bluuebunny/crossref_metadata_2025 huggingface dataset:
FHL3 negatively regulates human high-affinity IgE receptor β-chain gene expression by acting as a transcriptional co-repressor of MZF-1
Authors: TAKAHASHI Kyoko , MATSUMOTO Chiyuki , RA Chisei
Published: February 2005

The high-affinity IgE receptor FcεRI plays a key role in triggering allergic reactions. We recently reported that human FcεRI β-chain gene expression was down-regulated by a transcription factor, MZF-1, through an element in the fourth intron. In the present study, we found that this transcriptional repression by MZF-1 required FHL3 (four and a half LIM domain protein 3) as a cofactor. Yeast two-hybrid and immunoprecipitation assays demonstrated that FHL3 bound MZF-1 in vitro and in vivo. Overexpression of FHL3 in KU812 cells suppressed the β-chain promoter activity through the element in the fourth intron in an MZF-1-dependent manner. Furthermore, results from pull-down assays and gel-filtration chromatography employing nuclear extracts indicated that MZF-1 and FHL3 formed a complex of high molecular mass with some additional proteins in the nucleus. Granulocyte–macrophage colony-stimulating factor, which was reported to decrease FcεRI expression, induced the accumulation of FHL3 in the nucleus, in accordance with the repressive role of FHL3 in β-chain gene expression.
Substrate and product specificities of cis-type undecaprenyl pyrophosphate synthase
Authors: CHEN Annie P.-C. , CHANG Sing-Yang , LIN Yu-Chung , SUN Yang-Sheng , CHEN Chao-Tsen , WANG Andrew H.-J. , LIANG Po-Huang
Published: February 2005

UPPS (undecaprenyl pyrophosphate synthase) catalyses consecutive condensation reactions of FPP (farnesyl pyrophosphate) with eight isopentenyl pyrophosphates to generate C55 UPP, which serves as a lipid carrier for bacterial peptidoglycan biosynthesis. We reported the co-crystal structure of Escherichia coli UPPS in complex with FPP. Its phosphate head-group is bound to positively charged arginine residues and the hydrocarbon moiety interacts with hydrophobic amino acids including L85, L88 and F89, located on the α3 helix of UPPS. We now show that the monophosphate analogue of FPP binds UPPS with an eight times lower affinity (Kd=4.4 μM) compared with the pyrophosphate analogue, a result of a larger dissociation rate constant (koff=192 s−1). Farnesol (1 mM) lacking the pyrophosphate does not inhibit the UPPS reaction. GGPP (geranylgeranyl pyrophosphate) containing a larger C20 hydrocarbon tail is an equally good substrate (Km=0.3 μM and kcat=2.1 s−1) compared with FPP. The shorter C10 GPP (geranyl pyrophosphate) displays a 90-fold larger Km value (36.0±0.1 μM) but similar kcat value (1.7±0.1 s−1) compared with FPP. Replacement of L85, L88 or F89 with Ala increases FPP and GGPP Km values by the same amount, indicating that these amino acids are important for substrate binding, but do not determine substrate specificity. With GGPP as a substrate, UPPS still catalyses eight isopentenyl pyrophosphate condensation reactions to synthesize C60 product. Computer modelling suggests that the upper portion of the active-site tunnel, where cis double bonds of the product reside, may be critical for determining the final product chain length.
Gelsolin binds to polyphosphoinositide-free lipid vesicles and simultaneously to actin microfilaments
Authors: MÉRÉ Jocelyn , CHAHINIAN Anne , MACIVER Sutherland K. , FATTOUM Abdellatif , BETTACHE Nadir , BENYAMIN Yves , ROUSTAN Claude
Published: February 2005

Gelsolin is a calcium-, pH- and lipid-dependent actin filament severing/capping protein whose main function is to regulate the assembly state of the actin cytoskeleton. Gelsolin is associated with membranes in cells, and it is generally assumed that this interaction is mediated by PPIs (polyphosphoinositides), since an interaction with these lipids has been characterized in vitro. We demonstrate that non-PPI lipids also bind gelsolin, especially at low pH. The data suggest further that gelsolin becomes partially buried in the lipid bilayer under mildly acidic conditions, in a manner that is not dependent of the presence of PPIs. Our data also suggest that lipid binding involves a number of sites that are spread throughout the gelsolin molecule. Linker regions between gelsolin domains have been implicated by other work, notably the linker between G1 and G2 (gelsolin domains 1 and 2 respectively), and we postulate that the linker region between the N-terminal and C-terminal halves of gelsolin (between G3 and G4) is also involved in the interaction with lipids. This region is compatible with other studies in which additional binding sites have been located within G4–6. The lipid–gelsolin interactions reported in the present paper are not calcium-dependent, and are likely to involve significant conformational changes to the gelsolin molecule, as the chymotryptic digest pattern is altered by the presence of lipids under our conditions. We also report that vesicle-bound gelsolin is capable of binding to actin filaments, presumably through barbed end capping. Gelsolin bound to vesicles can nucleate actin assembly, but is less active in severing microfilaments.
Overexpression of troponin T in Drosophila muscles causes a decrease in the levels of thin-filament proteins
Authors: MARCO-FERRERES Raquel , ARREDONDO Juan J. , FRAILE Benito , CERVERA Margarita
Published: February 2005

