bluuebunny/crossref_metadata_2025 huggingface dataset:
Design and performance of a wireless sensor network for catchment‐scale snow and soil moisture measurements
Authors: Kerkez Branko , Glaser Steven D. , Bales Roger C. , Meadows Matthew W.
Published: August 2012

A wireless sensor network (WSN) was deployed as part of a water balance instrument cluster across a forested 1 km2headwater catchment in the southern Sierra Nevada of California. The network, which integrates readings from over 300 sensors, provides spatially representative measurements of snow depth, solar radiation, relative humidity, soil moisture, and matric potential. The ability of this densely instrumented watershed to capture catchment‐scale snow depth and soil moisture distributions is investigated through comparison with three comprehensive gridded surveys and 1 day of detailed lidar snow data. Statistical analysis shows that the network effectively characterized catchment‐wide distributions of snow depth, while offering a cost‐effective, reliable, and energy‐efficient means for collecting distributed data in real time. A temporal analysis of snow depth variability reveals that canopy cover is the major explanatory variable of snow depth and that under‐canopy measurements persistently show higher variability compared to those in open terrain. An analysis of soil moisture shows lower variability at deeper soil depth and a correlation between mean soil moisture and variability for shallow soils. A three‐phase design procedure was used to optimize the WSN deployment. First, as off‐the‐shelf performance of current WSN platforms for large‐scale, long‐term deployments cannot be guaranteed, statistics from a prototype deployment were analyzed. Two indicators of network performance, the packet delivery ratio and received signal strength indicator, showed that for our site conditions, a conservative 50 m node‐to‐node spacing would ensure low‐power, reliable, and robust network communications. Second, results from the prototype were used to refine hardware specifications and to guide the layout of the full 57‐node wireless network. Of these nodes, 23 were used actively for sensing, while the remaining 34 nodes were used as signal repeaters to ensure proper spatial radio coverage and robust network operations. Further analysis of network statistics is conducted during the third, operational, phase to validate system performance.
Atmospheric impact on the northwestern Pacific under a global warming scenario
Authors: Cheon Woo Geun , Park Young‐Gyu , Yeh Sang‐Wook , Kim Baek‐Min
Published: August 2012

Eleven climate models, one high‐resolution and ten low‐resolution, were analyzed to investigate the response of the northwestern Pacific under a global warming scenario. Application of scenario A1B of the Special Report on Emission Scenarios (SRES) weakens (intensifies) the southern (northern) part of the interior subtropical gyre both in high‐resolution and low‐resolution model. Such a dipole type change is mainly due to a basin‐scale dynamic atmosphere‐to‐ocean process. Namely, under global warming the Hadley circulation is weakened and expanded poleward. The Ferrel circulation is also displaced poleward, leading to weakening of ascending (descending) air motion and a high (low) sea level pressure anomaly in the northwestern (southeastern extratropical) North Pacific. Finally, a negative wind stress curl anomaly developed along the zero wind stress curl line of the present‐day climate to enhance the northern part of the gyre. The high‐resolution model results show greater changes in the structure of the Kuroshio and Kuroshio Extension, with strong intensification of the Kuroshio Extension front and jet, while in the low‐resolution models the changes are small. The Kuroshio between Taiwan and the southern coast of Japan is significantly intensified in the high‐resolution model results, but is slightly weakened in the ensemble of the low‐resolution models.
Seasonal variation of fractionated sea‐salt particles on the Antarctic coast
Authors: Hara K. , Osada K. , Yabuki M. , Yamanouchi T.
Published: August 2012

Aerosol sampling was conducted at Syowa Station, Antarctica (coastal station) in 2004–2006. SO42−depletion by mirabilite precipitation was identified from April through November. The fractionated sea‐salt particles were distributed in ultrafine– coarse modes. Molar ratios of Mg2+/Na+ and K+/Na+ were higher than in bulk seawater ratio during winter–spring. The Mg2+/Na+ ratio in aerosols greatly exceeded the upper limit in the case only with mirabilite precipitation. The temperature dependence of Mg2+/Na+ ratio strongly suggested that higher ratios of Mg2+/Na+ and K+/Na+were associated with sea‐salt fractionation by precipitation of mirabilite at −9°C, hydrohalite at ca. −23°C and other salts such as ikaite at ca. −5°C and gypsum at ca. −22°C during winter–spring. Mg‐salts with lower deliquescence relative humidity can be enriched gradually in the fractionated sea‐salt particles. Results suggests that sea‐salt fractionation can alter aerosol hygroscopicity and atmospheric chemistry in polar regions.
Magnetotail origins of auroral Alfvénic power
Authors: Zhang B. , Lotko W. , Brambles O. , Damiano P. , Wiltberger M. , Lyon J.
Published: August 2012

