bluuebunny/crossref_metadata_2025 huggingface dataset:
Method for Designing and Optimizing Random-Search Libraries for Strain Improvement
Authors: Klein-Marcuschamer Daniel , Stephanopoulos Gregory
Published: June 2010

Random searches have been the hallmark of directed evolution and have been extensively employed in the improvement of complex or poorly understood phenotypes such as tolerance to toxic compounds in the context of cellular engineering. While genome-wide mutagenesis followed by selection or screening has been a traditional means of phenotype improvement, the list of experimental methods for cellular engineering based on random searches is rapidly expanding. Adding to the confusion is the element of chance, which lengthens the process and most notably adds to the cost of phenotypic improvement programs. Here we present a method to systematize the effort of finding superior mutants by successively improving random libraries. The method, based on the quantification of phenotypic diversity, is then used to isolate more-robust strains.
Detection of Human Intestinal Catalase-Negative, Gram-Positive Cocci by rRNA-Targeted Reverse Transcription-PCR
Authors: Kubota Hiroyuki , Tsuji Hirokazu , Matsuda Kazunori , Kurakawa Takashi , Asahara Takashi , Nomoto Koji
Published: June 2010

An analytical system based on rRNA-targeted reverse transcription-quantitative PCR (RT-qPCR) for enumeration of catalase-negative, Gram-positive cocci was established. Subgroup- or species-specific primer sets targeting 16S or 23S rRNA from
Enterococcus
,
Streptococcus
, and
Lactococcus
were newly developed. The RT-qPCR method using these primers together with the previously reported primer sets specific for the
Enterococcus
genus, the
Streptococcus
genus, and several
Streptococcus
species was found to be able to quantify the target populations with detection limits of 10
3
to 10
4
cells per gram feces, which was more than 100 times as sensitive as the qPCR method (10
6
to 10
8
cells per gram feces). The RT-qPCR analysis of fecal samples from 24 healthy adult volunteers using the genus-specific primer sets revealed that
Enterococcus
and
Streptococcus
were present as intestinal commensals at population levels of log
10
6.2 ± 1.4 and 7.5 ± 0.9 per gram feces (mean ± standard deviation [SD]), respectively. Detailed investigation using species- or subgroup-specific primer sets revealed that the volunteers harbored unique
Enterococcus
species, including the
E. avium
subgroup, the
E. faecium
subgroup,
E. faecalis
, the
E. casseliflavus
subgroup, and
E. caccae
, while the dominant human intestinal
Streptococcus
species was found to be
S. salivarius
. Various
Lactococcus
species, such as
L. lactis
subsp.
lactis
or
L. lactis
subsp.
cremoris
,
L. garvieae
,
L. piscium
, and
L. plantarum
, were also detected but at a lower population level (log
10
4.6 ± 1.2 per gram feces) and prevalence (33%). These results suggest that the RT-qPCR method enables the accurate and sensitive enumeration of human intestinal subdominant but still important populations, such as Gram-positive cocci.
Cellular and Molecular Remodeling of the Endocytic Pathway during Differentiation of Trypanosoma brucei Bloodstream Forms
Authors: Vanhollebeke Benoit , Uzureau Pierrick , Monteyne Daniel , Pérez-Morga David , Pays Etienne
Published: June 2010

During the course of mammalian infection, African trypanosomes undergo extensive cellular differentiation, as actively dividing long slender (SL) forms progressively transform into intermediate (I) forms and finally quiescent G
1
/G
0
-locked short stumpy (ST) forms. ST forms maintain adaptations compatible with their survival in the mammalian bloodstream, such as high endocytic activity, but they already show preadaptations to the insect midgut conditions. The nutritional requirements of ST forms must differ from those of SL forms because the ST forms stop multiplying. We report that the uptake of several ligands was reduced in ST forms compared with that in SL forms. In particular, the haptoglobin-hemoglobin (Hp-Hb) complex was no longer taken up due to dramatic downregulation of its cognate receptor, TbHpHbR. As this receptor also allows uptake of trypanolytic particles from human serum, ST forms were resistant to trypanolysis by human serum lipoproteins. These observations allowed both flow cytometry analysis of SL-to-ST differentiation and the generation of homogeneous ST populations after positive selection upon exposure to trypanolytic particles. In addition, we observed that in ST forms the lysosome relocates anterior to the nucleus. Altogether, we identified novel morphological and molecular features that characterize SL-to-ST differentiation.
Geobacter uraniireducensNikR Displays a DNA Binding Mode Distinct from Other Members of the NikR Family
Authors: Benanti Erin L. , Chivers Peter T.
Published: June 2010

NikR is a nickel-responsive ribbon-helix-helix transcription factor present in many bacteria and archaea. The DNA binding properties ofEscherichia coliandHelicobacter pyloriNikR (factors EcNikR and HpNikR, respectively) have revealed variable features of DNA recognition. EcNikR represses a single operon by binding to a perfect inverted repeat sequence, whereas HpNikR binds to promoters from multiple genes that contain poorly conserved inverted repeats. These differences are due in large part to variations in the amino acid sequences of the DNA-contacting β-sheets, as well as residues preceding the β-sheets of these two proteins. We present here evidence of another variation in DNA recognition by the NikR protein fromGeobacter uraniireducens(GuNikR). GuNikR has an Arg-Gly-Ser β-sheet that binds specifically to an inverted repeat sequence distinct from those recognized by Ec- or HpNikR. The N-terminal residues that precede the GuNikR β-sheet residues are required for high-affinity DNA binding. Mutation of individual arm residues dramatically reduced the affinity of GuNikR for specific DNA. Interestingly, GuNikR tetramers are capable of binding cooperatively to the promoter regions of two different genes,nik(MN)1andnik(MN)2. Cooperativity was not observed for the closely relatedG. bemidjiensisNikR, which recognizes the same operator sequence. The cooperative mode of DNA binding displayed by GuNikR could affect the sensitivity of transporter gene expression to changes in intracellular nickel levels.
Genotypic differentiation inButomus umbellatus(Butomaceae) using isozymes and random amplified polymorphic DNAs
Authors: Fernando Danilo D. , Cass David D.
Published: June 2010