Formation of the contractile apparatus in muscle cells requires co-ordinated activation of several genes and the proper assembly of their products. To investigate the role of TnT (troponin T) in the mechanisms that control and co-ordinate thin-filament formation, we generated transgenic Drosophila lines that overexpress TnT in their indirect flight muscles. All flies that overexpress TnT were unable to fly, and the loss of thin filaments themselves was coupled with ultrastructural perturbations of the sarcomere. In contrast, thick filaments remained largely unaffected. Biochemical analysis of these lines revealed that the increase in TnT levels could be detected only during the early stages of adult muscle formation and was followed by a profound decrease in the amount of this protein as well as that of other thin-filament proteins such as tropomyosin, troponin I and actin. The decrease in thin-filament proteins is not only due to degradation but also due to a decrease in their synthesis, since accumulation of their mRNA transcripts was also severely diminished. This decrease in expression levels of the distinct thin-filament components led us to postulate that any change in the amount of TnT transcripts might trigger the down-regulation of other co-regulated thin-filament components. Taken together, these results suggest the existence of a mechanism that tightly co-ordinates the expression of thin-filament genes and controls the correct stoichiometry of these proteins. We propose that the high levels of unassembled protein might act as a sensor in this process.
The effect of the farnesyl protein transferase inhibitor SCH66336 on isoprenylation and signalling by the prostacyclin receptor
Authors: O'MEARA Sarah J. , KINSELLA B. Therese
Published: February 2005

Like Ras, farnesylation of the IP (prostacyclin receptor) is required for its efficient intracellular signalling, and hence the IP represents a potential target for inhibition by FTIs [FTase (farnesyl protein transferase) inhibitors]. Herein, the effect of SCH66336 on the isoprenylation and function of the human and mouse IPs overexpressed in human embryonic kidney 293 cells, and by the IP endogenously expressed in human erythroleukaemia cells, was investigated. SCH66336 yielded concentration-dependent decreases in IP-mediated cAMP generation (IC50 0.27–0.62 nM), [Ca2+]i mobilization (IC50 26.6–48.3 nM) and IP internalization, but had no effect on signalling by the non-isoprenylated β2 adrenergic receptor or β isoform of the TP (prostanoid thromboxane A2 receptor). Additionally, SCH66336 impaired IP-mediated crossdesensitization of TPα signalling (IC50 56.1 nM) and reduced farnesylation of the molecular chaperone protein HDJ-2 (IC50 3.1 nM). To establish whether farnesylation of the IP is inhibited and/or whether its ‘CaaX motif’ might undergo alternative geranylgeranylation in the presence of SCH66336, a series of chimaeric Ha (Harvey)-Ras fusions were generated by replacing its CaaX motif (-CVLS) with that of the IP (-CSLC) or, as controls, of Ki (Kirsten)-Ras 4B (-CVIM) or Rac 1 (-CVLL). Whereas SCH66336 had no effect on Ha-RasCVLL isoprenylation in vitro or in whole cells, it supported alternative geranylgeranylation of Ha-RasCVIM, but completely impaired isoprenylation of both Ha-RasCVLS and Ha-RasCSLC. These data confirm that the -CSLC motif of the IP is a direct target for inhibition by the FTI SCH66336, and in the presence of strong FTase inhibition, the IP does not undergo compensatory geranylgeranylation.
Oligomeric states of the voltage-dependent anion channel and cytochrome c release from mitochondria
Authors: ZALK Ran , ISRAELSON Adrian , GARTY Erez S. , AZOULAY-ZOHAR Heftsi , SHOSHAN-BARMATZ Varda
Published: February 2005

The VDAC (voltage-dependent anion channel) plays a central role in apoptosis, participating in the release of apoptogenic factors including cytochrome c. The mechanisms by which VDAC forms a protein-conducting channel for the passage of cytochrome c are not clear. The present study approaches this problem by addressing the oligomeric status of VDAC and its role in the induction of the permeability transition pore and cytochrome c release. Chemical cross-linking of isolated mitochondria or purified VDAC with five different reagents proved that VDAC exists as dimers, trimers or tetramers. Fluorescence resonance energy transfer between fluorescently labelled VDACs supports the concept of dynamic VDAC oligomerization. Mitochondrial cross-linking prevented both permeability transition pore opening and release of cytochrome c, yet had no effect on electron transport or Ca2+ uptake. Bilayer-reconstituted purified cross-linked VDAC showed decreased conductance and voltage-independent channel activity. In the dithiobis(succinimidyl propionate)-cross-linked VDAC, these channel properties could be reverted to those of the native VDAC by cleavage of the cross-linking. Cross-linking of VDAC reconstituted into liposomes inhibited the release of the proteoliposome-encapsulated cytochrome c. Moreover, encapsulated, but not soluble cytochrome c induced oligomerization of liposome-reconstituted VDAC. Thus the results indicate that VDAC exists in a dynamic equilibrium between dimers and tetramers and suggest that oligomeric VDAC may be involved in mitochondria-mediated apoptosis.
Lack of evidence for a role of TRB3/NIPK as an inhibitor of PKB-mediated insulin signalling in primary hepatocytes
Authors: IYNEDJIAN Patrick B.
Published: February 2005

