bluuebunny/crossref_metadata_2025 huggingface dataset:
Anaphase specific auto‐cleavage of separase
Authors: Zou Hui , Stemman Olaf , Anderson Jens S , Mann Matthias , Kirschner Marc W
Published: October 2002

Sister‐chromatid separation is triggered by a specific proteolytic cleavage of chromosomal cohesins catalyzed by the endopeptidase separase. Prior to anaphase, separase is inhibited independently by affinity binding to securin and by specific inhibitory phosphorylation. Here we show that separase itself is also subjected to proteolytic cleavages at three adjacent sites. The cleavages are auto‐catalyzed and occur specifically at anaphase coincident with separase activation. The cleaved fragments remain associated with each other and are catalytically active. Mapping of the cleavage sites reveals that all three sites are conserved in vertebrates underlining a significant function for this regulation.
The eye photoreceptor protein rhodopsin. Structural implications for retinal disease1
Authors: Garriga Pere , Manyosa Joan
Published: October 2002

Rhodopsin is the membrane receptor responsible for photoreception in the vertebrate retina. Its characteristic seven‐transmembrane helical structural motif is today widely recognised as a paradigm in signal transduction. Rhodopsin and the phototransduction system are frequently used as structural and mechanistic models for the G‐protein coupled receptor superfamily. Recent advances in the activation mechanism (as derived from the structural available data) and the implications for normal and pathological – in retinal disorders – visual function will be reviewed.
The regions of securin and cyclin B proteins recognized by the ubiquitination machinery are natively unfolded
Authors: Cox Cathleen J , Dutta Kaushik , Petri Edward T , Hwang William C , Lin Yaqiong , Pascal Steven M , Basavappa Ravi
Published: October 2002

The proteins securin and cyclin B are destroyed in mitosis by the ubiquitin/proteasome system. This destruction is important to mitotic progression. The N‐terminal regions of these proteins contain the sequence features recognized by the ubiquitination system. We have demonstrated using circular dichroism and 1‐D and 2‐D nuclear magnetic resonance that these rather substantial regions are natively unfolded. Based on these findings, we propose a model that helps to explain previously enigmatic observations.
Why glycine transporters have different stoichiometries
Authors: Supplisson Stéphane , Roux Michel J.
Published: October 2002

In the brain, neurons and glial cells compete for the uptake of the fast neurotransmitters, glutamate, GABA and glycine, through specific transporters. The relative contributions of glia and neurons to the neurotransmitter uptake depend on the kinetic properties, thermodynamic coupling and density of transporters but also on the intracellular metabolization or sequestration of the neurotransmitter. In the case of glycine, which is both an inhibitory transmitter and a neuromodulator of the excitatory glutamatergic transmission as a co‐agonist of N‐methyl D‐aspartate receptors, the glial (GlyT1b) and neuronal (GlyT2a) transporters differ at least in three aspects: (i) stoichiometries, (ii) reverse uptake capabilities and (iii) pre‐steady‐state kinetics. A 3 Na+/1 Cl−/gly stoichiometry was established for GlyT2a on the basis of a 2 charges/glycine flux ratio and changes in the reversal potential of the transporter current as a function of the extracellular glycine, Na+ and Cl− concentrations. Therefore, the driving force available for glycine uphill transport in neurons is about two orders of magnitude larger than for glial cells. In addition, GlyT2a shows a severe limitation for reverse uptake, which suggests an essential role of GlyT2a in maintaining a high intracellular glycine pool, thus facilitating the refilling of synaptic vesicles by the low affinity, low specificity vesicular transporter VGAT/VIAAT. In contrast, the 2 Na+/1 Cl−/gly stoichiometry and bi‐directional transport properties of GlyT1b are appropriate for the control of the extracellular glycine concentration in a submicromolar range that can modulate N‐methyl D‐aspartate receptors effectively. Finally, analysis of the pre‐steady‐state kinetics of GlyT1b and GlyT2a revealed that at the resting potential neuronal transporters are preferentially oriented outward, ready to bind glycine, which suggests a kinetic advantage in the uptake contest.
Stabilization signals: a novel regulatory mechanism in the ubiquitin/proteasome system
Authors: Dantuma Nico P , Masucci Maria G
Published: October 2002

The turnover of cellular proteins is a highly organized process that involves spatially and temporally regulated degradation by the ubiquitin/proteasome system. It is generally acknowledged that the specificity of the process is determined by constitutive or conditional protein domains, the degradation signals, that target the substrate for proteasomal degradation. In this review, we discuss a new type of regulatory domain: the stabilization signal. A model is proposed according to which protein half‐lives are determined by the interplay of counteracting degradation and stabilization signals.
Effects of copper on the expression of metal transporters in human intestinal Caco‐2 cells
Authors: Tennant Jason , Stansfield Matthew , Yamaji Sachie , Srai Surjit Kaila , Sharp Paul
Published: October 2002

Copper is an essential dietary trace metal, however the mechanisms involved in intestinal copper uptake are unclear. Two putative copper transporters are expressed in Caco‐2 cells, the divalent metal transporter (DMT1) and copper transporter (Ctr1). Our data demonstrate that copper could compete with iron for uptake via DMT1 and that DMT1 protein and mRNA expression were decreased following exposure (24 h) to high copper. Expression of Ctr1, which acts as a copper transporter in transfected cell lines, was unaffected by copper treatment. Interestingly, exposure to copper increased iron efflux from Caco‐2 cells and up regulated IREG1 (iron‐regulated mRNA) expression.
Cis and trans acting factors in the regulation of parathyroid hormone (PTH) mRNA stability by calcium and phosphate
Authors: Naveh-Many Tally , Bell Osnat , Silver Justin , Kilav Rachel
Published: October 2002

