bluuebunny/crossref_metadata_2025 huggingface dataset:
Impact of soil hydraulic parameter uncertainty on soil moisture modeling
Authors: Loosvelt Lien , Pauwels Valentijn R. N. , Cornelis Wim M. , De Lannoy Gabriëlle J. M. , Verhoest Niko E. C.
Published: March 2011

For simulations in basins where soil information is limited to soil type maps, a methodology is presented to quantify the uncertainty of soil hydraulic parameters arising from within‐soil‐class variability and to assess the impact of this uncertainty on soil moisture modeling. Continuous pedotransfer functions were applied to samples with different texture within each soil class to construct discrete probability distributions of the soil hydraulic parameters. When propagating the parameter distributions through a hydrologic model, a wide range of simulated soil moisture was generated within a single soil class. The pedotransfer function was found to play a crucial role in assessing the uncertainty in the modeled soil moisture, and the geographic origin of the pedotransfer function (region specific versus nonregion specific) highly affected the range and shape of the probability distribution of the soil hydraulic parameters. Furthermore, the modeled soil moisture distribution was found to be non‐Gaussian. An accurate uncertainty assessment therefore requires the characterization of its higher‐order moments. As an extension of this research, we have shown that applying continuous region‐specific pedotransfer functions to the central point of a soil class is a better alternative to standard (often nonregion‐specific) class pedotransfer functions for determining an average set of soil hydraulic parameters.
Consider the octopus
Authors: Morris Simon Conway
Published: March 2011

Being attacked by an octopus gives the opportunity to marvel at how convergent evolution created similar organs and senses in cephalopod and man.
Microbial rights?
Authors: Cockell Charles S
Published: March 2011

Our ability to disrupt habitats and manipulate living organisms requires a discussion of the ethics of microbiology, even if we argue that microbes themselves have no rights.
Therapeutic Hypothermia Influences Cell Genesis and Survival in the Rat Hippocampus following Global Ischemia
Authors: Silasi Gergely , Colbourne Frederick
Published: March 2011

Delayed hypothermia salvages CA1 neurons from global ischemic injury. However, the effects of this potent neuroprotectant on endogenous repair mechanisms, such as neurogenesis, have not been clearly examined. In this study, we quantified and phenotyped newly generated cells within the hippocampus following untreated and hypothermia-treated ischemia. We first show that CA1 pyramidal neurons did not spontaneously regenerate after ischemia. We then compared the level of neuroprotection when hypothermia was initiated either during or after ischemia. Treatment efficacy decreased with longer delays, but hypothermia delayed for up to 12 hours was neuroprotective. Although bromodeoxyuridine (BrdU) incorporation was elevated in ischemic groups, CA1 neurogenesis did not occur as the BrdU label did not colocalize with neuronal nuclei (NeuN) in any of the groups. Instead, the majority of BrdU-labeled cells were Iba-positive microglia, and neuroprotective hypothermia decreased the delayed generation of microglia during the third postischemic week. Conversely, hypothermia delayed for 12 hours significantly increased the survival of newly generated dentate granule cells at 4 weeks after ischemia. Thus, our findings show that CA1 neurogenesis does not contribute to hypothermic neuroprotection. Importantly, we also show that prolonged hypothermia positively interacts with postischemic repair processes, such as neurogenesis, resulting in improved functional outcome.
MONW Phenotype Is Associated With Advanced Colorectal Adenoma in Korean Men
Authors: Kim Moon‐Chan , Kim Chang‐Sup , Chung Tae‐Heum , Jeong Joseph , Lee Seon‐Ho , Kim Sung‐Ryul , Jung Seok‐Won , Park Neung‐Hwa , Yoo Cheol‐In
Published: March 2011

The aim of this study was to investigate whether there was a relationship between colorectal adenoma and metabolically obese but normal weight (MONW) among Korean men and women. The MONW phenotype is defined as a BMI <25, but fulfilling the metabolic syndrome (MS) criteria with a modified waist circumference (≥90 cm for men and ≥85 cm for women) appropriate for Korean. A total of 3,430 subjects (2,263 men and 1,167 women; 23–75 years old) were included in the study. Colorectal adenomas were diagnosed in 775 men and 199 women. The rate of advanced adenomas in males was 24.3% and in females 21.1%. A significant association between MONW and advanced colorectal adenoma was found in men (age‐adjusted odds ratio (OR) = 1.92, 95% confidence interval (CI): 1.06–3.47) but not in women (age‐adjusted OR = 1.80, 95% CI: 0.50–6.45). The findings suggest that men with MONW may have an increased risk of developing advanced colorectal adenoma whereas this does not seem true for females.
A Better Index of Body Adiposity
Authors: Bergman Richard N. , Stefanovski Darko , Buchanan Thomas A. , Sumner Anne E. , Reynolds James C. , Sebring Nancy G. , Xiang Anny H. , Watanabe Richard M.
Published: March 2011