The protein TRB3 (tribbles 3), also called NIPK (neuronal cell death-inducible protein kinase), was recently identified as a protein–protein interaction partner and an inhibitor of PKB (protein kinase B). To explore the hypothesis that TRB3/NIPK might act as a negative regulator of insulin signalling in the liver, this protein was overexpressed by adenoviral transduction of primary cultures of rat hepatocytes, and various aspects of insulin action were investigated. The insulin-induced phosphorylation of Ser-473 and Thr-308 of PKB was found to be undiminished in transduced hepatocytes with a molar excess of TRB3/NIPK over PKB of more than 25-fold. Consistent with unimpaired insulin activation of PKB, the stimulation of Ser-21 and Ser-9 phosphorylation of glycogen synthase kinase 3-α and -β, and the apparent phosphorylation level of 4E-BP1 (eukaryotic initiation factor 4-binding protein 1), were similar in transduced and control hepatocytes. The induction by insulin of the mRNAs encoding glucokinase and SREBF1 (sterol-regulatory-element-binding factor 1) were also normal in TRB3/NIPK hepatocytes. In contrast, the insulin-dependent induction of these two genes, as well as the activation of PKB, were shown to be suppressed in hepatocytes treated with the lipid ether compound PIA6 (phosphatidylinositol ether lipid analogue 6), a recently discovered specific inhibitor of PKB. Since TRB3/NIPK was reported to be increased in the liver of fasting mice, the effects of glucagon, glucocorticoids and insulin on the level of endogenous TRB3/NIPK mRNA in primary hepatocytes were investigated. No significant change in mRNA level occurred under any of the hormonal treatments. The present study does not support the hypothesis that the physiological role of TRB3/NIPK might be to put a brake on insulin signalling in hepatocytes.
A simple promoter containing two Sp1 sites controls the expression of sterol-regulatory-element-binding protein 1a (SREBP-1a)
Authors: ZHANG Chengkang , SHIN Dong-Ju , OSBORNE Timothy F.
Published: February 2005

The mammalian gene for SREBP-1 (sterol-regulatory-element-binding protein 1) contains two promoters that control the production of two proteins, SREBP-1a and -1c, and each contains a unique N-terminal transcriptional activation domain, but they are otherwise identical. The relative level of each mRNA varies from tissue to tissue and they respond differently to regulatory stimuli. SREBP-1c is more abundantly expressed in liver, where its level is also regulated by insulin and liver X receptor activators, and it is also autoregulated by SREBPs. In contrast, SREBP-1a mRNA levels are relatively low and constant in different tissues and few studies have specifically analysed its pattern of expression and regulation. In the present study, we show that the promoter for SREBP-1a is contained in a very small promoter-proximal region containing two Sp1 sites. The small and relatively simple structure for its promoter provides an explanation for the low level of SREBP-1a expression. Additionally, since Sp1 has been implicated in the modest regulation of several genes by insulin, its involvement in the expression of the SREBP-1a promoter provides an explanation for the modest insulin regulation observed in animal experiments.
The Smad3 linker region contains a transcriptional activation domain
Authors: WANG Guannan , LONG Jianyin , MATSUURA Isao , HE Dongming , LIU Fang
Published: February 2005

Transforming growth factor-β (TGF-β)/Smads regulate a wide variety of biological responses through transcriptional regulation of target genes. Smad3 plays a key role in TGF-β/Smad-mediated transcriptional responses. Here, we show that the proline-rich linker region of Smad3 contains a transcriptional activation domain. When the linker region is fused to a heterologous DNA-binding domain, it activates transcription. We show that the linker region physically interacts with p300. The adenovirus E1a protein, which binds to p300, inhibits the transcriptional activity of the linker region, and overexpression of p300 can rescue the linker-mediated transcriptional activation. In contrast, an adenovirus E1a mutant, which cannot bind to p300, does not inhibit the linker-mediated transcription. The native Smad3 protein lacking the linker region is unable to mediate TGF-β transcriptional activation responses, although it can be phosphorylated by the TGF-β receptor at the C-terminal tail and has a significantly increased ability to form a heteromeric complex with Smad4. We show further that the linker region and the C-terminal domain of Smad3 synergize for transcriptional activation in the presence of TGF-β. Thus our findings uncover an important function of the Smad3 linker region in Smad-mediated transcriptional control.
Knowing why and how to Innovate with Packaged Business Software
Authors: Swanson E Burton , Wang Ping
Published: February 2005

When firms move to adopt and implement a popular IT innovation, what knowledge must they have or gain, in order to be successful? Here we offer a model that explains a firm's success in terms of its adoption know-why and know-when and its implementation know-how. We examine this model in an exploratory survey of some 118 firms’ adoption and implementation of packaged business software in the 1990s. Using multivariate methods, we identify business coordination as know-why and management understanding and vendor support as know-how factors important to success, explaining nearly 60% of the variance. There is limited evidence that the right adoption know-why may help in acquiring or fostering the right implementation know-how. The findings serve to remind practitioners that they should attend carefully to adoption rationales, grounded in business benefits, when they innovate with new IT.
The structure of fluids confined in crystalline slitlike nanoscopic pores
Authors: Sałamacha L. , Patrykiejew A. , Sokołowski S. , Binder K.
Published: February 2005

Grand canonical and canonical ensemble Monte Carlo simulation methods are used to study the structure and phase behavior of Lennard-Jones fluids confined between the parallel (100) planes of the face centered cubic crystal. Thin slit pores with a width allowing for the formation of only up to five atomic layers are considered. The phase diagrams of the systems characterized by different pore width as well as by different strength of the fluid-pore walls potential are determined. It is shown that an enormously large number of different phase diagram topologies can occur, depending on the parameters of the problem (pore width, strength of the fluid-pore walls potential, etc).
Monte Carlo simulations of liquid crystals near rough walls
Authors: Cheung David L. , Schmid Friederike
Published: February 2005

