bluuebunny/crossref_metadata_2025 huggingface dataset:
Modulation of exogenous selenium in cadmium-induced changes in antioxidative metabolism, cadmium uptake, and photosynthetic performance in the 2 tobacco genotypes differing in cadmium tolerance
Authors: Liu Wenxing , Shang Shenghua , Feng Xue , Zhang Guoping , Wu Feibo
Published: September 2014

Hydroponic experiments were conducted using cadmium (Cd)–sensitive (cv Guiyan 1) and Cd-tolerant (Yunyan 2) tobacco cultivars to evaluate cultivar differences in response to Cd toxicity in the presence of selenium (Se). The results showed that addition of 3 µM Se in 50 µM Cd solution markedly reduced Cd accumulation in plants, alleviated Cd-induced growth inhibition, and increased nitrogen and chlorophyll contents as well as photosynthetic performance (i.e., net photosynthetic rate, stomatal conductance, and transpiration rate). External Se dramatically depressed Cd-induced O2•−, H2O2, and malondialdehyde accumulation, especially in the sensitive cultivar. Selenium significantly elevated Cd-depressed activities of superoxide dismutase, peroxidase, catalase, ascorbate peroxidase, glutathione-peroxidase, and glutathione reductase in the both cultivars after 7-d treatments. Meanwhile, Se counteracted Cd-induced alterations in certain nutrient elements; for example, it significantly increased Zn and Ca concentrations and reduced Mg concentration in both cultivars. Furthermore, Se significantly elevated Cd-depressed H+-K+-adenosine triphosphatase (ATPase), Na+-K+-ATPase, and Ca2+-Mg2+-ATPase activities. The beneficial effect of Se under Cd stress may be related mainly to the increased ATPase activity and reduced Cd uptake and reactive oxygen species accumulation, thus reducing the negative consequences of oxidative stress caused by Cd toxicity. Environ Toxicol Chem 2015;34:92–99. © 2014 SETAC
Application of a redox-proteomics toolbox to Daphnia magna challenged with model pro-oxidants copper and paraquat
Authors: Rainville Louis-Charles , Coelho Ana Varela , Sheehan David
Published: September 2014

The redox status of cells is involved in the regulation of several cellular stress–response pathways. It is frequently altered by xenobiotics, as well as by environmental stressors. As such, there is an increasing interest in understanding the redox status of proteins in different scenarios. Recent advances in proteomics enable researchers to measure oxidative lesions in a wide range of proteins. This opens the door to the sensitive detection of toxicity targets and helps decipher the molecular impact of pollutants and environmental stressors. The present study applies the measurement of protein carbonyls, the most common oxidative lesion of proteins, to gel-based proteomics in Daphnia magna. Daphnids were exposed to copper and paraquat, 2 well-known pro-oxidants. Catalase activity was decreased by paraquat, whereas global measurement of protein carbonyls and thiols indicated no change with treatment. Despite the absence of observed oxidative stress, 2-dimensional electrophoresis of the daphnid proteins and measurement of their carbonylation status revealed that 32 features were significantly affected by the treatments, showing higher sensitivity than single measurements. Identified proteins affected by copper indicated a decrease in the heat-shock response, whereas paraquat affected glycolysis. The present study demonstrates the applicability of redox-proteomics in daphnids, and indicates that the heat-shock response plays a counterintuitive role in metal resistance in daphnids. Environ Toxicol Chem 2015;34:84–91. © 2014 SETAC
Zebrafish as a model to investigate CNS myelination
Authors: Preston Marnie A. , Macklin Wendy B.
Published: September 2014

Myelin plays a critical role in proper neuronal function by providing trophic and metabolic support to axons and facilitating energy‐efficient saltatory conduction. Myelination is influenced by numerous molecules including growth factors, hormones, transmembrane receptors and extracellular molecules, which activate signaling cascades that drive cellular maturation. Key signaling molecules and downstream signaling cascades controlling myelination have been identified in cell culture systems. However, in vitro systems are not able to faithfully replicate the complex in vivo signaling environment that occurs during development or following injury. Currently, it remains time‐consuming and expensive to investigate myelination in vivo in rodents, the most widely used model for studying mammalian myelination. As such, there is a need for alternative in vivo myelination models, particularly ones that can test molecular mechanisms without removing oligodendrocyte lineage cells from their native signaling environment or disrupting intercellular interactions with other cell types present during myelination. Here, we review the ever‐increasing role of zebrafish in studies uncovering novel mechanisms controlling vertebrate myelination. These innovative studies range from observations of the behavior of single cells during in vivo myelination as well as mutagenesis‐ and pharmacology‐based screens in whole animals. Additionally, we discuss recent efforts to develop novel models of demyelination and oligodendrocyte cell death in adult zebrafish for the study of cellular behavior in real time during repair and regeneration of damaged nervous systems. GLIA 2015;63:177–193
GneimoSim: A modular internal coordinates molecular dynamics simulation package
Authors: Larsen Adrien B. , Wagner Jeffrey R. , Kandel Saugat , Salomon‐Ferrer Romelia , Vaidehi Nagarajan , Jain Abhinandan
Published: September 2014