Calcium and phosphate regulate parathyroid hormone (PTH) mRNA stability through differences in binding of parathyroid proteins to an element in its 3′‐untranslated region. One of the proteins is AUF1 (A+U‐rich element binding factor 1). An in vitro degradation assay showed that transcripts for PTH and chimeric growth hormone (GH)–PTH 63 nt, but not for native GH, were stabilized by PT proteins from rats on low calcium diets and destabilized by proteins from rats on low phosphate diets, correlating with PTH mRNA levels in vivo. In transfection experiments the 63 nt binding element destabilized mRNAs of reporter genes and this was prevented by over‐expression of AUF1. Our results identified a functional cis element in PTH mRNA. Differences in protein binding to this element determine PTH mRNA stability and its regulation by calcium and phosphate.
When reverse genetics meets physiology: the use of site‐specific recombinases in mice
Authors: Tronche François , Casanova Emilio , Turiault Marc , Sahly Iman , Kellendonk Christoph
Published: October 2002

The use of site‐specific recombinases enables the precise introduction of defined genetic mutations into the mouse genome. In theory, any deletion, point mutation, inversion or translocation can be modeled in mice. Because gene targeting is controlled both spatially and temporally, the function of a given gene can be studied in the desired cell types and at a specific time point. This ‘genetic dissection’ allows to define gene function in development, physiology or behavior. In this review, we focus on the technical possibilities of Cre and other site‐specific recombinases but also discuss their limitations.
Prion diseases: pathogenesis and public health concerns
Authors: Dormont Dominique
Published: October 2002

Transmissible spongiform encephalopathy (TSE) agents or prions induce neurodegenerative fatal diseases in humans and in some mammalian species. Human TSEs include Creutzfeldt–Jakob disease (CJD), Gerstmann–Sträussler–Scheinker syndrome, kuru and fatal familial insomnia. In animals, scrapie in sheep and goats, feline spongiform encephalopathy, transmissible mink encephalopathy, chronic wasting disease in wild ruminants, and bovine spongiform encephalopathy (BSE), which appeared in the UK in the mid‐1980s [Wells, G.A.H. et al. (1987) Vet. Rec. 121, 419–420], belong to the TSE group. Prions have biological and physicochemical characteristics that differ significantly from those of other microorganisms; for example, they are resistant to inactivation processes that are effective against conventional viruses, including those that alter nucleic acid structure or function. Alternatively, infectivity is highly susceptible to procedures that modify protein conformation. Today, the exact nature of prions remains unknown even though it is likely that they consist of protein only. At the biochemical level, TSEs are characterised by the accumulation, within the central nervous system of the infected individual, of an abnormal isoform of a particular protein from the host, the prion protein [Prusiner, S.B. (1982) Science 216, 136–144]. TSEs are transmissible among their species of origin, but they can also cross the species barrier and induce chronic infection and/or disease in other species. Transmissibility has been proven in natural situations such as the outbreak of CJD among patients treated with pituitary‐derived hormones and the appearance of BSE that affected UK cattle in the mid‐1980s.
E2F1 pathways to apoptosis
Authors: Ginsberg Doron
Published: October 2002

The E2F family of transcription factors plays a pivotal role in the regulation of cell proliferation and their activity is often deregulated in human tumors. Recent studies demonstrate that E2F1 can induce both proliferation and apoptosis. E2F1‐induced apoptosis occurs via multiple pathways, some of which induce stabilization and activation of the tumor suppressor p53. The pro‐apoptotic activity of E2F1 suggests that its deregulation constitutes an oncogenic stress that may target pre‐malignant cells to undergo apoptosis, thus preventing tumor development.
Characterization of a general amino acid permease from Hebeloma cylindrosporum
Authors: Wipf Daniel , Benjdia Mariam , Tegeder Mechthild , Frommer Wolf B
Published: October 2002

Besides a role in phosphate supply, ectomycorrhizas play a crucial role in nitrogen nutrition of plants. The ectomycorrhizal association between Hebeloma cylindrosporum and Pinus pinaster serves as a model system accessible to molecular manipulation. Hebeloma mycelium is able to take up and use amino acids as the sole nitrogen source. Suppression cloning allowed identification of a Hebeloma transporter (HcGAP1) mediating histidine uptake. HcGAP1 mediates secondary active uptake of a wide spectrum of different amino acids. The secondary active transport mechanism together with the expression in hyphae, but not in mycorrhizas, indicate a role in uptake of organic nitrogen from the soil.
p38 mitogen‐activated protein kinase dephosphorylation is regulated by protein phosphatase 2A in human platelets activated by collagen
Authors: Sundaresan Pavithra , Farndale Richard W
Published: October 2002