The effect of surface roughness on the structure of liquid crystalline fluids near solid substrates is studied by Monte Carlo simulations. The liquid crystal is modeled as a fluid of soft ellipsoidal molecules and the substrate is modeled as a hard wall that excludes the centers of mass of the fluid molecules. Surface roughness is introduced by embedding a number of molecules with random positions and orientations within the wall. It is found that the density and order near the wall are reduced as the wall becomes rougher, i.e., the number of embedded molecules is increased). Anchoring coefficients are determined from fluctuations in the reciprocal space order tensor. It is found that the anchoring strength decreases with increasing surface roughness.
A theoretical study for the reaction of vinyl cyanide C2H3CN(XA′1) with the ground state carbon atom C(P3) in cold molecular clouds
Authors: Su Hsiu-Fen , Kaiser R. I. , Chang A. H. H.
Published: February 2005

The reaction of the ground state atomic carbon, C(P3), with simple unsaturated nitrile, C2H3CN(XA′1) (vinyl cyanide), is investigated theoretically to explore the probable routes for the formation of carbon–nitrogen-bearing species in extraterrestrial environments particularly of ultralow temperature. Five collision complexes without entrance barrier as a result of the carbon atom addition to the π systems of C2H3CN are characterized. The B3YLP∕6–311G(d,p) level of theory is utilized in obtaining the optimized geometries, harmonic frequencies, and energies of the intermediates, transition states, and products along the isomerization and dissociation pathways of each collision complex. Subsequently, with the facilitation of computed RRKM rate constants at collision energy of 0–10kcal∕mol, the most probable paths for each collision complexes are determined, of which the CCSD(T)∕6–311G(d,p) energies are calculated. The major products predicted are exclusively due to the hydrogen atom dissociations, while the products of H2, CN, and CH2 decompositions are found negligible. Among many possible H-elimination products, cyano propargyl (p4) and 3-cyano propargyl (p5) are the most probable, in which p5 can be formed via two intermediates, cyano allene (i8) and cyano vinylmethylene (i6), while p4 is yielded from i8. The study suggests this class of reaction is an important route to the synthesis of unsaturated nitriles at the temperature as low as 10K, and the results are valuable for future chemical models of interstellar clouds.
Inelastic state-to-state scattering of OH (Π3∕22,J=3∕2,f) by HCl
Authors: Cireasa R. , van Beek M. C. , Moise A. , ter Meulen J. J.
Published: February 2005

Parity resolved state-to-state cross sections for inelastic scattering of OH (XΠ2) by HCl were measured in a crossed molecular beam experiment at the collision energy of 920cm−1. The OH (XΠ2) radicals were prepared in a single quantum state, Ω=3∕2, J=3∕2, MJ=3∕2, f, by means of electrostatic state selection in a hexapole field. The rotational distribution of the scattered OH radicals by HCl was probed by saturated LIF spectroscopy of the 0-0 band of the AΣ+2–XΠ2 transition. Relative state-to-state cross sections were measured for rotational excitations up to J=9∕2 within the Ω=3∕2 spin–orbit manifold and up to J=7∕2 within the Ω=1∕2 spin–orbit manifold. A propensity for spin–orbit conserving transitions was found, but no propensity for excitation into a particular Λ-doublet component of the same rotational state was evident. The data are presented and discussed in comparison with results previously obtained for collisions of OH with CO (Ecoll=450cm−1) and N2 (Ecoll=410cm−1) and with new data we have measured for the OH+CO system at a comparable collision energy (Ecoll=985cm−1). This comparison suggests that the potential energy surface (PES) governing the interaction between OH and HCl is more anisotropic than the PES’s governing the intermolecular interaction of OH with CO and N2.
Extensive generalization of renormalized coupled-cluster methods
Authors: Kowalski Karol , Piecuch Piotr
Published: February 2005

The recently developed completely renormalized (CR) coupled-cluster (CC) methods with singles, doubles, and noniterative triples or triples and quadruples [CR-CCSD(T) or CR-CCSD(TQ), respectively], which are based on the method of moments of CC equations (MMCC) [K. Kowalski and P. Piecuch, J. Chem. Phys. 113, 18 (2000)], eliminate the failures of the standard CCSD(T) and CCSD(TQ) methods at larger internuclear separations, but they are not rigorously size extensive. Although the departure from strict size extensivity of the CR-CCSD(T) and CR-CCSD(TQ) methods is small, it is important to examine the possibility of formulating the improved CR-CC methods, which are as effective in breaking chemical bonds as the existing CR-CCSD(T) and CR-CCSD(TQ) approaches, which are as easy to use as the CR-CCSD(T) and CR-CCSD(TQ) methods, and which can be made rigorously size extensive. This may be particularly useful for the applications of CR-CC methods and other MMCC approaches in calculations of potential energy surfaces of large many-electron systems and van der Waals molecules, where the additive separability of energies in the noninteracting limit is very important. In this paper, we propose different types of CR-CC approximations, termed the locally renormalized (LR) CCSD(T) and CCSD(TQ) methods, which become rigorously size extensive if the orbitals are localized on nointeracting fragments. The LR-CCSD(T) and LR-CCSD(TQ) methods rely on the form of the energy expression in terms of the generalized moments of CC equations, derived in this work, termed the numerator-denominator-connected MMCC expansion. The size extensivity and excellent performance of the LR-CCSD(T) and LR-CCSD(TQ) methods are illustrated numerically by showing the results for the dimers of stretched HF and LiH molecules and bond breaking in HF and H2O.
Hydrothermal reactions of formaldehyde and formic acid: Free-energy analysis of equilibrium
Authors: Matubayasi Nobuyuki , Nakahara Masaru
Published: February 2005

