Modeling the dynamic component of the geoid and topography of Venus
Authors: Pauer M. , Fleming K. , Čadek O.
Published: November 2006

We analyze the Venusian geoid and topography to determine the relative importance of isostatic, elastic and dynamic compensation mechanisms over different degree ranges. The geoid power spectrum plotted on a log‐log scale shows a significant change in its slope at about degree 40, suggesting a transition from a predominantly dynamic compensation mechanism at lower degrees to an isostatic and/or elastic mechanism at higher degrees. We focus on the dynamic compensation in the lower‐degree interval. We assume that (1) the flow is whole mantle in style, (2) the long‐wavelength geoid and topography are of purely dynamic origin, and (3) the density structure of Venus' mantle can be approximated by a model in which the mass anomaly distribution does not vary with depth. Solving the inverse problem for viscosity within the framework of internal loading theory, we determine the families of viscosity models that are consistent with the observed geoid and topography between degrees 2 and 40. We find that a good fit to the data can be obtained not only for an isoviscous mantle without a pronounced lithosphere, as suggested in some previous studies, but also for models with a high‐viscosity lithosphere and a gradual increase in viscosity with depth in the mantle. The overall viscosity increase across the mantle found for the latter group of models is only partially resolved, but profiles with a ∼100‐km‐thick lithosphere and a viscosity increasing with depth by a factor of 10–80, hence similar to viscosity profiles expected in the Earth's mantle, are among the best fitting models.
Iron in ice cores from Law Dome: A record of atmospheric iron deposition for maritime East Antarctica during the Holocene and Last Glacial Maximum
Authors: Edwards Ross , Sedwick Peter , Morgan Vin , Boutron Claude
Published: November 2006

Total dissolvable iron (TDFe) was measured in sections of ice cores recovered from Law Dome on the coast of Wilkes Land, East Antarctica. These samples include ice dating from the Last Glacial Maximum (LGM), the Last Deglaciation, and the early and mid Holocene as well as samples from the Anthropocene that have been dated with seasonal to annual resolution. Combining our TDFe concentration data with estimates of the ice accumulation rate, we estimate the atmospheric iron deposition for Law Dome and the adjacent Southern Ocean during these periods. Our results indicate that the atmospheric iron deposition flux to this region during the LGM (∼8 μmol Fe m−2 yr−1) was an order of magnitude higher than the average Holocene deposition flux (∼0.8 μmol Fe m−2 yr−1). This Holocene flux estimate is significantly higher than recent estimates of atmospheric iron deposition based on the analysis of iron in samples of the Dome C EPICA ice core, implying that there are significant meridional gradients in eolian iron flux to the Antarctic region. Our data also suggest that there have been significant variations in atmospheric iron deposition to Law Dome and adjacent ocean waters over seasonal to decadal timescales during the past century. Analysis of ice samples dating from calendar years 1927 to 1928 indicates an anomalously high flux of TDFe to the Law Dome region, amounting to around half the maximum LGM flux, possibly as a result of severe drought conditions on the Australian continent. Given that chronic iron deficiency is thought to limit phytoplankton production in much of the ocean around Antarctica, such large secular variations in atmospheric iron supply are likely to have had profound impacts on year‐to‐year primary production and ecosystem structure in Antarctic waters.
Unusual gray whale Eschrichtius robustus feeding in the summer of 2005 off the central Oregon Coast
Authors: Newell Carrie L. , Cowles Timothy J.
Published: November 2006

The climate of the North Pacific underwent an unusual event in the summer of 2005 with a very late spring transition. This event had profound effects on both resident gray whales (Eschrichtius robustus) and their food source, mysids, off Depoe Bay, Oregon. Near bottom swarms of gray whales' major prey item, Holmesimysis sculpta, were sparse until August, a marked contrast to normal years when mysid swarms are abundant all summer. A large percentage of mysid females had empty brood pouches in 2005 while in 2003 and 2004 all observed females had full brood pouches. Gray whales spent little time foraging and spent fewer days in residence than in earlier years. The 2005 resident whales also showed signs of poor body condition, reflecting a nutritional deficit.
Low frequency variability of South China Sea surface circulation from 11 years of satellite altimeter data
Authors: Fang Wendong , Guo Junjian , Shi Ping , Mao Qingwen
Published: November 2006

Eleven years of sea surface height from satellite altimetry data are used to describe the low frequency variability of South China Sea (SCS) surface circulation through Empirical Orthogonal Function (EOF) analysis. The annual variability clearly agrees with previous studies, revealing the SCS response to seasonal fluctuations of the overlaying monsoon winds. The summer eastward jet off west coast of SCS is shown from the second seasonal EOF mode. Two new patterns of year‐to‐year and decadal variability are presented for the first time from measurements. Long term positive trend appears from 1993 to 2001 and reverses the sign of its trend again from 2001 to 2003. Abnormal events occur in 1994–1995, in 1997–1998 and in 2002 with different spatial scales regarding both basin‐scale distribution and meso‐scale variability located off the western SCS. Association of these events with the El Niño‐Southern Oscillation is discussed.
Density variability at scales typical of gravity waves observed in Mars' thermosphere by the MGS accelerometer
Authors: Creasey John E. , Forbes Jeffrey M. , Keating Gerald M.
Published: November 2006

