bluuebunny/crossref_metadata_2025 huggingface dataset:
Wildfowl of Islay
Authors: Ogilvie M. A.
Published: July 2012

Synopsis

The island of Islay posssesses by far the largest population of wintering wildflowl in the Inner Hebrides; there are 18,000-20,000 barnacle geese Branta leucopsis and 4,000 Greenland white-fronted geese Anser albifrons jiavirostris. There is also a small flock of greylag geese A. anser. Most of the commoner dabbling and diving ducks spend the winter in small numbers, with a flock of 1,000 scaup Aythya marila the most important. A few hundred pairs of eider Somateria mollissima breed, and up to 3,000 wintering or moulting birds have occurred offshore. Other breeding duck are few in number, including up to five pairs of common scoter Melanitta nigra. Whooper swans Cygnus cygnus spent the winter in the past but are now common on passage only. Barnacle geese have trebled in numbers in the last twenty years, leading to complaints of agricultural damage, and a subsequent increase in shooting and disturbance followed by a recent decline in numbers. Annual data on populations, productivity and losses are presented. Greenland white-fronted geese have varied less in numbers, but shooting has increased and the situation is reviewed. All other wildfowl occurring on the island are dealt with briefly.
Forests of the Inner Hebrides—status and habitat
Authors: Bramwell A. G. , Cowie G. M.
Published: July 2012

Synopsis

Forestry development in the Inner Hebrides is largely confined to Islay, Jura, Mull, Skye, Raasay and Scalpay. Tue value of the forest industry is highlighted in producing a raw material for industry, providing employment and supporting the island infrastructure. Factors such as exposure, degraded soils and problems of marketing which force the forester to limit the choice of species to a few hardy saleable species are also described. Established consultation procedures are preserving the essential interests of competing land users by the rational apportionment of land to various uses and by good forest design. Creation of diversity in commercial plantations which is essential for habitat improvement by both natural means and modern management practices is described.

A checklist of vertebrate fauna which frequent these new forests is provided together with an assessment of their status.
Introduction: Opportunities, Artifacts, and Interpretation of Aberration-Corrected Electron Microscopy Data
Authors: Batson Phil , Smith Dave
Published: July 2012

A one-day pre-meeting workshop was held on August 7, 2011, immediately preceding the annual Microscopy and Microanalysis (M&M) 2011 meeting in Nashville, Tennessee. The workshop was organized by the Aberration-Corrected Electron Microscopy (ACEM) Focused Interest Group, with an Organizing Committee consisting of Phil Batson, Dave Muller, Larry Allard, Paul Voyles, Miofang Chi, and Mike O'Keefe.
Measurements of regional‐scale aerosol impacts on cloud microphysics over the East China Sea: Possible influences of warm sea surface temperature over the Kuroshio ocean current
Authors: Koike M. , Takegawa N. , Moteki N. , Kondo Y. , Nakamura H. , Kita K. , Matsui H. , Oshima N. , Kajino M. , Nakajima T. Y.
Published: July 2012

Cloud microphysical properties and aerosol concentrations were measured aboard an aircraft over the East China Sea and Yellow Sea in April 2009 during the Aerosol Radiative Forcing in East Asia (A‐FORCE) experiment. We sampled stratocumulus and shallow cumulus clouds over the ocean in 9 cases during 7 flights 500–900 km off the east coast of Mainland China. In this study we report aerosol impacts on cloud microphysical properties by focusing on regional characteristics of two key parameters, namely updraft velocity and aerosol size distribution. First, we show that the cloud droplet number concentration (highest 5%, Nc_max) correlates well with the accumulation‐mode aerosol number concentration (Na) below the clouds. We then show that Nc_maxcorrelates partly with near‐surface stratification evaluated as the difference between the sea surface temperature (SST) and 950‐hPa temperature (SST − T950). Cold air advection from China to the East China Sea was found to bring not only a large number of aerosols but also a dry and cold air mass that destabilized the atmospheric boundary layer, especially over the warm Kuroshio ocean current. Over this high‐SST region, greater updraft velocities and hence greater Nc_maxlikely resulted. We hypothesize that the low‐level static stability determined by SST and regional‐scale airflow modulates both the cloud microphysics (aerosol impact on clouds) and macro‐structure of clouds (cloud base and top altitudes, hence cloud liquid water path). Second, we show that not only higher aerosol loading in terms of total aerosol number concentration (NCN, D > 10 nm) but also larger aerosol mode diameters likely contributed to high Ncduring A‐FORCE. The mean Nc of 650 ± 240 cm−3was more than a factor of 2 larger than the global average for clouds influenced by continental sources. A crude estimate of the aerosol‐induced cloud albedo radiative forcing is also given.
Radiative forcing by light absorbing impurities in snow from MODIS surface reflectance data
Authors: Painter Thomas H. , Bryant Ann C. , Skiles S. McKenzie
Published: July 2012