The generalized Newton–Euler inverse mass operator (GNEIMO) method is an advanced method for internal coordinates molecular dynamics (ICMD). GNEIMO includes several theoretical and algorithmic advancements that address longstanding challenges with ICMD simulations. In this article, we describe the GneimoSim ICMD software package that implements the GNEIMO method. We believe that GneimoSim is the first software package to include advanced features such as the equipartition principle derived for internal coordinates, and a method for including the Fixman potential to eliminate systematic statistical biases introduced by the use of hard constraints. Moreover, by design, GneimoSim is extensible and can be easily interfaced with third party force field packages for ICMD simulations. Currently, GneimoSim includes interfaces to LAMMPS, OpenMM, and Rosetta force field calculation packages. The availability of a comprehensive Python interface to the underlying C++ classes and their methods provides a powerful and versatile mechanism for users to develop simulation scripts to configure the simulation and control the simulation flow. GneimoSim has been used extensively for studying the dynamics of protein structures, refinement of protein homology models, and for simulating large scale protein conformational changes with enhanced sampling methods. GneimoSim is not limited to proteins and can also be used for the simulation of polymeric materials.
Linking Organic Carbon, Water Content, and Nitrous Oxide Emission in a Reclaimed Coal Mine Soil
Authors: Dutta Tanushree , Stehouwer Richard C. , Dell Curtis J.
Published: September 2014

Mine‐land reclamation for biomass production is often achieved by means of large applications of N and organic C with amendments that could create soil conditions favorable for N2O production and emissions. To investigate this possibility, we conducted a laboratory experiment using mine soil collected from an active surface coal mine site near Philipsburg, Pennsylvania. During a 37‐d incubation period, we measured N2O and CO2fluxes from non‐amended soil and from soil amended with ammonium nitrate (L + F), composted poultry manure (Comp), poultry manure alone (Man) and mixed with 3 rates of paper mill sludge (PMS) to obtain carbon to nitrogen ratios of 14, 20 and 27 (Man + PMS14, 20 and 27), each at 60% and 80% water filled pore space (WFPS). Results showed that manure alone leads to a greater emission of N2O under laboratory conditions than with L + F. However, composting manure effectively reduced the emissions compared to that of L + F despite a large addition of organic C and N. Composted manure‐treated soil emitted less than all other manure‐based treatments at both 60% and 80% WFPS. The emissions were greater from soil amended with the Man + PMS treatments compared to non‐amended and L + F‐amended soil, and it increased during periods of intense microbial activity created by the application of manure and PMS. Higher water content increased emissions particularly during periods of intense microbial activity coupled with inorganic N availability. Cumulative N2O emissions from manure‐treated soils represented less than 0·1% loss of total applied N. Copyright © 2014 John Wiley & Sons, Ltd.
The proteome under translational control
Authors: Gawron Daria , Gevaert Kris , Van Damme Petra
Published: September 2014

A single eukaryotic gene can give rise to a variety of protein forms (proteoforms) as a result of genetic variation and multilevel regulation of gene expression. In addition to alternative splicing, an increasing line of evidence shows that alternative translation contributes to the overall complexity of proteomes. Identifying the repertoire of proteins and micropeptides expressed by alternative selection of (near‐)cognate translation initiation sites and different reading frames however remains challenging with contemporary proteomics. MS‐enabled identification of proteoforms is expected to benefit from transcriptome and translatome data by the creation of customized and sample‐specific protein sequence databases. Here, we focus on contemporary integrative omics approaches that complement proteomics with DNA‐ and/or RNA‐oriented technologies to elucidate the mechanisms of translational control. Together, these technologies enable to map the translation (initiation) landscape and more comprehensively define the inventory of proteoforms raised upon alternative translation, thus assisting in the (re‐)annotation of genomes.
Synthesis of unsaturation containing P(VDF‐co‐TrFE‐co‐CTFE) from P(VDF‐co‐CTFE) in one‐pot catalyzed with Cu(0)‐based single electron transfer living radical polymerization system
Authors: Hu Xin , Tan Shaobo , Gao Guoxin , Xie Yunchuan , Wang Qinzhuo , Li Na , Zhang Zhicheng
Published: September 2014

Poly(vinylidene fluoride‐co‐trifluoroethylene‐co‐chlorotrifluoroethylene) (P(VDF‐co‐TrFE‐co‐CTFE)) with internal double bond has been reported with high dielectric constant and energy density at room temperature, which is expected to serve as a promising dielectric film in high pulse discharge capacitors. An environmentally friendly one‐pot route, including the controllable hydrogenation via Cu(0) mediated single electron transfer radical chain transfer reaction (SET‐CTR) and dehydrochlorination catalyzed with N‐containing reagent, is successfully developed to synthesize P(VDF‐co‐TrFE‐co‐CTFE) containing unsaturation. The resultant polymer was carefully characterized with 1H NMR, 19F NMR, and FTIR. The composition of the resultant copolymer is strongly influenced by reaction conditions, including the reaction temperature, catalyst concentration, the types of ligands and solvents. The kinetics data of the chain transfer and elimination reaction demonstrate their well‐controlled feature of the strategy. By shifting the equilibrium between the CTR and elimination reactions dominated by N‐compounds serving as ligands in SET‐CTR and catalyst in the dehydrochlorination of P(VDF‐co‐CTFE), P(VDF‐co‐TrFE‐co‐CTFE) with tunable TrFE and double‐bond content could be synthesized in this one‐pot route. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2014, 52, 3429–3440
Protected hinge in the immunoglobulin G2‐A2 disulfide isoform
Authors: Liu Yaoqing Diana , Chou Robert Y.‐T. , Dillon Thomas M. , Poppe Leszek , Spahr Chris , Shi Stone D. H. , Flynn Gregory C.
Published: September 2014