Examination of the small‐scale density perturbations in Mars' thermosphere inferred from Mars Global Surveyor (MGS) accelerometer data reveals wave‐like structures consistent with gravity waves. The structures are interpreted to be horizontal with dominant wavelengths of 100–300 km observed along the orbital path. Density perturbations are significantly stronger in winter versus spring/summer, suggesting that the zonal mean winds play a major role in filtering these waves. There is also evidence of possible modulation by the mean winds due to local time differences. No correlation is found with the underlying topography, a source region on Earth for gravity waves. In fact, density perturbations in the northern hemisphere are observed to be greater than those in the southern hemisphere, which has a higher orographic variance. Over the Martian tropics, an observed source region for gravity waves, density perturbations are again not elevated, leaving questions on how gravity waves observed in the lower atmosphere are related to those observed in the thermosphere.
Modelling deep seasonal temperature changes in the Labrador Sea
Authors: Lu Youyu , Wright Daniel G. , Clarke R. Allyn
Published: November 2006

An eddy‐admitting model of the North Atlantic is applied to study the seasonal variations of temperature at 1000 m in the Labrador Sea. The model successfully reproduces the seasonal cycle of the near‐bottom temperature observed from a long‐term mooring deployed on the 1000 m isobath on the upper continental slope off Labrador. It also provides an estimate of the spatial distribution of the seasonal temperature variation in the whole Labrador Sea that can be interpreted in terms of the roles played by surface cooling, deep convection, lateral mixing and advection. The model results suggest that mixing along the steeply sloped isopycnal surfaces plays an important role in communicating the cold water formed by surface cooling to deep layers over the Labrador Slope in later winter. Upstream conditions are also communicated to the mooring site along the Slope through advection by the prevailing cyclonic circulation. In particular, the advection of warm water off Greenland contributes to the gradual warming from spring to winter at the mooring site.
Summer aridity in the United States: Response to mid‐Holocene changes in insolation and sea surface temperature
Authors: Diffenbaugh Noah S. , Ashfaq Moetasim , Shuman Bryan , Williams John W. , Bartlein Patrick J.
Published: November 2006

We examine the response of summer precipitation to mid‐Holocene insolation forcing and insolation‐induced changes in sea surface temperature. Using a high‐resolution nested climate modeling system, we find that mid‐Holocene insolation forcing results in drier‐than‐present conditions over the central continental United States (U.S.) and northern Rocky Mountains, as well as wetter‐than‐present conditions over the Atlantic seaboard and northwestern Great Plains. We find that changes in summer precipitation are dominated by changes in large‐scale processes, with similar patterns of change in the global and nested models. We also find that insolation‐induced changes in sea surface temperature do not change the basic pattern of precipitation response, primarily because the dynamical response is very similar with and without sea surface temperature changes. Notably, drier‐than‐present conditions over the central U.S. are associated with enhanced anticyclonic circulation aloft over the mid‐continent and reduced low‐level moisture content over the Gulf of Mexico and south‐central U.S., while wetter‐than‐present conditions over the Atlantic seaboard are associated with enhanced low‐level cyclonic circulation and elevated low‐level moisture content. The simulated patterns of precipitation and soil moisture agree with proxy moisture records from most regions, indicating both that insolation was the strongest determinant of mid‐Holocene summer aridity in the continental U.S. and that high‐resolution nested climate modeling systems are able to capture the basic response of midlatitude warm‐season aridity to changes in external climate forcing.
Dynamics of ionospheric O+ ions in the magnetosphere during the 24–25 September 1998 magnetic storm
Authors: Peroomian Vahé , El‐Alaoui Mostafa , Abdalla Maha Ashour , Zelenyi Lev M.
Published: November 2006

We have used the time‐dependent electric and magnetic fields obtained from a three‐dimensional global magnetohydrodynamic (MHD) simulation of the magnetosphere and large‐scale kinetic particle tracing to investigate the population of the magnetosphere by O+ ions from the dayside ion fountain during the 24–25 September 1998 magnetic storm. The MHD simulation used WIND data upstream of Earth as input. Ions were launched from both hemispheres on the dayside, and the ion launch rate was dynamically normalized to observations. We found that ionospheric O+ ions had access to the plasma sheet beyond a radial distance of 10 RE before the storm but gained access to the near‐Earth region and partial ring current soon after the storm sudden commencement (SSC). O+ ions already en route to the plasma sheet were accelerated and injected into the region nearly instantaneously after the SSC, resulting in a significant increase in the plasma sheet O+ number and energy densities. Significant changes to the magnetospheric configuration caused by the variations in solar wind dynamic pressure and IMF By and Bz, most notably the two pressure peaks at 000 UT and ∼0140 UT and the southward turning of the IMF at 0140 UT resulted in a relative absence of O+ ions from the magnetotail extending from ∼0140 UT to ∼0300 UT. After 0300 UT, the O+ density in the plasma sheet once again increased to >1 cm−3, and O+ was more abundant in the magnetotail compared even to the period immediately following the storm commencement. Prior to the storm, the average O+ energy density in the plasma sheet and ring current was 0.1–3 keV cm−3 and increased 20–30 keV cm−3 during the main phase of the storm, with peak values reaching 100 keV cm−3, consistent with the observations reported by Nosé et al. (2005).
Particle‐fluid simulation of the auroral current circuit
Authors: Vedin Jörgen , Rönnmark Kjell
Published: November 2006