The episodic deposition of dust and carbonaceous particles to snow decreases snow surface albedo and enhances absorption of solar radiation, leading to accelerated snowmelt, negative glacier mass balance, and the snow‐albedo feedback. Until now, no remote sensing retrieval has captured the spatial and temporal variability of this forcing. Here we present the MODIS Dust Radiative Forcing in Snow (MODDRFS) model that retrieves surface radiative forcing by light absorbing impurities in snow cover from Moderate Resolution Imaging Spectroradiometer (MODIS) surface reflectance data. Validation of MODDRFS with a 7‐year record of in situ measurements indicates the radiative forcing retrieval has positive bias at lower values and slight negative bias above 200 W m−2, subject to mixed pixel uncertainties. With bias‐correction, MODDRFS has a root mean squared error of 32 W m−2 and mean absolute error of 25 W m−2. We demonstrate MODDRFS in the Upper Colorado River Basin and Hindu Kush‐Himalaya.
Numerical modeling of the Mount Steller landslide flow history and of the generated long period seismic waves
Authors: Moretti L. , Mangeney A. , Capdeville Y. , Stutzmann E. , Huggel C. , Schneider D. , Bouchut F.
Published: July 2012

The rock‐ice avalanche that occurred in 2005 on Mount Steller, Alaska and the resulting long period seismic waves have been simulated for different avalanche scenarios (i.e., flow histories), with and without erosion processes taken into account. This 40–60 Mm3avalanche traveled about 10 km down the slope, mainly on top of a glacier, eroding a significant amount of ice. It was recorded by 7 broadband seismic stations. The simulations were compared with the recorded long period seismic signal and with the inverted flow history. The results show that, when erosion processes are taken into account, the simulations reproduce the observed signal at all the stations over a wide range of azimuths and source‐station distances (37–623 km). This comparison makes it possible to constrain the rheological parameters involved which should help constrain the volume of eroded material. Because landslides are continuously recorded by seismic networks, this method could significantly broaden quantitative insights into natural flow dynamics.
Aviation induced diurnal North Atlantic cirrus cover cycle
Authors: Graf Kaspar , Schumann Ulrich , Mannstein Hermann , Mayer Bernhard
Published: July 2012

Aviation induced cirrus (AIC) cover is identified from mean diurnal cycles of cirrus cover and air traffic density in the North Atlantic flight corridor. Traffic data for this region show an aviation “fingerprint” with two maxima during morning eastbound and afternoon westbound traffic. The same aviation fingerprint is found in cirrus cover. Cycle differences between west and east domain parts allow separating between aviation and natural diurnal changes. Cirrus cover is derived from 8 years of Meteosat infrared data. Linear contrail cover is estimated from the same data. Background cirrus without aviation impact is estimated from cirrus observations over the South Atlantic and from numerical weather prediction forecast. The cirrus cover cycle is well approximated by linear response to traffic density with fitted delay times of 2.3–4.1 h, implying AIC cover of 1–2%, more than expected from recent models.
The impact of the Indonesian Throughflow and tidal mixing on the summertime sea surface temperature in the western Indonesian Seas
Authors: Kida Shinichiro , Wijffels Susan
Published: July 2012

A numerical model is used to investigate how the Indonesian Throughflow and tidal mixing are affecting the seasonal cycle of the sea surface temperature (SST) in the Indonesian Seas. The SST in these seas is considered to play a major role on the development of the Australian Summer Monsoon. Based on a quantitative assessment of the heat budget, the Indonesian Throughflow is found to affect the SST in the western Indonesian Seas primarily during Austral summer. The Throughflow advects the warm water from the Pacific and maintains the warm SST when the Northwestern Monsoonal wind induces coastal upwelling along the northern side of the Nusa Tenggara and cools the SST. Such balance is supported by observations. The hydrographic sections show the isotherms tilting upward toward the northern coast of the Nusa Tenggara when satellite observations show slight decrease of the SST in the region. Tidal mixing is found to cool the SST during summer the most. This is because the Northwest Monsoonal wind induces coastal upwelling near where strong tidal mixing above seamount occurs and brings the tidally well‐mixed upper thermocline water to the surface. The surface Ekman flow also spreads this cool water around the Banda Sea where tidal mixing does not occur. The impact of tidal mixing on the SST is also found to come largely from that occurring above seamounts. The impact of tidal mixing on the continental shelves is limited to shelf‐breaks because cold subsurface water is necessary for enhanced vertical mixing to cool the SST.
Analyses of BlueSky Gateway PM2.5 predictions during the 2007 southern and 2008 northern California fires
Authors: Strand Tara M. , Larkin Narasimham , Craig Kenneth J. , Raffuse Sean , Sullivan Dana , Solomon Robert , Rorig Miriam , Wheeler Neil , Pryden Daniel
Published: July 2012

We evaluated predictions of hourly PM2.5surface concentrations produced by the experimental BlueSky Gateway air quality modeling system during two wildfire episodes in southern California (Case 1) and northern California (Case 2). In southern California, the prediction performance was dominated by the prevailing synoptic weather patterns, which differentiated the smoke plumes into two types: narrow and highly concentrated during an offshore flow, and diluted and well‐mixed during a light onshore flow. For the northern California fires, the prediction performance was dominated by terrain and the limitations of predicting concentrations in a narrow valley, rather than by the synoptic pattern, which did not differ much throughout the wildfire episode. There was an over‐prediction bias for the maximum values during this episode. When the predicted values were compared to observed values, the best performance results were for the onshore flow during the southern California fires, indicating that the coarse grid used by BlueSky Gateway appropriately represented these well‐mixed conditions. Overall, the southern California fire predictions were biased low and the model did not reproduce the high hourly concentrations (>240μg/m3) observed by the monitors. The predicted results performed well against the observations for the northern California fires, with a large number of predicted values within acceptable range of the observed values.
Geogenic and atmospheric sources for volatile organic compounds in fumarolic emissions from Mt. Etna and Vulcano Island (Sicily, Italy)
Authors: Tassi F. , Capecchiacci F. , Cabassi J. , Calabrese S. , Vaselli O. , Rouwet D. , Pecoraino G. , Chiodini G.
Published: July 2012