Obesity is a growing problem in the United States and throughout the world. It is a risk factor for many chronic diseases. The BMI has been used to assess body fat for almost 200 years. BMI is known to be of limited accuracy, and is different for males and females with similar %body adiposity. Here, we define an alternative parameter, the body adiposity index (BAI = ((hip circumference)/((height)1.5)–18)). The BAI can be used to reflect %body fat for adult men and women of differing ethnicities without numerical correction. We used a population study, the “BetaGene” study, to develop the new index of body adiposity. %Body fat, as measured by the dual‐energy X‐ray absorptiometry (DXA), was used as a “gold standard” for validation. Hip circumference (R = 0.602) and height (R = −0.524) are strongly correlated with %body fat and therefore chosen as principal anthropometric measures on which we base BAI. The BAI measure was validated in the “Triglyceride and Cardiovascular Risk in African‐Americans (TARA)” study of African Americans. Correlation between DXA‐derived %adiposity and the BAI was R = 0.85 for TARA with a concordance of C_b = 0.95. BAI can be measured without weighing, which may render it useful in settings where measuring accurate body weight is problematic. In summary, we have defined a new parameter, the BAI, which can be calculated from hip circumference and height only. It can be used in the clinical setting even in remote locations with very limited access to reliable scales. The BAI estimates %adiposity directly.
Identification and characterization of an inhibitory fibroblast growth factor receptor 2 (FGFR2) molecule, up-regulated in an Apert Syndrome mouse model
Authors: Wheldon Lee M. , Khodabukus Naila , Patey Susannah J. , Smith Terence G. , Heath John K. , Hajihosseini Mohammad K.
Published: March 2011

AS (Apert syndrome) is a congenital disease composed of skeletal, visceral and neural abnormalities, caused by dominant-acting mutations in FGFR2 [FGF (fibroblast growth factor) receptor 2]. Multiple FGFR2 splice variants are generated through alternative splicing, including PTC (premature termination codon)-containing transcripts that are normally eliminated via the NMD (nonsense-mediated decay) pathway. We have discovered that a soluble truncated FGFR2 molecule encoded by a PTC-containing transcript is up-regulated and persists in tissues of an AS mouse model. We have termed this IIIa–TM as it arises from aberrant splicing of FGFR2 exon 7 (IIIa) into exon 10 [TM (transmembrane domain)]. IIIa–TM is glycosylated and can modulate the binding of FGF1 to FGFR2 molecules in BIAcore-binding assays. We also show that IIIa–TM can negatively regulate FGF signalling in vitro and in vivo. AS phenotypes are thought to result from gain-of-FGFR2 signalling, but our findings suggest that IIIa–TM can contribute to these through a loss-of-FGFR2 function mechanism. Moreover, our findings raise the interesting possibility that FGFR2 signalling may be a regulator of the NMD pathway.
Biochemical correlation of activity of the α-dystroglycan-modifying glycosyltransferase POMGnT1 with mutations in muscle-eye-brain disease
Authors: Voglmeir Josef , Kaloo Sara , Laurent Nicolas , Meloni Marco M. , Bohlmann Lisa , Wilson Iain B. H. , Flitsch Sabine L.
Published: March 2011

Congenital muscular dystrophies have a broad spectrum of genotypes and phenotypes and there is a need for a better biochemical understanding of this group of diseases in order to aid diagnosis and treatment. Several mutations resulting in these diseases cause reduced O-mannosyl glycosylation of glycoproteins, including α-dystroglycan. The enzyme POMGnT1 (protein-O-mannose N-acetylglucosaminyltransferase 1; EC 2.4.1.-) catalyses the transfer of N-acetylglucosamine to O-linked mannose of α-dystroglycan. In the present paper we describe the biochemical characterization of 14 clinical mutants of the glycosyltransferase POMGnT1, which have been linked to muscle-eye-brain disease or similar conditions. Truncated mutant variants of the human enzyme (recombinant POMGnT1) were expressed in Escherichia coli and screened for catalytic activity. We find that three mutants show some activity towards mannosylated peptide substrates mimicking α-dystroglycan; the residues affected by these mutants are predicted by homology modelling to be on the periphery of the POMGnT1 surface. Only in part does the location of a previously described mutated residue on the periphery of the protein structure correlate with a less severe disease mutant.
Carnitine palmitoyltransferase 1A prevents fatty acid-induced adipocyte dysfunction through suppression of c-Jun N-terminal kinase
Authors: Gao Xuefei , Li Kuai , Hui Xiaoyan , Kong Xiangping , Sweeney Gary , Wang Yu , Xu Aimin , Teng Maikun , Liu Pentao , Wu Donghai
Published: March 2011

The adipocyte is the principal cell type for fat storage. CPT1 (carnitine palmitoyltransferase-1) is the rate-limiting enzyme for fatty acid β-oxidation, but the physiological role of CPT1 in adipocytes remains unclear. In the present study, we focused on the specific role of CPT1A in the normal functioning of adipocytes. Three 3T3-L1 adipocyte cell lines stably expressing hCPT1A (human CPT1A) cDNA, mouse CPT1A shRNA (short-hairpin RNA) or GFP (green fluorescent protein) were generated and the biological functions of these cell lines were characterized. Alteration in CPT1 activity, either by ectopic overexpression or pharmacological inhibition using etomoxir, did not affect adipocyte differentiation. However, overexpression of hCPT1A significantly reduced the content of intracellular NEFAs (non-esterified fatty acids) compared with the control cells when adipocytes were challenged with fatty acids. The changes were accompanied by an increase in fatty acid uptake and a decrease in fatty acid release. Interestingly, CPT1A protected against fatty acid-induced insulin resistance and expression of pro-inflammatory adipokines such as TNF-α (tumour necrosis factor-α) and IL-6 (interleukin-6) in adipocytes. Further studies demonstrated that JNK (c-Jun N terminal kinase) activity was substantially suppressed upon CPT1A overexpression, whereas knockdown or pharmacological inhibition of CPT1 caused a significant enhancement of JNK activity. The specific inhibitor of JNK SP600125 largely abolished the changes caused by the shRNA- and etomoxir-mediated decrease in CPT1 activity. Moreover, C2C12 myocytes co-cultured with adipocytes pre-treated with fatty acids displayed altered insulin sensitivity. Taken together, our findings have identified a favourable role for CPT1A in adipocytes to attenuate fatty acid-evoked insulin resistance and inflammation via suppression of JNK.
The expression of nicotinamideN-methyltransferase increases ATP synthesis and protects SH-SY5Y neuroblastoma cells against the toxicity of Complex I inhibitors
Authors: Parsons Richard B. , Aravindan Shylesh , Kadampeswaran Anusha , Evans Emily A. , Sandhu Kanwaljeet K. , Levy Elizabeth R. , Thomas Martin G. , Austen Brian M. , Ramsden David B.
Published: March 2011