The generation of Alfvénic Poynting flux in the central plasma sheet and its polar distribution at low altitude are studied using three dimensional global simulations of the solar wind‐magnetosphere‐ionosphere interaction. A 24‐hour event simulation (4–5 Feb 2004) driven by solar wind and interplanetary magnetic field data reproduces the global morphology of Alfvénic Poynting flux measured by the Polar satellite, including its dawn‐dusk asymmetry. Controlled simulations show that the dawn‐dusk asymmetry is regulated by the spatial variation in ionospheric conductance. The asymmetry disappears when the conductance is taken to be spatially uniform. The simulated Alfvénic Poynting flux is generated in the magnetotail by time‐variable, fast flows emerging from nightside reconnection. The simulated fast flows are more intense in the premidnight sector as observed; this asymmetry also disappears when the ionospheric conductance is spatially uniform. Analysis of the wave propagation in the plasma sheet source region, near xGSM ≈ −15 RE, shows that as the fast flow brakes, a portion of its kinetic energy is transformed into the electromagnetic energy of intermediate and fast magnetohydrodynamic waves. The wave power is dominantly compressional in the source region and becomes increasingly Alfvénic as it propagates along magnetic field lines toward the ionosphere.
The observation of Doppler shifts of subionospheric LF signal in possible association with earthquakes
Authors: Hayakawa M. , Kasahara Y. , Endoh T. , Hobara Y. , Asai S.
Published: August 2012

The Doppler‐shift observation of LF (f = 60 kHz) subionospheric signal from Saga (Kyushu) (with call sign of JJY) as observed at Chofu (CHF), has been used to investigate the properties of ionospheric perturbations possibly associated with earthquakes(EQs). The period of analysis is seismo‐active half a year from January 1, 2009 to June 30, 2009, and six EQs with magnitude greater than 5.0 (in a range from 5.1 to 5.8, which took place within the wave sensitive area of the JJY‐CHF path) are dealt with. It is found from the Doppler‐shift observation at CHF that the Doppler shifts are really observed and the components in the frequency ranges of AGW (atmospheric gravity wave) and AW (acoustic wave) in the Doppler shifts are clearly enhanced, at least, before each EQ. This observational fact would lend a strong support to the important role of atmospheric oscillation channel in the lithosphere‐atmosphere‐ionosphere coupling mechanism.
Direct estimate of water, heat, and salt transport through the Strait of Otranto
Authors: Yari Sadegh , Kovačević Vedrana , Cardin Vanessa , Gačić Miroslav , Bryden Harry L.
Published: August 2012

The transport of water volume, salt and heat was calculated using continuous measurements of currents in the Otranto Strait for a one‐year period in 1994–95. Temperature and salinity data sets, available from five hydrographic surveys, were used to obtain the seasonal temperature and salinity distributions at the Otranto transect. The Variational Inverse Method (VIM) was applied to reconstruct spatial distributions of the de‐tided low‐pass inflowing current component, salinity and temperature. Errors associated with estimates of transports are influenced by the data coverage: the higher the spatial resolution, the smaller the error and vice versa. Volume transport reaches a maximum in winter and spring and attains its minimum in summer. The obtained volume transport [∼1 Sv (106 m3s−1)] should be considered a lower limit value since in that period the Adriatic was producing relatively small quantities of deep water due to the inflow of low‐salinity (high buoyancy) waters and relatively mild winters. Comparing the mean advective heat input and the air‐sea heat loss, the same order of magnitude between the two has been obtained which is satisfactory considering the possible errors of the two approaches. The relative importance of the eddy heat transport to the total transport is estimated to be only about 5% and thus it can be neglected in a first approximation. The salt transport estimates show a net input, suggesting a salinity increase during the period of study; this was confirmed from the long‐term salinity data in the Southern Adriatic.
Analysis of rainfall‐induced slope instability using a field of local factor of safety
Authors: Lu Ning , Şener‐Kaya Başak , Wayllace Alexandra , Godt Jonathan W.
Published: August 2012

Slope‐stability analyses are mostly conducted by identifying or assuming a potential failure surface and assessing the factor of safety (FS) of that surface. This approach of assigning a single FS to a potentially unstable slope provides little insight on where the failure initiates or the ultimate geometry and location of a landslide rupture surface. We describe a method to quantify a scalar field of FS based on the concept of the Coulomb stress and the shift in the state of stress toward failure that results from rainfall infiltration. The FS at each point within a hillslope is called the local factor of safety (LFS) and is defined as the ratio of the Coulomb stress at the current state of stress to the Coulomb stress of the potential failure state under the Mohr‐Coulomb criterion. Comparative assessment with limit‐equilibrium and hybrid finite element limit‐equilibrium methods show that the proposed LFS is consistent with these approaches and yields additional insight into the geometry and location of the potential failure surface and how instability may initiate and evolve with changes in pore water conditions. Quantitative assessments applying the new LFS field method to slopes under infiltration conditions demonstrate that the LFS has the potential to overcome several major limitations in the classical FS methodologies such as the shape of the failure surface and the inherent underestimation of slope instability. Comparison with infinite‐slope methods, including a recent extension to variably saturated conditions, shows further enhancement in assessing shallow landslide occurrence using the LFS methodology. Although we use only a linear elastic solution for the state of stress with no post‐failure analysis that require more sophisticated elastoplastic or other theories, the LFS provides a new means to quantify the potential instability zones in hillslopes under variably saturated conditions using stress‐field based methods.
The wake structure behind a porous obstruction and its implications for deposition near a finite patch of emergent vegetation
Authors: Chen Zhengbing , Ortiz Alejandra , Zong Lijun , Nepf Heidi
Published: August 2012