In this paper, fluid source(s) and processes controlling the chemical composition of volatile organic compounds (VOCs) in gas discharges from Mt. Etna and Vulcano Island (Sicily, Italy) were investigated. The main composition of the Etnean and Volcano gas emissions is produced by mixing, to various degrees, of magmatic and hydrothermal components. VOCs are dominated by alkanes, alkenes and aromatics, with minor, though significant, concentrations of O‐, S‐ and Cl(F)‐substituted compounds. The main mechanism for the production of alkanes is likely related to pyrolysis of organic‐matter‐bearing sediments that interact with the ascending magmatic fluids. Alkanes are then converted to alkene and aromatic compounds via catalytic reactions (dehydrogenation and dehydroaromatization, respectively). Nevertheless, an abiogenic origin for the light hydrocarbons cannot be ruled out. Oxidative processes of hydrocarbons at relatively high temperatures and oxidizing conditions, typical of these volcanic‐hydrothermal fluids, may explain the production of alcohols, esters, aldehydes, as well as O‐ and S‐bearing heterocycles. By comparing the concentrations of hydrochlorofluorocarbons (HCFCs) in the fumarolic discharges with respect to those of background air, it is possible to highlight that they have a geogenic origin likely due to halogenation of both methane and alkenes. Finally, chlorofluorocarbon (CFC) abundances appear to be consistent with background air, although the strong air contamination that affects the Mt. Etna fumaroles may mask a possible geogenic contribution for these compounds. On the other hand, no CFCs were detected in the Vulcano gases, which are characterized by low air contribution. Nevertheless, a geogenic source for these compounds cannot be excluded on the basis of the present data.
Future changes and uncertainties in Asian precipitation simulated by multiphysics and multi–sea surface temperature ensemble experiments with high‐resolution Meteorological Research Institute atmospheric general circulation models (MRI‐AGCMs)
Authors: Endo Hirokazu , Kitoh Akio , Ose Tomoaki , Mizuta Ryo , Kusunoki Shoji
Published: July 2012

This study focuses on projecting future changes in mean and extreme precipitation in Asia, and discusses their uncertainties. Time‐slice experiments using a 20‐km‐mesh atmospheric general circulation (AGCM) were performed both in the present‐day (1979–2003) and the future (2075–2099). To assess the uncertainty of the projections, 12 ensemble projections (i.e., combination of 3 different cumulus schemes and 4 different sea surface temperature (SST) change patterns) were conducted using 60‐km‐mesh AGCMs. For the present‐day simulations, the models successfully reproduced the pattern and amount of mean and extreme precipitation, although the model with the Arakawa–Schubert (AS) cumulus scheme underestimated the amount of extreme precipitation. For the future climate simulations, in South Asia and Southeast Asia, mean and extreme precipitation generally increase, but their changes show marked differences among the projections, suggesting some uncertainty in their changes over these regions. In East Asia, northwestern China and Bangladesh, in contrast, mean and extreme precipitation show consistent increases among the projections, suggesting their increases are reliable for this model framework. Further investigation by analysis of variance (ANOVA) revealed that the uncertainty in the precipitation changes in South Asia and Southeast Asia are derived mainly from differences in the cumulus schemes, with an exception in the Maritime Continent where the uncertainty originates mainly from the differences in the SST pattern.
A probabilistic description of the bed load sediment flux: 3. The particle velocity distribution and the diffusive flux
Authors: Furbish David Jon , Roseberry John C. , Schmeeckle Mark W.
Published: July 2012

Particles transported as bed load within a specified streambed area possess at any instant a distribution of velocities. This distribution figures prominently in describing the rates of transport and dispersal of particles. High‐speed imaging of sand particles transported as bed load over a planar bed reveals that the probability density functions of the streamwise and cross‐stream particle velocities are exponential‐like. For quasi‐steady conditions the exponential‐like density of streamwise velocities reflects a balance among three fluxes in momentum space: (1) an advection of streamwise momentum whose magnitude and sign vary with the momentum state; (2) a diffusion of momentum from higher to lower values of momentum density; and (3) a drift of momentum from regions in momentum space having high average rates of generation of kinetic energy toward regions having low rates of generation of kinetic energy. The probability density of cross‐stream velocities similarly reflects a balance of fluxes of cross‐stream momentum. Whereas the average net force acting on particles is zero under steady conditions, the mean, variance and asymmetry of the distribution of forces acting on particles vary with the momentum state of the particles. Numerical simulations of particle motions that are faithful to these statistical properties reproduce key empirical results, namely, the exponential‐like velocity distribution and the nonlinear relation between hop distances and travel times. The simulations also illustrate how steady gradients in particle activity, the solid volume of particles in motion per unit streambed area, induce a diffusive flux as described in companion papers.
Changes in the intermediate water mass formation rates in the global ocean for the Last Glacial Maximum, mid‐Holocene and pre‐industrial climates
Authors: Wainer I. , Goes M. , Murphy L. N. , Brady E.
Published: July 2012

