bluuebunny/crossref_metadata_2025 huggingface dataset:
Ammonium Concentrations in Produced Waters from a Mesothermic Oil Field Subjected to Nitrate Injection Decrease through Formation of Denitrifying Biomass and Anammox Activity
Authors: Cornish Shartau Sabrina L. , Yurkiw Marcy , Lin Shiping , Grigoryan Aleksandr A. , Lambo Adewale , Park Hyung-Soo , Lomans Bart P. , van der Biezen Erwin , Jetten Mike S. M. , Voordouw Gerrit
Published: June 2010

Community analysis of a mesothermic oil field, subjected to continuous field-wide injection of nitrate to remove sulfide, with denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA genes indicated the presence of heterotrophic and sulfide-oxidizing, nitrate-reducing bacteria (hNRB and soNRB). These reduce nitrate by dissimilatory nitrate reduction to ammonium (e.g.,
Sulfurospirillum
and
Denitrovibrio
) or by denitrification (e.g.,
Sulfurimonas
,
Arcobacter
, and
Thauera
). Monitoring of ammonium concentrations in producing wells (PWs) indicated that denitrification was the main pathway for nitrate reduction in the field: breakthrough of nitrate and nitrite in two PWs was not associated with an increase in the ammonium concentration, and no increase in the ammonium concentration was seen in any of 11 producing wells during periods of increased nitrate injection. Instead, ammonium concentrations in produced waters decreased on average from 0.3 to 0.2 mM during 2 years of nitrate injection. Physiological studies with produced water-derived hNRB microcosms indicated increased biomass formation associated with denitrification as a possible cause for decreasing ammonium concentrations. Use of anammox-specific primers and cloning of the resulting PCR product gave clones affiliated with the known anammox genera “
Candidatus
Brocadia” and “
Candidatus
Kuenenia,” indicating that the anammox reaction may also contribute to declining ammonium concentrations. Overall, the results indicate the following: (i) that nitrate injected into an oil field to oxidize sulfide is primarily reduced by denitrifying bacteria, of which many genera have been identified by DGGE, and (ii) that perhaps counterintuitively, nitrate injection leads to decreasing ammonium concentrations in produced waters.
Differential Regulation of Six Heavy Metal Efflux Systems in the Response of
Myxococcus xanthus
to Copper
Authors: Moraleda-Muñoz Aurelio , Pérez Juana , Extremera Antonio Luis , Muñoz-Dorado José
Published: June 2010

Myxococcus xanthus
has to cope with changes in its environment during growth and development. Among these factors, the concentration of copper is crucial due to the essential toxic effect of this metal, which forces the cells to maintain a tight homeostasis. The
M. xanthus
copper response is more complex than that in other bacteria, which is reflected by the different copper sensitivities of growing and developing cells. In the present study, the participation in copper homeostasis of six heavy metal efflux systems encoded in the
M. xanthus
genome has been examined. Three of these pumps exhibit the signature sequences in transmembrane domain 4 of the Cus systems (Cus1, Cus2, and Cus3), while the other three exhibit the motifs of the Czc systems (Czc1, Czc2, and Czc3). The Cus2 and Cus3 systems are inducible by copper and monovalent metals, functioning as the main copper efflux pumps, while the Cus1 system is implicated in Zn
2+
homeostasis. The Czc systems are also differentially regulated either by divalent metals but not by copper (Czc1), by copper and divalent metals (Czc2), or by starvation (Czc3). The differential regulation of these six efflux systems ensures the proper completion of the
M. xanthus
life cycle in an environment with fluctuating concentrations of copper and other metals.
Identification and Elimination of the Competing
N
-Acetyldiaminopentane Pathway for Improved Production of Diaminopentane by
Corynebacterium glutamicum
Authors: Kind Stefanie , Jeong Weol Kyu , Schröder Hartwig , Zelder Oskar , Wittmann Christoph
Published: June 2010

The present work describes the development of a superior strain of
Corynebacterium glutamicum
for diaminopentane (cadaverine) production aimed at the identification and deletion of the underlying unknown
N
-acetyldiaminopentane pathway. This acetylated product variant, recently discovered, is a highly undesired by-product with respect to carbon yield and product purity. Initial studies with
C. glutamicum
DAP-3c, a previously derived tailor-made diaminopentane producer, showed that up to 20% of the product occurs in the unfavorable acetylated form. The strain revealed enzymatic activity for diaminopentane acetylation, requiring acetyl-coenzyme A (CoA) as a donor. Comparative transcriptome analysis of DAP-3c and its parent strain did not reveal significant differences in the expression levels of 17 potential candidates annotated as
N
-acetyltransferases. Targeted single deletion of several of the candidate genes showed NCgl1469 to be the responsible enzyme. NCgl1469 was functionally assigned as diaminopentane acetyltransferase. The deletion strain, designated
C. glutamicum
DAP-4, exhibited a complete lack of
N
-acetyldiaminopentane accumulation in medium. Hereby, the yield for diaminopentane increased by 11%. The mutant strain allowed the production of diaminopentane as the sole product. The deletion did not cause any negative growth effects, since the specific growth rate and glucose uptake rate remained unchanged. The identification and elimination of the responsible acetyltransferase gene, as presented here, display key contributions of a superior
C. glutamicum
strain producing diaminopentane as a future building block for bio-based polyamides.
Increased Lipid Accumulation in the Chlamydomonas reinhardtii
sta7-10
Starchless Isoamylase Mutant and Increased Carbohydrate Synthesis in Complemented Strains
Authors: Work Victoria H. , Radakovits Randor , Jinkerson Robert E. , Meuser Jonathan E. , Elliott Lee G. , Vinyard David J. , Laurens Lieve M. L. , Dismukes G. Charles , Posewitz Matthew C.
Published: June 2010