This experimental study describes the mean and turbulent flow structure in the wake of a circular array of cylinders, which is a model for a patch of emergent vegetation. The patch diameter, D, and patch density, a (frontal area per volume), are varied. The flow structure is linked to a nondimensional flow blockage parameter, CDaD, which is the ratio of the patch diameter and a drag length scale (CDa)−1. CD is the cylinder drag coefficient. The velocity exiting the patch, Ue, is reduced relative to the upstream velocity, U∞, and Ue/U∞ decreases as flow blockage (CDaD) increases. A predictive model is developed for Ue/U∞. The wake behind the patch contains two peaks in turbulence intensity. The first peak occurs directly behind the patch and is related to turbulence production within the patch at the scale of individual cylinders. The second peak in turbulence intensity occurs at distance Lwdownstream from the patch and is related to the wake‐scale vortices of the von Karman vortex street. The presence of the flowUe in the wake delays the formation of the von Karman vortex street until distance L1 (<Lw) behind the patch. Both L1 and Lw increase as Ue increases and thus as the flow blockage (CDaD) decreases. L1sets the distance behind the patch within which fine‐particle deposition can occur. BeyondLw, turbulence associated with the wake‐scale vortices inhibits deposition.
Multiple microRNAs induced by Cdx1 suppress Cdx2 in human colorectal tumour cells
Authors: Tagawa Takanobu , Haraguchi Takeshi , Hiramatsu Hiroaki , Kobayashi Kazuyoshi , Sakurai Kouhei , Inada Ken-Ichi , Iba Hideo
Published: August 2012

The mammalian transcriptional factors, Cdx1 and Cdx2 (Cdx is caudal-type homeobox) are paralogues and critical for the cellular differentiation of intestinal or colorectal epithelia. It has been reported previously that in Cdx1 transgenic or knockout mice, endogenous Cdx2 levels are inversely correlated with Cdx1 levels. Recently, we found that exogenous Cdx1 expression can suppress Cdx2 in a human colorectal tumour cell line, SW480, although the underlying molecular mechanisms were unclear. In the present study, we show that several microRNAs induced by exogenous Cdx1 expression directly bind to the CDX2 mRNA 3′UTR (untranslated region) to destabilize these transcripts, finally leading to their degradation. Using microarray analysis, we found that several miRNAs that were computationally predicted to target CDX2 mRNAs are up-regulated by exogenous Cdx1 expression in SW480 cells. Among these molecules, we identified miR-9, miR-16 and miR-22 as having the potential to suppress Cdx2 through the binding of the 3′UTR to its transcript. Importantly, simultaneous mutations of both the miR-9- and miR-16-binding sites in the CDX2 3′UTR were shown to be sufficient to block Cdx2 suppression. The results of the present study suggest a unique feature of miRNAs in which they contribute to homoeostasis by limiting the levels of transcription factors belonging to the same gene family.
Protein kinase Cϵ activity induces anti-inflammatory and anti-apoptotic genes via an ERK1/2- and NF-κB-dependent pathway to enhance vascular protection
Authors: Dumont Odile , Mylroie Hayley , Bauer Andrea , Calay Damien , Sperone Andrea , Thornton Clare , Hamdulay Shahir S. , Ali Nadira , Boyle Joseph J. , Choo Joan R. , Samarel Allen M. , Haskard Dorian O. , Randi Anna M. , Evans Paul C. , Mason Justin C.
Published: August 2012

Vascular endothelial injury predisposes to endothelial dysfunction and atherogenesis. We have investigated the hypothesis that PKCϵ (protein kinase Cϵ) is an important upstream regulator of cytoprotective pathways in vascular ECs (endothelial cells). Depletion of PKCϵ in human ECs reduced expression of the cytoprotective genes A1, A20 and Bcl-2. Conversely, constitutively active PKCϵ expressed in human ECs increased mRNA and protein levels of these cytoprotective genes, with up-regulation dependent upon ERK1/2 (extracellular-signal-regulated kinase 1/2) activation. Furthermore, inhibition of NF-κB (nuclear factor κB) by the pharmacological antagonist BAY 11-7085 or an IκB (inhibitor of NF-κB) SuperRepressor prevented cytoprotective gene induction. Activation of PKCϵ enhanced p65 NF-κB DNA binding and elevated NF-κB transcriptional activity. Importantly, although NF-κB activation by PKCϵ induced cytoprotective genes, it did not up-regulate pro-inflammatory NF-κB targets [E-selectin, VCAM-1 (vascular cell adhesion molecule 1) and ICAM-1 (intercellular adhesion molecule 1)]. Indeed, PKCϵ exhibited cytoprotective and anti-inflammatory actions, including inhibition of TNFα (tumour necrosis factor α)-induced JNK (c-Jun N-terminal kinase) phosphorylation and ICAM-1 up-regulation, a response attenuated by depletion of A20. Thus we conclude that PKCϵ plays an essential role in endothelial homoeostasis, acting as an upstream co-ordinator of gene expression through activation of ERK1/2, inhibition of JNK and diversion of the NF-κB pathway to cytoprotective gene induction, and propose that PKCϵ represents a novel therapeutic target for endothelial dysfunction.
Does endotoxaemia contribute to osteoarthritis in obese patients?
Authors: Metcalfe David , Harte Alison L. , Aletrari Mina Olga , Al Daghri Nasser M. , Al Disi Dara , Tripathi Gyanendra , McTernan Philip G.
Published: August 2012