The incompatibility between stationary kinetic and dynamic fluid descriptions of auroral electron acceleration has been an outstanding problem in space physics for decades. In this study we introduce a new numerical simulation model that provides a unified picture by including electron temperature variations consistent with collisionless kinetic theory in the fluid description. We demonstrate that this new particle‐fluid model can describe the partial reflection of Alfvén waves from the acceleration region, as well as the formation of a field‐aligned potential drop proportional to the upward current. This study also suggests that for example ion dynamics and high‐frequency waves must be added to the model before it properly can describe the return current region. Simulations based on the particle‐fluid concept can be applied to various processes in space physics and astrophysics where strong currents flowing along an inhomogeneous magnetic field will cause temperature increases and field‐aligned electric fields.
Relationship between the high‐latitude electric and magnetic turbulence and the Birkeland field‐aligned currents
Authors: Golovchanskaya I. V. , Ostapenko A. A. , Kozelov B. V.
Published: November 2006

We demonstrate the turbulent properties of the high‐latitude electric and magnetic fluctuations, observed by the low‐altitude polar‐orbiting Dynamic Explorer 2 (DE2) satellite, by means of spectrum analysis and examination of the probability density function (PDF) of the fluctuations. To gain insight into the origin of the underlying turbulence, we calculate turbulent field patterns from DE2 observations under different IMF conditions and compare them with the associated patterns of the Birkeland field‐aligned currents (FACs). A clear similarity of these two groups of distributions suggests a close, perhaps cause and effect relationship between the large‐scale FACs and turbulent fields. This finding gives more evidence for the association of the turbulence under study and discrete auroral features, which are known to arise in the regions of strong background FACs.
Climatologies of nighttime upper thermospheric winds measured by ground‐based Fabry‐Perot interferometers during geomagnetically quiet conditions: 2. High‐latitude circulation and interplanetary magnetic field dependence
Authors: Emmert J. T. , Hernandez G. , Jarvis M. J. , Niciejewski R. J. , Sipler D. P. , Vennerstrom S.
Published: November 2006

We analyze upper thermospheric (∼250 km) nighttime horizontal neutral wind patterns, during geomagnetically quiet (Kp < 3) conditions, over the following locations: South Pole (90°S), Halley (76°S, 27°W), Millstone Hill (43°N, 72°W), Søndre Strømfjord (67°N, 51°W), and Thule (77°N, 68°W). We examine the wind patterns as a function of magnetic local time and latitude, solar cycle, day of year, and the dawn‐dusk and north‐south components of the interplanetary magnetic field (IMF By and Bz). In magnetic coordinates, the quiet time high‐latitude wind patterns are dominated by antisunward flow over the polar cap, with wind speeds that generally increase with increasing solar extreme ultraviolet (EUV) irradiation. The winds are generally stronger during equinox than during winter, particularly over the South Pole in the direction of eastern longitudes. IMF By exerts a strong influence on the wind patterns, particularly in the midnight sector. During winter, By positive winds around midnight in the northern (southern) hemisphere are directed more toward the dusk (dawn) sector, compared to corresponding By negative winds; this behavior is consistent with the By‐dependence of statistical ionospheric convection patterns. The strength of the wind response to By tends to increase with increasing solar EUV irradiation, roughly in proportion to the increased wind speeds. Quiet time By effects are detectable at latitudes as low as that of Millstone Hill (magnetic latitude 53°N). Quiet time Bz effects are negligible except over the magnetic polar cap station of Thule.
Geomagnetic activity dependence of the inner magnetospheric proton distribution: An empirical approach for the 21–25 April 2001 storm
Authors: Milillo A. , Orsini S. , Massetti S. , Mura A.
Published: November 2006

The empirical approach in global modeling the proton distributions of the inner magnetosphere (Orsini et al., 2004) is here applied for a detailed analysis of the 21–25 April 2001 storm. This method, based on comparison of the Milillo et al. (2001) model with local proton spectra, results as a simple and powerful tool for inner magnetospheric studies. In this work we use the Los Alamos National Laboratory proton spectra in order to obtain the time‐evolving model parameters at different magnetic local times (MLT). We compare the model parameters with the geomagnetic indexes as well as with the solar wind data. The final outcome of this study is the analysis of the evolution of the magnetospheric populations during storms. This analysis shows that specific local characteristics of the proton fluxes, as the width of proton spectra, can be interpreted as global plasma distributions tracers. Furthermore, their temporal evolution is recurrent during any storm development, depending on solar wind characteristics. In particular, this study suggests the existence of a MLT‐dependent time delay between the solar wind disturbance arrival and the broadening of the energy spectra of proton fluxes in the inner magnetosphere. Finally, the model shows how the particles convected or injected from the nightside during storm main phase quickly decay or diffuse gaining energy so that the diffused particles play a major role during the recovery phase.
Critical single‐domain/multidomain grain sizes in noninteracting and interacting elongated magnetite particles: Implications for magnetosomes
Authors: Muxworthy Adrian R. , Williams Wyn
Published: November 2006