Human IgG2 consists of disulfide‐mediated structural isoforms, classified by the number of Fab arms disulfide‐linked to the heavy chain hinge. In the IgG2‐B isoform, both Fab arms are linked to the hinge region, and in IgG2‐A, neither Fab arm are linked to the hinge. IgG2‐A/B is a hybrid between these two forms, with only one Fab arm disulfide‐linked to the hinge. Within each of these isoform types are subtypes, with subtle disulfide‐linkage differences. Here we explored the structural basis for the A1 and A2 isoform subtypes. Whereas A1 isoform converts into the A/B and B isoforms under mild redox conditions, A2 does not. Characterization of the disulfide connectivities of A2 isoform revealed a similar structure to A1 isoform, with parallel inter heavy chain disulfide linkages in the hinge region. However, the hinge disulfides in A2 isoform were resistant to reduction under conditions where A1 isoform hinge disulfides became reduced and they required thermal treatment (>55°C) to obtain thiol‐dependent disulfide reduction. Structural analysis of the hinge region indicated that the protected disulfides were restricted to cysteines 219 and 220 of the upper hinge. Disruption of the upper hinge through insertion mutagenesis eliminated A2 isoform behavior. 1H NMR studies showed that the A1 isoform Fc glycan was more dynamic than that on A2 isoform and showed some other conformational differences. Results point to an IgG2‐A2 upper hinge region that is more akin to the interior of a globular protein than the flexible hinge region expected on an IgG.
A conservative adaptive wavelet method for the shallow‐water equations on the sphere
Authors: Aechtner M. , Kevlahan N. K.‐R. , Dubos T.
Published: September 2014

We introduce an innovative wavelet‐based approach to adjust local grid resolution dynamically to maintain a uniform specified error tolerance. Extending the work of Dubos and Kevlahan, a wavelet multiscale approximation is used to make the Thuburn‐Ringler‐Skamarock‐Klemp (TRiSK) model dynamically adaptive for the rotating shallow‐water equations on the sphere. This article focuses on the challenges encountered when extending the adaptive wavelet method to the sphere and ensuring an efficient parallel implementation using message passing interface (MPI). The wavelet method is implemented in Fortran 95 with an emphasis on computational efficiency and scales well up to processors for load‐unbalanced scenarios and up to at least processors for load‐balanced scenarios. The method is verified using standard smooth test cases and a nonlinear test case proposed by Galewsky et al. The dynamical grid adaption provides compression ratios of up to 50 times in a challenging homogenous turbulence test case. The adaptive code is about three times slower per active grid point than the equivalent non‐adaptive TRiSK code and about four times slower per active grid point than an equivalent spectral code. This computationally efficient adaptive dynamical core could serve as the foundation on which to build a complete climate or weather model.
Structural classification and similarity measurement of malware
Authors: Shi Hongbo , Hamagami Tomoki , Yoshioka Katsunari , Xu Haoyuan , Tobe Kazuhiro , Goto Shigeki
Published: September 2014

This paper proposes a new lightweight method that utilizes the growing hierarchical self‐organizing map (GHSOM) for malware detection and structural classification. It also shows a new method for measuring the structural similarity between classes. A dynamic link library (DLL) file is an executable file used in the Windows operating system that allows applications to share codes and other resources to perform particular tasks. In this paper, we classify different malware by the data mining of the DLL files used by the malware. Since the malware families are evolving quickly, they present many new problems, such as how to link them to other existing malware families. The experiment shows that our GHSOM‐based structural classification can solve these issues and generate a malware classification tree according to the similarity of malware families. © 2014 Institute of Electrical Engineers of Japan. Published by John Wiley & Sons, Inc.
Lowe on Modal Knowledge
Authors: Horvath Joachim ,   Philosophy Documentation Center
Published: September 2014

In recent work, E. J. Lowe presents an essence-based account of our knowledge of metaphysical modality that he claims to be superior to its main competitors. I argue that knowledge of essences alone, without knowledge of a suitable bridge principle, is insufficient for knowing that something is metaphysically necessary or metaphysically possible. Yet given Lowe’s other theoretical commitments, he cannot account for our knowledge of the needed bridge principle, and so his essence-basedmodal epistemology remains incomplete. In addition to that, Lowe’s account implies a psychologically unrealistic reconstruction of how we ordinarily acquire knowledge of metaphysical modalities. The discussion of Lowe’s suggestive essence-based account is also intended as a case study that illustrates amore general problem in the epistemology ofmodality: the great difficulty of explaining ourmodal knowledge in terms of a single overtly nonmodal kind of knowledge.The failure of Lowe’s account suggests that such a sweeping reductive explanation of ourmodal knowledge might simply not be available. This should be good news for those philosophers who champion less reductive or more pluralistic accounts of our modal knowledge.
Meaning, Expression and Extremely Strong Evidence
Authors: Zeman Dan ,   Philosophy Documentation Center
Published: September 2014