The chemical equilibria concerning formaldehyde and formic acid are computationally investigated in water over a wide range of thermodynamic conditions. The free energy is evaluated in the method of energy representation for the solvent effect on the decomposition processes of these two compounds. The solvation is found to suppress the production of nonpolar species from a polar. In the two competitive decomposition reactions of formic acid, the solvent strongly inhibits the decarboxylation (HCOOH→CO2+H2) and its effect is relatively weak for the decarbonylation (HCOOH→CO+H2O). The equilibrium weights for the two decomposition pathways of formic acid are determined by the equilibrium constant of the water-gas-shift reaction (CO+H2O→CO2+H2), which is an essential and useful process in fuel technology. The reaction control by the solvent is then examined for the water-gas-shift reaction. Through the comparison of the equilibrium constants in the absence and presence of solvent, even the favorable side of the reaction is shown to be tuned by the solvent density and temperature. The reaction equilibrium is further treated for aldehyde disproportionation reactions involving formaldehyde and formic acid. The disproportionation reactions are found to be subject to relatively weak solvent effects and to be dominated by the electronic contribution.
Four-component Hartree–Fock calculations of magnetic-field induced circular birefringence—Faraday effect—in noble gases and dihalogens
Authors: Ekström Ulf , Norman Patrick , Rizzo Antonio
Published: February 2005

The effects of relativity on the magnetic-field induced circular birefringence, or Faraday effect, in He, Ne, Ar, Xe, Rn, F2, Cl2, Br2, and I2 have been determined at the four-component Hartree–Fock level of theory. A measure of the birefringence is given by the Verdet constant, which is a third-order molecular property and thus relates to quadratic response functions. A fully analytical nonlinear polarization propagator approach is employed. The results are gauge invariant as a consequence of the spatial symmetries in the molecular systems. The calculations include electronic as well as vibrational contributions to the property. Comparison with experiment is made for He, Ne, Ar, Xe, and Cl2, and, apart from neon, the theoretical values of the Verdet constant are within 10% of the experimental ones. The inclusion of nonrelativistically spin-forbidden excitations in the propagator parametrization has significant effects on the dispersion in general, but such effects are in the general case largely explained by the use of a resonant-divergent propagator theory. In the present work we do, however, observe noticeable relativistic corrections to the Verdet constant in the off-resonant regions for systems with light elements (F2 and Cl2), and nonrelativistic results for the Verdet constant of Br2 are in error by 25% in the low-frequency region.
Fast and accurate Coulomb calculation with Gaussian functions
Authors: Füsti-Molnár László , Kong Jing
Published: February 2005

Coulomb interaction is one of the major time-consuming components in a density functional theory (DFT) calculation. In the last decade, dramatic progresses have been made to improve the efficiency of Coulomb calculation, including continuous fast multipole method (CFMM) and J-engine method, all developed first inside Q-Chem. The most recent development is the advent of Fourier transform Coulomb method developed by Fusti-Molnar and Pulay, and an improved version of the method has been recently implemented in Q-Chem. It replaces the least efficient part of the previous Coulomb methods with an accurate numerical integration scheme that scales in O(N2) instead of O(N4) with the basis size. The result is a much smaller slope in the linear scaling with respect to the molecular size and we will demonstrate through a series of benchmark calculations that it speeds up the calculation of Coulomb energy by several folds over the efficient existing code, i.e., the combination of CFMM and J-engine, without loss of accuracy. Furthermore, we will show that it is complementary to the latter and together the three methods offer the best performance for Coulomb part of DFT calculations, making the DFT calculations affordable for very large systems involving thousands of basis functions.
Nonlinear response of the benzene molecule to strong magnetic fields
Authors: Pagola G. I. , Caputo M. C. , Ferraro M. B. , Lazzeretti P.
Published: February 2005

The fourth-rank hypermagnetizability tensor of the benzene molecule has been evaluated at the coupled Hartree–Fock level of accuracy within the conventional common-origin approach, adopting gaugeless basis sets of increasing size and flexibility. The degree of convergence of theoretical tensor components has been estimated allowing for two different coordinate systems. It is shown that a strong magnetic field perpendicular to the plane of the molecule causes a distortion of the electron charge density, which tends to concentrate in the region of the C–C bonds. This charge contraction has a dynamical origin, and can be interpreted as a feedback effect in terms of the classical Lorentz force acting on the electron current density.
Blue up-conversion Tm3+-doped fiber laser pumped by a multiline Raman source
Authors: Talavera D. V. , Mejía E. B.
Published: February 2005

We report laser oscillation at 481 nm when pumping a Tm3+-doped fluorozirconate fiber by two Raman-generated signals at 1117 and 1175 nm. A superior efficiency was achieved when pumping with both lines. For example, the conversion efficiency was 20% when pumping with 83 mW of 1117 nm and reached 33% when copumping with 29 mW of 1175 nm. As higher powers of the copumping signal were applied, a powerful amplified spontaneous emission at ∼790nm started to compete with 481 nm. The slope efficiency evolved from 16% to 48% when pumping with a simpler, noncontrolled Raman source that provided a single- to multi wavelength evolving spectrum.
Structure control of CdS nanobelts and their luminescence properties
Authors: Wang Chunrui , Ip K. M. , Hark S. K. , Li Quan
Published: February 2005