NNMT (nicotinamide N-methyltransferase, E.C. 2.1.1.1) catalyses the N-methylation of nicotinamide to 1-methylnicotinamide. NNMT expression is significantly elevated in a number of cancers, and we have previously demonstrated that NNMT expression is significantly increased in the brains of patients who have died of Parkinson's disease. To investigate the cellular effects of NNMT overexpression, we overexpressed NNMT in the SH-SY5Y cell line, a tumour-derived human dopaminergic neuroblastoma cell line with no endogenous expression of NNMT. NNMT expression significantly decreased SH-SY5Y cell death, which correlated with increased intracellular ATP content, ATP/ADP ratio and Complex I activity, and a reduction in the degradation of the NDUFS3 [NADH dehydrogenase (ubiquinone) iron–sulfur protein 3] subunit of Complex I. These effects were replicated by incubation of SH-SY5Y cells with 1-methylnicotinamide, suggesting that 1-methylnicotinamide mediates the cellular effects of NNMT. Both NNMT expression and 1-methylnicotinamide protected SH-SY5Y cells from the toxicity of the Complex I inhibitors MPP+ (1-methyl-4-phenylpyridinium ion) and rotenone by reversing their effects upon ATP synthesis, the ATP/ADP ratio, Complex I activity and the NDUFS3 subunit. The results of the present study raise the possibility that the increase in NNMT expression that we observed in vivo may be a stress response of the cell to the underlying pathogenic process. Furthermore, the results of the present study also raise the possibility of using inhibitors of NNMT for the treatment of cancer.
Impaired hepatic insulin signalling in PON2-deficient mice: a novel role for the PON2/apoE axis on the macrophage inflammatory response
Authors: Bourquard Noam , Ng Carey J. , Reddy Srinivasa T.
Published: March 2011

Hepatic glucose metabolism is strongly influenced by oxidative stress and pro-inflammatory stimuli. PON2 (paraoxonase 2), an enzyme with undefined antioxidant properties, protects against atherosclerosis. PON2-deficient (PON2-def) mice have elevated hepatic oxidative stress coupled with an exacerbated inflammatory response from PON2-deficient macrophages. In the present paper, we demonstrate that PON2 deficiency is associated with inhibitory insulin-mediated phosphorylation of hepatic IRS-1 (insulin receptor substrate-1). Unexpectedly, we observed a marked improvement in the hepatic IRS-1 phosphorylation state in PON2-def/apoE (apolipoprotein E)−/− mice, relative to apoE−/− mice. Factors secreted from activated macrophage cultures derived from PON2-def and PON2-def/apoE−/− mice are sufficient to modulate insulin signalling in cultured hepatocytes in a manner similar to that observed in vivo. We show that the protective effect on insulin signalling in PON2-def/apoE−/− mice is directly associated with altered production of macrophage pro-inflammatory mediators, but not elevated intracellular oxidative stress levels. We further present evidence that modulation of the macrophage inflammatory response in PON2-def/apoE−/− mice is mediated by a shift in the balance of NO and ONOO− (peroxynitrite) formation. Our results demonstrate that PON2 plays an important role in hepatic insulin signalling and underscores the influence of macrophage-mediated inflammatory response on hepatic insulin sensitivity.
Function of the CysD domain of the gel-forming MUC2 mucin
Authors: Ambort Daniel , van der Post Sjoerd , Johansson Malin E. V. , MacKenzie Jenny , Thomsson Elisabeth , Krengel Ute , Hansson Gunnar C.
Published: March 2011

The colonic human MUC2 mucin forms a polymeric gel by covalent disulfide bonds in its N- and C-termini. The middle part of MUC2 is largely composed of two highly O-glycosylated mucin domains that are interrupted by a CysD domain of unknown function. We studied its function as recombinant proteins fused to a removable immunoglobulin Fc domain. Analysis of affinity-purified fusion proteins by native gel electrophoresis and gel filtration showed that they formed oligomeric complexes. Analysis of the individual isolated CysD parts showed that they formed dimers both when flanked by two MUC2 tandem repeats and without these. Cleavages of the two non-reduced CysD fusion proteins and analysis by MS revealed the localization of all five CysD disulfide bonds and that the predicted C-mannosylated site was not glycosylated. All disulfide bonds were within individual peptides showing that the domain was stabilized by intramolecular disulfide bonds and that CysD dimers were of non-covalent nature. These observations suggest that CysD domains act as non-covalent cross-links in the MUC2 gel, thereby determining the pore sizes of the mucus.
Structures of the substrate-binding protein provide insights into the multiple compatible solute binding specificities of the Bacillus subtilis ABC transporter OpuC
Authors: Du Yang , Shi Wei-Wei , He Yong-Xing , Yang Yi-Hu , Zhou Cong-Zhao , Chen Yuxing
Published: March 2011