This short paper follows up on the exchange between Ray Buchanan and Wayne Davis (this journal) concerning the theory of speaker meaning put forward by Davis in previous work. I briefly present Davis’ main tenets, Buchanan’s objections, Davis’ replies, and then offer a new case that enforces the problem raised by Buchanan to Davis’ theory for speaker meaning.
Novel fermentation process strengthening strategy for production of propionic acid and vitamin B12 by Propionibacterium freudenreichii
Authors: Wang Peng , Jiao Youjing , Liu Shouxin
Published: September 2014

An efficient fermentation-strengthening approach was developed to improve the anaerobic production of propionic acid and vitamin B12 by co-fermentation with Propionibacterium freudenreichii. Vitamin B12 production from glucose resulted in relatively high productivity (0.35 mg/L h) but a low propionic acid yield (0.55 g/g). By contrast, glycerol gave a high propionic acid yield (0.63 g/g) but low productivity (0.16 g/L h). Co-fermentation of glycerol and glucose with a gradual addition strategy gave high yields (propionic acid: 0.71 g/g; vitamin B12: 0.72 mg/g) and productivities (propionic acid: 0.36 g/L h; vitamin B12: 0.36 mg/L h). Finally, the integrated feedstock and fermentation system strengthening strategy was demonstrated as an efficient method for the economic production of bio-based propionic acid and vitamin B12.
The transition to adulthood around the Mediterranean: Contributions of the special issue
Authors: Tagliabue Semira , Lanz Margherita , Beyers Wim
Published: September 2014

This analysis of the papers in the special issue on the transition to adulthood around the Mediterranean calls attention to the role of the family of origin in the transition itself. All the papers analyzed a specific aspect of family relationships, focusing especially on the parent–child relationship. Moreover, several outcomes were considered, such as identity, psychological well‐being, life satisfaction, and criteria of adulthood, highlighting the multidimensional features of the transitional phase young people are facing. Together, these papers make a great contribution to the current literature, especially for the ones linked to the Mediterranean area, and provide both foundation and new paths for future research.
A‐to‐I editing on tRNAs: Biochemical, biological and evolutionary implications
Authors: Torres Adrian Gabriel , Piñeyro David , Filonava Liudmila , Stracker Travis H. , Batlle Eduard , Ribas de Pouplana Lluis
Published: September 2014

Inosine on transfer RNAs (tRNAs) are post‐transcriptionally formed by a deamination mechanism of adenosines at positions 34, 37 and 57 of certain tRNAs. Despite its ubiquitous nature, the biological role of inosine in tRNAs remains poorly understood. Recent developments in the study of nucleotide modifications are beginning to indicate that the dynamics of such modifications are used in the control of specific genetic programs. Likewise, the essentiality of inosine‐modified tRNAs in genome evolution and animal biology is becoming apparent. Here we review our current understanding on the role of inosine in tRNAs, the enzymes that catalyze the modification and the evolutionary link between such enzymes and other deaminases.
Neonatal hypoxic–ischemic encephalopathy reduces c‐Fos activation in the rat hippocampus: evidence of a long‐lasting effect
Authors: Souza Andressa , Dussan‐Sarria Jairo Alberto , Medeiros Liciane Fernandes , Souza Ana Cláudia , Oliveira Carla , Scarabelot Vanessa Leal , Adachi Lauren Naomi , Winkelmann‐Duarte Elisa Cristiana , Philippi‐Martins Bárbara Beatriz , Netto Carlos Alexandre , Caumo Wolnei , Torres Iraci L.S.
Published: September 2014

The effect of neonatal hypoxic–ischemic encephalopathy (HIE) on maturation of nociceptive pathways has been sparsely explored. To investigate whether neonatal HIE alters neuronal activity, nociceptive behavior, and serum neuroplasticity mediators (brain‐derived neurotrophic factor [BDNF] and tumor necrosis factor‐α [TNF]) in the short, medium, and long term. Neonate male Wistar rats were randomized to receive a brain insult that could be either ischemic (left carotid artery ligation [LCAL]), hypoxic (8% oxygen chamber), hypoxic–ischemic (LCAL and hypoxic chamber), sham‐ischemic, or sham‐hypoxic. Neuronal activity (c‐Fos activation at region CA1 and dentate gyrus of the hippocampus), nociceptive behavior (von Frey, tail‐flick, and hot‐plate tests), neuroplasticity mediators (BDNF, TNF), and a cellular injury marker (lactase dehydrogenase [LDH]) were assessed in blood serum 14, 30, and 60 days after birth. Neonatal HIE persistently reduced c‐Fos activation in the ipsilateral hippocampal region CA1; however, contralateral c‐Fos reduction appeared only 7 weeks after the event. Neonatal HIE acutely reduced the paw withdrawal threshold (von Frey test), but this returned to normal by the 30th postnatal day. Hypoxia reduced serum LDH levels. Serum neuroplasticity mediators increased with age, and neonatal HIE did not affect their ontogeny. Neonatal HIE‐induced reduction in neuronal activity occurs acutely in the ipsilateral hippocampal region CA1 and persists for at least 60 days, but the contralateral effect of the insult is delayed. Alterations in the nociceptive response are acute and self‐limited. Serum neuroplasticity mediators increase with age, and remain unaffected by HIE.
Direct measurement of shear properties of microfibers
Authors: Behlow H. , Saini D. , Oliveira L. , Durham L. , Simpson J. , Serkiz S. M. , Skove M. J. , Rao A. M.
Published: September 2014