The critical size for stable single‐domain (SD) behavior has been calculated as a function of grain elongation for magnetite grains using a numerical micromagnetic algorithm. Importantly, for the first time, we consider the contribution of intergrain magnetostatic interactions on the SD/multidomain (MD) critical size (d0). For individual grains our numerical estimates for d0 for elongated grains are lower than that determined by previous analytical and numerical calculations. Nevertheless, the inclusion of magnetostatic interactions into the model was found to increase d0 to values significantly higher than any previously published estimates of d0 for individual grains. Therefore the model calculations show that there is a relatively wide range of grain sizes within which depending on the degree of magnetostatic interactions and elongation, a grain can be either SD or MD. The model results are compared to observations of magnetosomes found in magnetotactic bacteria. The newly calculated upper d0 limit for the interacting grains now accommodates the largest magnetosomes reported in the literature. These large magnetosomes were previously thought to be MD, suggesting that evolutionary processes are highly efficient at optimizing magnetosome grain size and spatial distribution.
Influence of systematic error correction on the temporal behavior of an ocean model
Authors: Drecourt Jean‐Philippe , Haines Keith , Martin Matthew
Published: November 2006

This paper derives an approach to systematic correction of errors in the mean dynamic topography (MDT) used for altimeter data assimilation in ocean circulation models. An a priori error covariance is used to help identify bias in the MDT. The method is then demonstrated in the operational Forecasting Ocean Assimilation Model (FOAM) from the U.K. Met Office. Two independent MDTs are compared: the original MDT currently used in the model and a new product of the European project Gravity and Ocean Circulation in the North Atlantic (GOCINA) which has an a priori error covariance field associated with it. A third MDT is then derived by estimating and correcting the systematic error in the GOCINA MDT using off‐line bias calculations. The results are compared using diagrams that split the traditional root‐mean‐square error (RMSE) in the model sea level into two independent measures, a systematic error and a variable or dynamical error. The dynamical error is a measure of the capacity of the model to represent the temporal variations of the observations, in this case the time‐varying altimetry. It is shown that the dynamic sea level error can be improved by the choice of MDT despite the fact that it is formally independent. In this way it is demonstrated that the bias correction method derived for the MDT also leads to improvement in the forecasting of altimetric sea level anomalies in the FOAM model.
Tidal dynamics in channels: 2. Complex channel networks
Authors: Hill A. E. , Souza A. J.
Published: November 2006

Intricate networks of tidal channels such as those found in fjordic, barrier island, and branching estuarine systems are often at risk from contaminant inputs and can be important as spawning grounds or migration pathways for marine organisms. These intricate systems are rarely spatially resolved in regional‐scale numerical tidal models, and setting up a specific detailed numerical model for the purpose of rapidly assessing the likely tidal behavior of such geometrically complex systems carries a high overhead. Here we describe a straightforward algorithm (implemented in MATLAB) which permits rapid assessment of the linear tidal dynamics in an arbitrarily complex network of tidal channels. The method needs only a minimum of input data, namely, (1) the forcing tidal elevation amplitude and phase at the entrances of those channels directly exposed to the open sea and (2) the length, width, and depth of each channel. The performance of the method is tested against results from the finite element regional‐scale numerical model of Foreman et al. (1993) in the fjordic region of western Canada.
Sampling uncertainty properties of cloud fraction estimates from random transect observations
Authors: van de Poll H. M. , Grubb H. , Astin I.
Published: November 2006

Cloud cover is conventionally estimated from satellite images as the observed fraction of cloudy pixels. Active instruments such as radar and Lidar observe in narrow transects that sample only a small percentage of the area over which the cloud fraction is estimated. As a consequence, the fraction estimate has an associated sampling uncertainty, which usually remains unspecified. This paper extends a Bayesian method of cloud fraction estimation, which also provides an analytical estimate of the sampling error. This method is applied to test the sensitivity of this error to sampling characteristics, such as the number of observed transects and the variability of the underlying cloud field. The dependence of the uncertainty on these characteristics is investigated using synthetic data simulated to have properties closely resembling observations of the spaceborne Lidar NASA‐LITE mission. Results suggest that the variance of the cloud fraction is greatest for medium cloud cover and least when conditions are mostly cloudy or clear. However, there is a bias in the estimation, which is greatest around 25% and 75% cloud cover. The sampling uncertainty is also affected by the mean lengths of clouds and of clear intervals; shorter lengths decrease uncertainty, primarily because there are more cloud observations in a transect of a given length. Uncertainty also falls with increasing number of transects. Therefore a sampling strategy aimed at minimizing the uncertainty in transect derived cloud fraction will have to take into account both the cloud and clear sky length distributions as well as the cloud fraction of the observed field. These conclusions have implications for the design of future satellite missions. This paper describes the first integrated methodology for the analytical assessment of sampling uncertainty in cloud fraction observations from forthcoming spaceborne radar and Lidar missions such as NASA's Calipso and CloudSat.
ISLSCP Initiative II global data sets: Surface boundary conditions and atmospheric forcings for land‐atmosphere studies
Authors: Hall Forrest G. , Brown de Colstoun Eric , Collatz George J. , Landis David , Dirmeyer Paul , Betts Alan , Huffman George J. , Bounoua Lahouari , Meeson Blanche
Published: November 2006