In clonal plants like Butomus umbellatus, pollination between ramets commonly leads to geitonogamy since even distant ramets may belong to a common genet. A prior knowledge as to which ramets are genotypically different is essential to establish a cross-pollination treatment. Ramets from three introduced populations of B. umbellatus in western Canada (Hatzic Lake, British Columbia; Sturgeon River, Alberta; St. Andrews, Manitoba) were analyzed using isozyme and random amplified polymorphic DNA (RAPD) markers. Protein electrophoresis failed to reveal any difference in the banding patterns of 150 ramets using 16 enzyme systems. However, 5 of the 16 RAPD primers used were helpful in revealing polymorphism in terms of fragment amplifications. Three genets were differentiated, i.e., two from Hatzic Lake and one from both Sturgeon River and St. Andrews. Since B. umbellatus is largely unexamined, our data also represent a preliminary contribution on the genetic organization of this colonizing clonal aquatic species. Keywords: Butomus umbellatus, isozyme, RAPD, clone, genet, ramet.
Acid phosphatase isoforms in dry seeds and during seedling development in barley (Hordeum vulgare)
Authors: Pasqualini S. , Batini P. , Ederli L. , Panara F. , Antonielli M.
Published: June 2010

The acid phosphatase activity in the soluble, membrane, and cell wall fractions from Hordeum vulgare in dry seeds and during seedling development was investigated. The acid phosphatase activities were also assayed in barley roots and coleoptiles at different developmental stages. Electrophoretic patterns of multiple acid phosphatases in seeds, endosperms and embryos, and growing roots and coleoptiles are shown. The enzyme activity shows a rapid decrease in both roots and coleoptiles during growth. Using nondenaturing polyacrylamide gel electrophoresis, multiple acid phosphatase forms were found in all the organs examined. However, no qualitative differences in the location of bands were observed between root and coleoptile extract at various stages of development. The coleoptile cell wall fraction showed an acid phosphatase form characterized by a very low electrophoretic mobility that was not found in the soluble fraction. Keywords: barley, Hordeum vulgare L., acid phosphatase, isoforms, seedlings growth.
Maximum decomposition limits of forest litter types: a synthesis
Authors: Berg Björn , Johansson Maj-Britt , Ekbohm Gunnar , McClaugherty Charles , Rutigliano Flora , Santo Amalia Virzo De
Published: June 2010

We used long-term litter decomposition data to estimate final decomposition levels using an asymptotic function. The estimated final limit values for decomposition were compared with available chemical data for the different litter types. A total of 41 limit values were estimated from as many different decomposition studies, and 20 different litter types were incubated in eight different forest systems. The limit values estimated varied with litter type. They ranged from about 35 to about 100% decomposition and were linearly related to the initial litter concentrations of N, Mn, and Ca in the newly shed litter. For these three nutrients, there are causal relationships to lignin degradation and to the lignin-degrading microbial community. Using all available data, we made simple and multiple linear regressions and obtained a negative linear relationship between limit value and initial N concentration ([Formula: see text]; n = 41; p < 0.001). For needle litter alone, we obtained a better relationship ([Formula: see text]; n = 23; p < 0.001). Manganese concentrations in litter gave a positive relationship ([Formula: see text]; n = 25; p < 0.001), with a clear improvement when needle litter was tested for alone ([Formula: see text]; n = 16; p < 0.001). Calcium alone gave a barely significant relationship. When combining nutrients in multiple linear relationships we obtained high R2 values, indicating that the models were good. Thus for all sites and litter types, N, Mn, and Ca combined gave an [Formula: see text] value of 0.640 with n = 25 (p < 0.001). All needle litters combined gave an [Formula: see text] of 0.745 (n = 16; p < 0.001). The significance of this finding is discussed. Keywords: litter decomposition, limit values, maximum decomposition, nitrogen, manganese, calcium.
Endophytic fungi in branches of Norway spruce with particular reference to Tryblidiopsis pinastri
Authors: Barklund Pia , Kowalski T.
Published: June 2010

A variety of endophytic fungi were isolated from the branches of Norway spruce (Picea abies). We found that as internodes age, the composition of endophytic species gradually changes, both qualitatively and quantitatively. One of the dominating species, Tryblidiopsis pinastri, was most common in young internodes. In contrast, three other common species, Phialocephala scopiformis, Geniculosporium serpens, and Tapesia livido-fusca, were most frequently isolated from old internodes. Mollisia spp. were also common components of the endophytic flora of the Norway spruce in Sweden. Keywords: Picea abies, Tryblidiopsis pinastri, Phialocephala scopiformis, Geniculosporium spp., Tapesia spp., Mollisia spp.
Gas exchange and growth of three arctic tree-line tree species under different soil temperature and drought preconditioning regimes
Authors: Landhäusser Simon M. , Wein Ross W. , Lange Petra
Published: June 2010