OA (osteoarthritis) is a degenerative condition associated with obesity. A number of metabolic explanations have been proposed to explain the association between obesity and OA in non-weight-bearing joints; however, none of these hypotheses have been demonstrated empirically. In the present Hypothesis article, we recognize that obesity is associated with compromised gut mucosa, translocation of microbiota and raised serum LPS (lipopolysaccharide). The consequent activation of the innate immune response leads to increased serum titres of inflammatory mediators in obese patients, with both local and systemic markers of inflammation associated with onset and progression of OA. Furthermore, a number of workers have shown that articular cartilage repair is impaired by a range of inflammatory mediators, both in vitro and in vivo. We propose that metabolic endotoxaemia, caused by impaired gastric mucosa and low-grade chronic inflammation, may contribute to the onset and progression of OA in obese patients. This may account for the association between obesity and OA at non-weight-bearing joints which cannot be explained by biomechanical factors.
Well-posedness of the viscous boussinesq system in besov spaces of negative regular index s = −1
Authors: Deng Chao , Cui Shangbin
Published: August 2012

This paper is concerned with well-posedness of the natural convection in a viscous incompressible fluid. We first prove that the n-dimensional Boussinesq system is well-posed for initial data \documentclass[12pt]{minimal}\begin{document}$(\vec{u}_0,\theta _0)$\end{document}(u⃗0,θ0) either belonging to \documentclass[12pt]{minimal}\begin{document}$({B}^{-1}_{\infty ,1}\cap {B^{-1,1}_{\infty ,\infty }})\times {B}^{-1}_{p,r}$\end{document}(B∞,1−1∩B∞,∞−1,1)×Bp,r−1 or to \documentclass[12pt]{minimal}\begin{document}${B^{-1,1}_{\infty ,\infty }}\times {B}^{-1,\varepsilon }_{p,\infty }$\end{document}B∞,∞−1,1×Bp,∞−1,ɛ with 1 ⩽ r ⩽ ∞, \documentclass[12pt]{minimal}\begin{document}$\frac{n}{2}
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Stability of a viscous pinching thread
Authors: Eggers Jens
Published: August 2012

We consider the dynamics of a fluid thread near pinch-off, in the limit that inertial effects can be neglected. There exists an infinite hierarchy of similarity solutions corresponding to pinch-off. Only one of the similarity solutions (the “ground state”) is stable, all other solutions are linearly unstable to perturbations, and thus cannot be observed. Eigenvalues and eigenfunctions are calculated analytically.
Polyhedral duality in Bell scenarios with two binary observables
Authors: Fritz Tobias
Published: August 2012

For the Bell scenario with two parties and two binary observables per party, it is known that the no-signaling polytope is the polyhedral dual (polar) of the Bell polytope. Computational evidence suggests that this duality also holds for three parties. Using ideas of Werner, Wolf, Żukowski, and Brukner, we prove this for any number of parties by describing a simple linear bijection mapping (facet) Bell inequalities to (extremal) no-signaling boxes and vice versa. Furthermore, a symmetry-based technique for extending Bell inequalities (respectively, no-signaling boxes) with two binary observables from n parties to n + 1 parties is described; the Mermin–Klyshko family of Bell inequalities arises in this way, as well as 11 of the 46 classes of facet Bell inequalities for three parties. Finally, we ask whether the set of quantum correlations is self-dual with respect to our transformation. We find this not to be the case in general, although it holds for two parties on the level of correlations. This self-duality implies Tsirelson's bound for the CHSH inequality.
On the discrete spectrum of quantum layers
Authors: Lu Zhiqin , Rowlett Julie
Published: August 2012

Consider a quantum particle trapped between a curved layer of constant width built over a complete, non-compact, $\mathcal C^2$C2 smooth surface embedded in $\mathbb {R}^3$R3. We assume that the surface is asymptotically flat in the sense that the second fundamental form vanishes at infinity, and that the surface is not totally geodesic. This geometric setting is known as a quantum layer. We consider the quantum particle to be governed by the Dirichlet Laplacian as Hamiltonian. Our work concerns the existence of bound states with energy beneath the essential spectrum, which implies the existence of discrete spectrum. We first prove that if the Gauss curvature is integrable, and the surface is weakly κ-parabolic, then the discrete spectrum is non-empty. This result implies that if the total Gauss curvature is non-positive, then the discrete spectrum is non-empty. Next, we prove that if the Gauss curvature is non-negative, then the discrete spectrum is non-empty. Finally, we prove that if the surface is parabolic, then the discrete spectrum is non-empty if the layer is sufficiently thin.
Enhanced persistence of fog under illumination for carbon nanotube fog condensation nuclei
Authors: Banerjee Saumyabrata , Tripathi Sachchida N. , Das Utpal , Ranjan Raju , Jadhav Nilesh , Singh Vivek P. , Jariwala Chinmay , Sonkar Sumit , Sarkar Sabyasachi
Published: August 2012

Black carbon (BC) emissions have increased over South Asia and more persistent winter fogs are common during last decade. However, a physical mechanism connecting these two is still unknown. A significant fraction of BC is known to be in the form of carbon-nanotube (CNT). We have investigated the effects of two different sets of fog condensation nuclei, viz., inorganic salts (sodium chloride and ammonium sulphate) and BC (graphite and CNT) on the dissipation of chamber generated fog under dark and halogen lamp illuminated conditions at a controlled temperature, relative humidity, and fog condensation nuclei distribution. We found that, for inorganic salts, fog dissipates at a faster rate under illumination than in dark conditions showing similar trends for both sodium chloride and ammonium chloride. On the contrary, fog is found to be more persistent, for illuminated conditions, in the case of BC. Moreover, fog persistence is found to be more than twice for CNT compared to graphite in illuminated conditions. CNT is known to be an extremely effective absorber of light which leads to microscopic heating and subsequent evaporation which inhibits droplet growth. Small droplets have large residence time leading to longer fog persistence. This hitherto unknown mechanism may be responsible for persistent fog in India during last decade.
Physicochemical characterization of point defects in fluorine doped tin oxide films
Authors: Akkad Fikry El , Joseph Sudeep
Published: August 2012