We report herein the publication and evaluation of the International Satellite Land Surface Climatology Project (ISLSCP) Initiative II global interdisciplinary data record. The record consists of 52 data sets, with a common series in the 10‐year period 1985 to 1996. Selected data series extend well beyond this period. All series are coregistered to a common grid and gap‐filled for continuity using uniform procedures. We describe briefly the individual data sets within the collection; provide user guidance; and contrast, compare and evaluate those data sets containing similar parameters (land cover, NDVI, albedo, precipitation and near‐surface meteorology). We also describe the process used to develop the Initiative II collection which involved a broad international scientific community focused on addressing a well‐defined set of carbon, water and energy cycle questions within the context of a specific set of analysis tools. The communities that drove the definition of the Initiative II collection were investigators within the international scientific communities of the Global Energy and Water cycle Experiment, GEWEX, program (http://www.gewex.org/); the International Geosphere/Biosphere Program IGBP (http://www.igbp.kva.se); and the U.S. Global Change Research Program, USGCRP (http://www.usgcrp.gov/). Finally, we report usage statistics based on access and download of files from the ISLSCP Initiative II collection available at http://www.daac.ornl.gov.
A global inventory of stratospheric fluorine in 2004 based on Atmospheric Chemistry Experiment Fourier transform spectrometer (ACE‐FTS) measurements
Authors: Nassar R. , Bernath P. F. , Boone C. D. , McLeod S. D. , Skelton R. , Walker K. A. , Rinsland C. P. , Duchatelet P.
Published: November 2006

Total fluorine (FTOT) in the stratosphere has been determined using Atmospheric Chemistry Experiment Fourier transform spectrometer (ACE‐FTS) measurements of HF, COF2, COClF, CF4, CCl3F (CFC‐11), CCl2F2 (CFC‐12), CHClF2 (HCFC‐22), CCl2FCClF2 (CFC‐113), CH3CClF2 (HCFC‐142b), CH2FCF3 (HFC‐134a), and SF6. The retrieval of HFC‐134a (CH2FCF3) from spaceborne measurements had not been carried out prior to this work. Measurements of these species have been supplemented by data from models to extend the altitude range of the profiles and have also been complemented by estimates of 15 minor fluorine species. Using these data, separate fluorine budgets were determined in five latitude zones (60°–82°N, 30°–60°N, 30°S–30°N, 30°–60°S, and 60°–82°S) by averaging over the period of February 2004 to January 2005 inclusive, when possible. Stratospheric FTOT profiles in each latitude zone are nearly linear, with mean stratospheric FTOT values ranging from 2.50 to 2.59 ppbv (with a 1σ precision of 0.04–0.07 ppbv and an estimated accuracy of 0.15 ppbv) for each zone. The highest mean FTOT value occurred in the tropics, which is qualitatively consistent with increasing levels of stratospheric fluorine and the mean stratospheric circulation pattern.
Aerosol optical properties during the 2004 New England Air Quality Study–Intercontinental Transport and Chemical Transformation: Gulf of Maine surface measurements—Regional and case studies
Authors: Sierau Berko , Covert David S. , Coffman Derek J. , Quinn Patricia K. , Bates Timothy S.
Published: November 2006

We report results from the 2004 New England Air Quality Study–Intercontinental Transport and Chemical Transformation (NEAQS‐ITCT) based on measurements of aerosol optical properties in the marine boundary layer of the Gulf of Maine. The in situ data collected on board the NOAA research vessel Ronald H. Brown includes extensive properties of aerosol scattering coefficient, absorption coefficient, and optical depth at multiple wavelengths in the visible. From these, intensive properties were derived, including the Ångström exponent of scattering, single scattering albedo, and submicrometer fraction of scattering. The optical particle properties were sorted by time and location on the basis of aerosol source regions and air mass back trajectories. The results indicate a large degree of temporal and spatial variability in the observed parameters: up to 80% in the scattering and absorption coefficients, 55% in the Ångström exponent, 16% in the single scattering albedo, and 25% in the submicrometer fraction of scattering. The variability is mainly due to the multitude of aerosol sources and transport pathways in the study area. During NEAQS 2004 the mean scattering coefficients were about 20 to 40% lower than those measured during NEAQS 2002 but showed a similar variability. The mean absorption coefficient for the aerosol during NEAQS 2002 was about 80% larger than that measured during NEAQS 2004. The modal parameters of the volume‐size distributions and refractive index and density of the particles were consistent with the aerosol models used in the MODIS land and ocean aerosol retrieval algorithms.
Comparison of two methods to identify live benthic foraminifera: A test between Rose Bengal and CellTracker Green with implications for stable isotope paleoreconstructions
Authors: Bernhard Joan M. , Ostermann Dorinda R. , Williams David S. , Blanks Jessica K.
Published: November 2006

The conventional method to distinguish live from dead benthic foraminifers uses Rose Bengal, a stain that reacts with both live and dead cytoplasm. CellTracker Green CMFDA is a fluorogenic probe causing live cells to fluoresce after proper incubation. To determine the more accurate viability method, we conducted a direct comparison of Rose Bengal staining with CellTracker Green labeling. Eight multicore tops were analyzed from Florida Margin (SE United States; 248–751 m water depths), near Great Bahama Bank (259–766 m), and off the Carolinas (SE United States; 220 and 920 m). On average, less than half the Rose Bengal–stained foraminifera were actually living when collected. Thus, while Rose Bengal can significantly overestimate abundance, combined analyses of CellTracker Green and Rose Bengal can provide insights on population dynamics and effects of episodic events. Initial stable isotope analyses indicate that the CellTracker Green method does not significantly affect these important paleoceanographic proxies.
Open Standards and Resources in Systems Biology: collaborative scale-up toward virtual life
Authors: Le Novere Nicolas
Published: November 2006