The compatible solute ABC (ATP-binding cassette) transporters are indispensable for acquiring a variety of compatible solutes under osmotic stress in Bacillus subtilis. The substrate-binding protein OpuCC (Opu is osmoprotectant uptake) of the ABC transporter OpuC can recognize a broad spectrum of compatible solutes, compared with its 70% sequence-identical paralogue OpuBC that can solely bind choline. To explore the structural basis of this difference of substrate specificity, we determined crystal structures of OpuCC in the apo-form and in complex with carnitine, glycine betaine, choline and ectoine respectively. OpuCC is composed of two α/β/α globular sandwich domains linked by two hinge regions, with a substrate-binding pocket located at the interdomain cleft. Upon substrate binding, the two domains shift towards each other to trap the substrate. Comparative structural analysis revealed a plastic pocket that fits various compatible solutes, which attributes the multiple-substrate binding property to OpuCC. This plasticity is a gain-of-function via a single-residue mutation of Thr94 in OpuCC compared with Asp96 in OpuBC.
hZwint-1 bridges the inner and outer kinetochore: identification of the kinetochore localization domain and the hZw10-interaction domain
Authors: Vos Larissa J. , Famulski Jakub K. , Chan Gordon K. T.
Published: March 2011

Accurate chromosome segregation in mitosis is required to maintain genetic stability. hZwint-1 [human Zw10 (Zeste white 10)-interacting protein 1] is a kinetochore protein known to interact with the kinetochore checkpoint protein hZw10. hZw10, along with its partners Rod (Roughdeal) and hZwilch, form a complex which recruits dynein–dynactin and Mad1–Mad2 complexes to the kinetochore and are essential components of the mitotic checkpoint. hZwint-1 localizes to the kinetochore in prophase, before hZw10 localization, and remains at the kinetochore until anaphase, after hZw10 has dissociated. This difference in localization timing may reflect a role for hZwint-1 as a structural kinetochore protein. In addition to hZw10, we have found that hZwint-1 interacts with components of the conserved Ndc80 and Mis12 complexes in yeast two-hybrid and GST (glutathione transferase) pull-down assays. Furthermore, hZwint-1 was found to have stable FRAP (fluorescence recovery after photobleaching) dynamics similar to hHec1, hSpc24 and hMis12. As such, we proposed that hZwint-1 is a structural protein, part of the inner kinetochore scaffold and recruits hZw10 to the kinetochore. To test this, we performed mutagenesis-based domain mapping to determine which regions of hZwint-1 are necessary for kinetochore localization and which are required for interaction with hZw10. hZwint-1 localizes to the kinetochore through the N-terminal region and interacts with hZw10 through the C-terminal coiled-coil domain. The two domains are at opposite ends of the protein as expected for a protein that bridges the inner and outer kinetochore.
The neurosteroid dehydroepiandrosterone could improve somatic cell reprogramming
Authors: Shoae‐Hassani Alireza , Sharif Shiva , Verdi Javad
Published: March 2011

Expression of four major reprogramming transgenes, including Oct4, Sox2, Klf4 and c‐myc, in somatic cells enables them to have pluripotency. These cells are iPSC (induced pluripotent stem cell) that currently show the greatest potential for differentiation into cells of the three germ lineages. One of the issues facing the successful reprogramming and clinical translation of iPSC technology is the high rate of apoptosis after the reprogramming process. Reprogramming is a stressful process, and the p53 apoptotic pathway plays a negative role in cell growth and self‐renewal. Apoptosis via the p53 pathway serves as a major barrier in nuclear somatic cell reprogramming during iPSC generation. DHEA (dehydroepiandrosterone) is an abundant steroid that is produced at high levels in the adrenal cells, and withdrawal of DHEA increases the levels of p53 in the epithelial and stromal cells, resulting in increased levels of apoptotic cells; meanwhile, DHEA decreases cellular apoptosis. DHEA could improve the efficacy of reprogramming yield due to a decrease in apoptosis via the p53 pathway and an increase in cell viability.
Note: Quantitative (artifact-free) surface potential measurements using Kelvin force microscopy
Authors: Mélin T. , Barbet S. , Diesinger H. , Théron D. , Deresmes D.
Published: March 2011

The measurement of local surface potentials by Kelvin force microscopy (KFM) can be sensitive to external perturbations which lead to artifacts such as strong dependences of experimental results (typically in a ∼1 V range) with KFM internal parameters (cantilever excitation frequency and/or the projection phase of the KFM feedback-loop). We analyze and demonstrate a correction of such effects on a KFM implementation in ambient air. Artifact-free KFM measurements, i.e., truly quantitative surface potential measurements, are obtained with a ∼30 mV accuracy.
Experimental setup for camera-based measurements of electrically and optically stimulated luminescence of silicon solar cells and wafers
Authors: Hinken David , Schinke Carsten , Herlufsen Sandra , Schmidt Arne , Bothe Karsten , Brendel Rolf
Published: March 2011

We report in detail on the luminescence imaging setup developed within the last years in our laboratory. In this setup, the luminescence emission of silicon solar cells or silicon wafers is analyzed quantitatively. Charge carriers are excited electrically (electroluminescence) using a power supply for carrier injection or optically (photoluminescence) using a laser as illumination source. The luminescence emission arising from the radiative recombination of the stimulated charge carriers is measured spatially resolved using a camera. We give details of the various components including cameras, optical filters for electro- and photo-luminescence, the semiconductor laser and the four-quadrant power supply. We compare a silicon charged-coupled device (CCD) camera with a back-illuminated silicon CCD camera comprising an electron multiplier gain and a complementary metal oxide semiconductor indium gallium arsenide camera. For the detection of the luminescence emission of silicon we analyze the dominant noise sources along with the signal-to-noise ratio of all three cameras at different operation conditions.
Patterned anvils for high pressure measurements at low temperature
Authors: Welzel Oliver P. , Grosche F. Malte
Published: March 2011