The physical and chemical properties of spray deposited FTO films are studied using FESEM, x-ray diffraction (XRD), x-ray photoelectron spectroscopy (XPS), electrical and optical measurements. The results of XRD measurements showed that the films are polycrystalline (grain size 20–50 nm) with Rutile structure and mixed preferred orientation along the (200) and (110) planes. An angular shift of the XRD peaks after F-doping is observed and interpreted as being due to the formation of substitutional fluorine defects (FO) in presence of high concentration of oxygen vacancies (VO) that are electrically neutral. The electrical neutrality of oxygen vacancies is supported by the observation that the electron concentration n is two orders of magnitude lower than the VO concentration calculated from chemical analyses using XPS measurements. It is shown that an agreement between XPS, XRD, and Hall effect results is possible provided that the degree of deviation from stoichiometry is calculated with the assumption that the major part of the bulk carbon content is involved in O-C bonds. High temperature thermal annealing is found to cause an increase in the FO concentration and a decrease in both n and VO concentrations with the increase of the annealing temperature. These results could be interpreted in terms of a high temperature chemical exchange reaction between the SnO2 matrix and a precipitated fluoride phase. In this reaction, fluorine is released to the matrix and Sn is trapped by the fluoride phase, thus creating substitutional fluorine FO and tin vacancy VSn defects. The enthalpy of this reaction is determined to be approximately 2.4 eV while the energy of formation of a VSn through the migration of SnSn host atom to the fluoride phase is approximately 0.45 eV.
The effects of charge transfer on the aqueous solvation of ions
Authors: Soniat Marielle , Rick Steven W.
Published: August 2012

Ab initio-based charge partitioning of ionic systems results in ions with non-integer charges. This charge-transfer (CT) effect alters both short- and long-range interactions. Until recently, the effects of CT have been mostly neglected in molecular dynamics (MD) simulations. The method presented in this paper for including charge transfer between ions and water is consistent with ab initio charge partitioning and does not add significant time to the simulation. The ions of sodium, potassium, and chloride are parameterized to reproduce dimer properties and aqueous structures. The average charges of the ions from MD simulations (0.900, 0.919, and −0.775 for Na+, K+, and Cl−, respectively) are consistent with quantum calculations. The hydration free energies calculated for these ions are in agreement with experimental estimates, which shows that the interactions are described accurately. The ions also have diffusion constants in good agreement with experiment. Inclusion of CT results in interesting properties for the waters in the first solvation shell of the ions. For all ions studied, the first shell waters acquire a partial negative charge, due to the difference between water-water and water-ion charge-transfer amounts. CT also reduces asymmetry in the solvation shell of the chloride anion, which could have important consequences for the behavior of chloride near the air-water interface.
Oxidation stress evolution and relaxation of oxide film/metal substrate system
Authors: Dong Xuelin , Feng Xue , Hwang Keh-Chih
Published: August 2012

Stresses in the oxide film/metal substrate system are crucial to the reliability of the system at high temperature. Two models for predicting the stress evolution during isothermal oxidation are proposed. The deformation of the system is depicted by the curvature for single surface oxidation. The creep strain of the oxide and metal, and the lateral growth strain of the oxide are considered. The proposed models are compared with the experimental results in literature, which demonstrates that the elastic model only considering for elastic strain gives an overestimated stress in magnitude, but the creep model is consistent with the experimental data and captures the stress relaxation phenomenon during oxidation. The effects of the parameter for the lateral growth strain rate are also analyzed.
Low frequency pressure modulation of indium antimonide
Authors: Hallock Gary A. , Meier Mark A.
Published: August 2012

A lumped parameter resonator capable of generating megapascal pressures at low frequency (kilohertz) is described. Accelerometers are used to determine the applied pressure, and are calibrated with a piezoelectric sample. A laser diagnostic was also developed to measure the pressure in semiconductor samples through the band gap pressure dependence. In addition, the laser diagnostic has been used to measure the attenuation coefficient α of commercially available indium antimonide (InSb) wafers. The resonator and laser diagnostic have been used with InSb samples to verify the pressure response.
Phase diagram of supercooled water confined to hydrophilic nanopores
Authors: Limmer David T. , Chandler David
Published: August 2012

We present a phase diagram for water confined to cylindrical silica nanopores in terms of pressure, temperature, and pore radius. The confining cylindrical wall is hydrophilic and disordered, which has a destabilizing effect on ordered water structure. The phase diagram for this class of systems is derived from general arguments, with parameters taken from experimental observations and computer simulations and with assumptions tested by computer simulation. Phase space divides into three regions: a single liquid, a crystal-like solid, and glass. For large pores, radii exceeding 1 nm, water exhibits liquid and crystal-like behaviors, with abrupt crossovers between these regimes. For small pore radii, crystal-like behavior is unstable and water remains amorphous for all non-zero temperatures. At low enough temperatures, these states are glasses. Several experimental results for supercooled water can be understood in terms of the phase diagram we present.
A study of the anisotropy of stress in a fluid confined in a nanochannel
Authors: Hartkamp Remco , Ghosh A. , Weinhart T. , Luding S.
Published: August 2012