Low soil temperatures and water availability are thought to be major factors determining the distribution of tree species at the arctic tree line. A comparative study examined the response of Betula papyrifera, Populus balsamifera, and Picea mariana seedlings to different soil temperatures and drought regimes in a growth chamber experiment. Morphological and ecophysiological responses (net assimilation rate, stomatal conductance to water vapour, and residual conductance) of these tree line tree species were measured and compared. Mean biomass accumulation of the deciduous species was greater than that of Picea mariana with increasing soil temperatures. Root biomass showed an increase of 30% in the three species between the soil temperatures of 3 and 15 °C. Response of ecophysiological variables to increased soil temperature was greater in B. papyrifera and Populus balsamifera than in Picea mariana. In a second experiment, drought-preconditioned B. papyrifera and Populus balsamifera seedlings were subjected to a 6-day water-withholding treatment. Drought decreased shoot mass and increased the root to shoot ratio equally in B. papyrifera and Populus balsamifera. Drought-preconditioned B. papyrifera and Populus balsamifera seedlings responded differently to the 6-day water-withholding treatment. Betula papyrifera used a water-conserving strategy and maintained low net assimilation rates and low water use after drought preconditioning, whereas in Populus balsamifera greater net assimilation rates were associated with drought preconditioning. These results are consistent with the distribution of these three tree species at the arctic tree line. Keywords: Picea mariana, Populus balsamifera, Betula papyrifera, drought preconditioning, soil temperature, arctic tree line.
Small-subunit rRNA gene sequences from representatives of selected families of the Gigartinales and Rhodymeniales (Rhodophyta). 2. Recognition of the Halymeniales ord.nov.
Authors: Saunders G. W. , Kraft G. T.
Published: June 2010

Nucleotide sequences of the nuclear, small-subunit ribosomal RNAs, as inferred from polymerase chain reaction amplified products, are introduced for representatives of the Dumontiaceae, Endocladiaceae, Halymeniaceae, and Kallymeniaceae of the order Cryptonemiales sensu Kylin, the Mychodeaceae, Phyllophoraceae, Schizymeniaceae, and Sebdeniaceae of the order Gigartinales sensu Kylin, and the Lomentariaceae and Rhodymeniaceae of the order Rhodymeniales. The new sequences are included in phylogenetic analyses incorporating previously published sequences from additional families of the orders Ahnfeltiales, Ceramiales, Gigartinales, Gracilariales, Palmariales, Plocamiales, and Rhodymeniales. We used the molecular data to test the validity of the taxonomic merger of the orders Gigartinales and Cryptonemiales that was proposed by G.T. Kraft and P.A. Robins in 1985. With only two exceptions (the families Halymeniaceae and Sebdeniaceae), phylogenetic analyses of the SSU data support a monophyletic origin for a combined Gigartinales–Cryptonemiales. We therefore propose the resurrection of a redefined Cryptonemiales to consist, at this time, of only the Halymeniaceae and Sebdeniaceae. Because virtually no elements of the original or recent definitions of the Cryptonemiales survive in the characterization of this taxon, we followed procedures allowed by the International Code of Botanical Nomenclature to designate it the Halymeniales ord.nov. Analysis of molecular data further indicates that the Rhodymeniales is a monophyletic assemblage distinct from both the Gigartinales and Halymeniales; it should not be merged with the Gigartinales as is occasionally suggested. Keywords: Cryptonemiales, Gigartinales, Halymeniaceae, Halymeniales, phylogeny, Rhodophyta, Sebdeniaceae, small-subunit rRNA, systematics.
Parasitism of yeasts by lignicolous Basidiomycota and other fungi
Authors: Hutchison Leonard J. , Barron G. L.
Published: June 2010

On water agar, hyphae of certain fungi are able to attack microcolonies and even solitary cells of yeasts belonging to the genera Candida, Cryptococcus, Pichia, Rhodotorula, and Sporidiobolus. The ability to attack yeasts is particularly common among the Basidiomycota and 100 of 195 isolates tested positive. In the Ascomycota and Deuteromycota, only 12 of 128 isolates tested positive. Two species of the Oomycota and 10 species of the Zygomycota tested negative. Two types of initial responses were recorded: (i) a chemotropic response in which directional hyphae are attracted to microcolonies or solitary cells, and (ii) a contact response in which hyphae reach yeast colonies by chance and subsequently attack them. In both cases the invading fungus produces coralloid masses of branched assimilative hyphae within the yeast colonies. Yeast cells are utilized as a nutrient source by the invading fungus in either of two ways: (i) the walls of yeast cells are lysed releasing the contents that are absorbed by the coralloid hyphae or (ii) branched hyphae from the invading fungus attach to the yeast cells, penetrate the walls, and absorb the contents. Both methods involve necrotrophic mycoparasitism. Keywords: yeasts, Basidiomycota, necrotrophic mycoparasitism, wood decay, nitrogen requirements.
Far-red light stimulates internode elongation, cell division, cell elongation, and gibberellin levels in bean
Authors: Beall Frederick D. , Yeung Edward C. , Pharis Richard P.
Published: June 2010