The accumulation of bioenergy carriers was assessed in two starchless mutants of
Chlamydomonas reinhardtii
(the
sta6
[ADP-glucose pyrophosphorylase] and
sta7
-
10
[isoamylase] mutants), a control strain (CC124), and two complemented strains of the
sta7
-
10
mutant. The results indicate that the genetic blockage of starch synthesis in the
sta6
and
sta7
-
10
mutants increases the accumulation of lipids on a cellular basis during nitrogen deprivation relative to that in the CC124 control as determined by conversion to fatty acid methyl esters. However, this increased level of lipid accumulation is energetically insufficient to completely offset the loss of cellular starch that is synthesized by CC124 during nitrogen deprivation. We therefore investigated acetate utilization and O
2
evolution to obtain further insights into the physiological adjustments utilized by the two starchless mutants in the absence of starch synthesis. The results demonstrate that both starchless mutants metabolize less acetate and have more severely attenuated levels of photosynthetic O
2
evolution than CC124, indicating that a decrease in overall anabolic processes is a significant physiological response in the starchless mutants during nitrogen deprivation. Interestingly, two independent
sta7
-
10
:
STA7
complemented strains exhibited significantly greater quantities of cellular starch and lipid than CC124 during acclimation to nitrogen deprivation. Moreover, the complemented strains synthesized significant quantities of starch even when cultured in nutrient-replete medium.
Comparative Analyses of Two Thermophilic Enzymes Exhibiting both β-1,4 Mannosidic and β-1,4 Glucosidic Cleavage Activities from
Caldanaerobius polysaccharolyticus
Authors: Han Yejun , Dodd Dylan , Hespen Charles W. , Ohene-Adjei Samuel , Schroeder Charles M. , Mackie Roderick I. , Cann Isaac K. O.
Published: June 2010

The hydrolysis of polysaccharides containing mannan requires endo-1,4-β-mannanase and 1,4-β-mannosidase activities. In the current report, the biochemical properties of two endo-β-1,4-mannanases (Man5A and Man5B) from
Caldanaerobius polysaccharolyticus
were studied. Man5A is composed of an N-terminal signal peptide (SP), a catalytic domain, two carbohydrate-binding modules (CBMs), and three surface layer homology (SLH) repeats, whereas Man5B lacks the SP, CBMs, and SLH repeats. To gain insights into how the two glycoside hydrolase family 5 (GH5) enzymes may aid the bacterium in energy acquisition and also the potential application of the two enzymes in the biofuel industry, two derivatives of Man5A (Man5A-TM1 [TM1 stands for truncational mutant 1], which lacks the SP and SLH repeats, and Man5A-TM2, which lacks the SP, CBMs, and SLH repeats) and the wild-type Man5B were biochemically analyzed. The Man5A derivatives displayed endo-1,4-β-mannanase and endo-1,4-β-glucanase activities and hydrolyzed oligosaccharides with a degree of polymerization (DP) of 4 or higher. Man5B exhibited endo-1,4-β-mannanase activity and little endo-1,4-β-glucanase activity; however, this enzyme also exhibited 1,4-β-mannosidase and cellodextrinase activities. Man5A-TM1, compared to either Man5A-TM2 or Man5B, had higher catalytic activity with soluble and insoluble polysaccharides, indicating that the CBMs enhance catalysis of Man5A. Furthermore, Man5A-TM1 acted synergistically with Man5B in the hydrolysis of β-mannan and carboxymethyl cellulose. The versatility of the two enzymes, therefore, makes them a resource for depolymerization of mannan-containing polysaccharides in the biofuel industry. Furthermore, on the basis of the biochemical and genomic data, a molecular mechanism for utilization of mannan-containing nutrients by
C. polysaccharolyticus
is proposed.
Transport of Preproteins by the Accessory Sec System Requires a Specific Domain Adjacent to the Signal Peptide
Authors: Bensing Barbara A. , Sullam Paul M.
Published: June 2010

The accessory Sec (SecA2/Y2) systems of streptococci and staphylococci are dedicated to the transport of large serine-rich repeat (SRR) glycoproteins to the bacterial cell surface. The means by which the glycosylated preproteins are selectively recognized by the accessory Sec system have not been fully characterized. In
Streptococcus gordonii
, the SRR glycoprotein GspB has a 90-residue amino-terminal signal sequence that is essential for transport by SecA2/Y2 but is not sufficient to mediate the transport of heterologous proteins by this specialized transporter. We now report that a preprotein must remain at least partially unfolded prior to transport by the accessory Sec system. In addition, a region of approximately 20 residues from the amino-terminal end of mature GspB (the
a
ccessory
S
ec
t
ransport or AST domain) is essential for SecA2/Y2-dependent transport. The replacement of several AST domain residues with glycine strongly interferes with export, which suggests that a helical conformation may be important. Analysis of GspB variants with alterations in the AST domain, in combination with the results with a SecY2 variant, indicates that the AST domain is essential both for targeting to the SecA2/Y2 translocase and for initiating translocation through the SecY2 channel. The combined results suggest a unique mechanism that ensures the transport of a single substrate by the SecA2/Y2 system.
Wearing someone else's shoes
Authors: Rae Kym
Published: June 2010