The practise of Systems Biology relies on interfaces. Interfaces between the entities we study: the paradigm moved from a physical object centric view toward a relationship-centric one; interfaces between tools: From the retrieval of the primary data to the fine analysis of a model's behaviour, one uses many tools, more or less well connected; interfaces between individuals: To build any non-trivial mechanistic model requires to merge existing work and gather external expertise.If we want these interfaces to be generic enough to allow for anybody to leverage on existing toolkits, a fundamental requirement is the existence of community-developed well supported standards, but also open resources where to find the "lego" blocks. Over the last half-decade, several efforts have been launched in that direction,whether concerning encoding format, ontologies or databases. Some of them are now well-established in the field and play a significant role to improve its coherence but also to increase the size and the quality of quantitative models.
DARPP-32 is a robust integrator of dopamine and glutamate signals
Authors: Le Novere Nicolas , Fernandez Eric , Schiappa Renaud , Girault Jean-Antoine
Published: November 2006

Integration of neurotransmitter and neuromodulator signals in the striatum plays a central role in the functions and dysfunctions of the basal ganglia. DARPP-32 is a key actor of this integration in the GABAergic medium-size spiny neurons, in particular in response to dopamine and glutamate. When phosphorylated by cAMP-dependent protein kinase (PKA) DARPP-32 inhibits protein phosphatase-1 (PP1), whereas when phosphorylated by cyclin-dependent kinase 5 (CDK5) it inhibits PKA. DARPP-32 is also regulated by casein kinases and by several protein phosphatases. These complex and intricate regulations make simple predictions of DARPP-32 dynamic behaviour virtually impossible. We used detailed quantitative modelling of the regulation of DARPP-32 phosphorylation to improve our understanding of its function. The models included all the combinations of the three best characterized phosphorylation sites of DARPP-32, their regulation by kinases and phosphatases, and the regulation of those enzymes by cAMP and Ca2+ signals. Dynamic simulations allowed to observe the temporal relationships between cAMP and Ca2+ signals. We confirmed that the proposed regulation of protein phosphatase-2A (PP2A) by calcium can account for the observed decrease of Threonine 75 phosphorylation upon glutamate receptor activation. Sensitivity analysis showed that CDK5 activity is a major regulator of the response, as previously suggested. Conversely, the regulation of PP2A by PKA or by calcium, had little effect on the function of DARPP-32 in these conditions. The simulations showed that DARPP-32 is not only a robust signal integrator, but also a coincidence detector, the delay between cAMP and calcium signals affecting the response to the latter. This integration did not depend on the concentration of DARPP-32, while the absolute response on PP1 varied linearly. In silico mutants showed that Ser137 phosphorylation affects the coincidence detector function, and that constitutive phosphorylation in Ser137 transforms DARPP-32 in a quasi-irreversible switch. This work is a first attempt to better understand the complex interactions between cAMP and Ca2+ regulation of DARPP-32. Progressive inclusion of additional components should lead to a realistic model of signalling networks underlying the function of striatal neurons.
Quantum Stratonovich calculus and the quantum Wong-Zakai theorem
Authors: Gough John
Published: November 2006

We extend the Itō-to-Stratonovich analysis or quantum stochastic differential equations, introduced by Gardiner and Collett for emission (creation), absorption (annihilation) processes, to include scattering (conservation) processes. Working within the framework of quantum stochastic calculus, we define Stratonovich calculus as an algebraic modification of the Itō one and give conditions for the existence of Stratonovich time-ordered exponentials. We show that conversion formula for the coefficients has a striking resemblance to Green’s function formulas from standard perturbation theory. We show that the calculus conveniently describes the Markov limit of regular open quantum dynamical systems in much the same way as in the Wong-Zakai approximation theorems of classical stochastic analysis. We extend previous limit results to multiple-dimensions with a proof that makes use of diagrammatic conventions.
Atomic displacement free interfaces and atomic registry in SiO2∕(1×1) Si(100)
Authors: Shaw Justin M. , Herbots N. , Hurst Q. B. , Bradley D. , Culbertson R. J. , Atluri V. , Queeney K. T.
Published: November 2006

We use ion beam analysis to probe the structure and interface of ultrathin thermal oxide films grown on (1×1) Si(100) surfaces prepared using the Herbots-Atluri [U.S. patent No. 6,613,677 (Sept. 2, 2003)] wet chemical clean. We discover that these oxide layers are structurally registered with the substrate lattice with no interfacial structural disorder. Registry of Si atoms is most pronounced along ⟨111⟩ directions relative to the Si substrate, consistent with a β-cristobalite epitaxial phase. This structurally registered phase transitions to an amorphous structure approximately 2nm from the interface.
Prediction of the thermosonic signal from fatigue cracks in metals using vibration damping measurements
Authors: Morbidini Marco , Cawley Peter , Barden Tim , Almond Darryl , Duffour Philippe
Published: November 2006