We present molecular dynamics simulations of planar Poiseuille flow of a Lennard-Jones fluid at various temperatures and body forces. Local thermostatting is used close to the walls to reach steady-state up to a limit body force. Macroscopic fields are obtained from microscopic data by time- and space-averaging and smoothing the data with a self-consistent coarse-graining method based on kernel interpolation. Two phenomena make the system interesting: (i) strongly confined fluids show layering, i.e., strong oscillations in density near the walls, and (ii) the stress deviates from the Newtonian fluid assumption, not only in the layered regime, but also much further away from the walls. Various scalar, vectorial, and tensorial fields are analyzed and related to each other in order to understand better the effects of both the inhomogeneous density and the anisotropy on the flow behavior and rheology. The eigenvalues and eigendirections of the stress tensor are used to quantify the anisotropy in stress and form the basis of a newly proposed objective, inherently anisotropic constitutive model that allows for non-collinear stress and strain gradient by construction.
Structural, vibrational, and thermal properties of densified silicates: Insights from molecular dynamics
Authors: Bauchy M.
Published: August 2012

Structural, vibrational, and thermal properties of densified sodium silicate (close to NS2) are investigated with classical molecular dynamics simulations of the glass and the liquid state. A systematic investigation of the glass structure with respect to density was performed. We observe a repolymerization of the network manifested by a transition from a tetrahedral to an octahedral silicon environment, the decrease of the amount of non-bridging oxygen atoms and the appearance of threefold coordinated oxygen atoms (triclusters). Anomalous changes in the medium range order are observed, the first sharp diffraction peak showing a minimum of its full-width at half maximum according to density. Generic vibrational trends are observed, such as the shift of the Boson peak intensity to higher frequencies and the decrease of its intensity. Finally, we show that the thermal behavior of the liquid can be reproduced by the Birch-Murnaghan equation of states, thus allowing us to compute the isothermal compressibility.
Spectral analysis of mixing in chaotic flows via the mapping matrix formalism: Inclusion of molecular diffusion and quantitative eigenvalue estimate in the purely convective limit
Authors: Gorodetskyi O. , Giona M. , Anderson P. D.
Published: August 2012

This paper extends the mapping matrix formalism to include the effects of molecular diffusion in the analysis of mixing processes in chaotic flows. The approach followed is Lagrangian, by considering the stochastic formulation of advection-diffusion processes via the Langevin equation for passive fluid particle motion. In addition, the inclusion of diffusional effects in the mapping matrix formalism permits to frame the spectral properties of mapping matrices in the purely convective limit in a quantitative way. Specifically, the effects of coarse graining can be quantified by means of an effective Péclet number that scales as the second power of the linear lattice size. This simple result is sufficient to predict the scaling exponents characterizing the behavior of the eigenvalue spectrum of the advection-diffusion operator in chaotic flows as a function of the Péclet number, exclusively from purely kinematic data, by varying the grid resolution. Simple but representative model systems and realistic physically realizable flows are considered under a wealth of different kinematic conditions–from the presence of large quasi-periodic islands intertwined by chaotic regions, to almost globally chaotic conditions, to flows possessing “sticky islands”–providing a fairly comprehensive characterization of the different numerical phenomenologies that may occur in the quantitative analysis of mapping matrices, and ultimately of chaotic mixing processes.
Radial resolution enhancement of the NSTX Thomson scattering diagnostic
Authors: LeBlanc B. P. , Diallo A. , Labik G. , Stevens D. R.
Published: August 2012

Current magnetic confinement plasma physics research has increased the demand for radial resolution in profile diagnostics, in particular in the edge and pedestal regions. On NSTX, an upgrade of the existing multi-point Thomson scattering diagnostic has been implemented in order to respond to the research program needs. Twelve new radial channels have been added bringing the total number of positions to 42. Four previously un-instrumented fiber bundles were put in service. Eight existing “active” fiber bundles were divided in two sub-bundles each in order to increase spatial resolution. Twelve radial channels now cover the pedestal region with a resolution near one centimeter. Fifteen radial channels cover the core and internal transport barrier regions. Two additional channels were added, one near the inner edge and one in the outer scrape-off layer. The intersection of the focused viewing optics field of view with a finite-width laser beam results in major-radius cross talk between adjacent fiber sub-bundles. A discussion and calculation of the cross talk will be presented.
Measuring the absolute deuterium–tritium neutron yield using the magnetic recoil spectrometer at OMEGA and the NIF
Authors: Casey D. T. , Frenje J. A. , Gatu Johnson M. , Séguin F. H. , Li C. K. , Petrasso R. D. , Glebov V. Yu. , Katz J. , Knauer J. P. , Meyerhofer D. D. , Sangster T. C. , Bionta R. M. , Bleuel D. L. , Döppner T. , Glenzer S. , Hartouni E. , Hatchett S. P. , Le Pape S. , Ma T. , MacKinnon A. , Mckernan M. A. , Moran M. , Moses E. , Park H.-S. , Ralph J. , Remington B. A. , Smalyuk V. , Yeamans C. B. , Kline J. , Kyrala G. , Chandler G. A. , Leeper R. J. , Ruiz C. L. , Cooper G. W. , Nelson A. J. , Fletcher K. , Kilkenny J. , Farrell M. , Jasion D. , Paguio R.
Published: August 2012