This paper recounts a journey of discovery by a scientist who inadvertently takes on coordination of an ArtsHealth programme. The dynamics of role change are explored showcasing the vulnerabilities and fears that often accompany these career adjustments. The associated ArtsHealth programme (Gomeroi gaaynggal)works with Aboriginal and Torres Strait Islander women in Australia throughout their pregnancy to improve understanding of issues that impact the health of themselves and their developing baby. By wearing someone else shoes, the scientist is immersed in the project and must confront issues including skill mix, learning and cultural diversity.
Introducing spirituality, religion and culture curricula in the psychiatry residency programme: Table 1
Authors: Kozak Leila , Boynton Lorin , Bentley Jacob , Bezy Emma
Published: June 2010

A growing body of research suggests that religion and spirituality may have a positive effect on mental and physical health. Medical schools have been increasingly offering courses in spirituality and health, particularly about the multi-cultural dimensions of religion and spirituality. There is a trend towards integrating the teaching of cross-cultural issues related to spirituality and religion into medical education. This trend is particularly evident in the field of psychiatry, where an increasing number of residency programmes are developing curriculum in this area. This article describes a specific curriculum in spirituality, religion and culture that was introduced in 2003 at the University of Washington Psychiatry Residency Program in Seattle, Washington. Reflections about the present and future of subject areas such as spirituality and religion in medical education and psychiatry residency are discussed.
FUZZYART NEURAL NETWORK FOR PROTEIN CLASSIFICATION
Authors: ANGADI ULAVAPPA B. , VENKATESULU M.
Published: June 2010

One of the major research directions in bioinformatics is that of predicting the protein superfamily in large databases and classifying a given set of protein domains into superfamilies. The classification reflects the structural, evolutionary and functional relatedness. These relationships are embodied in hierarchical classification such as Structural Classification of Protein (SCOP), which is manually curated. Such classification is essential for the structural and functional analysis of proteins. Yet, a large number of proteins remain unclassified. We have proposed an unsupervised machine-learning FuzzyART neural network algorithm to classify a given set of proteins into SCOP superfamilies. The proposed method is fast learning and uses an atypical non-linear pattern recognition technique. In this approach, we have constructed a similarity matrix from p-values of BLAST all-against-all, trained the network with FuzzyART unsupervised learning algorithm using the similarity matrix as input vectors and finally the trained network offers SCOP superfamily level classification. In this experiment, we have evaluated the performance of our method with existing techniques on six different datasets. We have shown that the trained network is able to classify a given similarity matrix of a set of sequences into SCOP superfamilies at high classification accuracy.
IMPROVING THE INTER-CORPORA COMPATIBILITY FOR PROTEIN ANNOTATIONS
Authors: WANG YUE , KIM JIN-DONG , SÆTRE RUNE , PYYSALO SAMPO , OHTA TOMOKO , TSUJII JUN'ICHI
Published: June 2010

Although there are several corpora with protein annotation, incompatibility between the annotations in different corpora remains a problem that hinders the progress of automatic recognition of protein names in biomedical literature. Here, we report on our efforts to find a solution to the incompatibility issue, and to improve the compatibility between two representative protein-annotated corpora: the GENIA corpus and the GENETAG corpus. In a comparative study, we improve our insight into the two corpora, and a series of experimental results show that most of the incompatibility can be removed.
Electromagnetic Interference Analysis of DC–DC Converters Based on Piezoelectric Transformers
Authors: Liu Yuan-Ping , Vasic Dejan , Wu Wen-Jong , Costa François , Lee Chih-Kung
Published: June 2010

Power electronic converters based on piezoelectric transformers (PTs) have been widely adopted in recent years owning to their many inherent advantages, such as safety, low profile, and high power density. However, few studies have been conducted about noise emitted by PT converters. In this work, we studied the conducted electromagnetic interference (EMI) characteristics in a 10 W PT-based DC–DC converter. The different sources and specific couplings of EMI in this PT are presented. The experimental setup that allows us to study the various propagation paths and to measure the relevant impedances will be shown. A model that focuses on the parasitic impedances of the PT connected to the rectifier will be proposed. This model can show the paths of common noises in detail. We can observe that the EMI behaviours of PT-based converters are related to the isolated characteristics of the PT and the voltage waveforms of the connected circuits. Two connection methods between the PT and its driving circuit are discussed by both simulation and experiment to validify our model.
Electronic Structure of Sr2AlNbO6: Dielectric and X-ray Photoemission Spectroscopy Study
Authors: Dutta Alo , Sinha Tripurari Prasad , Shannigrahi Santiranjan
Published: June 2010

The dielectric property and the electronic structure of double perovskite oxide strontium aluminium niobate, Sr2AlNbO6 (SAN), synthesised by a solid state reaction technique are investigated. The Rietveld refinement of the X-ray diffraction data of the sample shows the cubic phase with the F
m3m structure (lattice parameter, a = 7.7789 Å). The compound shows significant frequency dispersion in its dielectric properties. The Cole–Cole model is used to study the dielectric relaxation of SAN. The scaling behavior of loss tangent suggests that the relaxation describes the same mechanism at various temperatures. The electronic structure of SAN is studied by the first principles full potential linearized augmented plane wave method. Its valence band consists mainly of the O 2p states hybridised with the Nb 4d states. The calculated density of states is used to compare the valence band X-ray photoemission spectra of the sample.
Dielectric Function and Electronic Excitations of Functionalized DNA Thin Films
Authors: Lee Hosuk , Lee Hosun , Lee Jung Eun , Lee U Rha , Choi Dong Hoon
Published: June 2010