As novel fibers with enhanced mechanical properties continue to be synthesized and developed, the ability to easily and accurately characterize these materials becomes increasingly important. Here we present a design for an inexpensive tabletop instrument to measure shear modulus (G) and other longitudinal shear properties of a micrometer-sized monofilament fiber sample, such as nonlinearities and hysteresis. This automated system applies twist to the sample and measures the resulting torque using a sensitive optical detector that tracks a torsion reference. The accuracy of the instrument was verified by measuring G for high purity copper and tungsten fibers, for which G is well known. Two industrially important fibers, IM7 carbon fiber and Kevlar® 119, were also characterized with this system and were found to have G = 16.5 ± 2.1 and 2.42 ± 0.32 GPa, respectively.
A low phase noise microwave frequency synthesis for a high-performance cesium vapor cell atomic clock
Authors: François B. , Calosso C. E. , Danet J. M. , Boudot R.
Published: September 2014

We report the development, absolute phase noise, and residual phase noise characterization of a 9.192 GHz microwave frequency synthesis chain devoted to be used as a local oscillator in a high-performance cesium vapor cell atomic clock based on coherent population trapping (CPT). It is based on frequency multiplication of an ultra-low phase noise 100 MHz oven-controlled quartz crystal oscillator using a nonlinear transmission line-based chain. Absolute phase noise performances of the 9.192 GHz output signal are measured to be −42, −100, −117 dB rad2/Hz and −129 dB rad2/Hz at 1 Hz, 100 Hz, 1 kHz, and 10 kHz offset frequencies, respectively. Compared to current results obtained in a state-of-the-art CPT-based frequency standard developed at LNE-SYRTE, this represents an improvement of 8 dB and 10 dB at f = 166 Hz and f = 10 kHz, respectively. With such performances, the expected Dick effect contribution to the atomic clock short term frequency stability is reported at a level of 6.2 × 10−14 at 1 s integration time, that is a factor 3 higher than the atomic clock shot noise limit. Main limitations are pointed out.
A geophysical shock and air blast simulator at the National Ignition Facility
Authors: Fournier K. B. , Brown C. G. , May M. J. , Compton S. , Walton O. R. , Shingleton N. , Kane J. O. , Holtmeier G. , Loey H. , Mirkarimi P. B. , Dunlop W. H. , Guyton R. L. , Huffman E.
Published: September 2014

The energy partitioning energy coupling experiments at the National Ignition Facility (NIF) have been designed to measure simultaneously the coupling of energy from a laser-driven target into both ground shock and air blast overpressure to nearby media. The source target for the experiment is positioned at a known height above the ground-surface simulant and is heated by four beams from the NIF. The resulting target energy density and specific energy are equal to those of a low-yield nuclear device. The ground-shock stress waves and atmospheric overpressure waveforms that result in our test system are hydrodynamically scaled analogs of full-scale seismic and air blast phenomena. This report summarizes the development of the platform, the simulations, and calculations that underpin the physics measurements that are being made, and finally the data that were measured. Agreement between the data and simulation of the order of a factor of two to three is seen for air blast quantities such as peak overpressure. Historical underground test data for seismic phenomena measured sensor displacements; we measure the stresses generated in our ground-surrogate medium. We find factors-of-a-few agreement between our measured peak stresses and predictions with modern geophysical computer codes.
New experimental platform to study high density laser-compressed matter
Authors: Gauthier M. , Fletcher L. B. , Ravasio A. , Galtier E. , Gamboa E. J. , Granados E. , Hastings J. B. , Heimann P. , Lee H. J. , Nagler B. , Schropp A. , Gleason A. , Döppner T. , LePape S. , Ma T. , Pak A. , MacDonald M. J. , Ali S. , Barbrel B. , Falcone R. , Kraus D. , Chen Z. , Mo M. , Wei M. , Glenzer S. H.
Published: September 2014

We have developed a new experimental platform at the Linac Coherent Light Source (LCLS) which combines simultaneous angularly and spectrally resolved x-ray scattering measurements. This technique offers a new insights on the structural and thermodynamic properties of warm dense matter. The < 50 fs temporal duration of the x-ray pulse provides near instantaneous snapshots of the dynamics of the compression. We present a proof of principle experiment for this platform to characterize a shock-compressed plastic foil. We observe the disappearance of the plastic semi-crystal structure and the formation of a compressed liquid ion-ion correlation peak. The plasma parameters of shock-compressed plastic can be measured as well, but requires an averaging over a few tens of shots.
Predicting the sensitivity of the beryllium/scintillator layer neutron detector using Monte Carlo and experimental response functions
Authors: Styron J. D. , Cooper G. W. , Ruiz C. L. , Hahn K. D. , Chandler G. A. , Nelson A. J. , Torres J. A. , McWatters B. R. , Carpenter Ken , Bonura M. A.
Published: September 2014