A magnetic recoil spectrometer (MRS) has been installed and extensively used on OMEGA and the National Ignition Facility (NIF) for measurements of the absolute neutron spectrum from inertial confinement fusion implosions. From the neutron spectrum measured with the MRS, many critical implosion parameters are determined including the primary DT neutron yield, the ion temperature, and the down-scattered neutron yield. As the MRS detection efficiency is determined from first principles, the absolute DT neutron yield is obtained without cross-calibration to other techniques. The MRS primary DT neutron measurements at OMEGA and the NIF are shown to be in excellent agreement with previously established yield diagnostics on OMEGA, and with the newly commissioned nuclear activation diagnostics on the NIF.
Integrated x-ray reflectivity measurements of elliptically curved pentaerythritol crystals
Authors: Haugh M. J. , Regan S. P. , Jacoby K. D. , Ross P. W. , Magoon J. , Barrios M. A. , Emig J. A. , Shoup M. J. , Fournier K. B.
Published: August 2012

The elliptically curved pentaerythritol (PET) crystals used in the Supersnout 2 x-ray spectrometer on the National Ignition Facility at Lawrence Livermore National Laboratory have been calibrated photometrically in the range of 5.5–16 keV. The elliptical geometry provides broad spectral coverage and minimizes the degradation of spectral resolution due to the finite source size. The reflectivity curve of the crystals was measured using a x-ray line source. The integrated reflectivity (RI) and width of its curve (ΔΘ) were the measurements of major interest. The former gives the spectrometer throughput, and the latter gives the spectrometer resolving power. Both parameters are found to vary considerably with the radius of curvature of the crystal and with spectral energy. The results are attributed to an enhanced mosaic effect due to the increase in curvature. There are also contributions from the crystal cleaving and gluing processes.
Mechanisms of bridge-mediated electron transfer: A TDDFT electronic dynamics study
Authors: Ding Feizhi , Chapman Craig T. , Liang Wenkel , Li Xiaosong
Published: August 2012

We present a time-dependent density functional theory approach for probing the dynamics of electron transfer on a donor-bridge-acceptor polyene dye scaffold. Two kinds of mechanisms, namely, the superexchange mechanism and the sequential mechanism, may be involved in the electron transfer process. In this work, we have focused on the crossover between these two charge transfer mechanisms on a series of donor-bridge-acceptor polyene dye systems with varying lengths of conjugated bridges. A number of methods and quantities are used to assist in the analysis, including the phase relationship of charge evolution and frequency domain spectra of the time-dependent dipole. Our simulations show that the superexchange mechanism plays a dominant role in the electron transfer from donor to acceptor when the bridge length is small, and the sequential mechanism becomes more important as the polyene bridge is lengthened. Full Ehrenfest dynamics with nuclear motion show that molecular vibrations play a very small role in such ultrafast charge transfer processes.
Mixing coarse-grained and fine-grained water in molecular dynamics simulations of a single system
Authors: Riniker Sereina , van Gunsteren Wilfred F.
Published: August 2012

The use of a supra-molecular coarse-grained (CG) model for liquid water as solvent in molecular dynamics simulations of biomolecules represented at the fine-grained (FG) atomic level of modelling may reduce the computational effort by one or two orders of magnitude. However, even if the pure FG model and the pure CG model represent the properties of the particular substance of interest rather well, their application in a hybrid FG/CG system containing varying ratios of FG versus CG particles is highly non-trivial, because it requires an appropriate balance between FG-FG, FG-CG, and CG-CG energies, and FG and CG entropies. Here, the properties of liquid water are used to calibrate the FG-CG interactions for the simple-point-charge water model at the FG level and a recently proposed supra-molecular water model at the CG level that represents five water molecules by one CG bead containing two interaction sites. Only two parameters are needed to reproduce different thermodynamic and dielectric properties of liquid water at physiological temperature and pressure for various mole fractions of CG water in FG water. The parametrisation strategy for the FG-CG interactions is simple and can be easily transferred to interactions between atomistic biomolecules and CG water.
Evaluation of the operating space for density fluctuation measurements employing 2D imaging reflectometry
Authors: Ren X. , Tobias B. J. , Che S. , Domier C. W. , Luhmann N. C. , Muscatello C. M. , Kramer G. , Valeo E.
Published: August 2012

Microwave imaging reflectometry provides broad poloidal coverage as a density fluctuation measurement tool. 2D imaging systems are evaluated for DIII-D relevant conditions using a full-wave reflectometer code, FWR2D. Reasonable correlation of the synthetic diagnostic signal with density fluctuations at the plasma cutoff surface for a wide range of fluctuation parameters is evaluated and achieved for coherent oscillations; also the frequency spectra are compared for relevant fluctuations. The consequences of non-idealities inherent to imaging fluctuations away from the plasma midplane, where receiving antennas view the plasma cutoff at oblique angles, are evaluated for the optimization of these systems.
Structural, electrical, and magnetic properties of Ce doped La0.7Ca0.3MnO3 thin films
Authors: Khare Amit , Choudhary R. J. , Sanyal S. P.
Published: August 2012