Thermosonics (also known as ultrasound stimulated thermography or sonic infrared imaging) is a potentially attractive nondestructive testing method for the detection of contacting interface-type defects such as fatigue cracks in metals and delaminations in composites. A high power acoustic horn is typically used to excite a complex vibration field, which causes the defect interfaces to rub and dissipate energy as heat. The resulting local increase in temperature at one of the specimen surfaces can then be measured by an infrared camera. In this study a set of steel beams with fatigue cracks of different depth and variable partial crack opening was tested. Each beam was instrumented with strain gages across the crack and at the back face for the measurement of both the “breathing” behavior of the cracks and the excited vibration. The heat released at the crack was predicted from the measured vibration and an experimental estimate of the additional damping introduced in the specimens by each crack. The cracks were modeled analytically as nonuniform heat sources. Hence the temperature rise expected on the monitoring surface of the specimens could be predicted and compared with the infrared camera measurements. The results show good linear correlation between predictions and measurements, thus validating the prediction algorithm. The relationship between the vibration input and the thermal output will allow, as a longer-term goal, the prediction of the general threshold level of vibration needed for reliable crack detection.
Characterization of terahertz electromagnetic waves from coherent longitudinal optical phonons in GaAs/AlAs multiple quantum wells
Authors: Mizoguchi K. , Mizumoto A. , Nakayama M. , Saito S. , Syouji A. , Sakai K. , Yamamoto N. , Akahane K.
Published: November 2006

The characteristics of terahertz (THz) electromagnetic waves emitted from coherent GaAs-like longitudinal optical (LO) phonons in GaAs/AlAs multiple quantum wells were investigated. It was found that the amplitude of the THz wave from the coherent LO phonon is increased linearly with increasing number of periods of the quantum well. This result demonstrates that the THz wave originates from the superposition of the oscillatory polarization induced by the coherent GaAs-like LO phonon in each quantum-well layer. The amplitude of the THz wave is proportional to the excitation-power density below about 0.4 μJ∕cm2, and its radiation power reaches about 1 μW at the excitation-power density of 2 μJ∕cm2. Moreover, the amplitude of the THz wave shows a sinusoidal change with the polarization angle of the pump pulse. These results indicate that the coherent LO phonon emitting the THz wave is generated through the combination of the following two mechanisms: impulsive stimulated Raman scattering and instantaneous screening of the surface electric field.
The Hall dynamo effect and nonlinear mode coupling during sawtooth magnetic reconnection
Authors: Ding W. X. , Brower D. L. , Deng B. H. , Almagri A. F. , Craig D. , Fiksel G. , Mirnov V. , Prager S. C. , Sarff J. S. , Svidzinski V.
Published: November 2006

During magnetic reconnection associated with sawtooth activity in a reversed field pinch, we observe a large fluctuation-induced Hall electromotive force, ⟨δJ×δB⟩∕nee, which is capable of modifying the equilibrium current. This Hall dynamo effect is determined in the hot plasma core by laser Faraday rotation which measures equilibrium and fluctuating magnetic field and current density. We find that the Hall dynamo is strongest when nonlinear mode coupling between three spatial Fourier modes of the resistive tearing instability is present. Mode coupling alters the phase relation between magnetic and current density fluctuations for individual Fourier modes leading to a finite Hall effect. Detailed measurements of the spatial and temporal dynamics for the dominant core resonant mode under various plasma configurations are described providing evidence regarding the origin of the Hall dynamo.
Focused ion beam induced deflections of freestanding thin films
Authors: Kim Y.-R. , Chen P. , Aziz M. J. , Branton D. , Vlassak J. J.
Published: December 2006

Prominent deflections are shown to occur in freestanding silicon nitride thin membranes when exposed to a 50keV gallium focused ion beam for ion doses between 1014 and 1017ions∕cm2. Atomic force microscope topographs were used to quantify elevations on the irradiated side and corresponding depressions of comparable magnitude on the back side, thus indicating that what at first appeared to be protrusions are actually the result of membrane deflections. The shape in high-stress silicon nitride is remarkably flat-topped and differs from that in low-stress silicon nitride. Ion beam induced biaxial compressive stress generation, which is a known deformation mechanism for other amorphous materials at higher ion energies, is hypothesized to be the origin of the deflection. A continuum mechanical model based on this assumption convincingly reproduces the profiles for both low-stress and high-stress membranes and provides a family of unusual shapes that can be created by deflection of freestanding thin films under beam irradiation.
Isomolar-semigrand ensemble molecular dynamics: Application to vapor-liquid equilibrium of the mixture methane/ethane
Authors: Morrow Timothy I. , Maginn Edward J.
Published: November 2006

The isomolar-semigrand ensemble molecular dynamics (iSGMD) method is applied to the simulation of the binary system methane/ethane. The vapor-liquid equilibrium properties of this system at a temperature of 192.37K are computed using the Gibbs-Duhem integration method. The iSGMD method, which resembles conventional hybrid Monte Carlo (MC) but is applicable to phase equilibrium calculations, is designed to overcome the difficulties associated with performing standard Monte Carlo-type particle transformations in liquid systems that are very dense and/or are comprised of complex molecules with many intramolecular degrees of freedom. This work shows that particle transformations using the iSGMD method for the simple system methane/ethane are at least 25 times more successful than standard MC-type transformations. The P-x-y curve for the system methane/ethane at 192.37K computed using iSGMD simulations agrees very well with the experimental P-x-y curve as well as results of a previous MC study.
Effect of catalyst oxidation on the growth of carbon nanotubes by thermal chemical vapor deposition
Authors: Sato Hideki , Hori Yasunori , Hata Koichi , Seko Kazuyuki , Nakahara Hitoshi , Saito Yahachi
Published: December 2006