A methodology for obtaining empirical curves relating absolute measured scintillation light output to beta energy deposited is presented. Output signals were measured from thin plastic scintillator using NIST traceable beta and gamma sources and MCNP5 was used to model the energy deposition from each source. Combining the experimental and calculated results gives the desired empirical relationships. To validate, the sensitivity of a beryllium/scintillator-layer neutron activation detector was predicted and then exposed to a known neutron fluence from a Deuterium-Deuterium fusion plasma (DD). The predicted and the measured sensitivity were in statistical agreement.
Robust and efficient variational fitting of Fock exchange
Authors: Mejía-Rodríguez Daniel , Köster Andreas M.
Published: September 2014

We propose a new variational fitting approach for Fock exchange that requires only the calculation of analytical three-center electron repulsion integrals. It relies on localized molecular orbitals and Hermite Gaussian auxiliary functions. The working equations along with a detailed description of the implementation are presented. The computational performance of the new algorithm is analyzed by benchmark calculations on systems with different dimensionality. Comparison with standard four-center and three-center electron repulsion integral Hartree-Fock calculations shows an excellent accuracy-performance relation.
Polarizability anisotropy relaxation in nanoconfinement: Molecular simulation study of water in cylindrical silica pores
Authors: Milischuk Anatoli A. , Ladanyi Branka M.
Published: September 2014

We report the results of a molecular simulation study of polarizability anisotropy relaxation for water confined in approximately cylindrical silica pores, with diameters in the range from 20 to 40 Å. In our calculations, we use a polarizability model that includes molecular and interaction-induced components. In agreement with optical Kerr effect experimental data, we find strong confinement effects on the relaxation rate of water polarizability anisotropy. Given that water molecular polarizability anisotropy is small, much of the intensity of the polarizability anisotropy response comes from the interaction-induced component. However, we find that, at longer times, the relaxation properties of this component strongly resemble those of collective reorientation, the mechanism by which the molecular polarizability anisotropy relaxes. We also find that the relevant collective orientational relaxation differs considerably from single molecule reorientation and that this difference varies with the extent of confinement. Our investigation of the effects of axial-radial pore anisotropy indicates that these effects play a minor role in water polarizability anisotropy relaxation in this pore diameter range.
Mean properties and free energy of a few hard spheres confined in a spherical cavity
Authors: Urrutia I. , Pastorino C.
Published: September 2014

We use analytical calculations and event-driven molecular dynamics simulations to study a small number of hard sphere particles in a spherical cavity. The cavity is also taken as the thermal bath so that the system thermalizes by collisions with the wall. In that way, these systems of two, three, and four particles, are considered in the canonical ensemble. We characterize various mean and thermal properties for a wide range of number densities. We study the density profiles, the components of the local pressure tensor, the interface tension, and the adsorption at the wall. This spans from the ideal gas limit at low densities to the high-packing limit in which there are significant regions of the cavity for which the particles have no access, due the conjunction of excluded volume and confinement. The contact density and the pressure on the wall are obtained by simulations and compared to exact analytical results. We also obtain the excess free energy for N = 4, by using a simulated-assisted approach in which we combine simulation results with the knowledge of the exact partition function for two and three particles in a spherical cavity.
A rigorous bound on the vertical transport of heat in Rayleigh-Bénard convection at infinite Prandtl number with mixed thermal boundary conditions
Authors: Whitehead Jared P. , Wittenberg Ralf W.
Published: September 2014

A rigorous upper bound on the Nusselt number is derived for infinite Prandtl number Rayleigh-Bénard convection for a fluid constrained between no-slip, mixed thermal vertical boundaries. The result suggests that the thermal boundary condition does not affect the qualitative nature of the heat transport. The bound is obtained with the use of a nonlinear, stably stratified background temperature profile in the bulk, notwithstanding the lack of boundary control of the temperature due to the Robin boundary conditions.
On combining temperature and pressure effects on structural properties of crystals with standard ab initio techniques
Authors: Erba A.
Published: September 2014

A general-purpose, fully automated, computationally efficient implementation is presented of a series of techniques for the simultaneous description of pressure and temperature effects on structural properties of materials, by means of standard ab initio simulations. Equilibrium volume, bulk modulus, thermal expansion coefficient, equation-of-state, Grüneisen parameter, constant-pressure and constant-volume specific heats are computed as a function of temperature and pressure for the simple crystal of diamond and compared with accurate experimental data. Convergence of computed properties with respect to super-cell size is critically discussed. The effect on such properties of the adopted exchange-correlation functional of the density-functional-theory is discussed by considering three different levels of approximation (including hybrids): it is found to be rather small for the temperature dependence of equilibrium volume and bulk modulus, whereas it is quite large as regards their absolute values.
An antenna-coupled split-ring resonator for biosensing
Authors: Torun H. , Cagri Top F. , Dundar G. , Yalcinkaya A. D.
Published: September 2014

An antenna-coupled split-ring resonator-based microwave sensor is introduced for biosensing applications. The sensor comprises a metallic ring with a slit and integrated monopole antennas on top of a dielectric substrate. The backside of the substrate is attached to a metallic plate. Integrated antennas are used to excite the device and measure its electromagnetic characteristics. The resonant frequency of the device is measured as 2.12 GHz. The characteristics of the device with dielectric loading at different locations across its surface are obtained experimentally. The results indicate that dielectric loading reduces the resonant frequency of the device, which is in good agreement with simulations. The shift in resonant frequency is employed as the sensor output for biomolecular experiments. The device is demonstrated as a resonant biomolecular sensor where the interactions between heparin and fibroblast growth factor 2 are probed. The sensitivity of the device is obtained as 3.7 MHz/(μg/ml) with respect to changes in concentration of heparin.
Laser energy deposition effectiveness on shock-wave boundary-layer interactions over cylinder-flare combinations
Authors: Osuka T. , Erdem E. , Hasegawa N. , Majima R. , Tamba T. , Yokota S. , Sasoh A. , Kontis K.
Published: September 2014