Multiprobe high pressure measurements require electrical leads in the sample chamber. Compared to conventional wire-based techniques, metallic tracks patterned onto the anvil surface improve reliability and ease of use, and enable novel and more demanding measurements under high pressure. We have developed new anvil designs based on sputter-deposited tracks on alumina and moissanite anvils. These anvils allow convenient and reliable measurements of electrical transport properties or of the magnetic susceptibility under hydrostatic conditions, as demonstrated by test measurements on Pb and Ca3Ru2O7.
Simultaneous polarized neutron reflectometry and anisotropic magnetoresistance measurements
Authors: Demeter J. , Teichert A. , Kiefer K. , Wallacher D. , Ryll H. , Menéndez E. , Paramanik D. , Steitz R. , Van Haesendonck C. , Vantomme A. , Temst K.
Published: March 2011

A novel experimental facility to carry out simultaneous polarized neutron reflectometry (PNR) and anisotropic magnetoresistance (AMR) measurements is presented. Performing both techniques at the same time increases their strength considerably. The proof of concept of this method is demonstrated on a CoO/Co bilayer exchange bias system. Although information on the same phenomena, such as the coercivity or the reversal mechanism, can be separately obtained from either of these techniques, the simultaneous application optimizes the consistency between both. In this way, possible differences in experimental conditions, such as applied magnetic field amplitude and orientation, sample temperature, magnetic history, etc., can be ruled out. Consequently, only differences in the fundamental sensitivities of the techniques can cause discrepancies in the interpretation between the two. The almost instantaneous information obtained from AMR can be used to reveal time-dependent effects during the PNR acquisition. Moreover, the information inferred from the AMR measurements can be used for optimizing the experimental conditions for the PNR measurements in a more efficient way than with the PNR measurements alone.
Microstructural and magnetic properties of (La0.7Sr0.3MnO3)0.7:(Mn3O4)0.3 nanocomposite thin films
Authors: Bi Zhenxing , Weal Emily , Luo Hongmei , Chen Aiping , MacManus-Driscoll Judith L. , Jia Quanxi , Wang Haiyan
Published: March 2011

Epitaxial (La0.7Sr0.3MnO3)0.7:(Mn3O4)0.3 (LSMO:Mn3O4) nanocomposite thin films were grown on SrTiO3 (001) substrate by a pulsed laser deposition technique. The nanocomposite structures vary from triangular domains, to vertically aligned columns, and finally to smaller spherical domains as the deposition frequency varies from 1, 5, to 10 Hz, respectively. The strain in LSMO is systematically tuned, but that of the Mn3O4 phase is relatively stable as the deposition frequency increases. The tunable strain is found directly related to the different domain and grain boundary (GB) structures. Physical properties including saturation magnetization, Curie temperature (TC), magnetoresistance and metal–insulator transition temperature (TMI), all show systematic trends as the deposition frequency varies. This study reveals that the domain/GBs tunability achieved in nanocomposite thin films can affect the lattice strain and further tune their ferromagnetic properties.
Doped, porous iron oxide films and their optical functions and anodic photocurrents for solar water splitting
Authors: Kronawitter Coleman X. , Mao Samuel S. , Antoun Bonnie R.
Published: March 2011

The fabrication and morphological, optical, and photoelectrochemical characterization of doped iron oxide films is presented. The complex index of refraction and absorption coefficient of polycrystalline films are determined through measurement and modeling of spectral transmission and reflection data using appropriate dispersion relations. Photoelectrochemical characterization for water photo-oxidation reveals that the conversion efficiencies of electrodes are strongly influenced by substrate temperature during their oblique-angle physical vapor deposition. These results are discussed in terms of the films’ morphological features and the known optoelectronic limitations of iron oxide films for application in solar water splitting devices.
Experimental arrangements suitable for the acquisition of inelastic neutron scattering spectra of heterogeneous catalysts
Authors: Silverwood Ian P. , Hamilton Neil G. , McFarlane Andrew , Ormerod R. Mark , Guidi Tatiana , Bones Jonathan , Dudman Michael P. , Goodway Christopher M. , Kibble Mark , Parker Stewart F. , Lennon David
Published: March 2011

Inelastic neutron scattering (INS) is increasingly being used for the characterization of heterogeneous catalysts. As the technique is uniquely sensitive to hydrogen atoms, vibrational spectra can be obtained that emphasize a hydrogenous component or hydrogen-containing moieties adsorbed on to an inorganic support. However, due to sensitivity constraints, the technique typically requires large sample masses (∼10 g catalyst). A reaction system is hereby described that enables suitable quantities of heterogeneous catalysts to be appropriately activated and operated under steady-state conditions for extended periods of time prior to acquisition of the INS spectrum. In addition to ex situ studies, a cell is described which negates the need for a sample transfer stage between reaction testing and INS measurement. This cell can operate up to temperatures of 823 K and pressures up to 20 bar. The apparatus is also amenable to adsorption experiments at the gas–solid interface.
Terahertz localized surface plasmon resonance of periodic silicon microring arrays
Authors: Grant J. , Shi X. , Alton J. , Cumming D. R. S.
Published: March 2011