Single crystalline CdS (hexagonal) nanobelts have been synthesized using thermal evaporation at temperatures ranging from 1000to1200°C. These nanobelts universally grow along the [120] crystalline direction. The nanobelts fabricated at 1000°C appear to be much more uniform than those at 1200°C. Moreover, the surface of the nanobelts grown at 1200°C is rough compared to that of the former, which is due to the secondary growth of CdS crystallites on the nanobelts’ surfaces at higher temperatures, as induced by the surface polarity. Cathodoluminescence and photoluminescence studies disclose the different electronic structure qualities of the two samples. The growth mechanisms of the nanobelts and the luminescence differences of the two samples are discussed.
Magnetic anomalies and canting effects in nanocrystalline spinel copper ferrites CuxFe3−xO4
Authors: Stewart S. J. , Mercader R. C. , Vandenberghe R. E. , Cernicchiaro G. , Scorzelli R. B.
Published: February 2005

The magnetic behavior of nanocrystalline copper spinel ferrites CuxFe3−xO4 (0.42⩽x⩽1) exhibiting different degrees of crystallinity, have been investigated by means of in-field Mössbauer and dc magnetic measurements. The samples were obtained by a coprecipitation method and were subsequently high-energy ball milled for different times, which induced a progressive improvement of the ferrite crystallinity and cation redistribution. Their magnetism shows some peculiar features; at 5K, the virgin magnetization curves remain outside the main hysteresis loop for applied fields of ≈1T and display an S-shaped form. Below 60K, the field-cooled hysteresis loops are shifted toward the negative field direction. In addition, in the same temperature range, the field-cooled magnetization of the samples with poorest crystallinity decreases sharply due to the spin freezing at the surface. The in-field Mössbauer spectra at 4.2K show that the magnetic moments of the Fe3+ ions are in a canted spin state for both the tetrahedral and octahedral sites of the spinel structure, and evidence a decrease of the average spin canting with the degree of crystallinity. After calcination at 950°C, the coprecipitated sample no longer displays the magnetic anomalous and canting features. We explain our results as due to the partially disordered surface within the frame of the core-shell model rather than to the effect of cation redistribution.
Large-eddy simulation of low frequency oscillations of the Dean vortices in turbulent pipe bend flows
Authors: Rütten F. , Schröder W. , Meinke M.
Published: February 2005

Large-eddy simulations are performed to investigate turbulent flows through 90° pipe bends that feature unsteady flow separation, unstable shear layers, and an oscillation of the Dean vortices. Single bends with curvature radii of one- and three-pipe diameters are considered at the Reynolds number range 5000–27 000. The numerically computed distributions of the time-averaged velocities, Reynolds stress components, and power spectra of the velocities are validated by comparison with particle image velocimetry measurements. The power spectra of the overall forces onto the pipe walls are determined. The spectra exhibit a distinct peak in the high frequency range that is ascribed to vortex shedding at the inner side of the bends and shear layer instability. At the largest Reynolds number the spectra also exhibit an oscillation at a frequency much lower than that commonly observed at vortex shedding from separation. It turns out that the associated flow pattern is similar to the swirl switching phenomenon earlier found in experimental studies with which the present results are compared. It is shown that the low frequency oscillation perceptible on the entire wall is caused by the two Dean vortices whose strength vary in time and which as such alternately dominate the flow field.
Control of finite-dimensional quantum systems: Application to a spin-12 particle coupled with a finite quantum harmonic oscillator
Authors: Rangan C. , Bloch A. M.
Published: February 2005

In this paper, we consider the problem of the controllability of a finite-dimensional quantum system in both the Schrödinger and interaction pictures. Introducing a Quantum Transfer Graph, we elucidate the role of Lie algebra rank conditions and the complex nature of the control matrices. We analyze the example of a sequentially coupled N-level system: a spin-12 particle coupled to a finite quantum harmonic oscillator. This models an important physical paradigm of quantum computers—the trapped ion. We describe the control of the finite model obtained, under the right conditions, from the original infinite-dimensional system.
Bulk synthesis of carbon-filled silicon carbide nanotubes with a narrow diameter distribution
Authors: Borowiak-Palen E. , Ruemmeli M. H. , Gemming T. , Knupfer M. , Biedermann K. , Leonhardt A. , Pichler T. , Kalenczuk R. J.
Published: February 2005

We report on a simple and low-cost route to produce SiC nanotubes without the need for the more usual oxide based reactions using a high temperature substitution reaction between multiwall carbon nanotubes as a frame and Si powder. Local scale studies using transmission and scanning electron microscopy are also presented. The SiC nanotubes are carbon filled and open ended. Both their mean diameter and diameter distribution are smaller than previously reported for SiC nanotubes. Bulk scale studies using Raman and infrared as a probe showed the sample to be comprised of multiple polytypes and that finite size effects are present.
Minority carrier diffusion length measurements in 6H–SiC
Authors: Polyakov Alexander Y. , Li Qiang , Huh Sung Wook , Skowronski Marek , Lopatiuk Olena , Chernyak Leonid , Sanchez Edward
Published: February 2005

Minority carrier diffusion lengths were measured as a function of temperature and position along the growth axis of lightly nitrogen doped boules of 6H–SiC grown by the physical vapor transport technique. It is shown that the diffusion lengths increase from 1to2microns in the seed portion of the boule to about 4microns in the tail portion of the boules. Deep levels transient spectroscopy measurements revealed the presence of deep electron traps with the activation energies of 0.35eV, 0.5eV, 0.65eV, and 1eV. The densities of all these traps decrease when moving from seed to tail of the boules. A good correlation between the change of the lifetime values and the density of the 0.65eV and 1eV electron traps was observed. The measured lifetimes show an increase with temperature following a power law that suggests that the hole capture could be determined by cascade capture process.
Surface tension and viscosity of liquid and undercooled tantalum measured by a containerless method
Authors: Paradis Paul-François , Ishikawa Takehiko , Yoda Shinichi
Published: February 2005