The paleoclimate version of the National Center for Atmospheric Research Community Climate System Model version 3 (NCAR‐CCSM3) is used to analyze changes in the water formation rates in the Atlantic, Pacific, and Indian Oceans for the Last Glacial Maximum (LGM), mid‐Holocene (MH) and pre‐industrial (PI) control climate. During the MH, CCSM3 exhibits a north‐south asymmetric response of intermediate water subduction changes in the Atlantic Ocean, with a reduction of 2 Sv in the North Atlantic and an increase of 2 Sv in the South Atlantic relative to PI. During the LGM, there is increased formation of intermediate water and a more stagnant deep ocean in the North Pacific. The production of North Atlantic Deep Water (NADW) is significantly weakened. The NADW is replaced in large extent by enhanced Antarctic Intermediate Water (AAIW), Glacial North Atlantic Intermediate Water (GNAIW), and also by an intensified of Antarctic Bottom Water (AABW), with the latter being a response to the enhanced salinity and ice formation around Antarctica. Most of the LGM intermediate/mode water is formed at 27.4 <σθ < 29.0 kg/m3, while for the MH and PI most of the subduction transport occurs at 26.5 < σθ < 27.4 kg/m3. The simulated LGM Southern Hemisphere winds are more intense by 0.2–0.4 dyne/cm2. Consequently, increased Ekman transport drives the production of intermediate water (low salinity) at a larger rate and at higher densities when compared to the other climatic periods.
TEC ingestion into NeQuick 2 to model the East African equatorial ionosphere
Authors: Nigussie M. , Radicella S. M. , Damtie B. , Nava B. , Yizengaw E. , Ciraolo L.
Published: July 2012

NeQuick 2 ionospheric empirical model depends on global ionospheric coefficients that are estimated from unevenly distributed ionosonde measurements. In regions, like Africa, where very few observational data were available until recently, the model estimated the ionospheric peak parameters by interpolation. When one wants to employ the model to specify the ionosphere where very few data have been used for model development, the performances of the model need careful validation. This study investigates the performances of NeQuick 2 in the East African region by assisting the model with measurements from a single Global Positioning System (GPS) receiver, which has been deployed recently. This can be done by first calculating an effective ionization level that drives NeQuick 2 to compute slant total electron content (sTEC) which fits, in the least square sense, with the measurements taken from a single GPS receiver. We then quantify the performances of NeQuick 2 in reproducing the measured TEC by running the model at four other locations, where GPS stations are available, using the same effective ionization level that we calculated from a single GPS station as a driver of the model. Finally, the performances of the model before and after data ingestion have been investigated by comparing the model results with the experimental sTEC and vertical TEC (vTEC) obtained from the four test stations. Three months data during low solar activity conditions have been used for this study. We have shown that the capability of NeQuick 2, in describing the East African region of the ionosphere, can be improved substantially by data ingestion. We found that the model after ingestion reproduces the experimental TEC better as far as about 620 km away from the reference station than that before adaptation. The statistical comparisons of the performances of the model in reproducing sTEC before and after ingestion are also discussed in this study.
Substrate binds in the S1 site of the F253A mutant of LeuT, a neurotransmitter sodium symporter homologue
Authors: Wang Hui , Gouaux Eric
Published: July 2012

LeuT serves as the model protein for understanding the relationships between structure, mechanism and pharmacology in neurotransmitter sodium symporters (NSSs). At the present time, however, there is a vigorous debate over whether there is a single high‐affinity substrate site (S1) located at the original, crystallographically determined substrate site or whether there are two high‐affinity substrates sites, one at the primary or S1 site and the other at a second site (S2) located at the base of the extracellular vestibule. In an effort to address the controversy over the number of high‐affinity substrate sites in LeuT, one group studied the F253A mutant of LeuT and asserted that in this mutant substrate binds exclusively to the S2 site and that 1 mM clomipramine entirely ablates substrate binding to the S2 site. Here we study the binding of substrate to the F253A mutant of LeuT using ligand binding and X‐ray crystallographic methods. Both experimental methods unambiguously show that substrate binds to the S1 site of the F253A mutant and that binding is retained in the presence of 1 mM clomipramine. These studies, in combination with previous work, are consistent with a mechanism for LeuT that involves a single high‐affinity substrate binding site.
NEDDylation regulates E2F‐1‐dependent transcription
Authors: Loftus Sarah J , Liu Geng , Carr Simon M , Munro Shonagh , La Thangue Nicholas B
Published: July 2012

The ubiquitin‐like molecule NEDD8 modifies cullin‐RING ubiquitin E3 ligases. NEDD8 has been shown to have a few additional substrates, but the extent to which this modification targets non‐cullins and the functional significance of such modifications remain unclear. Here, we demonstrate that the cell‐cycle‐regulating transcription factor E2F‐1 is a substrate for NEDD8 post‐translational modification. NEDDylation results in decreased E2F‐1 stability, lower transcriptional activity and slower cell growth. The lysine residues in E2F‐1 targeted for NEDDylation can also be methylated, pointing to a possible interplay between these modifications. These results identify a new mode of E2F‐1 regulation and highlight the emerging role of NEDD8 in regulating transcription factor stability and function.
Cardiovascular disease is associated with high-fat-diet-induced liver damage and up-regulation of the hepatic expression of hypoxia-inducible factor 1α in a rat model
Authors: Burgueño Adriana L. , Gianotti Tomas F. , Mansilla Noelia G. , Pirola Carlos J. , Sookoian Silvia
Published: July 2012