The contributions of cell division and cell elongation and the potential role of gibberellins in the far-red light stimulation of bean internode elongation were investigated. When bean plants, Phaseolus vulgaris cv. Kentucky Wonder, were grown in white light supplemented with far-red light a significant increase, up to threefold, in internode elongation was observed. Microscopic examination revealed that cell lengths were also increased but by a lower magnitude than internode length. Cell-labeling studies with [3H]thymidine showed that nuclei labeling was increased in internodes receiving supplemental far-red light. Thus far-red light induced increased internode elongation is a result of both increased cell elongation and increased cell division. Gibberellins A1, A20, A19, A44, and A4 and kaurenoic acid were identified in extracts of internode tissue by gas chromatography – mass spectroscopy using [2H2]-labeled internal standards for quantification. It thus appears that the early C-13 hydroxylation pathway is operative in the elongating internode. Endogenous GA1 and GA20 were approximately twofold higher in the first internodes of plants receiving supplemental far-red light. A comparison of the metabolism of exogenously supplied [2H2]GA19 suggested that GA turnover was greater in tissues exposed to supplemental far-red light. These results indicate that both cell division and elongation contribute to the enhanced elongation response of bean internodes to far-red light and that these processes are correlated with an increase in GA levels and (or) metabolism. Keywords: Phaseolus, gibberellins, phytochrome, far-red light.
Isozyme variation, morphology, and growth response to temperature in Pythium ultimum
Authors: Barr D. J. S. , Warwick S. I. , Désaulniers N. L.
Published: June 2010

A worldwide collection of 60 isolates of Pythium ultimum and 37 asexual (sexually sterile) isolates presumed to be P. ultimum were compared by isozyme analysis, morphological characters, and their growth rate at different temperatures. Isolates were separated into 10 multilocus genotypes as defined by nine isozyme loci. Five genotypes (U1–U5) comprising 85 isolates differed from each other merely by homo- or hetero-zygous states at one and (or) two loci. Four isolates in genotype U6 produced zoospores and were presumed to be var. sporangiiferum. They differed at one locus from genotypes U1–U5. Genotypes U7, U8, U9, and U10 differed from U1–U5 at one, two, three, and five loci, respectively. Sexual isolates occurred in genotypes U1–U3 and U6–U10, and asexual isolates in genotypes U2–U6. Only minor differences were detected in morphology in six isolates (genotypes U8–U10). A single isolate (genotype U10) differed in growth rate from all others. Isozyme analysis is an effective means of distinguishing P. ultimum from nine other species included for comparative purposes and for identifying asexual isolates that cannot be positively identified by morphology. Keywords: Pythium ultimum var. ultimum, Pythium ultimum var. sporangiiferum, isozymes.
Molecular systematics of E-strain mycorrhizal fungi: Wilcoxina and its relationship to Tricharina (Pezizales)
Authors: Egger Keith N.
Published: June 2010

Nuclear-encoded ribosomal RNA gene sequences (rDNA) spanning 107 base pairs at the 3′ end of the 18S gene, the 5′ internal transcribed spacer region (ITS1), and across divergent domain D1 near the 5′ end of the 28S gene were analyzed to infer a phylogeny for taxa of the E-strain mycorrhizal fungal genus Wilcoxina and to determine their relationship to representatives of the genus Tricharina. The phylogeny suggests that Wilcoxina and Tricharina, although related, should be maintained as separate genera. Wilcoxina taxa formed a distinct group that exhibited interspecific variation of 37.6% in the ITS1 region. Wilcoxina alaskana was the most distant taxon, which is consistent with its growth on an unusual substrate (rotting wood). It remains to be confirmed that this taxon is mycorrhizal. A cryptic Wilcoxina species, known only from root isolates, was found. Sequence analysis of the ITS1 region distinguished two varieties of Wilcoxina mikolae: var. mikolae and var. tetraspora. Among the taxa of Tricharina examined there was 31.2% variation in the ITS1 region. The most divergent taxon in the Tricharina group was Tricharina praecox, although sequence analysis was unable to distinguish the varieties described within this species. The remaining taxa in Tricharina formed a tight group with only 10.2% interspecific divergence in the ITS1 region. There is sequence evidence that at least two taxa are included in Tricharina gilva as presently delineated. As the sole report of mycorrhiza formation in Tricharina is shown to be based upon a misidentification, it therefore appears that only Wilcoxina taxa are mycorrhizal. Keywords: E-strain, Wilcoxina, Tricharina, mycorrhiza, ribosomal DNA, phylogeny.
Cosegregation of Avr4 and Avr6 in Phytophthora sojae
Authors: Gijzen Mark , Förster Helga , Coffey Michael D. , Tyler Brett
Published: June 2010

The F2 progeny resulting from a cross of Phytophthora sojae race 2 (avirulent on Rps4 and Rps6) and race 7 (virulent on Rps4 and Rps6) were tested for their ability to cause disease on soybean plants carrying the Rps4 or the Rps6 resistance genes. Of 55 F2 progeny analyzed, 41 individuals were avirulent on both of these genes and 14 were virulent on Rps4 and Rps6, indicating that avirulence on Rps4 and Rps6 is dominant and linked. These results support the suggestion that the soybean–Phytophthora relationship is a gene for gene interaction and that the presumptive Avr4 and Avr6 genes are either tightly linked or identical. Keywords: avirulence, genetic mapping, Glycine max, incomplete dominance, Phytophthora megasperma f.sp. glycinea.
A NOTE ON KILLING VECTOR FIELDS OF BIANCHI TYPE II SPACETIMES IN TELEPARALLEL THEORY OF GRAVITATION
Authors: SHABBIR GHULAM , KHAN SUHAIL
Published: June 2010

The aim of this paper is to classify Bianchi type II spacetimes according to their teleparallel Killing vector fields using the direct integration technique. Studying teleparallel Killing vector fields in the above spacetimes, it turns out that the dimensions of the teleparallel Killing vector fields are 4, 5 or 7. A brief comparison between teleparallel and general relativity Killing vector fields are given. It is shown that for the above spacetimes in the presence of torsion we get more conservation laws which are different from the theory of general relativity.
A DYNAMICAL, CONFINING MODEL AND BULK VISCOSITY OF QCD MATTER AT FINITE TEMPERATURE
Authors: JIANG YU , WANG BIN , SUN WEI-MIN , ZONG HONG-SHI
Published: June 2010