The effects of repetitive laser-pulse energy depositions (5.5 mJ/pulse) onto a shock wave-boundary layer interaction region over cylinder-flare model in a Mach 1.92 flow are experimentally investigated. Depending on the nose shape and the flare angle, the flow patterns are subdivided to two; separated flow in which a slip line and a strong separation shock wave originated in the nose-cylinder junction appears, and a non-separated flow in which a slip line is not observed and the re-attachment shock wave is much weaker. At flare angles around 30°, the separation can be suppressed by laser energy deposition even of down to 5 kHz. The Schlieren-visualized flow patterns are well correlated to the drag characteristics, in which a larger drag is obtained without separation. A possible scenario of the separation control is that the disturbance introduced by the baroclinic vortex ring induced the boundary layer transition so that it became robust against the adverse pressure gradient. Under marginal conditions, dual mode flow patterns, that is, a partial and full suppression modes are obtained under the same operation conditions.
Coupled ion acoustic and drift waves in magnetized superthermal electron-positron-ion plasmas
Authors: Adnan Muhammad , Mahmood S. , Qamar Anisa
Published: September 2014

Linear and nonlinear coupled drift-ion acoustic waves are investigated in a nonuniform magnetoplasma having kappa distributed electrons and positrons. In the linear regime, the role of kappa distribution and positron content on the dispersion relation has been highlighted; it is found that strong superthermality (low value of κ) and addition of positrons lowers the phase velocity via decreasing the fundamental scalelengths of the plasmas. In the nonlinear regime, first, coherent nonlinear structure in the form of dipoles and monopoles are obtained and the boundary conditions (boundedness) in the context of superthermality and positron concentrations are discussed. Second, in case of scalar nonlinearity, a Korteweg–de Vries-type equation is obtained, which admit solitary wave solution. It is found that both compressive and rarefactive solitons are formed in the present model. The present work may be useful to understand the low frequency electrostatic modes in inhomogeneous electron positron ion plasmas, which exist in astrophysical plasma situations such as those found in the pulsar magnetosphere.
Phase behaviors and membrane properties of model liposomes: Temperature effect
Authors: Wu Hsing-Lun , Sheng Yu-Jane , Tsao Heng-Kwong
Published: September 2014

The phase behaviors and membrane properties of small unilamellar vesicles have been explored at different temperatures by dissipative particle dynamics simulations. The vesicles spontaneously formed by model lipids exhibit pre-transition from gel to ripple phase and main transition from ripple to liquid phase. The vesicle shape exhibits the faceted feature at low temperature, becomes more sphere-like with increasing temperature, but loses its sphericity at high temperature. As the temperature rises, the vesicle size grows but the membrane thickness declines. The main transition (Tm) can be identified by the inflection point. The membrane structural characteristics are analyzed. The inner and outer leaflets are asymmetric. The length of the lipid tail and area density of the lipid head in both leaflets decrease with increasing temperature. However, the mean lipid volume grows at low temperature but declines at high temperature. The membrane mechanical properties are also investigated. The water permeability grows exponentially with increasing T but the membrane tension peaks at Tm. Both the bending and stretching moduli have their minima near Tm. Those results are consistent with the experimental observations, indicating that the main signatures associated with phase transition are clearly observed in small unilamellar vesicles.
Effect of shear stress on electromagnetic behaviors in superconductor-ferromagnetic bilayer structure
Authors: Yong Huadong , Zhao Meng , Jing Ze , Zhou Youhe
Published: September 2014

In this paper, the electromagnetic response and shielding behaviour of superconductor-ferromagnetic bilayer structure are studied. The magnetomechanical coupling in ferromagnetic materials is also considered. Based on the linear piezomagnetic coupling model and anti-plane shear deformation, the current density and magnetic field in superconducting strip are obtained firstly. The effect of shear stress on the magnetization of strip is discussed. Then, we consider the magnetic cloak for superconductor-ferromagnetic bilayer structure. The magnetic permeability of ferromagnetic material is obtained for perfect cloaking in uniform magnetic field with magnetomechanical coupling in ferromagnet. The simulation results show that the electromagnetic response in superconductors will change by applying the stress only to the ferromagnetic material. In addition, the performance of invisibility of structure for non-uniform field will be affected by mechanical stress. It may provide a method to achieve tunability of superconducting properties with mechanical loadings.
Electron impact rotationally elastic total cross section for formamide
Authors: Vinodkumar Minaxi , Limbachiya Chetan , Desai Hardik , Vinodkumar P. C.
Published: September 2014