Collagen and the cross‐linked collagen‐related peptide (CRP‐XL) each induced platelet p38 mitogen‐activated protein kinase (p38) phosphorylation after 2 min. Subsequent dephosphorylation occurred in platelets activated with collagen, but not with CRP‐XL, demonstrating glycoprotein VI‐independent regulation of p38. Okadaic acid and fostriecin, inhibitors specific for protein phosphatase 2A (PP2A), blocked p38 dephosphorylation, and PP2A co‐immunoprecipitated with phospho‐p38. In addition, use of phenylarsine oxide suggested that tyrosine phosphatases and PP2A may act in concert to dephosphorylate p38. Finally, regulation of p38 in collagen‐stimulated Glanzmann's platelets was indistinguishable from that in normal platelets, showing that p38 regulation is independent of integrin αIIbβ3.
Derivation of structural restraints using a thiol‐reactive chelator
Authors: Dvoretsky Alex , Gaponenko Vadim , Rosevear Paul R
Published: October 2002

Recognition and identification of protein folds is a prerequisite for high‐throughput structural genomics. Here we demonstrate a simple protocol for covalent attachment of a short and more rigid metal‐chelating tag, thiol‐reactive EDTA, by chemical modification of the single cysteine residue in barnase(H102C). Conjugation of the metal‐chelating tag provides the advantage of allowing a greater range of paramagnetic metal substitutions. Substitution of Yb3+, Mn2+, and Co2+ permitted measurement of metal–amide proton distances, dipolar shifts, and residual dipolar couplings. Paramagnetic‐derived restraints are advantageous in the NMR structure elucidation of large protein complexes and are shown sufficient for validation of homology‐based fold predictions.
Proteome analysis of lipofuscin in human retinal pigment epithelial cells
Authors: Schutt F. , Ueberle B. , Schnölzer M. , Holz F.G. , Kopitz J.
Published: October 2002

Excessive accumulation of lipofuscin in postmitotic retinal pigment epithelial cells is a common pathogenetic pathway in various blinding retinal diseases including age‐related macular degeneration, which is now the most common cause of registerable blindness in the industrialized nations. To better understand the role of lipofuscin accumulation and to manipulate the pathogenetic mechanisms on both experimental and therapeutic levels we analyzed the proteome of isolated human ocular lipofuscin granules from human RPE cells. After homogenization and fractionation by gradient ultracentrifugation of the RPE/choroid complex from 10 pairs of human donors, protein compounds were separated by 2D gel electrophoresis and analyzed using matrix‐assisted laser desorption/ionization mass spectrometry and HPLC‐coupled electrospray tandem mass spectrometry. Besides a better understanding of downstream pathways, this approach may provide new targets for therapeutic interventions in a currently untreatable disease.
The effect of 12‐O‐tetradecanoylphorbol‐13‐acetate on Sertoli cell morphology and cytoskeletal organization: an in vitro study by means of cryo‐SEM and fluorescent techniques
Authors: Panagopoulou Evridiki , Kouloukoussa Mirsini , Voloudaki‐Baltatzi Irene , Kittas Christos , Marinos Evangelos
Published: October 2002

By means of cryo‐scanning electron microscopy (cryo‐SEM) and fluorescent techniques, evidence is provided on how 12‐O‐tetradecanoylphorbol‐13‐acetate (TPA) affects Sertoli cell morphology and F‐actin and vinculin organization in vitro. In order to visualize the morphological changes, the cells were observed with cryo‐SEM. F‐actin was localized using rhodamine (TRI)–phalloidin and vinculin using a primary monoclonal antibody and a second TRI‐conjugated antibody. The results indicate that after the addition of 10−7 M TPA, Sertoli cells begin to round up and their cytoplasm is retracted towards a central region. Actin bundle organization is disrupted and vinculin assumes a punctuate distribution throughout the cell. Thus, the reorganization of actin and vinculin and subsequent changes in cell morphology seem to be brought about by TPA affecting not only actin but also the protein vinculin which interacts with actin. A discussion is made concerning the effect of TPA on cytoskeletal reorganization, which is closely related to cell transformation.
Chemotherapy‐induced cardiotoxicity: current practice and prospects of prophylaxis
Authors: Gharib M.I. , Burnett A.K.
Published: October 2002

Cardiotoxicity is a potential side effect of few chemotherapeutic agents. The anthracycline class of cytotoxic antibiotics are the most famous, but other chemotherapeutic agents can also cause serious cardiotoxicity and are not so well recognised. Examples include cyclophosphamide, ifosfamide, mitomycin and fluorouracil. Prediction and hence prophylaxis has always been a difficult task. Ideal monitoring techniques, upon which efficient prophylaxis depends, are yet to be determined. Current prophylaxis relies upon early detection of systolic and/or diastolic dysfunction. While somewhat useful, in some cases by the time defects are detected progression of chemotherapy‐induced cardiomyopathy is beyond prevention. Prophylaxis would be much more efficient if a biochemical marker of myocardiocyte damage could be reliably used to stop further chemotherapy at the correct time before irreversible progressive ‘macroscopic’ damage becomes evident upon imaging. Work is currently progressing to identify the role of markers such as troponins and natriuretic peptides in this regard.
CNMs/CMs as Primary Care Providers: Scope of Practice Issues
Authors: Sullivan Nancy H.
Published: October 2002

Since the proliferation of managed care organizations and the expansion of the central role of the primary care provider in the early 1990s, certified nurse‐midwives and certified midwives have debated the merits and drawbacks of their inclusion in this category of provider. The present article explores the history of primary care and reviews the most commonly accepted definition of primary care. The boundaries of scope of practice in primary care and the legal and economic ramifications of certified nurse‐midwives/certified midwives practice in this area are discussed.
Journal Reviews
Authors: Zeidenstein Laura
Published: October 2002

Distribution of genital tract trauma in childbirth and related postnatal pain. Albers L, Garcia J, Renfrew M, McCandlish R, Elbourne D. Birth 1999;26:11–5.