CVD (cardiovascular disease) is associated with abnormal liver enzymes, and NAFLD (non-alcoholic fatty liver disease) is independently associated with cardiovascular risk. To gain insights into the molecular events underlying the association between liver enzymes and CVD, we developed an HFD (high-fat diet)-induced NAFLD in the SHR (spontaneously hypertensive rat) and its control WKY (Wistar–Kyoto) rat strain. We hypothesized that hepatic induction of Hif1a (hypoxia-inducible factor 1α) might be the link between CVD and liver injury. Male SHRs (n=13) and WKY rats (n=14) at 16 weeks of age were divided into two experimental groups: standard chow diet and HFD (10 weeks). HFD-fed rats, irrespective of the strain, developed NAFLD; however, only HFD-SHRs had focus of lobular inflammation and high levels of hepatic TNFα (tumour necrosis factor α). SHRs had significantly higher liver weight and ALT (alanine aminotransferase) levels, irrespective of NAFLD. Liver abundance of Hif1a mRNA and Hif1α protein were overexpressed in SHRs (P<0.04) and were significantly correlated with ALT levels (R=0.50, P<0.006). This effect was not reverted by a direct acting splanchnic vasodilator (hydralazine). Angiogenesis may be induced by the HFD, but the disease model showed significantly higher hepatic Vegf (vascular endothelial growth factor) levels (P<0.025) even in absence of dietary insult. Hif1a mRNA overexpression was not observed in other tissues. Liver mRNA of Nr1d1 (nuclear receptor subfamily 1, group D, member 1; P<0.04), Ppara [Ppar (peroxisome-proliferatoractivated receptor) α; P<0.05], Pparg (Pparγ; P<0.001) and Sirt1 (Sirtuin 1; P<0.001) were significantly upregulated in SHRs, irrespective of NAFLD. Sirt1 and Hif1a mRNAs were significantly correlated (R=0.71, P<0.00002). In conclusion, CVD is associated with Hif1a-related liver damage, hepatomegaly and reprogramming of liver metabolism, probably to compensate metabolic demands.
Ameloblastic Carcinoma of the Maxilla with Extension into the Ethmoidal Air Cells and Close Proximity to the Anterior Skull Base: A Rare Case Presentation
Authors: Perumal Colin J.
Published: July 2012

A case of an ameloblastic carcinoma with extension to the anterior skull base as a result of prolonged misdiagnosis is being presented. Radical surgery and radiotherapy was performed due to involvement of the ethmoidal air sinuses and close proximity to the cranial fossa. Diagnostic tests showed no evidence of metastasis. The patient was treated with surgery, adjuvant radiotherapy, and prosthetic rehabilitation.
Free Flap Reconstruction for Complex Scalp and Forehead Defects with Associated Full-Thickness Calvarial Bone Resections
Authors: Larrañaga Juan , Rios Alfredo , Franciosi Edgardo , Mazzaro Eduardo , Figari Marcelo
Published: July 2012

Extensive defects of the scalp and forehead associated with calvarial bone resections demand complex reconstructions. Free flaps offer vascularized tissue of excellent quality and quantity. We report six patients with extensive scalp and forehead defects associated with calvarial bone resections reconstructed with free flaps. Five patients also required a cranioplasty. The flaps used were two anterolateral thigh flaps, one vastus lateralis flap, one myocutaneous latissimus dorsi flap, one latissimus dorsi flap, and one radial forearm flap. All flaps survived with no partial necrosis. There were no donor site complications. One patient presented an exposure of the alloplastic material used for cranioplasty. We strongly recommend the use of free flaps for this kind of reconstruction.
High bandwidth differential amplifier for shock experiments
Authors: Ross P. W. , Tran V. , Chau R.
Published: July 2012

We developed a high bandwidth differential amplifier for gas gun shock experiments of low-resistance metals. The circuit has a bandwidth up to 1 GHz, and is capable of measuring signals of ≤1.5 V with a common mode rejection of 250 V. Conductivity measurements of gas gun targets are measured by flowing high currents through the targets. The voltage is measured across the target using a technique similar to a four-point probe. Because of the design of the current source and load, the target voltage is ∼250 V relative to ground. Since the expected voltage change in the target is <1 V, the differential amplifier must have a large common mode rejection. Various amplifying designs are shown, although the increased amplification decreases bandwidth. Bench tests show that the amplifier can withstand significant common mode dc voltage and measure 10 ns, and 50 mV signals.
Structure and dynamics of water in nonionic reverse micelles: A combined time-resolved infrared and small angle x-ray scattering study
Authors: van der Loop Tibert H. , Panman Matthijs R. , Lotze Stephan , Zhang Jing , Vad Thomas , Bakker Huib J. , Sager Wiebke F. C. , Woutersen Sander
Published: July 2012