Electrostatic levitation and multibeam radiative heating overcame contamination and sample position stability problems associated with handling of liquid tantalum. This approach allowed the measurements of the surface tension and the viscosity of the superheated and undercooled states of tantalum using the oscillation drop method. The measurements of the surface tension could be expressed as σ(T)=2.15×103−0.21(T−Tm)mNm−1 over the 2970–3400K interval, where Tm is the melting temperature (3290K). The value at Tm agrees well with the scarce data appearing in the literature. Similarly, on the 3000–3400K temperature range, the viscosity was determined as η(T)=0.0035exp[213.3∕(RT)](mPas).
Mass-analyzed CFx+ (x=1,2,3) ion beam study on selectivity of SiO2-to-SiN etching and a-C:F film deposition
Authors: Yanai Ken-ichi , Karahashi Kazuhiro , Ishikawa Kenji , Nakamura Moritaka
Published: February 2005

To clarify the origins of high selectivity in SiO2-to-SiN etching in fluorocarbon gas plasma, mass-analyzed CFx+ (x=1,2,3) ions with a definite kinetic energy of 250–2000eV were irradiated on SiN and SiO2 surfaces. Selectivity in SiO2-to-SiN etching varies greatly for different CFx+ ions. For CF3+ ions, the etch yield of SiN is almost the same as that of SiO2, causing poor selectivity. For CF+ ions, on the other hand, the etch yield of SiN is much smaller than that of SiO2. An amorphous fluorinated carbon (a-C:F) film grows without any neutral radicals on the SiN surface at energies below 1250eV and on the SiO2 surface at energies below 500eV due to CF+ ion irradiation. The difference in threshold energy of a-C:F film deposition causes high selectivity in SiO2-to-SiN etching. Slight etching of substrate films first takes place at the initial stage of deposition, then etching stops, and a homogeneous a-C:F film is grown. Accumulated carbons during the initial etching reaction modify the surface reaction layer, which causes drastic changes in reactions such as etching to “etch stop” and a-C:F film growth.
Efficient excitation of cavity resonances of subwavelength metallic gratings
Authors: Quémerais P. , Barbara A. , Le Perchec J. , López-Ríos T.
Published: February 2005

One-dimensional rectangular metallic gratings enable enhanced transmission of light for specific resonance frequencies. Two kinds of modes participating in enhanced transmission have already been demonstrated: waveguide modes and surface plasmon polaritons. Since the original article by Hessel and Oliner [Appl. Opt. 4, 1275 (1965)] pointing out the existence of waveguide modes, little progress was made in their understanding. We present here a careful analysis, and show that the coupling between the light and such resonances can be tremendously improved using an evanescent wave. This leads to enhanced localization of light in cavities, yielding, in particular, a very selective light transmission through these gratings.
Effects of donor concentration on the electrical properties of Nb-doped BaTiO3 thin films
Authors: Liu Lifeng , Guo Haizhong , Lü Huibin , Dai Shouyu , Cheng Bolin , Chen Zhenghao
Published: February 2005

Thin films of BaNbxTi1−xO3(0<x⩽0.5) were epitaxially grown on MgO substrates by laser molecular beam epitaxy. The thin films undergo tetragonal to cubic and semiconductor to metal transitions with Nb concentrations as shown by x-ray diffraction and electrical resistivity measurements. Room temperature resistivities are found to decrease monotonically with increasing Nb concentration and range from 101 to 10−4Ωcm. The fact that the temperature dependence of resistivity of the thin films can be fitted well using a small polaron model reveals the polaronic nature of the charge carriers in the thin films. This conclusion is further confirmed by the existence of localized states within the band gap of BaTiO3 as revealed by synchrotron radiation-based ultraviolet photoelectron spectroscopy.
An extension of Faxen’s laws for nonisothermal flow around a sphere
Authors: Mohan Aruna , Brenner Howard
Published: February 2005

In the presence of temperature gradients, the enforcement of the no-slip boundary condition on the velocity of a gas at its boundary with a solid leads to predictions inconsistent with experimental observations. It is known that Maxwell’s [J. C. Maxwell, Philos. Trans. R. Soc. London 170, 231 (1879)] thermal slip condition must instead be applied, as, for example, in the cases of thermophoresis and thermal transpiration. In addition to gases, the motion of particles in otherwise stationary liquids has also been explained by the use of a similarly constituted thermal slip condition. We use this slip condition to generalize Faxen’s laws for incompressible creeping Stokes flow around a heat-conducting sphere in the presence of temperature gradients, for the case of an arbitrary undisturbed Stokes flow far from the sphere. These laws are confirmed by showing their agreement with known results for thermophoretic particle motion. By way of illustration, Faxen’s laws are used to calculate the force and torque acting on a small spherical particle in a laterally insulated capillary tube under an externally imposed temperature gradient. These results have potential applications with respect to the motion of particles in nonisothermal, fluid-filled porous media, microelectromechanical systems devices, and in aerosol technology. The basic scheme is also generally applicable to situations in which the slip is induced by other externally imposed gradients, such as in the case of electrophoretic particle motion arising from an electric potential gradient.
Thermal lens study of the OH− influence on the fluorescence efficiency of Yb3+-doped phosphate glasses
Authors: Jacinto C. , Oliveira S. L. , Nunes L. A. O. , Catunda T. , Bell M. J. V.
Published: February 2005