In this paper we calculate the thermodynamic quantities and bulk viscosity in a simple confining Dyson–Schwinger equation model of two-flavor QCD. Our results show that the velocity of sound shows a sharp increase around [Formula: see text] and at the phase transition temperature [Formula: see text] the derivative of the velocity with respect to T has a distinct change. It is also found that the trace anomaly increases sharply below the phase transition point and the bulk viscosity has a peak located at [Formula: see text] which is almost the same as the peak of the trace anomaly. A comparison of our results with those in the previous literature is given.
EXTENDED UNCERTAINTY PRINCIPLE AND THE GEOMETRY OF (ANTI)-DE SITTER SPACE
Authors: MIGNEMI S.
Published: June 2010

It has been proposed that on (anti)-de Sitter background, the Heisenberg uncertainty principle should be modified by the introduction of a term proportional to the cosmological constant. We show that this modification of the uncertainty principle can be derived straightforwardly from the geometric properties of (anti)-de Sitter spacetime. We also discuss the connection between the so-called extended generalized uncertainty principle and triply special relativity.
DID ARTISTS DISCOVER CHAOS BEFORE SCIENTISTS?
Authors: FORTUNA LUIGI , FRASCA MATTIA
Published: June 2010

Chaos was historically discovered with the Lorenz attractor in 1963. Several artworks, created before that date, by post-war artists such as Fontana, Crippa, Mathieu and Tobey, seem to anticipate forms and shapes typically shown by chaotic systems. In this paper, we juxtapose these masterpieces with some strange attractors of dynamical system theory in a timeline leading to the question whether artists discovered chaos before scientists.
NON-EXISTENCE, MONOTONICITY FOR POSITIVE SOLUTIONS OF SEMILINEAR ELLIPTIC SYSTEM IN $\mathbb{R}_+^N$
Authors: GUO YUXIA
Published: June 2010

In this paper, by using the Alexandrov–Serrin method of moving plane combined with integral inequality, we prove some non-existence results for positive weak solution of semilinear elliptic system in the half-space [Formula: see text].
GLOBAL ERROR BOUNDS WITH EXPONENTS FOR MULTIFUNCTIONS WITH SET CONSTRAINTS
Authors: HUANG HUI
Published: June 2010

In this paper, higher order strongly convex-graph multifunctions are introduced. Using the normal cones, we give some characterizations for higher order strongly convex-graph multifunctions. Moreover, in terms of the coderivatives, we present some sufficient conditions for multifunctions with set constraints to have global error bounds with exponents in Banach spaces.
LEGENDRIAN HELIX AND CABLE LINKS
Authors: DING FAN , GEIGES HANSJÖRG
Published: June 2010

Traynor ([11]) has described an example of a two-component Legendrian "circular helix link" Λ0 ⊔ Λ1 in the 1-jet space J1(S1) of the circle (with its canonical contact structure) that is topologically but not Legendrian isotopic to the link Λ1 ⊔ Λ0. We give a complete classification of the Legendrian realizations of this topological link type, as well as all other "cable links" in J1(S1).
THE LAPW CALCULATION OF ELECTRONIC STRUCTURE OF ANATASE TiO2 DOPED WITH TRANSITION METAL ATOMS
Authors: LIAO BIN , WU XIANYING , LIANG HONG , ZHANG XU , HOU XINGGANG , LIU ANDONG
Published: June 2010

The electronic density of states (DOS) and energy bands of doped anatase TiO2 are studied by the full potential linearized augmented plane wave (FPLAPW) method based on the density functional theory. After doping with transition metal atoms, the band gap of TiO2 is narrowed, doping with transition metal cation makes both valence bands and conduction bands move towards lower position.
SELECTIVE EXCITATION OF HIGH VIBRATIONAL STATES OF HYDROGEN FLUORIDE IN A THERMAL ENVIRONMENT BY ULTRAFAST INFRARED LASER PULSES
Authors: NIU KAI , DONG LI-QING , CONG SHU-LIN
Published: June 2010

The selective excitation of the high ground vibrational state of rotationless HF in an unobserved quasi-resonant thermal environment under the control of a single pulse and pulse train is studied using the reduced density matrix theory. It is shown that the pulse train can enhance the population transfer probability. The numerical results reveal that the vibrational relaxation process is affected by the distribution of the environment frequency and the molecule–environment coupling intensity. The effects of the molecule–environment coupling parameter and the overlapping pulses on the population of the target state of HF are also discussed.
THEORETICAL STUDY OF QUASI-CLASSICAL CALCULATIONS FOR THE REACTION Sr + CH3Br
Authors: LI YA-MIN , WANG SHUO
Published: June 2010

The first quasi-classical trajectory (QCT) calculation for the exothermic reaction Sr + CH3Br is carried out based on a constructed London–Eyring–Polanyi–Sato (LEPS) potential energy surface (PES). By QCT calculation, the product SrBr vibration distributions are obtained. The result is in good comparison with the experimental one by Keijzer JF et al. [Chem. Phys.207:261, 1996]. Furthermore, the reaction product SrBr angular distribution and rotational alignment are also obtained. The products are dominantly forward-scattered and the alignment effect is obvious. Fast dynamics mechanism is proposed upon the calculation results.
QUANTUM DYNAMICAL CALCULATION OF ALL ROVIBRATIONAL STATES OF HO2 FOR TOTAL ANGULAR MOMENTUM J = 0–10
Authors: CHEN WENWU , POIRIER BILL
Published: June 2010