We study the structure and reorientation dynamics of nanometer-sized water droplets inside nonionic reverse micelles (water/Igepal-CO-520/cyclohexane) with time-resolved mid-infrared pump-probe spectroscopy and small angle x-ray scattering. In the time-resolved experiments, we probe the vibrational and orientational dynamics of the O-D bonds of dilute HDO:H2O mixtures in Igepal reverse micelles as a function of temperature and micelle size. We find that even small micelles contain a large fraction of water that reorients at the same rate as water in the bulk, which indicates that the polyethylene oxide chains of the surfactant do not penetrate into the water volume. We also observe that the confinement affects the reorientation dynamics of only the first hydration layer. From the temperature dependent surface-water dynamics, we estimate an activation enthalpy for reorientation of 45 ± 9 kJ mol−1 (11 ± 2 kcal mol−1), which is close to the activation energy of the reorientation of water molecules in ice.
Direct dynamics simulation of dioxetane formation and decomposition via the singlet ·O–O–CH2–CH2· biradical: Non-RRKM dynamics
Authors: Sun Rui , Park Kyoyeon , de Jong Wibe A. , Lischka Hans , Windus Theresa L. , Hase William L.
Published: July 2012

Electronic structure calculations and direct chemical dynamics simulations are used to study the formation and decomposition of dioxetane on its ground state singlet potential energy surface. The stationary points for 1O2 + C2H4, the singlet ·O–O–CH2–CH2· biradical, the transition state (TS) connecting this biradical with dioxetane, and the two transition states and gauche ·O–CH2–CH2–O· biradical connecting dioxetane with the formaldehyde product molecules are investigated at different levels of electronic structure theory including UB3LYP, UMP2, MRMP2, and CASSCF and a range of basis sets. The UB3LYP/6-31G* method was found to give representative energies for the reactive system and was used as a model for the simulations. UB3LYP/6-31G* direct dynamics trajectories were initiated at the TS connecting the ·O–O–CH2–CH2· biradical and dioxetane by sampling the TS's vibrational energy levels, and rotational and reaction coordinate energies, with Boltzmann distributions at 300, 1000, and 1500 K. This corresponds to the transition state theory model for trajectories that pass the TS. The trajectories were directed randomly towards both the biradical and dioxetane. A small fraction of the trajectories directed towards the biradical recrossed the TS and formed dioxetane. The remainder formed 1O2 + C2H4 and of these ∼ 40% went directly from the TS to 1O2 + C2H4 without getting trapped and forming an intermediate in the ·O–O–CH2–CH2· biradical potential energy minimum, a non-statistical result. The dioxetane molecules which are formed dissociate to two formaldehyde molecules with a rate constant two orders of magnitude smaller than that predicted by Rice–Ramsperger–Kassel–Marcus theory. The reaction dynamics from dioxetane to the formaldehyde molecules do not follow the intrinsic reaction coordinate or involve trapping in the gauche ·O–CH2–CH2–O· biradical potential energy minimum. Important non-statistical dynamics are exhibited for this reactive system.
A full-dimensional wave packet dynamics study of the photodetachment spectra of ${\rm FCH}_{4}^{-}$ FCH 4−
Authors: Palma Juliana , Manthe Uwe
Published: July 2012

The low-resolution photodetachment spectrum of \documentclass[12pt]{minimal}\begin{document}${\rm FCH}_4^-$\end{document} FCH 4− is studied in full dimensionality employing the multi-configurational time-dependent Hartree approach and potential energy surfaces recently developed by Bowman and co-workers. The computed spectrum qualitatively agrees with the low-resolution spectrum measured by Neumark and co-workers. It displays two peaks which can be assigned to different vibrational states of methane in the quasi-bound F·CH4 van der Waals complex. The first intense peak correlates to methane in its vibrational ground state while the second much smaller peak results from methane where one of the bending modes is excited. The present simulations consider only a single potential energy surface for the neutral FCH4 system and thus do not include spectral contributions arising from transitions to excited electronic states correlating to the F(2P) + CH4 asymptote. Considering the quantitative differences between the computed and the experimental spectra, one cannot decide whether beside the vibrational excitation of the methane fragment also electronic excitation of FCH4 contributes to the second peak in the experimental photodetachment spectrum.
Dynamical simulation of dipolar Janus colloids: Equilibrium structure and thermodynamics
Authors: Hagy Matthew C. , Hernandez Rigoberto
Published: July 2012

The static microstructures and thermodynamics of a colloidal dispersion of dipolar Janus (DJ) particles—that is, dipolar spheres in which each hemisphere is specified by a different charge interaction—have been investigated through simulation. DJ particles are modeled at a high level of detail with pairwise potentials represented as a sum of a spherically symmetric soft repulsion and an orientation-dependent electrostatic component using continuous potentials. The latter is important because it allows for the use of conventional molecular dynamics simulations, and is in contrast to the patch model and dipolar hard sphere model, which are discontinuous and therefore do not. The electrostatics are represented through a rigorous pointwise (PW) covering of two different hemispheres filled by points of corresponding charge. An isotropic coarse-graining (CG) of the PW models serves as a limit of the structure wherein the orientations of the DJ particles can be pairwise averaged. Over the range of volume fractions and DJ charge densities studied—consistent with reversible structures absent of long-range correlations—the CG model agrees well with the PW model with respect to equilibrium structure (isotropic pair correlation) and ensemble free energy. Time-dependent relaxation simulations of the PW model suggest that chain structures are not expected in liquid phases in contrast to that which has been observed for point dipole models of simple polar fluids.
The effects of adsorbed water layers on the apparent height of nanostructures in ambient amplitude modulation atomic force microscopy
Authors: Santos Sergio , Verdaguer Albert , Chiesa Matteo
Published: July 2012