We measure the dielectric functions of organic-soluble, functionalized DNAs bearing functional moieties in the near-infrared, visible, and ultra-violet spectra by using spectroscopic ellipsometry. Natural double-stranded DNA is dissolved in water and reacted with carbazole-based trimethyl ammonium bromide, cetyltrimethylammonium bromide, and chalcone-terminated trimethyl ammonium bromide. The functional DNA products are all precipitated and filtered for washing and drying. We successfully prepare functionalized DNAs that are insoluble in water but soluble in organic solvents. The thin films are fabricated by using the spin coating technique after preparing solutions in either homogeneous or mixed organic solvents. We measure the ultraviolet–visible absorbance spectra of the films. The absorbance spectra show that the optical energy gaps of the functionalized DNAs change little even though the DNAs are connected to the complex molecules by electrostatic interaction. From the measured ellipsometric angles, we estimate the dielectric functions by using parametric optical constant model and layer model analysis. Depending on the nature of the attached complex molecules, the dielectric functions change, new optical structures develop below and above band gaps arising from the side molecules, and the optical energy gaps of the DNAs are altered slightly by weak coupling to the tethered complex molecules.
Photochemical Deposition of GaSxOy Thin Films from Aqueous Solutions
Authors: Chowdhury Supria , Ichimura Masaya
Published: June 2010

Photochemical deposition (PCD) is a technique of film preparation from solutions by UV light illumination. In this study, GaS
x
O
y
thin films were prepared on fluorine-doped-tin-oxide-coated glass substrates by PCD from an aqueous solution of Ga2(SO4)3 and Na2S2O3. GaS
x
O
y
is a wide-band-gap semiconductor and suitable as a buffer layer material in solar cells. The as-deposited films were characterized by Auger electron spectroscopy, scanning electron microscopy and optical transmission spectroscopy. The O/Ga ratio was close to the stoichiometric ratio, 1.5, and the S/Ga ratio is much smaller, less than 0.3 for a film deposited under the optimum conditions. The film exhibited a wide energy band gap of 3.5 eV and a resistivity of the order of 102 Ω cm.
85Rb D1-Line Coherent-Population-Trapping Atomic Clock for Low-Power Operation
Authors: Goka Shigeyoshi
Published: June 2010

A 85Rb D1-line coherent-population-trapping (CPT) atomic clock with a natural-mixture Rb gas cell is demonstrated. D1-line excitation can generate a larger CPT resonance amplitude, and the choice of 85Rb rather than conventional 87Rb is because of its lower ground-state hyperfine-splitting frequency. The frequency deviation for the D1 line was measured using the same experimental setup as that for the D2 line except for the vertical-cavity surface-emitting laser (VCSEL) wavelength and RF power. In the case of D1-line excitation, the CPT resonance amplitude was 1.5 times that for the D2 line, and the light shift sensitivity was one-half that for the D2 line. The Allan standard deviations for the 85Rb D1 line, estimated from the frequency deviations, are <2.5×10-12 per day. In addition, the required RF is 1.5 GHz and its power is only -8.0 dBm.
Optoelectronic Properties of the p-MnZnO/n-Si Structure Photodiodes in a Strong Magnetic Field
Authors: Chen Lung-Chien , Tien Ching-Ho , Hsu Ya-Ying
Published: June 2010

Photodiodes with a p-MnZnO/n-Si substrate structure were fabricated. Mn-doped p-type ZnO (MnZnO) films were deposited by ultrasonic spray pyrolysis on a (100)-oriented silicon substrate. A dark current and a photocurrent of ∼4.31×10-7 and 6.95×10-4 A, respectively, were measured at a reverse bias of 2 V, and a photocurrent-to-dark current contrast ratio of almost four orders of magnitude was observed. When a p-MnZnO/n-Si structure photodiode was applied a strong magnetic field of 0.5 T, the photocurrent slightly increases to ∼1.24×10-3 A at a reverse bias of 2 V. This may be attributed to the Auger recombination effect due to the applied magnetic field.
Direct Observation of Fluctuations in the Number and Individual Electronic Properties of Interface Traps in Nanoscale Metal–Oxide–Semiconductor Field-Effect Transistors
Authors: Tsuchiya Toshiaki , Mori Yuki , Morimura Yuta , Mogami Tohru , Ohji Yuzuru
Published: June 2010

Fluctuations in not only the number but also the individual electronic properties of interface traps in small-gate-area metal–oxide–semiconductor field-effect transistors (MOSFETs) containing just a few interface traps have been directly observed. This observation is based on an understanding of a newly observed phenomenon in the charge pumping characteristics, i.e., on-time (or off-time)-dependent charge pumping characteristics. It is shown that the fluctuation in the number of interface traps contained in an individual MOSFET is fairly large, and that there are various interface traps with individual carrier capture rates. These fluctuations may have an impact on the variation in threshold voltage of future digital metal–insulator–semiconductor devices.
Effect of Overlayer Viscoelasticity on Resonant Characteristics of a Quartz Crystal Resonator
Authors: Suh Yong Kweon , Kim Young Han
Published: June 2010