The energy levels and wavefunctions for all rovibrational bound states of HO2 are systematically computed, for all total angular momentum values J = 0–10. The calculations are performed using ScalIT, a suite of software modules designed to enable quantum dynamics and related calculations to be performed on massively parallel computing architectures. This is the first-ever application of ScalIT to a real (and very challenging) molecular application. The codes, and in particular, the algorithms (optimal separable basis, preconditioned inexact spectral transform, phase space optimized discrete variable representation basis) are so efficient that in fact, the entire calculation can be performed on a single CPU — although parallel scalability over a small number of CPUs is also evaluated, and found to be essentially perfect in this regime. For the lowest 11 vibrational states, the rotational levels for J = 0–10 fit fairly well to a rigid rotor model, with all vibrational-state-dependent rotational constants, B eff (v), close to values obtained from a previous calculation for J = 0 and 1 [J Chem Phys107:2705, 1997]. However, comparatively larger discrepancies with the rigid-rotor model are found at the higher J values, manifesting in the observed K-splitting (along the O–O bond) of rovibrational levels. This supports earlier work [J Chem Phys113:11055, 2000] suggesting that Coriolis coupling is quite important for this system.
MICRO-CONSTITUENT BASED VISCOELASTIC FINITE ELEMENT ANALYSIS OF BIOLOGICAL CELLS
Authors: CHENG F. , UNNIKRISHNAN G. U. , REDDY J. N.
Published: June 2010

A viscoelastic analysis of the biological cell considering the microcellular material properties is carried out in this work. Three separate regions of the cell: the actin cortex, cytoplasm and nucleus are considered. The outer cortex and cytoplasm are modeled using standard linear viscoelastic model (SLS) and standard neo-Hookean viscoelastic solid, and a linear elastic material model is considered for the nucleus. The effect of the material properties of cytoplasm and actin cortex on the derivable parameters from three major experimental studies of magnetic twisting cytometry (MTC) and atomic force microscopy (AFM) and micropipette aspiration (MPA) are analyzed using the finite element method. The bead center displacement for the MTC, reaction force for AFM, and aspiration length ratio for the MPA are the major quantities derived from the finite element analysis. A number of parametric studies are also conducted and it is observed that SLS and SnHS models predict nearly identical results for the material constants.
UNCERTAINTY QUANTIFICATION IN STOCHASTIC SYSTEMS USING POLYNOMIAL CHAOS EXPANSION
Authors: SEPAHVAND K. , MARBURG S. , HARDTKE H.-J.
Published: June 2010

In recent years, extensive research has been reported about a method which is called the generalized polynomial chaos expansion. In contrast to the sampling methods, e.g., Monte Carlo simulations, polynomial chaos expansion is a nonsampling method which represents the uncertain quantities as an expansion including the decomposition of deterministic coefficients and random orthogonal bases. The generalized polynomial chaos expansion uses more orthogonal polynomials as the expansion bases in various random spaces which are not necessarily Gaussian. A general review of uncertainty quantification methods, the theory, the construction method, and various convergence criteria of the polynomial chaos expansion are presented. We apply it to identify the uncertain parameters with predefined probability density functions. The new concepts of optimal and nonoptimal expansions are defined and it demonstrated how we can develop these expansions for random variables belonging to the various random spaces. The calculation of the polynomial coefficients for uncertain parameters by using various procedures, e.g., Galerkin projection, collocation method, and moment method is presented. A comprehensive error and accuracy analysis of the polynomial chaos method is discussed for various random variables and random processes and results are compared with the exact solution or/and Monte Carlo simulations. The method is employed for the basic stochastic differential equation and, as practical application, to solve the stochastic modal analysis of the microsensor quartz fork. We emphasize the accuracy in results and time efficiency of this nonsampling procedure for uncertainty quantification of stochastic systems in comparison with sampling techniques, e.g., Monte Carlo simulation.
ESTIMATION OF ANISOTROPIC PLASTIC PROPERTIES OF ENGINEERING STEELS FROM SPHERICAL IMPRESSIONS
Authors: YONEDA KEISHI , YONEZU AKIO , HIRAKATA HIROYUKI , MINOSHIMA KOHJI
Published: June 2010

This study proposes a method of reverse analysis to estimate the anisotropic plastic properties of engineering steels by spherical indentation. The method takes into consideration materials that obey the work-hardening law and show in-plane anisotropic yield stress. Finite element analysis was first carried out to compute the indentation behavior of such materials, showing that a permanent impression exhibited an anisotropic shape which was strongly dependent on the orthotropic axis. Based on the anisotropy of the impression geometry, we developed a simple approach to determine the yield stress, work-hardening exponent and yield stress ratio. The approach consists of several functions related to the parameters of two impression geometries, produced by dual spherical indentations with different indentation forces. Since the present method uses only two impression geometries and does not necessitate indentation force — displacement curves (indentation curves), it is a particularly useful technique to evaluate "indistinguishable materials" which are special sets of materials with distinct plastic properties, yet yield almost identical indentation curves.
DEFENSE HOLE DESIGN FOR A SHEAR DOMINANT LOADED PLATE
Authors: AKOUR SALIH N. , NAYFEH JAMAL F. , NICHOLSON DAVID W.
Published: June 2010