Ambient amplitude modulation atomic force microscopy (AM AFM) is one of the most broadly used techniques as it is versatile and can provide measurements of single nanostructures routinely. Nevertheless, the technique typically measures an apparent height of nanostructures that does not coincide with the true height. Here, we carry out an exhaustive study of the several possibilities that arise in the presence and in the absence of adsorbed water layers when measuring the height of nanostructures. A method to control whether water layers are perturbed and whether intermittent mechanical contact occurs is provided. We show that the predicted range of apparent heights in the several interaction regimes is as large as the experimental values that are routinely obtained. In one extreme the apparent height might be larger than the true height even when sample deformation occurs. In the other, height reversal might occur even when sample deformation is much smaller than the loss of height. A main mechanism leading to such a broad range of measurements is identified in terms of the presence of water layers and the long range character of the resulting forces. In short, due to these long range effects, the gap in separation in the two amplitude branches, i.e., the attractive and the repulsive regimes, might be an order of magnitude larger in the presence of water than in its absence.
Precise description of single and double ionization of hydrogen molecule in intense laser pulses
Authors: Vafaee Mohsen , Sami Firoozeh , Shokri Babak , Buzari Behnaz , Sabzyan Hassan
Published: July 2012

A new simulation box setup is introduced for the precise description of the wavepacket evolution of two electronic systems in intense laser pulses. In this box, the regions of the hydrogen molecule H2, and singly and doubly ionized species, \documentclass[12pt]{minimal}\begin{document}${\rm H}_{2}^+$\end{document}H2+ and \documentclass[12pt]{minimal}\begin{document}${\rm H}_{2}^{+2}$\end{document}H2+2, are well discernible and their time-dependent populations are calculated at different laser field intensities. In addition, some new regions are introduced and characterized as quasi-double ionization and their time-dependencies on the laser field intensity are calculated and analyzed. The adopted simulation box setup is special in that it assures proper evaluation of the second ionization. In this study, the dynamics of the electrons and nuclei of the hydrogen molecule are separated based on the adiabatic approximation. The time-dependent Schrödinger and Newton equations are solved simultaneously for the electrons and the nuclei, respectively. Laser pulses of 390 nm wavelength at four different intensities (i.e., 1 × 1014, 5 × 1014, 1 × 1015, and 5 × 1015 W cm−2) are used in these simulations. Details of the central H2 region are also presented and discussed. This region is divided into four sub-regions related to the ionic state H+H− and covalent (natural) state HH. The effect of the motion of nuclei on the enhanced ionization is discussed. Finally, some different time-dependent properties are calculated, their dependencies on the intensity of the laser pulse are studied, and their correlations with the populations of different regions are analyzed.
Atomistic picture of isothermal volume relaxation behavior of atactic polystyrene glass provided by a molecular dynamics simulation
Authors: Chen Xiaoyu , Ye Yuanfeng , Hao Lingyun
Published: July 2012

Using an atomistic molecular dynamics (MD) simulation, we study the volume relaxation behavior of atactic polystyrene and attempt to correlate this macroscopic behavior with certain microscopic aspects. To this end, the gyration radius, the dimensionless relative shape anisotropy, the mean-squared displacement, and the non-Gaussian parameter are examined simultaneously. Our result shows that the structures characterized at different length scales change in a self-similar way and these changes are intimately correlated to the translational mobility of atoms. The initial incubation of structural changes at the different scales originates from the restriction of mobility due to the cage effect. The applicability of the MD simulation to the investigation of the bulk properties is discussed.
Dipolar transformations of two-dimensional quantum dots arrays proven by electron energy loss spectroscopy
Authors: Moctezuma R. E. , Nossa J. F. , Camacho A. , Carrillo J. L. , Rubí J. M.
Published: July 2012

Dipolar transformations of two-dimensional arrays of quantum dots are investigated theoretically. Homogeneous and non-homogeneous two-dimensional distributions are modeled by considering sections of the quantum dot array with different confinement potential. The dipolar transformations are tested by means of simulation of the dispersion of electrons of a beam traveling parallel to the plane of the quantum dot array. We calculate the electron energy loss function as a function of the temperature for different non-homogeneous distributions, considering several confinement potentials and coupling potentials among the quantum dots. Our results indicate that it would be possible by electron energy loss spectroscopy experiments to detect these dipolar transformations.
An adaptive pseudospectral method for wave packet dynamics
Authors: Kieri Emil , Holmgren Sverker , Karlsson Hans O.
Published: July 2012

We solve the time-dependent Schrödinger equation for molecular dynamics using a pseudospectral method with global, exponentially decaying, Hagedorn basis functions. The approximation properties of the Hagedorn basis depend strongly on the scaling of the spatial coordinates. Using results from control theory we develop a time-dependent scaling which adaptively matches the basis to the wave packet. The method requires no knowledge of the Hessian of the potential. The viability of the method is demonstrated on a model for the photodissociation of IBr, using a Fourier basis in the bound state and Hagedorn bases in the dissociative states. Using the new approach to adapting the basis we are able to solve the problem with less than half the number of basis functions otherwise necessary. We also present calculations on a two-dimensional model of CO2 where the new method considerably reduces the required number of basis functions compared to the Fourier pseudospectral method.
Density functional theory for encapsidated polyelectrolytes: A comparison with Monte Carlo simulation
Authors: Jin Zhehui , Wu Jianzhong
Published: July 2012