Reviewed by: Suzanne Seger, CNM, MSN, Mount Sinai Medical Center Midwifery Service, New York, New York.

Association between method of delivery and maternal rehospitalization. Lydon‐Rochelle M, Holt VL, Martin DP, Easterling TR. J Am Med Assoc 2000;283(18):2411–6.

Reviewed by: Kimberly A. Whitfill, MSN, CNM, Assistant Clinical Professor, Columbia University School of Nursing/Nurse‐Midwifery Program, New York, New York.

Is it necessary to suture all lacerations after a vaginal birth? Lundquist M, Olsson A, Nissen E, Norman M. Birth 2000;27:79–85.

Reviewed by: Kathy Rosenberg, CNM, MS, Katonah, New York.

Effect of a screening‐based prevention policy on prevalence of early‐onset group B streptococcal sepsis. Brozanski BS, Jones JG, Krohn MA, Sweet RL. Obstet Gynecol 2000;95:496–501.

Reviewed by: Jessica Lynn, GNM, MSN, Columbia University School of Nursing, New York, New York.
Structure and property of glycine’s derivatives bound by multications (H+, Li+, and Na+): A theoretical study
Authors: Ai Hongqi , Bu Yuxiang , Han Keli
Published: October 2002

The calculations using several different methods (B3P86, MP2, MP3, MP4SDQ, and CCSD) and basis sets [6-31G*, 6-31+G*, and 6-311+G(2df,2pd)] have been first performed for 15 glycine derivatives (one Gly–2H+, one Gly–3H+, five Gly–H+Li+ isomers, three Gly–H+Na+ isomers, three Gly–Li+Na+ isomers, and two Gly–2Na+ isomers) formed by multications (H+, Li+ or Na+) and different active sites of a glycine molecule. These calculations yield accurate geometric structures, relative energies, bond energies, vibrational frequencies, infrared intensities, and charge distributions. The comparisons of relative energy for each isomer show that both Gly–2H+ and Gly–3H+ derived from the most stable neutral glycine hold the lowest energies among their respective corresponding isomers. For the Gly–2H+, two protons are, respectively, bound to the amino nitrogen and the syn carbonyl oxygen of the most stable neutral glycine molecule. On the basis of the Gly–2H+, the derivative Gly–3H+ can be generated when the third proton binds to the hydroxyl oxygen. For five Gly–H+Li+ isomers, three Gly–H+Na+ isomers, three Gly–Li+Na+ isomers, and two Gly–2Na+ isomers, each of their corresponding ground state possesses the structure with the heavier cation coordinated to carbonyl oxygen and the lighter one to the anti-amino nitrogen of another kinds of neutral glycine molecule. The bond energies first reveal that some of these derivatives must surmount an activation energy barrier in the course of some cation (proton) dissociating from it. The origin of these barriers are investigated and discussed. Finally characteristic frequency calculations imply that the study is very important in the search of the glycine derivatives by rotational spectroscopy, or for the identification of their isomers by their infrared bands.
Calculation of the energy levels of weakly bound molecular trimers: Application to (H2)3
Authors: Costa Luı́s S. , Clary David C.
Published: October 2002

A quantum-mechanical procedure is described for calculating the ro-vibrational states of weakly bound molecular clusters using a basis function approach. The method involves using a body fixed Jacobi-type coordinate system, which provides an orthogonal kinetic-energy operator. The evaluation of all angular degrees of freedom is performed analytically through a suitable expansion of the potential. The radial degrees of freedom are treated numerically with a discrete variable representation. The approach is applied to the (H2)2 and (H2)3 systems treating the H2 monomers as rigid bodies. For zero total angular momentum, it is found that (H2)3 has only one bound-state for each symmetry, with the ortho–ortho–ortho symmetry being the most stable.
Adiabatic time-dependent density functional methods for excited state properties
Authors: Furche Filipp , Ahlrichs Reinhart
Published: October 2002

This work presents theory, implementation, and validation of excited state properties obtained from time-dependent density functional theory (TDDFT). Based on a fully variational expression for the excited state energy, a compact derivation of first order properties is given. We report an implementation of analytic excited state gradients and charge moments for local, gradient corrected, and hybrid functionals, as well as for the configuration interaction singles (CIS) and time-dependent Hartree–Fock (TDHF) methods. By exploiting analogies to ground state energy and gradient calculations, efficient techniques can be transferred to excited state methods. Benchmark results demonstrate that, for low-lying excited states, geometry optimizations are not substantially more expensive than for the ground state, independent of the molecular size. We assess the quality of calculated adiabatic excitation energies, structures, dipole moments, and vibrational frequencies by comparison with accurate experimental data for a variety of excited states and molecules. Similar trends are observed for adiabatic excitation energies as for vertical ones. TDDFT is more robust than CIS and TDHF, in particular, for geometries differing significantly from the ground state minimum. The TDDFT excited state structures, dipole moments, and vibrational frequencies are of a remarkably high quality, which is comparable to that obtained in ground state density functional calculations. Thus, yielding considerably more accurate results at similar computational cost, TDDFT rivals CIS as a standard method for calculating excited state properties in larger molecules.
High resolution C1s and S2p photoelectron spectra of thiophene
Authors: Giertz A. , Bässler M. , Björneholm O. , Wang H. , Feifel R. , Miron C. , Karlsson L. , Svensson S. , Børve K. J. , Sæthre L. J.
Published: October 2002