Baseline data is produced for designing an optimum Defense Hole System (DHS) for a large plate with a circular hole in shear dominant-load range. Stress concentration associated with circular holes for tensile/shear ratio ranging from 0% to 25% is reduced by 13.5% to 16.67%, respectively. This reduction is achieved by introducing auxiliary elliptical holes (i.e., DHS) along the principal stress directions. Each pair lies along the same principal direction has the same geometry and placement on either side of the main hole. These holes are placed in the low stress regions. With such reduction in the maximum stress level, the improvement in fatigue life of a structural part can be very significant. Both redesign optimization and parametric optimization techniques are utilized to reach the optimum solutions and to generate the baseline data. Finite Element Analysis (FEA) is used to evaluate the stresses and to optimize the size and location of the DHS. The optimum cases are validated using the RGB-photoelasticity technique. Three main goals are achieved by introducing such holes: maximum stress reduction, working as crack arrest in case a crack propagates, and material reduction.
INTERFACIAL SHEAR EFFECT ON HERRINGBONE PATTERN OF THIN FILMS ON COMPLIANT SUBSTRATES
Authors: SONG J.
Published: June 2010

A stiff thin film on a heated compliant substrate may buckle when the system is cooled due to the thermal expansion mismatch between the film and substrate. Highly ordered herringbone patterns are observed as the system continues to cool. A theoretical model for the herringbone pattern coupling the interfacial shear traction is developed to understand the underlying mechanism. It is shown that the interfacial shear traction plays a key role on the formation of the herringbone pattern. Its effects on the buckling wavelength and amplitude are also given in the paper. The results agree well with experiments and therefore provide valuable guide to the precise design and control of the buckling profile in many applications ranging from stretchable electronics to micro/nanoscale surface patterning and precision metrology.
KINESIN AND DYNEIN SMART NANOMOTORS: TOWARDS BIO-NANOROBOTIC SYSTEMS
Authors: KHATAEE H. R. , KHATAEE A. R.
Published: June 2010

The majority of active transport in cells is driven by two classes of intelligent nanomotors, kinesin and dynein. The intelligence of kinesin and dynein nanomotors is the key toward developing intelligent bio-nanosystems for various nanotechnological applications. The first step in this regard is the ability to determine the structure, behavior, and properties of basic bio-nanocomponents, such as proteins. Therefore, in this paper we have described structures and mechanisms of kinesin and dynein protein nanomotors. Kinesin and dynein nanomotors are multi-protein complexes which are responsible for various dynamical processes for transporting single molecules over small distances to cell movement and growth. They convert the chemical energy into mechanical work directly rather than via an intermediate energy. Kinesin and dynein protein nanomotors are self-guiding systems. They have evolved to enable movement on their polymer filaments, either on cellular or supra-cellular levels, to recognize the direction of movement. Kinesin and dynein nanomotors have different properties, but in the cell they are known to cooperate and even to compete with each others during their function. It has been indicated that kinesin and dynein nanomotors can be defined as ideal bio-nanocomponents for bio-nanorobotic systems because of their small size, perfect structure, smart and high efficiency.
SENSITIVIY OF A NANOCANTILEVER-BASED MASS SENSOR
Authors: PRABAKAR K. , JAYAPANDIAN J. , TYAGI A. K. , SUNDAR C. S. , RAJ BALDEV
Published: June 2010

In the present work, mass and position sensitivity of a nanocantilever is simulated using finite element analysis. Changes in resonant frequency of various modes of a polysilicon cantilever, with a gold coating of different thickness, area, and spatial distribution is simulated. It is found that for a uniform increase in gold coating thickness, torsional mode gives an order higher mass sensitivity than vertical bending and lateral bending modes. In other cases, sensitivity is highly dependent on the position of the coating and is explained on the basis of flexural rigidity. Apart from this, simulations were performed for a point mass (gold cube) loading at various positions along the length and width axis of the cantilever. Further, for localized mass loading, cantilever was tailored for enhanced sensitivity. It is found that by introducing a step discontinuity in thickness of the cantilever, the mass sensitivity increases by two orders of magnitude and it depends on the position of step from free end, step thickness, and step width.
FABRICATION OF NANOPOROUS CHITOSAN MEMBRANES
Authors: WANG XIAOLIANG , LI XIANG , STRIDE ELEANOR , EDIRISINGHE MOHAN
Published: June 2010

Naturally derived biopolymers have been widely used for biomedical applications such as drug carriers, wound dressings, and tissue engineering scaffolds. Chitosan is a typical polysaccharide of great interest due to its biocompatibility and film-formability. Chitosan membranes with controllable porous structures also have significant potential in membrane chromatography. Thus, the processing of membranes with porous nanoscale structures is of great importance, but it is also challenging and this has limited the application of these membranes to date. In this study, with the aid of a carefully selected surfactant, polyethyleneglycol stearate-40, chitosan membranes with a well controlled nanoscale structure were successfully prepared. Additional control over the membrane structure was obtained by exposing the suspension to high intensity, low frequency ultrasound. It was found that the concentration of chitosan/surfactant ratio and the ultrasound exposure conditions affect the structural features of the membranes. The stability of nanopores in the membrane was improved by intensive ultrasonication. Furthermore, the stability of the blended suspensions and the intermolecular interactions between chitosan and the surfactant were investigated using scanning electron microscope and Fourier transform infrared spectroscopy (FTIR) analysis, respectively. Hydrogen bonds and possible reaction sites for molecular interactions in the two polymers were also confirmed by FTIR analysis.
CONSTRUCTAL DESIGN OF NANOFLUIDS FOR ONE-DIMENSIONAL STEADY HEAT CONDUCTION SYSTEMS
Authors: BAI CHAO , WANG LI QIU
Published: June 2010