We demonstrate the absorption characteristics of silicon microring resonators at terahertz frequencies. Simulation and experimental data show a dipolar localized surface plasmon resonance (DLSPR) absorption peak. We demonstrate that the frequency position and magnitude of the DLSPR peak may be tuned by varying the geometry and thickness of the microring or by modification of the silicon impurity concentration. Finite difference time domain simulations reveal that there is a strong enhancement of the electric field at the resonant frequency. The absorption properties of our resonator are described in terms of effective optical constants and reveal that the silicon microring is an electric resonator. Surface plasmon resonators are efficient terahertz absorbers and have potential applications in security imaging, biological analysis, spectroscopy and nondestructive testing.
Optimizing facet coating of quantum cascade lasers for low power consumption
Authors: Bai Y. , Darvish S. R. , Bandyopadhyay N. , Slivken S. , Razeghi M.
Published: March 2011

Typical high power consumption (∼10 W) of mid-infrared quantum cascade lasers (QCLs) has been a serious limitation for applications in battery powered systems. A partial high-reflection (PHR) coating technique is introduced for power downscaling with shorter cavity lengths. The PHR coating consists of a double layer dielectric of SiO2 and Ge. With this technique, a 4.6 μm QCL with an ultra low threshold power consumption of less than a watt (0.83 W) is demonstrated in room temperature continuous wave operation. At 25°C, the maximum output power and wall plug efficiency are 192 mW and 8.6%, respectively.
Electric field control of magnetic anisotropies and magnetic coercivity in Fe/BaTiO3(001) heterostructures
Authors: Brivio S. , Petti D. , Bertacco R. , Cezar J. C.
Published: March 2011

Magnetoelectric effects in Fe/BaTiO3(001) heterostructures have been investigated via magneto-optical Kerr effect as a function of temperature. We find major modifications of magnetic anisotropies and magnetic coercivity induced by the application of electric fields perpendicular to the interface. Changes in the coercive magnetic field, on the order of 100% at 250 K (in the orthorhombic phase of BaTiO3) and 40% at 300 K (in the tetragonal phase), which are linked to the ferroelectric behavior of BaTiO3, are reported.
Cryogenic microwave imaging of metal–insulator transition in doped silicon
Authors: Kundhikanjana Worasom , Lai Keji , Kelly Michael A. , Shen Zhi-Xun
Published: March 2011

We report the instrumentation and experimental results of a cryogenic scanning microwave impedance microscope. The microwave probe and the scanning stage are located inside the variable temperature insert of a helium cryostat. Microwave signals in the distance modulation mode are used for monitoring the tip-sample distance and adjusting the phase of the two output channels. The ability to spatially resolve the metal–insulator transition in a doped silicon sample is demonstrated. The data agree with a semiquantitative finite element simulation. Effects of the thermal energy and electric fields on local charge carriers can be seen in the images taken at different temperatures and dc biases.
Dependence of transport on adatom location for armchair-edge graphene nanoribbons
Authors: Chen Xiongwen , Song Kehui , Zhou Benhu , Wang Haiyan , Zhou Guanghui
Published: March 2011

We study the transport property for armchair-edge graphene nanoribbons (AGNRs) with an adatom coupling to a semi-infinite quantum wire. Using the nonequilibrium Green’s function (NEGF) approach with tight-binding approximation, we demonstrate that the tunneling current through the system is sensitively dependent on both the AGNR width and adatom location. Interestingly, when the adatom locates onto a carbon atom in the 3jth chain from the edge of a metallic AGNR, the system shows a transmission gap accompanied by a threshold voltage like a semiconducting AGNR. This effect may be useful in scanning tunneling microscopy experimental characterization on graphene samples.
A gyrokinetic collision operator for magnetized Lorentz plasmas
Authors: Liu Chang , Qin Hong , Ma Chenhao , Yu Xiongjie
Published: March 2011

A gyrocenter collision operator for magnetized Lorentz plasmas is derived using the Fokker–Plank method. The gyrocenter collision operator consists of drift and diffusion terms in the gyrocenter coordinates, including the diffusion of the gyrocenter, which does not exist for the collision operator in the particle phase space coordinates. The gyrocenter collision operator also depends on the transverse electric field explicitly, which is crucial for the correct treatment of collisional effects and transport in the gyrocenter coordinates. The gyrocenter collision operator derived is applied to calculate the particle and heat transport fluxes in a magnetized Lorentz plasma with an electric field. The particle and heat transport fluxes calculated from our gyrocenter collision operator agree exactly with the classical Braginskii’s result [S. I. Braginskii, Reviews of Plasma Physics (Consultants Bureau, New York, 1965), Vol. 1, p. 205: P. Helander and D. J. Sigmar, Collisional Transport in Magnetized Plasmas (Cambridge University, Cambridge, 2002), p. 65], which validates the correctness of our collision operator. To calculate the transport fluxes correctly, it is necessary to apply the pullback transformation associated with gyrocenter coordinate transformation in the presence of collisions, which also serves as a practical algorithm for evaluating collisional particle and heat transport fluxes in the gyrocenter coordinates.
High-level direct-dynamics variational transition state theory calculations including multidimensional tunneling of the thermal rate constants, branching ratios, and kinetic isotope effects of the hydrogen abstraction reactions from methanol by atomic hydrogen
Authors: Meana-Pañeda Rubén , Truhlar Donald G. , Fernández-Ramos Antonio
Published: March 2011