Vibrationally resolved C1s and S2p photoelectron spectra of the thiophene molecule have been recorded using monochromated synchrotron radiation at photon energies of 330 eV and 210 eV, respectively. The photoelectron bands contain complex vibrational structures which are analyzed using ab initio and curve-fitting procedures. The analysis is in good agreement with the experimental spectrum which enables identification of two chemically shifted carbon 1s core hole states. We were also able to determine the molecular-field splitting of the S2p3/2 ionic state to about 99 meV. The molecular-field splitting was moreover calculated using second-order Møller–Plesset perturbation theory, confirming the result from the fitting procedure.
Landau model of the smectic C–isotropic phase transition
Authors: Mukherjee Prabir K. , Pleiner Harald , Brand Helmut R.
Published: October 2002

We propose a Landau model to describe the smectic C–isotropic phase transition. A general Landau theory for the coupled orientational and translational order parameters and including the tilt angle is developed. The conditions for the smectic C–isotropic phase transition and the stability conditions of the smectic C phase are calculated. On the basis of this model it is argued that the smectic C–isotropic phase transition is always first order. We present a detailed analysis of the question under which conditions a direct smectic C–isotropic phase transition prevails in comparison to smectic A–isotropic and nematic–isotropic transitions. The theoretical results are found to be in qualitative agreement with all published experimental results.
A theoretical study on decomposition of formic acid in sub- and supercritical water
Authors: Yagasaki Takuma , Saito Shinji , Ohmine Iwao
Published: October 2002

The mechanisms of the dissociation of formic acid in subcritical and supercritical water are investigated theoretically. In this dissociation, water molecules around a formic acid play a role of a catalyst by transferring a proton along their locally formed hydrogen bond network. There are two channels of the dissociation, that is, the dehydration (HCOOH→CO+H2O) starting from the trans-formed formic acid and the decarboxylation (HCOOH→CO2+H2) from the cis-formed formic acid. The effects of hydration on these channels in sub- and supercritical water are analyzed by calculating the free energy and analyzing the water molecular coordination by the Monte Carlo method and molecular dynamics calculations. It is found that the hydration is stronger in the decarboxylation (via the cis-path) than in the dehydration (via the trans-path). The number of “catalytic” water molecules coordinated to the cis-formed formic acid, leading to decarboxylation, in supercritical is almost the same as that in subcritical water. On the other hand, the catalytic water molecular coordination on the trans-formed formic acid, leading to the dehydration, is found to be much more reduced in supercritical water than that in subcritical water. These facts manifest how the decarboxylation becomes more favorable than the dehydration in supercritical water, whereas both dissociation channels are equally probable in subcritical water.
Quantum dynamics for dissipative systems: A hydrodynamic perspective
Authors: Burghardt Irene , Møller Klaus B.
Published: October 2002

This paper explores the hydrodynamic description of quantum densities evolving under the effects of dissipation. For illustration, we refer to analytical solutions for a harmonic system and Markovian dissipation, and derive expressions for the hydrodynamic moments and a hydrodynamic force that represents a generalization of the quantum force of Bohmian dynamics. Beyond this, we draw general conclusions on the dynamical transition, induced by dissipation, to a classical-like regime. In this context, the relation between the quantum-mechanical hydrodynamic picture and its classical-statistical analogue is investigated. This has some bearing upon mixed quantum-classical schemes emerging from the hydrodynamic description.
Lattice spring model of filled polymers and nanocomposites
Authors: Buxton Gavin A. , Balazs Anna C.
Published: October 2002

Mechanical properties of homopolymers containing either solid spheres, rods, or platelets are compared using a three-dimensional lattice spring model, and thus, the effects of filler geometry on the mechanical behavior of the composite are isolated. In addition, the properties of exfoliated and intercalated nanocomposites are examined and the source of the increased reinforcement efficiency in nanocomposites, as a consequence of platelet exfoliation, is elucidated. Viscoelastic deformations are explicitly incorporated in the lattice spring model and, thus, the mechanical response of these filled polymer materials are determined.
Volume effects on the molecular mobility close to glass transition in supercooled phenylphthalein-dimethylether. II
Authors: Paluch Marian , Casalini Riccardo , Best Andreas , Patkowski Adam
Published: October 2002

Pressure–volume–temperature measurements in phenylphthalein-dimethylether (PDE) are reported, in combination with recently published dynamic light scattering data obtained under high pressure. We discuss the role that volume and thermal effects play in controlling the dynamics in the vicinity of the glass transition. Although volume is not the unique thermodynamical parameter characterizing the relaxation dynamics in PDE, its contribution to the super-Arrhenius behavior of the relaxation times in the vicinity of the glass transition is remarkable. The contribution of volume to the temperature dependence of the relaxation times has been characterized by means of the ratio of the activation energy at constant volume to the enthalpy of activation at constant pressure, EV/HP. We point out that this quantity is correlated with the temperature behavior of the nonexponentiallity parameter, βKWW. Moreover, the τ(T,P) values were analyzed in terms of an extension of the Adam–Gibbs model. It was shown that this model gives a satisfactory interpretation of the pressure sensitivity of the dynamics (d log10(τ)/dP)|T in terms of thermodynamic properties of the material.
Polyimide-waveguide-based thermal optical switch using total-internal-reflection effect
Authors: Yang Jianyi , Zhou Qingjun , Chen Ray T.
Published: October 2002