The generalized equations correlating the resonant characteristics, such as frequency and admittance, and rheological properties of an overlayer applied on the electrode interaface of a quartz crystal resonator are derived from the mechanics of the quartz movement using an electric equivalent circuit. The resulting correlations generalize the relationship between the resonant characteristics and the rheological properties of an overlayer leading to multiple sets of viscosity and elastic shear modulus for a given set of resonant characteristics. The extreme cases of the generalized equations are in accordance with the results of previous studies of separate problems. In the case of a Newtonian fluid overlayer, the derived correlation of the resonant frequency explains the experimental result of the viscosity effect on the frequency. The experimental results for a spin-coated polyethylene are analyzed using the full equations as well as the approximated ones leading to the good agreement between the two, and the agreement implies that we can employ the equivalent circuit theory – not so much different from that without an overlayer – in analyzing the experimental data with the quartz crystal resonator.
Synthesis and Magnetic Property of Multiferroic BiMnO3 Nanoparticles in the Pores of Mesoporous Silica
Authors: Tajiri Takayuki , Harazono Manabu , Deguchi Hiroyuki , Mito Masaki , Kohno Atsushi , Kohiki Shigemi
Published: June 2010

The mesoporous silica material SBA-15 was prepared with control pore size for use as a nanoparticle synthesis template. The X-ray diffraction results show that the nanopores were ordered in a hexagonal structure. The pore size was controlled by the synthesis conditions. Nanoparticles of the multiferroic compound BiMnO3 with an average size of about 14 nm were successfully synthesized in the pores of SBA-15, and their magnetic properties were investigated. The prepared BiMnO3 nanoparticles showed both antiferromagnetic and ferromagnetic behavior, whereas BiMnO3 bulk crystals consistently showed ferromagnetic behavior. The prepared BiMnO3 nanoparticles exhibited unique magnetic size effects: the appearance of antiferromagnetic behavior and the coexistence of antiferromagnetic and ferromagnetic components.
Surface Smoothing of Polycrystalline Substrates with Gas Cluster Ion Beams
Authors: Mashita Takafumi , Toyoda Noriaki , Yamada Isao
Published: June 2010

The surface smoothing of polycrystalline materials is difficult owing to the etching rate dependence on crystalline orientation. In this study, surface smoothing with a gas cluster ion beam (GCIB) was studied in polycrystalline substrates such as poly-SiC (surface roughness, 0.3 nm) and yttrium aluminum garnet (YAG; surface roughness, 1.1 nm). Before irradiation, there were many scratches induced by mechanical polishing on poly-SiC. These scratches were removed after Ar-GCIB irradiation. Additional O2-GCIB irradiation for asperity removal showed improvement in the average roughness of poly-SiC to 0.3 nm. Similarly, the scratches on the as-polished surface of YAG disappeared and the YAG surface roughness decreased to 0.7 nm with Ar-GCIB irradiation without inducing an etching rate difference between grains. It was also shown that polycrystalline diamond or poly-Si films can be smoothed using GCIB. These results indicate that GCIB polishing is suitable for the surface planarization of polycrystalline materials.
Refilling and Planarization of Patterned Surface with Amorphous Carbon Films by Using Gas Cluster Ion Beam Assisted Deposition
Authors: Toyoda Noriaki , Hirota Tomokazu , Mashita Takafumi , Yamada Isao
Published: June 2010

Planarization of nano-structured surface has become important for various devices such as the bit patterned media or discrete track media for next generation storage devices. In this study, gas cluster ion beam (GCIB) assisted deposition was used to deposit amorphous carbon film on line-and-space pattern to realize simultaneous refilling and planarization. As GCIB irradiations induce dense energy depositions, the density of the amorphous carbon film deposited with GCIB assisted deposition became high compared to the other chemical vapor deposition (CVD) based deposition technique. The line-and-space pattern was refilled and planarized by deposition of amorphous carbon films by using Ar-GCIB assisted deposition. The thickness required for planarization with amorphous carbon deposition using Ar-GCIB assisted deposition was approximately the initial peak-to-valley height of the line-and-space pattern. Thus, very effective refilling and planarization is realized by using GCIB assisted deposition.
Shape-Dependent Magnetic Moment and Formation Energy of Fe Heterostructures on Cu(111): An Ab initio Study
Authors: Choi Heechae , Chung Yong-Chae
Published: June 2010

Shape-dependent magnetic moment and island formation energy of Fe adatoms on a Cu(111) surface were systematically investigated using the density functional theory based first-principles calculations. The calculated formation energy of a Fe nanoisland was linearly proportional to the number of Fe–Fe bondings within the island, regardless of the number of Fe atoms or the shape. The magnetic moments of Fe nanoisland atoms were determined by two key factors, the numbers of Fe–Fe bondings and the angles between the Fe–Fe bondings. The magnetic moment of the Fe atom that had the highest number of Fe–Fe bondings was the minimum in all the island models. Through the analysis of the decomposed Fe 3d-electron density of states, we found that the shape-dependency of Fe heterostructures magnetism on Cu(111) results from the preference of Fe atoms to fill certain 3d-electron orbitals according to the Fe–Fe bonding angles.
Magnetic Anisotropy of Ni-Doped ZnO Nanocrystalline Thin Films
Authors: Subramanian Munisamy , Ran Fan-Yong , Tanemura Masaki , Hihara Takehiko , Soga Tetsuo , Jimbo Takashi
Published: June 2010