We report a detailed theoretical study of the hydrogen abstraction reaction from methanol by atomic hydrogen. The study includes the analysis of thermal rate constants, branching ratios, and kinetic isotope effects. Specifically, we have performed high-level computations at the MC3BB level together with direct dynamics calculations by canonical variational transition state theory (CVT) with the microcanonically optimized multidimensional tunneling (μOMT) transmission coefficient (CVT/μOMT) to study both the CH3OH + H → CH2OH + H2 (R1) reaction and the CH3OH + H → CH3O + H2 (R2) reaction. The CVT/μOMT calculations show that reaction R1 dominates in the whole range \documentclass[12pt]{minimal}\begin{document}$298\le T(\rm K)\le 2500$\end{document}298≤T(K)≤2500 and that anharmonic effects on the torsional mode about the C–O bond are important, mainly at high temperatures. The activation energy for the total reaction sum of R1 and R2 reactions changes substantially with temperature and, therefore, the use of straight-line Arrhenius plots is not valid. We recommend the use of new expressions for the total R1 + R2 reaction and for the R1 and R2 individual reactions.
A combined ion-sputtering and electron-beam annealing device for the in vacuo postpreparation of scanning probes
Authors: Eder Georg , Schlögl Stefan , Macknapp Klaus , Heckl Wolfgang M. , Lackinger Markus
Published: March 2011

We describe the setup, characteristics, and application of an in vacuo ion-sputtering and electron-beam annealing device for the postpreparation of scanning probes (e.g., scanning tunneling microscopy (STM) tips) under ultrahigh vacuum (UHV) conditions. The proposed device facilitates the straightforward implementation of a common two-step cleaning procedure, where the first step consists of ion-sputtering, while the second step heals out sputtering-induced defects by thermal annealing. In contrast to the standard way, no dedicated external ion-sputtering gun is required with the proposed device. The performance of the described device is demonstrated by SEM micrographs and energy dispersive x-ray characterization of electrochemically etched tungsten tips prior and after postprocessing.
A molecular theory for two-photon and three-photon fluorescence polarization
Authors: Leeder J. M. , Andrews D. L.
Published: March 2011

In the analysis of molecular structure and local order in heterogeneous samples, multiphoton excitation of fluorescence affords chemically specific information and high-resolution imaging. This report presents the results of an investigation that secures a detailed theoretical representation of the fluorescence polarization produced by one-, two-, and three-photon excitations, with orientational averaging procedures being deployed to deliver the fully disordered limits. The equations determining multiphoton fluorescence response prove to be expressible in a relatively simple, generic form, and graphs exhibit the functional form of the multiphoton fluorescence polarization. Amongst other features, the results lead to the identification of a condition under which the fluorescence produced through the concerted absorption of any number of photons becomes completely unpolarized. It is also shown that the angular variation of fluorescence intensities is reliable indicator of orientational disorder.
Power-law dependence of the melting temperature of ubiquitin on the volume fraction of macromolecular crowders
Authors: Waegele Matthias M. , Gai Feng
Published: March 2011

The dependence of the melting temperature increase (ΔTm) of the protein ubiquitin on the volume fraction (φ) of several commonly used macromolecular crowding agents (dextran 6, 40, and 70 and ficoll 70) was quantitatively examined and compared to a recently developed theoretical crowding model, i.e., ΔTm ∼ (Rg/Rc)αφα/3. We found that in the current case this model correctly predicts the power-law dependence of ΔTm on φ but significantly overestimates the role of the size (i.e., Rc) of the crowding agent. In addition, we found that for ubiquitin the exponent α is in the range of 4.1−6.5, suggesting that the relation of α = 3/(3ν − 1) is a better choice for estimating α based on the Flory coefficient (ν) of the polypeptide chain. Taken together these findings highlight the importance of improving our knowledge and theoretical treatment of the microcompartmentalization of the commonly used model crowding agents.
Ultrafast photo-excitation dynamics in isolated, neutral water clusters
Authors: Liu H. T. , Müller J. P. , Beutler M. , Ghotbi M. , Noack F. , Radloff W. , Zhavoronkov N. , Schulz C. P. , Hertel I. V.
Published: March 2011

Using the efficient nonlinear conversion scheme which was recently developed in our group [M. Beutler, M. Ghotbi, F. Noack, and I. V. Hertel, Opt. Lett. 134, 1491 (2010); M. Ghotbi, M. Beutler, and F. Noack, ibid 35, 3492 (2010)] to provide intense sub-50 fs vacuum ultraviolet laser pulses we have performed the first real time study of ultrafast, photo-induced dynamics in the electronically excited \documentclass[12pt]{minimal}\begin{document}$\tilde{A}$\end{document}Ã-state of water clusters (H2O)n and (D2O)n, n = 2–10. Three relevant time scales, 1.8–2.5, 10–30, and 50–150 fs, can be distinguished which—guided by the available theoretical results—are attributed to H (D)-ejection, OH (OD) dissociation, and a nonadiabatic transition through a conical intersection, respectively. While a direct quantitative comparison is only very preliminary, the present results provide a crucial test for future modeling of excited state dynamics in water clusters, and should help to unravel some of the many still unresolved puzzles about water.
Xe+ formation following photolysis of Au–Xe: A velocity map imaging study
Authors: Hopkins W. Scott , Woodham Alex P. , Plowright Richard J. , Wright Timothy G. , Mackenzie Stuart R.
Published: March 2011

The photodissociation dynamics of Au–Xe leading to Xe+ formation via the Ξ1/2–X2Σ+ (v′, 0) band system (41 500–41 800 cm−1) have been investigated by velocity map imaging. Five product channels have been indentified, which can be assigned to photoinduced charge transfer followed by photodissociation in either the neutral or the [Au–Xe]+ species. For the neutral species, charge transfer occurs via a superexcited Rydberg state prior to dissociative ionization, while single-photon excitation of the gold atom in Au+–Xe accesses an (Au+)*–Xe excited state that couples to a dissociative continuum in Au–Xe+. Mechanisms by which charge transfer occurs are proposed, and branching ratios for Xe+ formation via the superexcited Rydberg state are reported. The bond dissociation energy for the first excited state of Au+–Xe is determined to be ∼9720 ± 110 cm−1.
Development of radially movable multichannel Reynolds stress probe system for a cylindrical laboratory plasma
Authors: Nagashima Yoshihiko , Inagaki Shigeru , Kamakaki Kunihiro , Arakawa Hiroyuki , Yamada Takuma , Shinohara Shunjiro , Kawai Yoshinobu , Yagi Masatoshi , Fujisawa Akihide , Itoh Sanae -I. , Itoh Kimitaka , Takase Yuichi
Published: March 2011