A total-internal-reflection waveguide switch with an X junction was designed and fabricated by using the thermo-optic effect of polyimide materials. Experimental results show that the crosstalk is below −28 dB at the wavelength of 1.55 μm. The switching power with the current electrode is 132 mW, which can be reduced to 20–30 mW with an optimized design together with electroplating to form a thick conducting path.
Direct determination of free exciton binding energy from phonon-assisted luminescence spectra in GaN epilayers
Authors: Xu S. J. , Liu W. , Li M. F.
Published: October 2002

Investigation of variable-temperature longitudinal optical (LO) phonon-assisted luminescence spectra of free excitons and free electrons in heteroepitaxial GaN thin films has been conducted. It is found that thermal broadening of the LO phonon-assisted photoluminescence peaks is much slower than those of the peaks of their parents so that the first-order LO peaks of the free exciton transition and the band-to-band transition can be well resolved even at room temperature, leading to a direct determination of the band A free exciton binding energy as 25.4±0.9 meV. At the same time, we demonstrate that the simple hydrogenlike model still is a good approximation to describe the energy level structure of free excitons in GaN.
GaAs(311) templates for molecular beam epitaxy growth: surface morphologies and reconstruction
Authors: Wang Z. M. , Yazdanpanah V. R. , Shultz J. L. , Salamo G. J.
Published: October 2002

Morphologies of GaAs(311) surfaces grown by molecular beam epitaxy were investigated by in situ reflection high-energy electron diffraction and scanning tunnelling microscope. In addition to the (8×1) reconstruction, two surface phases, GaAs(311)A-(4×1) and GaAs(311)B-(2×1) were observed. Both of these surfaces are characterized by wider, atomically smooth terraces with much lower structural anisotropy, when compared to the (8×1) reconstructed GaAs(311) surfaces. The observed surfaces have potential as templates for the growth of organized quantum dots, wires, and wells.
Micromechanical cantilever as an ultrasensitive pH microsensor
Authors: Bashir R. , Hilt J. Z. , Elibol O. , Gupta A. , Peppas N. A.
Published: October 2002

We report on a pH sensor with ultrahigh sensitivity based on a microcantilever structure with a lithographically-defined crosslinked copolymeric hydrogel. Silicon-on-insulator wafers were used to fabricate cantilevers on which a polymer consisting of poly(methacrylic acid) (PMAA) with poly(ethylene glycol) dimethacrylate was patterned using free-radical UV polymerization. As the pH around the cantilever was increased above the pKa of PMAA, the polymer network expanded and resulted in a reversible change in surface stress causing the microcantilever to bend. Excellent mechanical amplification of polymer swelling as a function of pH change within the dynamic range was obtained, with a maximum deflection sensitivity of 1 nm/5×10−5 ΔpH.
Dynamic etching of silicon for broadband antireflection applications
Authors: Striemer C. C. , Fauchet P. M.
Published: October 2002

An electrochemical etching technique has been developed that provides continuous control over the porosity of a porous silicon layer as a function of etching depth. Thin films with engineered porosity gradients, and thus a controllable gradient in the index of refraction, have been used to demonstrate broadband antireflection properties on silicon wafer and solar cell substrates. A simulation was also developed to examine the effects of specific porosity profiles on film reflectivity.
Gradient nanostructures for interfacing microfluidics and nanofluidics
Authors: Cao Han , Tegenfeldt Jonas O. , Austin Robert H. , Chou Stephen Y.
Published: October 2002

It is difficult to introduce long genomic DNA molecules into nanometer scale fluidic channels directly from the macroscale world because of the steep entropic barrier caused by necessary stretching of the polymer. We present a very simple technique using optical lithography to fabricate continuous spatial gradient structures which smoothly narrow the cross section of a volume from the micron to the nanometer length scale, greatly reducing the local entropic barrier to nanochannel entry. This technique, diffraction gradient lithography, can be very valuable for the fabrication of micro/nano total analysis systems.
High-resolution atomic force microscope nanotip grown by self-field emission
Authors: Oon C. H. , Thong J. T. L. , Lei Y. , Chim W. K.
Published: October 2002

A technique to grow a single tungsten filament tip on a tapping mode atomic force microscope (AFM) tip by a process of self-field emission in the presence of tungsten carbonyl is demonstrated. Such filaments have a tip radius of 1–2 nm and are grown to lengths ranging from 400 nm to 3 μm and a shank diameter of about 60–90 nm. Images of germanium nanocrystals and porous alumina membranes show much higher resolution and definition than standard AFM tips. The tip shows no degradation even after 10 h of scanning, demonstrating its utility as a practical tip. The self-aligned nature of the growth makes it a very simple nanotip fabrication technique.
Magnetic gradiometer based on a high-transition temperature superconducting quantum interference device for improved sensitivity of a biosensor
Authors: Lee SeungKyun , Myers W. R. , Grossman H. L. , Cho H.-M. , Chemla Y. R. , Clarke John
Published: October 2002