We report structural and magnetization properties of nickel-doped zinc oxide thin films prepared on Si substrates by spray pyrolysis technique. Grazing angle X-ray diffraction measurements confirm the wurtzite structure of Zn1-xNixO films and no secondary phase was found for ZnO thin films doped with 5% Ni or less. Hysteresis measurements demonstrate that the Ni-doped ZnO films are magnetically anisotropic and they exhibit intrinsic ferromagnetic behavior at room temperature. Higher magnetization in 3 kOe is observed for a field applied perpendicular to the sample surface compared with the in-plane direction.
Density Functional Theory Method for Study of the Mechanism of C–H Bond Formation on Finite-Sized Graphene Surface
Authors: Tachikawa Hiroto , Iyama Tetsuji
Published: June 2010

The structures and electronic states of hydrogenated graphenes with a finite size have been investigated by a density functional theory (DFT) method. Five graphenes of various sizes (n=2, 4, 7, 14, and 19, where n indicates the number of benzene rings in graphene) were examined as models of a hydrogenated graphene system. The harmonic vibrational frequency corresponding to a C–H stretching mode showed a linear relationship between the frequency and the C–H bond length. The C–H bond formed by the addition of hydrogen atoms was completely polarized as Cδ-–Hδ+ in an equilibrium structure. It was found that the activation barrier is formed by hybridization from sp2 to sp3 in the transition region. The mechanism of C–H bond formation on a graphene surface was discussed on the basis of theoretical results.
Atomic-Scale Investigation of the Ti/Al(001) Interface: A Molecular Dynamics Simulation
Authors: Yoon Geunsup , Lee Soon-Gun , Kim Byung-Hyun , Chung Yong-Chae
Published: June 2010

The intermixing characteristics of Ti thin film deposited on Al(001) substrate at atomic level were investigated by molecular dynamics simulation. The intermixing at Ti/Al(001) interface was limited within only the topmost layer of the Al(001) substrate at 300 K with 0.1 eV incident energy of a Ti atom. The mixing characteristics for Ti/Al(001) such as layer coverage function and mixing length were significantly different from those of the transition metals (TM; Fe, Co, and Ni)/Al(001) systems. The different intermixing behavior can be explained in terms of local acceleration and incorporation energy barrier.
Characterization of Antisticking Layers for UV Nanoimprint Lithography Molds with Scanning Probe Microscopy
Authors: Kurihara Masaaki , Hatakeyama Sho , Yamada Noriko , Shimomura Takeya , Nagai Takaharu , Yoshida Kouji , Tomita Tatsuya , Hoga Morihisa , Hayashi Naoya , Ohtani Hiroyuki , Fujihira Masamichi
Published: June 2010

Antisticking layers (ASLs) on UV nanoimprint lithography (UV-NIL) molds were characterized by scanning probe microscopies (SPMs) in addition to macroscopic analyses of work of adhesion and separation force. Local physical properties of the ASLs were measured by atomic force microscopy (AFM) and friction force microscopy (FFM). The behavior of local adhesive forces measured with AFM on several surfaces was consistent with that of work of adhesion obtained from contact angle. The ASLs were coated by two different processes, i.e., one is a vapor-phase process and the other a spin-coating process. The homogeneity of the ASLs prepared by the vapor-phase process was better than that of those prepared by the spin-coating process. In addition, we measured the thicknesses of ASL patterns prepared by a lift-off method to investigate the effect of the ASL thicknesses on critical dimensions of the molds with ASLs and found that this effect is not negligible.
Numerical Simulation of Glass Imprinting for Molding Temperature Prediction
Authors: Yasui Manabu , Arai Masahiro , Ito Hiroaki , Ino Tomohiro , Takahashi Masaharu , Kaneko Satoru , Hirabayashi Yasuo , Maeda Ryutaro
Published: June 2010

For optimizing the conditions of glass imprinting, many researchers commonly use the trial-and-error method. Therefore, it is advantageous to carry out a preliminary analysis of glass imprinting. The viscoelastic property of glass is necessary for MEMS-ONE in which a viscoelastic model is used. Assuming glass materials to be viscoelastic boies, the relaxation share modulus was measured by the creep test based on traditional thermo-viscoelastic theory. The Williams–Landel–Ferry (WLF) equation is applied using the temperature dependence of liquid viscosity. We compared experimental results with the analytic results of MEMS-ONE simulation under the conditions of fixed pressure (3.56 MPa) and time (10 min). The object of evaluation is the height of the central position prong. The molding temperature can be predicted within 10 °C error by the simulation.
Comprehensive Study of Microgel Electrode for On-Chip Electrophoretic Cell Sorting
Authors: Hattori Akihiro , Yasuda Kenji
Published: June 2010

We have developed an on-chip cell sorting system and microgel electrode for applying electrostatic force in microfluidic pathways in the chip. The advantages of agarose electrodes are 1) current-driven electrostatic force generation, 2) stability against pH change and chemicals, and 3) no bubble formation caused by electrolysis. We examined the carrier ion type and concentration dependence of microgel electrode impedance, and found that CoCl2 has less than 1/10 of the impedance from NaCl, and the reduction of the impedance of NaCl gel electrode was plateaued at 0.5 M. The structure control of the microgel electrode exploiting the surface tension of sol-state agarose was also introduced. The addition of 1% (w/v) trehalose into the microgel electrode allowed the frozen storage of the microgel electrode chip. The experimental results demonstrate the potential of our system and microgel electrode for practical applications in microfluidic chips.
Fabrication of a Wheatstone-Bridge Integrated SU-8 Cantilever
Authors: Ahn Jun-Hyung , Park Chang-Sin , Lee Dong-Weon
Published: June 2010