We have studied the structural, transport, and magnetic properties of La0.7Ca0.3−xCexMnO3 (x = 0.0, 0.025, 0.05, 0.1, and 0.15) manganite thin films on LaAlO3 (100) substrate prepared by pulsed laser deposition technique. The grown films are single phase and epitaxial in nature as revealed by x-ray diffraction and in-plane phi-scan. The temperature dependent resistivity measurements of these films reveal a metal–semiconductor transition at TP and transition temperature is found to shift lower temperature with Ce doping. Resistivity data at high temperature have been fitted with the variable range hopping model to estimate the density of states at Fermi level {N (EF)}, while at low temperature electron–electron, electron–phonon, and electron-magnon processes contribute to scattering of carriers. It was observed that N(EF) decreases with Ce doping leads to a decrease in conductivity of the Ce doped samples. We have observed maximum magnetoresistance value ∼90% near the TP. Magnetization measurements reveal that long-range ferromagnetic ordering in all samples and that saturation magnetic moment increases as x increases.
Measuring the diurnal pattern of leaf hyponasty and growth in Arabidopsis - a novel phenotyping approach using laser scanning
Authors: Dornbusch Tino , Lorrain Séverine , Kuznetsov Dmitry , Fortier Arnaud , Liechti Robin , Xenarios Ioannis , Fankhauser Christian
Published: August 2012

Plants forming a rosette during their juvenile growth phase, such as Arabidopsis thaliana (L.) Heynh., are able to adjust the size, position and orientation of their leaves. These growth responses are under the control of the plants circadian clock and follow a characteristic diurnal rhythm. For instance, increased leaf elongation and hyponasty – defined here as the increase in leaf elevation angle – can be observed when plants are shaded. Shading can either be caused by a decrease in the fluence rate of photosynthetically active radiation (direct shade) or a decrease in the fluence rate of red compared with far-red radiation (neighbour detection). In this paper we report on a phenotyping approach based on laser scanning to measure the diurnal pattern of leaf hyponasty and increase in rosette size. In short days, leaves showed constitutively increased leaf elevation angles compared with long days, but the overall diurnal pattern and the magnitude of up and downward leaf movement was independent of daylength. Shade treatment led to elevated leaf angles during the first day of application, but did not affect the magnitude of up and downward leaf movement in the following day. Using our phenotyping device, individual plants can be non-invasively monitored during several days under different light conditions. Hence, it represents a proper tool to phenotype light- and circadian clock-mediated growth responses in order to better understand the underlying regulatory genetic network.
Fuel treatment effects on tree mortality following wildfire in dry mixed conifer forests, Washington State, USA
Authors: Prichard Susan J. , Kennedy Maureen C.
Published: August 2012

Fuel reduction treatments are increasingly used to mitigate future wildfire severity in dry forests, but few opportunities exist to assess their effectiveness. We evaluated the influence of fuel treatment, tree size and species on tree mortality following a large wildfire event in recent thin-only, thin and prescribed burn (thin-Rx) units. Of the trees that died within the first 3 years, most died in the first year regardless of treatment. First-year mortality was much higher in control and thin-only units (65 and 52%) than in thin-Rx units (37%). Cumulative third-year mortality followed a similar trend (78 and 64% in control and thin-only units) v. 43% in thin-Rx units. Percentage crown scorch is a strong predictor of mortality and is highly dependent on fuel treatment. Across all treatments, Pinus ponderosa had a lower probability of post-fire mortality than did Pseudotsuga menziesii. Finally, the probability of beetle attack on surviving trees was highest in large-diameter trees within thin-only treatments and lowest within thin-Rx treatments. This study contributes further evidence supporting the effectiveness of thinning and prescribed burning on mitigating post-fire tree mortality. We also present evidence that a combination of thinning and prescribed burning is associated with lower incidence of post-fire bark beetle attack.
Structure of androcam supports specialized interactions with myosin VI
Authors: Joshi Mehul K. , Moran Sean , Beckingham Kathleen M. , MacKenzie Kevin R.
Published: August 2012

Androcam replaces calmodulin as a tissue-specific myosin VI light chain on the actin cones that mediate
D. melanogaster
spermatid individualization. We show that the androcam structure and its binding to the myosin VI structural (Insert 2) and regulatory (IQ) light chain sites are distinct from those of calmodulin and provide a basis for specialized myosin VI function. The androcam N lobe noncanonically binds a single Ca
2+
and is locked in a “closed” conformation, causing androcam to contact the Insert 2 site with its C lobe only. Androcam replacing calmodulin at Insert 2 will increase myosin VI lever arm flexibility, which may favor the compact monomeric form of myosin VI that functions on the actin cones by facilitating the collapse of the C-terminal region onto the motor domain. The tethered androcam N lobe could stabilize the monomer through contacts with C-terminal portions of the motor or recruit other components to the actin cones. Androcam binds the IQ site at all calcium levels, constitutively mimicking a conformation adopted by calmodulin only at intermediate calcium levels. Thus, androcam replacing calmodulin at IQ will abolish a Ca
2+
-regulated, calmodulin-mediated myosin VI structural change. We propose that the N lobe prevents androcam from interfering with other calmodulin-mediated Ca
2+
signaling events. We discuss how gene duplication and mutations that selectively stabilize one of the many conformations available to calmodulin support the molecular evolution of structurally and functionally distinct calmodulin-like proteins.