A new radially movable multichannel azimuthal probe system has been developed for measuring azimuthal and radial profiles of electrostatic Reynolds stress (RS) per mass density of microscale fluctuations for a cylindrical laboratory plasma. The system is composed of 16 probe units arranged azimuthally. Each probe unit has six electrodes to simultaneously measure azimuthal and radial electric fields for obtaining RS. The advantage of the system is that each probe unit is radially movable to measure azimuthal RS profiles at arbitrary radial locations as well as two-dimensional structures of fluctuations. The first result from temporal observation of fluctuation azimuthal profile presents that a low-frequency fluctuation (1–2 kHz) synchronizes oscillating Reynolds stress. In addition, radial scanning of the probe system simultaneously demonstrates two-dimensional patterns of mode structure and nonlinear forces with frequency f = 1.5  kHz and azimuthal mode number m = 1.
Assessment and prediction of thermal transport at solid–self-assembled monolayer junctions
Authors: Duda John C. , Saltonstall Christopher B. , Norris Pamela M. , Hopkins Patrick E.
Published: March 2011

Self-assembled monolayers (SAMs) have recently garnered much interest due to their unique electrical, chemical, and thermal properties. Several studies have focused on thermal transport across solid–SAM junctions, demonstrating that interface conductance is largely insensitive to changes in SAM length. In the present study, we have investigated the vibrational spectra of alkanedithiol-based SAMs as a function of the number of methylene groups forming the molecular backbone via Hartree–Fock methods. In the case of Au–alkanedithiol junctions, it is found that despite the addition of nine new vibrational modes per added methylene group, only one of these modes falls below the maximum phonon frequency of Au. In addition, the alkanedithiol one-dimensional density of normal modes (modes per unit energy per unit length) is nearly constant regardless of chain length, explaining the observed insensitivity. Furthermore, we developed a diffusive transport model intended to predict interface conductance at solid–SAM junctions. It is shown that this predictive model is in an excellent agreement with prior experimental data available in the literature.
Stabilizing effect of a nonresonant radio frequency drive on the m=1 diocotron instability
Authors: Maero G. , Paroli B. , Pozzoli R. , Romé M.
Published: March 2011

It has been experimentally shown that the rotation radius of a non-neutral plasma column around the longitudinal axis of a Malmberg–Penning trap experiences a growth in amplitude (m=1 diocotron instability), leading to the loss of the plasma on the surface of the confining electrodes. A new stabilization mechanism has been investigated with the help of systematic experiments in the ELTRAP (ELectron TRAP) device where a high-frequency, low-amplitude drive has been applied on an azimuthally sectored electrode. An effective confining force is created, which reduces the offset of the column from the center. This interpretation and its theoretical analysis show a qualitative agreement with the experimental findings, where a net confinement effect is present for a wide range of drive amplitudes and frequencies.
Electron cyclotron current drive in low collisionality limit: On parallel momentum conservation
Authors: Marushchenko N. B. , Beidler C. D. , Kasilov S. V. , Kernbichler W. , Maaßberg H. , Prater R. , Harvey R. W.
Published: March 2011

A comprehensive treatment of the models used in ray- and beam-tracing codes to calculate the electron cyclotron current drive (ECCD) by means of the adjoint technique, based on the adjoint properties of the collision and Vlasov operators appearing in the drift-kinetic equation, is presented. Particular attention is focused on carefully solving the adjoint drift-kinetic equation (generalized Spitzer problem) with parallel momentum conservation in the like-particle collisions. The formulation of the problem is valid for an arbitrary magnetic configuration. Only the limit of low collisionality is considered here, which is of relevance for high-temperature plasmas. It is shown that the accurate solution of the adjoint drift-kinetic equation with parallel momentum conservation significantly differs (apart from the suprathermal electron portion) from that calculated in the high-speed-limit, which is most commonly used in the literature. For high-temperature plasmas with significant relativistic effects, the accuracy of the resulting numerical models is demonstrated by ray-tracing calculations and benchmark results are presented. It is found that the ECCD efficiency calculated for ITER with parallel momentum conservation significantly exceeds the predictions obtained with the high-speed-limit model.
Ab initiointeratomic decay widths of excited states by applying Stieltjes imaging to Lanczos pseudospectra
Authors: Kopelke S. , Gokhberg K. , Averbukh V. , Tarantelli F. , Cederbaum L. S.
Published: March 2011

Electronically excited states of atoms and molecules in an environment may decay in interatomic processes by transferring excess energy to neighboring species and ionizing them. The corresponding interatomic decay width is the most important characteristic of the decay allowing to calculate its efficiency and the final states’ distribution. In this paper we present calculations of interatomic widths by the Fano–Stieltjes method applied to Lanczos pseudospectra, which has been previously shown to provide accurate autoionization widths in atoms and molecules. The use of Lanczos pseudospectra allows one to avoid the full diagonalization bottleneck and makes the method applicable to larger systems. We apply the present method to the calculation of interatomic decay widths in NeMg, NeAr and HCN·Mgn, n = 1, 2 clusters. The results are compared with widths obtained analytically and by other ab initio methods where available.