We describe the design and fabrication of an SU-8 cantilever with an integrated Wheatstone-bridge configuration. A photolithographic process of SU-8 on an anisotropically wet-etched Si substrate is used to produce reliable sharp tips. Changes in the surface stress on the cantilever are detected by an integrated Au piezoresistor. Preliminary results of the measurement are presented for cantilever evaluation. The fabricated SU-8 cantilever has a resonance frequency of about 4.5 kHz, which yields a spring constant of approximately 0.15 N/m. These cantilevers are very suitable for the nondestructive atomic force microscope (AFM) analysis of fragile biological samples, such as cells and body fluids.
Two-Step Deformation Mechanism of Self-Forming Three-Dimensional Carbon Micro Structures
Authors: Usuda Keisuke , Hoshino Takayuki , Morishima Keisuke
Published: June 2010

We have developed a novel fabrication method for three-dimensional carbon micro structures using a carbon-microelectromechanical system (C-MEMS) and a thermomechanical deformation technique. Three-dimensional carbon micro structures could be fabricated as pyrolyzed SU-8 film with sputtered Au layer. The SU-8 film with sputtered Au layer was deformed autonomously by thermal deformation. Fabrication of three dimensional structures from two dimensional films is like origami structure. In this paper, we investigated deformation behaviour, including temperature-dependent deformation, shape-dependent deformation, and size-dependent deformation to design carbon structures. We found a two-step deformation. The SU-8 film with sputtered Au layer was deformed toward the Au-inside direction by thermal expansion at temperatures under 200 °C. However, it was deformed toward the Au-outside direction by the glass transition between 200 and 300 °C. Shape- and size-dependent deformations were also confirmed. This process could allow fabrication of various micro devices such as large surface area electrodes for micro fuel cells, microreactors, and microsensors.
Characterization of Four-Points-Pinned Ring-Shaped Silicon Microelectromechanical Systems Resonator
Authors: Oka Tomohiro , Tanigawa Hiroshi , Suzuki Kenichiro
Published: June 2010

A four-points-inner-pinned ring-shaped microelectromechanical systems (MEMS) resonator has been investigated. The simulated comparison between disk- and ring-shaped resonators indicates that the amplitudes of the ring-shaped resonators are more than ten times larger than those of the disk-shaped ones for modes with the same resonant frequency. Three types of anchor configuration for the ring-shaped resonators, inner-pinned, outer-pinned, and center-fixed, were compared. The results show that, for the inner-pinned ring-shaped resonator, three fundamental resonant modes occur close to each other, although this resonator is the smallest and does not suffer from the effect of misalignment as a result of one mask fabrication. A new method to identify each fundamental resonant mode has been proposed and successfully adapted for evaluating the frequency characteristics of fabricated resonators. The fabricated ring-shaped resonator had a radial-contour-common (RCC) resonant mode at 1.615 MHz with a Q-factor of over 30,000. These values agreed at 98.9% accuracy with those of the simulated resonator.
Performance Analysis of a Convection-Based Tilt Sensor
Authors: Choi Ju Chan , Kong Seong Ho
Published: June 2010

This paper presents fabrication sequence and performance improving methods for convection-based tilt sensor. Also a packaging method to minimize the effect of environmental temperature fluctuation is proposed. Both electrolytic solution-based and air convection-based tilt sensors realized using micro-electro-mechanical-system (MEMS) technology have been previously reported by our research group. Although the MEMS-based electrolytic tilt sensor shows merited characteristics, such as wider operating tilt range, lower cost and compactness, compared to commercialized conventional electrolytic tilt sensors, it still suffers from metal electrode corrosion, electrolyte deterioration, surface tension of the electrolyte, and difficulty in packaging. In order to avoid those demerits, convective tilt sensor using air medium instead of electrolytic solution has been proposed and its fundamental performances has also been demonstrated in the previous works. In this paper, the effect of air medium condition on sensitivity of proposed convective tilt sensor has been investigated. In addition, a packaging method utilizing the Peltier device is presented to minimize environmental thermal effect without additional temperature compensation circuit. It is expected that this technique can be similarly applied to improve the performance and reliability of other sensors using gas media.
Micro-Electro-Mechanical System/Field-Effect-Transistor Hybrid Switch for Energy Scavenging System
Authors: Kim Hoseong , Kang Sungmuk , Park Kyungjin , Park Jaewoo , Kim Yu-Rae , Baek Chang-Wook
Published: June 2010

An innovative micro-electro-mechanical system/metal–oxide–semiconductor field-effect-transistor (MEMS/MOSFET) hybrid switch is presented. The main switch of the hybrid device is a MOSFET switch whose gate voltage is supplied through a MEMS switch. The electrostatic operation mechanism and inherent hysteresis characteristics of MEMS switch combined with the characteristics of MOSFET provides a high current handling capability, a low power consumption, self-referencing, a high noise immunity, and an ease of control and all of these advantages are experimentally demonstrated in practical circuits. This hybrid switch can be employed in energy scavenging system and in other electronic devices in order to save standby energy.
Structure and internal deformation of the Arnaboll Thrust Sheet, NW Scotland: implications for strain localization in thrust belts
Authors: Wibberley Christopher A. J. , Butler Robert W. H.
Published: June 2010