We describe a gradiometer based on a high-transition temperature superconducting quantum interference device (SQUID) that improves the sensitivity of a SQUID-based biosensor. The first-derivative gradiometer, fabricated from a single layer of YBa2Cu3O7−x, has a baseline of 480 μm and a balance against uniform fields of 1 part in 150. Used in our SQUID “microscope,” it reduces the response to parasitic magnetic fields generated by the measurement process to the level of the SQUID noise. The gradiometer-based microscope is two orders of magnitude more sensitive to superparamagnetic nanoparticles bound to biological targets than our earlier magnetometer-based microscope.
Structural disorder and loss of piezoelectric properties in α-quartz at high temperature
Authors: Haines J. , Cambon O. , Keen D. A. , Tucker M. G. , Dove M. T.
Published: October 2002

The piezoelectric properties of α-quartz-based resonators, characterized by the mechanical quality factor, Q, are found to degrade beginning above 300 °C. This is well below the transition at 573 °C to the β phase, which in principle limits the piezoelectric response of this material. This gradual loss of piezoelectric response can be linked to the increase in structural disorder in α-quartz found in total neutron scattering measurements. Analysis of these data by reverse Monte Carlo modeling indicates that between 200 and 400 °C, the local disorder in the instantaneous structure of α-quartz becomes comparable to that of β-quartz.
Single-photon emission of CdSe quantum dots at temperatures up to 200 K
Authors: Sebald K. , Michler P. , Passow T. , Hommel D. , Bacher G. , Forchel A.
Published: October 2002

We report on the generation of triggered single photons obtained from epitaxially grown self-assembled CdSe/Zn(S,Se) quantum dots for temperatures up to 200 K. At low temperatures (T<40 K) photon correlation experiments under pulsed excitation show nearly perfect single-photon emission from an individual CdSe quantum dot. For higher temperatures (T>40 K) an increasing multi-photon emission probability due to spectrally overlapping acoustic phonon sidebands of neighboring quantum dots is observed. We found that the multi-photon emission probability of a bare quantum dot (background subtracted) is strongly suppressed at 200 K if compared to a Poissonian light source of the same average intensity. Our results demonstrate the large potential of self-assembled CdSe/Zn(S,Se) quantum dots for nonclassical light generation at temperatures up to 200 K.
Relationship between the Li ionic conduction and the local structures in B-site substituted perovskite compounds, (Li0.1La0.3)1+xMxNb1−xO3 (M=Zr, Ti; x=0, 0.05)
Authors: Nakayama Masanobu , Ikuta Hiromasa , Uchimoto Yoshiharu , Wakihara Masataka , Terada Yasuko
Published: October 2002

Generally, it is known that the activation energy for the Li+ conduction in the perovskite-type oxides such as (Li,La)NbO3 decreases with the expansion of the lattice. However, our previous results showed an increase in the activation energy with Zr doping at B site in spite of lattice expansion. In the present study, the local structure of B site substituted perovskite oxides, (Li0.1La0.3)1+xMxNb1−xO3 (M=Zr, Ti; x=0, 0.05), has been investigated using the extended x-ray absorption fine structure (EXAFS) technique with a view to explore the divergence exerted by Zr-doped perovskites. The EXAFS measurement revealed that the Li+ migration pathway in the Zr-doped samples is subjected to contract due to the local lattice distortion around the Zr-doped site.
Short inversions and conserved gene cluster
Authors: Sankoff David
Published: October 2002

Motivation: Two independent sets of recent observations on newly sequenced microbial genomes pertain to the prevalence of short inversion as a gene order rearrangement process and to the lack of conservation of gene order within conserved gene clusters. We propose a model of inversion where the key parameter is the length of the inverted fragment.

Results: We show that there is a qualitative difference in the pattern of evolution when the inversion length is small with respect to the cluster size and when it is large. This suggests an explanation of the lack of parallel gene order in conserved clusters and raises questions about the statistical validity of putative functionally selected gene clusters if these have only been tested against inappropriate null hypotheses.

Contact: sankoff@poste.umontreal.ca
Neutron irradiation effect on radio-frequency magnetron-sputtered GaN thin films and Au/GaN Schottky diodes
Authors: Wang Ching-Wu
Published: October 2002

The microstructural and luminescent properties of pre-irradiated and neutron-irradiated sputtered GaN thin films were systematically investigated. Analytical results revealed that the optimal (1×1013 n/cm2) neutron irradiation fluence could not only promote the crystallinity of GaN thin films, but also effectively repress the occurrence of deep level luminescence in the photoluminescence spectrum due to the creation of nitrogen-related deep electron traps (Et1). Moreover, from both the Fourier transform infrared spectroscopy and yellow band emission results, it is strongly suggested that Ga–H complexes in the vicinity of the nitrogen vacancy, forming the Et2 trap, possibly act as the origin of yellow band emission in GaN material. The superior I–V characteristics resulting from the optimal (1×1013 n/cm2) neutron irradiation fluence on the Au/sputtered GaN Schottky diode were attributed mainly to the superior crystallinity, creating the fewer deep electron traps of Et1, leading to a smaller turn-on voltage as well as a larger conduction current in the forward-biased situation. In the reverse-biased condition, the smaller leakage current and the larger breakdown voltage were suggested to probably be due to the presence of fewer nitrogen vacancies and/or less Ga–Au compound formation at the Au/GaN junction.
Experimental simulation of integrated optoelectronic sensors based on III nitrides
Authors: Starikov D. , Boney C. , Medelci N. , Um J.-W. , Bensaoula A. , Sanz M. Larios , Fox G. E.
Published: October 2002