In this work, the thermal lens (TL) technique is used to determine the fluorescence quantum efficiency (η) of Yb3+-doped phosphate glasses. The role of nonradiative processes such as energy migration among Yb ions and the interaction with OH− radicals are presented and discussed. Two sets of samples with the same Yb concentrations were prepared, one at ambient conditions (set A) and the other in N2 atmosphere (set N). The TL technique was shown to be very sensitive to the amount of OH radicals. Moreover, the η values obtained from the TL method are in good agreement with the calculate ones (based on lifetime measurements). The results indicate that TL can be a valuable technique to evaluate the quantum efficiency and nonradiative rates in ion-doped materials.
Passive-matrix addressing of viologen–TiO2 displays
Authors: Edwards M. O. M.
Published: February 2005

The electric driving of 3×3 electrochromic passive-matrix displays, based on porous TiO2 films with surface-attached viologen molecules, is studied. A nonuniform contrast between dark and light pixels is obtained by a well-known addressing method for liquid-crystal passive-matrix displays. An alternative addressing method is developed. The method is capable of displaying arbitrary image patterns with uniform contrast.
Polymer thin-film transistors fabricated by dry transfer of polymer semiconductor
Authors: Park Joonhyung , Shim Sang-Oak , Lee Hong H.
Published: February 2005

A dry transfer technique is applied to the semiconductor layer formation in fabricating polymer thin-film transistors (TFTs). This method removes the solvent compatibility problem that is typically encountered in solution processing of polymer semiconductor and polymer gate dielectric such that any pair of the two polymers can be admitted to the fabrication of polymer TFTs. When the technique is used in place of spin coating of the active layer, the mobility increases by almost an order of magnitude, primarily because the deleterious effects are removed that a solvent can have on the underlying dielectric layer. Annealing of the active layer is also made possible by the method, which results in a significant improvement in the on∕off ratio of the device.
Magnetoresistance of single magnetic vortices
Authors: Vavassori P. , Grimsditch M. , Metlushko V. , Zaluzec N. , Ilic B.
Published: February 2005

The magnetoresistance in a 1μm Permalloy disk, that develops a vortex state during reversal, has been experimentally measured and modeled. The agreement between measurements and numerical simulations shows that the conventional anisotropic magnetoresistance effect is the main source of magnetoresistance. The results demonstrate that magnetoresistance can be used to determine the chirality of the vortex thereby improving the chances that patterned dot arrays could be used in data storage technology.
Infrared spectroscopy of ZnO nanoparticles containing CO2 impurities
Authors: Hlaing Oo W. M. , McCluskey M. D. , Lalonde A. D. , Norton M. G.
Published: February 2005

Impurities play a major role in determining the optical and electrical properties of semiconductor nanoparticles. In this work, the presence and source of CO2 impurities in ZnO nanoparticles were studied by IR absorption spectroscopy. Isotopic substitution was used to verify the vibrational frequency assignment. Isochronal annealing experiments were performed to study the formation and stability of the molecular impurities. Our results indicate that the molecules are much more stable than CO2 adsorbed on bulk ZnO surfaces. By comparing our observations with similar results from IR spectroscopy of CO2 trapped in carbon nanotubes [C. Matranga, L. Chen, M. Smith, E. Bittner, J. K. Johnson, and B. Bockrath, J. Phys. Chem. B 107, 12930 (2003)], we conclude that the molecules are trapped in the ZnO nanoparticles.
Tunable hollow waveguide Bragg grating with low-temperature dependence
Authors: Sakurai Yasuki , Yokota Yasushi , Matsutani Akihiro , Koyama Fumio
Published: February 2005

We demonstrate a tunable hollow waveguide Bragg grating with low-temperature dependence. We fabricated a distributed Bragg reflector consisting of a grating loaded slab semiconductor hollow waveguide with a variable air-core. A change in an air-core thickness enables us to achieve a tunable propagation constant of several percents resulting in a large shift of several tens of nanometers in Bragg wavelength. We demonstrate 10nm continuous wavelength tuning of a peak reflectivity. This value corresponds to a propagation constant change of 0.64%, which is larger than that of thermo-optic effects or electro-optic effects. The measured temperature sensitivity of the peak wavelength is as low as 0.016nm∕K, which is seven times smaller than that of conventional semiconductor waveguide devices.
α-Helix formation in a photoswitchable peptide tracked from picoseconds to microseconds by time-resolved IR spectroscopy
Authors: Bredenbeck Jens , Helbing Jan , Kumita Janet R. , Woolley G. Andrew , Hamm Peter
Published: February 2005

Photo-triggered α-helix formation of a 16-residue peptide featuring a built-in conformational photoswitch is monitored by time-resolved IR spectroscopy. An experimental approach with 2-ps time resolution and a scanning range up to 30 μs is used to cover all time scales of the peptide dynamics. Experiments are carried out at different temperatures between 281 and 322 K. We observe single-exponential kinetics of the amide I′ band at 322 K on a time scale comparable to a recent temperature-jump folding experiment. When lowering the temperature, the kinetics become slower and nonexponential. The transition is strongly activated. Spectrally dispersed IR measurements provide multiple spectroscopic probes simultaneously in one experiment by resolving the amide I′ band, isotope-labeled amino acid residues, and side chains. We find differing relaxation dynamics at different spectral positions.