This paper reports computational results of the total cross sections for electron impact on formamide (HCONH2) over a wide range of energies from 0.01 eV to 5 keV. Total cross sections over such a wide range are reported for the first time as the earlier reported data is up to maximum of 12 eV. Below ionization threshold of the target, we performed ab initio calculations using UK molecular R-Matrix code within static, exchange plus polarization (SEP), and close coupling approximations. Twenty eight target states are included in close coupling formalism. Total 350 channels and 2410 configuration state functions are included in the calculations. We observe a π* shape resonance at 3.41 eV and a σ* resonance at 15.3 eV as against similar resonances reported at 3.77 eV and 14.9 eV, respectively, by Goumans et al. [J. Chem. Theory Comput. 5, 217 (2009)] using SEP model. The cross sections at higher energies are evaluated using the spherical complex optical potential formalism. The two methods are found to be consistent with a smooth cross over at 18 eV. The vertical excitation energies, electronic excitation cross sections, differential cross sections, momentum transfer, and total cross sections are computed. In absence of experimental data, we compared our computed total cross sections with available other theoretical results.
Influence of Bi on the Er luminescence in yttrium-erbium disilicate thin films
Authors: Scarangella Adriana , Miritello Maria , Priolo Francesco
Published: September 2014

The influence of bismuth on erbium optical properties at 1.54 μm has been investigated in yttrium-erbium disilicate thin films synthesized by magnetron co-sputtering and implanted with two Bi different doses. The Bi depth distribution and the evolution of its oxidation states after annealing treatments at 1000 °C in two atmospheres, O2 and N2, have been investigated. It was found that only in O2 the Bi3+ valence state is prevalent, thanks to the enhanced Bi mobility in the oxidizing ambient, as demonstrated by Rutherford backscattering spectrometry. At lower Bi content, although the formation of Bi0 metallic nanoparticles that are deleterious non radiative channels for Er luminescence, efficient energy transfer from Bi to Er has been obtained only in O2. It is due to the excitation of ultraviolet broad Bi3+ absorption band and the energy transfer to Er ions. We have evaluated that in this case, Er effective excitation cross section increased by a factor of 5 in respect with the one for direct Er absorption at 488 nm. At higher Bi dose, this mechanism is absent, but an increased Er optical efficiency at 1.54 μm has been observed under resonant excitation. It is due to the contribution of a fraction of Er ions having an increased lifetime. This phenomenon is associated with the formation of Bi agglomerates, induced at higher Bi doses, which well isolate Er from non-radiative quenching centers. The increased decay time assures higher optical efficiency at 1.54 μm.
Double metal waveguide InGaAs/AlInAs quantum cascade lasers emitting at 24 μm
Authors: Ohtani K. , Beck M. , Faist J.
Published: September 2014

A study on far-infrared In0.53Ga0.47As/Al0.48In0.52As quantum cascade lasers operating with a double metal waveguide is presented. To increase the laser upper state lifetime, a diagonal bound-to-continuum transition scheme is used in the active region. The observed threshold current density at 50 K is 5.7 kA/cm2, and the maximum operation temperature is 240 K. The laser emission wavelength is 24.4 μm, which is the longest wavelength in the mid-infrared quantum cascade lasers so far reported.
Charge-carrier transport and recombination in heteroepitaxial CdTe
Authors: Kuciauskas Darius , Farrell Stuart , Dippo Pat , Moseley John , Moutinho Helio , Li Jian V. , Allende Motz A. M. , Kanevce Ana , Zaunbrecher Katherine , Gessert Timothy A. , Levi Dean H. , Metzger Wyatt K. , Colegrove Eric , Sivananthan S.
Published: September 2014

We analyze charge-carrier dynamics using time-resolved spectroscopy and varying epitaxial CdTe thickness in undoped heteroepitaxial CdTe/ZnTe/Si. By employing one-photon and nonlinear two-photon excitation, we assess surface, interface, and bulk recombination. Two-photon excitation with a focused laser beam enables characterization of recombination velocity at the buried epilayer/substrate interface, 17.5 μm from the sample surface. Measurements with a focused two-photon excitation beam also indicate a fast diffusion component, from which we estimate an electron mobility of 650 cm2 (Vs)−1 and diffusion coefficient D of 17 cm2 s−1. We find limiting recombination at the epitaxial film surface (surface recombination velocity Ssurface = (2.8 ± 0.3) × 105 cm s−1) and at the heteroepitaxial interface (interface recombination velocity Sinterface = (4.8 ± 0.5) × 105 cm s−1). The results demonstrate that reducing surface and interface recombination velocity is critical for photovoltaic solar cells and electronic devices that employ epitaxial CdTe.
Dynamics of polymer film formation during spin coating
Authors: Mouhamad Y. , Mokarian-Tabari P. , Clarke N. , Jones R. A. L. , Geoghegan M.
Published: September 2014

Standard models explaining the spin coating of polymer solutions generally fail to describe the early stages of film formation, when hydrodynamic forces control the solution behavior. Using in situ light scattering alongside theoretical and semi-empirical models, it is shown that inertial forces (which initially cause a vertical gradient in the radial solvent velocity within the film) play a significant role in the rate of thinning of the solution. The development of thickness as a function of time of a solute-free liquid (toluene) and a blend of polystyrene and poly(methyl methacrylate) cast from toluene were fitted to different models as a function of toluene partial pressure. In the case of the formation of the polymer blend film, a concentration-dependent (Huggins) viscosity formula was used to account for changes in viscosity during spin coating. A semi-empirical model is introduced, which permits calculation of the solvent evaporation rate and the temporal evolution of the solute volume fraction and solution viscosity.