Reliable, miniature, multifunctional, real-time optoelectronic sensors can be fabricated by using III nitride materials that have several advantages over the conventional semiconductors. Recent advances in these materials allow integrated optoelectronic devices with tunable spectral characteristics. In addition, optically transparent sapphire substrates and commercially beneficial silicon wafers can be used for the device fabrication. Two concepts of the integrated optoelectronic sensor development are presented in this work. These concepts were investigated by fabrication and testing simulators based on III nitride and Si commercial components. The fabricated devices exhibit multifunctionality expressed by the ability to perform measurements of optical absorption (metallic salts solutions), reflection (interface with commonly used solvents), scattering (alumina powder slurries), and fluorescence (chlorophyll, fluorescein, pyrene, anthracene, and Escherichia coli strains carrying plasmids which encode fluorescent proteins). These measurements indicate the applicability of the III nitride and Si-based components and their layout according to the described concepts for the development of integrated multifunctional optoelectronic sensors.
Tunable emission from InAs quantum dots on InP nanotemplates
Authors: Lefebvre J. , Poole P. J. , Aers G. C. , Chithrani D. , Williams R. L.
Published: October 2002

Selective area chemical beam epitaxy is used to fabricate submicron [100]-oriented InP ridges with well-defined, defect-free (011) sidefacets and (001) tops. Following the deposition of two monolayers of InAs on such nanotemplates and subsequent capping with InP, photoluminescence spectra show for wider ridges strong emission from a thin InAs quantum well and, as the ridge width is reduced, a gradual appearance of a quantum dot emission at lower energy. The method allows continuous tuning on a given sample in a single growth run of both the quantum dot density and the emission wavelength. The result is a consequence of adatom diffusion from the ridge sidefacets onto the top (001) facet, which increases the amount of InAs beyond the critical thickness for three-dimensional nucleation to occur. Compared with growth on planar InP(001) substrates, InAs self-assembled quantum dots grown on these nanotemplates are more uniform as revealed by a twofold reduction in emission linewidth at 4 K.
Investigation of in situ trench etching process and Bosch process for fabricating high-aspect-ratio beams for microelectromechanical systems
Authors: Kok Kitt Wai , Yoo Won Jong , Sooriakumar K. , Pan J. Sheng , Lee E. Y.
Published: October 2002

The etching processes and mechanisms for sidewall formation were investigated for the in situ trench etching and releasing process, using a magnetically enhanced reactive ion etcher (MERIE), and for the Bosch process, using an inductively coupled plasma (ICP) etcher. For the Bosch process, almost vertical sidewall profiles were obtained up to etching depth of ∼100 μm. The average height of the scallops on the sidewall was ∼70 nm and the average erosion underneath the mask was ∼0.4 μm, when trenches 50 μm deep were formed. This limited the fabrication capability of small feature sized microelectromechanical system structures of less than ∼1 μm. For the in situ processes using MERIE, the reactive ion etching (RIE) lag was significant when the etching depth reached ∼50 μm. The RIE lag was significantly reduced when the ICP was used at pressure below 50 mTorr. Scallops and undercuts were not observed when the in situ process was used. Anger electron spectroscopy and x-ray photoelectron spectroscopy analysis revealed that the sidewall passivation layer from the in situ process consisted of SiOx (1<x<2, where x varies with sidewall thickness) and small amount of F.
Formation and removal of composite halogenated silicon oxide and fluorocarbon films deposited on chamber walls during plasma etching of multiple film stacks
Authors: Ullal Saurabh J. , Singh Harmeet , Daugherty John , Vahedi Vahid , Aydil Eray S.
Published: October 2002

In the shallow trench isolation process, a stack of thin films on a Si wafer must be etched using different gas discharges. During plasma etching of a thin-film stack consisting of an organic antireflection coating, Si3N4 and Si with Cl2, CHF3/CF4 and Cl2/O2 discharges, respectively, halogenated silicon oxide and fluorocarbon films form on the chamber walls. The chemical nature of these films and the methods for removing them were studied using multiple plasma and surface diagnostics. We find that the film which deposits on the chamber walls is a composite consisting primarily of two components, a halogenated silicon oxide film—created during Cl2/O2 etching of Si—and a fluorocarbon film formed during CF4/CHF3 etching of Si3N4. The halogenated silicon oxide film can be removed by etching with F formed by dissociation in SF6 plasma, while the fluorocarbon film is etched by O atoms created in O2 plasma. A sequential SF6 and O2 plasma process can be used to etch the composite film, but even an O2 plasma maintained under proper conditions was found to remove this film. During the removal of the fluorocarbon film by O2 discharge, the etching products released into the gas phase dissociate to produce F, which can etch the oxide film. Thus, the fluorocarbon film serves as a solid source of F allowing the removal of all of the composite film including the oxide component with O2 plasma alone. However, O2 plasma cleaning conditions must be optimized to allow high residence time for F atoms to react with the oxide film.