We report a heat treatment of catalyst in air that drastically enhances a growth of carbon nanotubes (CNTs) by means of thermal chemical vapor deposition (CVD). An Fe catalyst film deposited on a Si substrate was heat treated at 700°C in air before the acetylene CVD. The growth rate of the CNTs grown with the heat treatment was more than seven times higher than that of growth without the heat treatment. A scanning electron microscopy observation showed that the heat treatment in air promotes a granulation of the Fe catalyst. X-ray photoelectron spectroscopy and reflection high energy electron diffraction analyses showed that the heat treatment in air promotes an oxidation of the catalyst film and formation of Fe2O3 nanoparticles, suggesting that the heat treatment of Fe catalyst in air prevented the formation of Fe silicide that would deactivate the catalyst effect of Fe. The Fe2O3 nanoparticles do not agglomerate and can keep their original particles size. Thus the catalyst can maintain a catalyst activity during CNTs growth and, as a result, gives a growth enhancement of CNTs.
Asymmetric C13–C13 polarization transfer under dipolar-assisted rotational resonance in magic-angle spinning NMR
Authors: Ohashi Ryutaro , Takegoshi K.
Published: December 2006

A two-dimensional (2D) homonuclear exchange NMR spectrum in solids often shows an asymmetric cross-peak pattern, which disturbs a quantitative analysis of peak intensities. When magnetization is prepared using cross polarization (CP), the asymmetry can naively be ascribed to nonequilibrium initial magnetization. We show, however, that the CP effect cannot fully explain the observed mixing-time dependence of the peak intensities in 2D C13–C13 exchange spectra of [2,3-C13] l-alanine (2,3-Ala) under C13–H1 dipolar-assisted rotational resonance (DARR) recoupling, which has recently been proposed for a broadband recoupling method under magic-angle spinning. We develop a theory to describe polarization transfer in a two-spin system under DARR recoupling. By taking into account the effects of the partial spectral overlap among C13 signals, which is a unique feature of DARR recoupling, and H1–H1 flip-flop exchange, we can successfully explain the observed mixing-time dependence of the peak intensities of 2D C13–C13 DARR exchange spectra of 2,3-Ala. A simple initial-rate analysis is also examined.
Vortex state and effect of anisotropy in sub-100-nm magnetic nanodots
Authors: Mejía-López J. , Altbir D. , Romero A. H. , Batlle X. , Roshchin Igor V. , Li Chang-Peng , Schuller Ivan K.
Published: November 2006

Magnetic properties of Fe nanodots are simulated using a scaling technique and Monte Carlo method, in good agreement with experimental results. For the 20-nm-thick dots with diameters larger than 60nm, the magnetization reversal via vortex state is observed. The role of magnetic interaction between dots in arrays in the reversal process is studied as a function of nanometric center-to-center distance. When this distance is more than twice the dot diameter, the interaction can be neglected and the magnetic properties of the entire array are determined by the magnetic configuration of the individual dots. The effect of crystalline anisotropy on the vortex state is investigated. For arrays of noninteracting dots, the anisotropy strongly affects the vortex nucleation field and coercivity, and only slightly affects the vortex annihilation field.
Photoreflectance determination of the wetting layer thickness in the InxGa1−xAs∕GaAs quantum dot system for a broad indium content range of 0.3–1
Authors: Sęk G. , Poloczek P. , Ryczko K. , Misiewicz J. , Löffler A. , Reithmaier J. P. , Forchel A.
Published: November 2006

We have investigated a set of InxGa1−xAs∕GaAs quantum dot structures grown by solid source molecular beam epitaxy for a wide range of In content ranging from 30% to pure InAs∕GaAs dots. It is well known that in a self-assembled growth mode, the dots are formed on a thin layer of the InxGa1−xAs material, which is called wetting layer (WL). The WL thickness is driven by the strain, i.e., lattice mismatch between the layer and substrate materials. Usually, the WL quantum well is not optically active in emission type of experiments (the whole radiative recombination goes through the dot states) and even if so, the heavy hole ground state transition is probed only. In order to detect all the possible transitions, e.g., transitions related to light hole and possible higher order heavy hole states (including those transitions, which are nominally parity forbidden), we have used modulation spectroscopy in a form of photomodulated reflectivity measurements. This is an absorptionlike method, which has been proven to be highly sensitive to even very low intensity transitions in low-dimensional semiconductor structures. The aim of this work is to determine in a contactless optical manner the thickness of the wetting layer as a function of indium content starting with very low content and low-strain structures (at the limit of self-assembled dot creation) up to typical InAs dots on gallium arsenide with the effective wetting layer as thin as 1.5 ML. The observed optical transitions have been identified based on energy level calculations for thin rectangular wells and using effective mass approximation in an envelope function approach in which the well width has been treated as a fitting parameter to the experimental data.