Genome packaging inside viral capsids is strongly influenced by the molecular size and the backbone structure of RNA/DNA chains and their electrostatic affinity with the capsid proteins. Coarse-grained models are able to capture the generic features of non-specific interactions and provide a useful testing ground for theoretical developments. In this work, we use the classical density functional theory (DFT) within the framework of an extended primitive model for electrolyte solutions to investigate the self-organization of flexible and semi-flexible linear polyelectrolytes in spherical capsids that are permeable to small ions but not polymer segments. We compare the DFT predictions with Monte Carlo (MC) simulation for the density distributions of polymer segments and small ions at different backbone flexibilities and several solution conditions. In general, the agreement between DFT and MC is near quantitative except when the simulation results are noticeably influenced by the boundary effects. The numerical efficiency of the DFT calculations makes it promising as a useful tool for quantification of the structural and thermodynamic properties of viral nucleocapsids in vivo and at conditions pertinent to experiments.
Note: Grazing incidence small and wide angle x-ray scattering combined with imaging ellipsometry
Authors: Körstgens V. , Meier R. , Ruderer M. A. , Guo S. , Chiang H.-Y. , Perlich J. , Roth S. V. , Gehrke R. , Müller-Buschbaum P.
Published: July 2012

The combination of grazing incidence small angle x-ray scattering (GISAXS) and grazing incidence wide angle x-ray scattering (GIWAXS) with optical imaging ellipsometry is presented as an upgrade of the available measurement techniques at the wiggler beamline BW4 of the Hamburger Synchrotronstrahlungslabor. The instrument is introduced with the description of the alignment procedure to assure the measurement of imaging ellipsometry and GISAXS/GIWAXS on the same sample spot. To demonstrate the possibilities of the new instrument examples of morphological investigation on films made of poly(3-hexylthiophene) and [6,6]-phenyl-C61 butyric acid methyl ester as well as textured poly(9,9-dioctylfluorene-alt-benzo-thia-diazole) are shown.
Physical conditions for fast reconnection evolution in space plasmas
Authors: Ugai M.
Published: July 2012

The present paper studies physical conditions for fast reconnection mechanism involving slow shocks to evolve spontaneously in space (high-temperature) plasmas. This is fundamental for onset mechanisms of geomagnetic substorms and solar flares. It is demonstrated that reconnection evolution strongly depends on effective resistivity available in space plasmas as well as on dimensions of initial current sheet. If a current sheet is sufficiently thin, fast reconnection spontaneously evolves only when resistivity is locally enhanced around X reconnection point. This is because in space plasmas reconnection flows cause vital current concentration locally around X point. For current-driven anomalous resistivity, the resulting resistivity is automatically localized around X point, so fast reconnection mechanism can be realized. On the other hand, for uniform or Spitzer resistivity, any fast reconnection cannot grow; in particular, Spitzer resistivity is reduced around X point because of Joule heating. Regarding reconnection simulations (either fluid or particle), unless numerical resistivities are made negligibly small, they seriously mask the effects of physical resistivity, leading to a misleading conclusion that reconnection evolution is little influenced by plasma resistivity.
Non-volatile memory transistor based on Pt nanocrystals with negative differencial resistance
Authors: Mikhelashvili V. , Shneider Y. , Meyler B. , Atiya G. , Yofis S. , Cohen-Hyams T. , Kaplan W. D. , Lisiansky M. , Roizin Y. , Salzman J. , Eisenstein G.
Published: July 2012

We report on the structural and electrical characteristics of non-volatile memory (NVM) transistors and capacitors that use Pt nanocrystals (NCs) for charge storage. The transistor exhibits a memory window of 0.6 V for a sweep of ±2.5 V which increases to 11.5 V at ±10 V. The trapped charges (electron and hole) density for a ±10 V write/erase signal are 2.9 × 1013 cm−2. At small source to drain voltages (VSD) and for delay times longer than 0.1 ms, negative differential resistance (NDR) type behavior of the transistor source to drain ISD-VSD characteristics is revealed. The physical mechanism responsible for the NDR is related to the dynamics of electron injection (by tunneling through the thin bottom oxide) and their trapping by the Pt NCs. The large storage capability and relatively low program/erase voltages as well as the use of Pt, that is a Fab friendly material, make the described NVM transistors promising for practical applications.
Three dimensional nano-seeding assembly of ferromagnetic Fe/LaSrFeO4 nano-hetero dot array
Authors: Okada K. , Sakamoto T. , Fujiwara K. , Hattori A. N. , Kanki T. , Tanaka H.
Published: July 2012

Well-ordered ferromagnetic Fe nanodots/LaSrFeO4 nanocomposites have been fabricated by self-assembled crystal growth on La-SrTiO3 substrates having Fe nanoseed array fabricated by nanoimprint lithography (NIL). The Fe nanoseeds with spacing of 200 nm make possible the formation of perfectly arranged Fe/LaSrFeO4 nanocomposites; phase-separated Fe nanodots and the LaSrFeO4 matrix grew only on the nanoseeds and on the area except nanoseeds, respectively. A calculation based on a surface diffusion model has indicated that the nanoseed spacing required for the formation of the perfectly arranged nanocomposite is less than 400 nm. Magnetic force microscopy revealed an arrangement of isolated ferromagnetic domain corresponding to Fe nanodots grown on the Fe nanoseeds. The combination of self-assembled growth and NIL gives a route of the rational formation of high-density ferromagnetic memory devices.