Descriptions of structural evolution across thrust belts commonly assume a transition from ductile to brittle deformation, reflecting a progressive reduction in temperature accompanying exhumation. The universality of this model is challenged here using field relationships at Ben Arnaboll, in the northern part of the Moine Thrust Belt. Deformation in the Arnaboll Thrust Sheet, an allochthonous basement body of amphibolite-facies gneisses and pegmatite sheets, carried onto Cambrian sediments, includes widely distributed, low-displacement shears developed under greenschist facies with ingress of water. These ductile deformations post-date the emplacement of the thrust sheet as they link kinematically to breaching thrust structures emanating from the footwall of the Arnaboll Thrust. The thrust itself records a transition from mylonitic (ductile) to strongly localized (brittle) deformation that pre-dates the breaching thrusts and therefore the deformation within the thrust sheet itself. The structure of breaching thrusts charts an up-dip transition from localized slip to distributed shearing analogous to the trishear in fold-thrust complexes, Therefore deformation of the Arnaboll Thrust Sheet shows a return from strongly localized translation-dominated brittle deformation to more broadly distributed ductile deformation. This is likely to have been promoted by the ingress of water and the concomitant reaction-enhanced weakening of the basement.
Shear localization in solids: insights for mountain building processes from a frame-indifferent ideal material model
Authors: Patton Regan L. , Watkinson A. John
Published: June 2010

Tectonic and orogenic processes, reflecting the dynamic nature of the planet, provide myriad examples of the failure of Earth materials under load. Despite this wealth of data, the shear localization process remains a difficult physical modelling problem, lying at the frontiers of complex and non-linear systems research. We present a non-conventional continuum-physics approach to address this problem, based on the mathematical properties of differential grade-2 (DG-2) materials. We choose this material because it is both frame-indifferent, and general enough to include other, simpler materials as special cases. DG-2 materials in pure shear exhibit a dynamic rescaling mechanism, associated with localized shearing, which links the spatial and temporal scales of this process in a self-consistent manner, independent of the observer. On typical thermal timescales, the thermomechanical competence of DG-2 materials depends on the ratio of thermal to mechanical diffusivities, κ/χ. On this basis, we hypothesize the effective rigidity of Earth materials, pertaining when the thermomechanical competence is greater than unity. This theory, applied to the whole Earth, suggests the existence of isopycnal ‘detachment’ zones at systematic, globally correlated depths beneath orogens, consistent with a variety of geological data.
Bacterial biomineralization: new insights from
Myxococcus
-induced mineral precipitation
Authors: González-Muñoz Maria Teresa , Rodriguez-Navarro Carlos , Martínez-Ruiz Francisca , Arias Jose Maria , Merroun Mohamed L. , Rodriguez-Gallego Manuel
Published: June 2010

Bacteria have contributed to the formation of minerals since the advent of life on Earth. Bacterial biomineralization plays a critical role on biogeochemical cycles and has important technological and environmental applications. Despite the numerous efforts to better understand how bacteria induce/mediate or control mineralization, our current knowledge is far from complete. Considering that the number of recent publications on bacterial biomineralization has been overwhelming, here we attempt to show the importance of bacteria–mineral interactions by focusing in a single bacterial genus,
Myxococcus
, which displays an unusual capacity of producing minerals of varying compositions and morphologies. First, an overview of the recent history of bacterial mineralization, the most common bacteriogenic minerals and current models on bacterial biomineralization is presented. Afterwards a description of myxobacteria is presented, followed by a section where
Myxococcus
-induced precipitation of a number of phosphates, carbonates, sulphates, chlorides, oxalates and silicates is described and discussed in lieu of the information presented in the first part. As concluding remarks, implications of bacterial mineralization and perspectives for future research are outlined. This review strives to show that the mechanisms which control bacterial biomineralization are not mineral- or bacterial-specific. On the contrary, they appear to be universal and depend on the environment in which bacteria dwell.
Seasonal record from recent fluvial tufa deposits (Monasterio de Piedra, NE Spain): sedimentological and stable isotope data
Authors: Arenas C. , Osácar C. , Sancho C. , Vázquez-Urbez M. , Auqué L. , Pardo G.
Published: June 2010

Physical and hydrochemical parameters and sedimentation rates were monitored twice a year from August 1999 to March 2003 at the Monasterio de Piedra area (NE Spain). Different tufa facies related to distinct fluvial subenvironments were characterized and the isotopic composition of water was analysed seasonally. Sedimentary features (thickness, texture and structure) and stable isotope composition of the seasonal record on tablets were analysed. The seasonal intervals were identified from six-monthly thickness measurements on tablets.

Sedimentation rates had a strong seasonal pattern with higher values in warm periods than in cool ones, although erosive events and sporadic, warmer-than-normal climate conditions altered it. Three main types of fluvial facies were studied in detail: dense, stromatolitic tufa; dense to porous, massive tufa; and spongy, moss- and alga-bearing, crudely laminated tufa. Textural features of deposits from warm and cool periods had a variable pattern.

The sediment δ
18
O composition showed a rhythmic variation, with higher values in cool periods and lower in warm ones, caused by the fractionation due to seasonal temperature variations. The calculated temperatures for a theoretical equilibrium precipitation accord with the actual measured temperatures. The sediment δ
13
C composition had an irregular pattern, indicating that other parameters than temperature intervened in the fluvial system.