We perform a constructal design of nanofluid particle volume fraction for four heat-conduction systems and four types of nanofluids to address whether nanofluids with uniformly-dispersed particles always offer the optimal global performance. The constructal volume fraction is obtained to minimize the system overall temperature difference and overall thermal resistance. The constructal thermal resistance is an overall property fixed only by the system global geometry and the average thermal conductivity of nanofluids used in the system. Efforts to enhance the thermal conductivity of nanofluids are important to reduce the constructal overall thermal resistance. The constructal nanofluids that maximize the system performance depend on both the type of nanofluids and the system configuration, and are always having a nonuniform particle volume fraction for all the cases studied in the present work. Nanofluids research and development should thus focus on not only nanofluids but also systems that use them.
On the Weak Relatively Nonexpansive Mappings in Banach Spaces
Authors: Xu Yongchun , Su Yongfu
Published: June 2010

In recent years, the definition of weak relatively nonexpansive mapping has been presented and studied by many authors. In this paper, we give some results about weak relatively nonexpansive mappings and give two examples which are weak relatively nonexpansive mappings but not relatively nonexpansive mappings in Banach space "Equation missing" and "Equation missing".
An Active Fault-Tolerant PWM Tracker for Unknown Nonlinear Stochastic Hybrid Systems: NARMAX Model and OKID-Based State-Space Self-Tuning Control
Authors: Wang Chu-Tong , Tsai Jason S. H. , Chen Chia-Wei , Lin You , Guo Shu-Mei , Shieh Leang-San
Published: June 2010

An active fault-tolerant pulse-width-modulated tracker using the nonlinear autoregressive moving average with exogenous inputs model-based state-space self-tuning control is proposed for continuous-time multivariable nonlinear stochastic systems with unknown system parameters, plant noises, measurement noises, and inaccessible system states. Through observer/Kalman filter identification method, a good initial guess of the unknown parameters of the chosen model is obtained so as to reduce the identification process time and enhance the system performances. Besides, by modifying the conventional self-tuning control, a fault-tolerant control scheme is also developed. For the detection of fault occurrence, a quantitative criterion is exploited by comparing the innovation process errors estimated by the Kalman filter estimation algorithm. In addition, the weighting matrix resetting technique is presented by adjusting and resetting the covariance matrix of parameter estimates to improve the parameter estimation for faulty system recovery. The technique can effectively cope with partially abrupt and/or gradual system faults and/or input failures with fault detection.
On Some Layer‐Based Risk Measures with Applications to Exponential Dispersion Models
Authors: Furman Olga , Furman Edward
Published: June 2010

Layer‐based counterparts of a number of well‐known risk measures have been proposed and studied. Namely, some motivations and elementary properties have been discussed, and the analytic tractability has
been demonstrated by developing closed‐form expressions in the general framework of exponential dispersion models.
Infinite Boundary Value Problems for Second‐Order Nonlinear Impulsive Differential Equations with Supremum
Authors: Shi Piao-Piao , Wang Wen-Xia
Published: June 2010

We investigate the infinite boundary value problems for second‐order
impulsive differential equations with supremum by establishing a new comparison result
and using the lower and upper solution method, and obtain the existence results for their
maximal and minimal solutions.
Sliding Mode Observer and Control Design with Adaptive Parameter Estimation for a Supersonic Flight Vehicle
Authors: Bahrami M. , Ebrahimi B. , Ansarifar G. R.
Published: June 2010

Design and synthesis of a nonlinear generic supersonic flight vehicle longitudinal dynamics control for angle-of-attack, AOA, output tracking in the atmospheric flight is presented based on sliding mode control. A sliding mode observer is invoked to estimate AOA which is difficult to measure in practice. Large parameter uncertainties accommodation envisaged by designing adaptive mechanisms for both the control and observer and high chattering authority due to large deviations of aerodynamic coefficients arising from wind-tunnel measurements are inhibited. The employed method enables the sliding mode control design to exhibit the desired dynamic properties during the entire output-tracking process. Simulations results are presented to demonstrate the performance, robustness, and stability.
Fixed Point in Topological Vector Space-Valued Cone Metric Spaces
Authors: Azam Akbar , Beg Ismat , Arshad Muhammad
Published: June 2010

We obtain common fixed points of a pair of mappings satisfying a generalized contractive type condition in TVS-valued cone metric spaces. Our results generalize some well-known recent results in the literature.
A Metabolic Model of Human Erythrocytes: Practical Application of the E-Cell Simulation Environment
Authors: Yachie-Kinoshita Ayako , Nishino Taiko , Shimo Hanae , Suematsu Makoto , Tomita Masaru
Published: June 2010

The human red blood cell (RBC) has long been used for modeling of complex biological networks, for elucidation of a wide variety of dynamic phenomena, and for understanding the fundamental topology of metabolic pathways. Here, we introduce our recent work on an RBC metabolic model using the E-Cell Simulation Environment. The model is sufficiently detailed to predict the temporal hypoxic response of each metabolite and, at the same time, successfully integrates modulation of metabolism and of the oxygen transporting capacity of hemoglobin. The model includes the mechanisms of RBC maintenance as a single cell system and the functioning of RBCs as components of a higher order system. Modeling of RBC metabolism is now approaching a fully mature stage of realistic predictions at the molecular level and will be useful for predicting conditions in biotechnological applications such as long-term cold storage of RBCs.