bluuebunny/crossref_metadata_2025 huggingface dataset:
Age-associated decline in mitochondrial respiration and electron transport in Drosophila melanogaster
Authors: Ferguson Melissa , Mockett Robin J. , Shen Yi , Orr William C. , Sohal Rajindar S.
Published: August 2005

The principal objective of the present study was to identify specific alterations in mitochondrial respiratory functions during the aging process. Respiration rates and the activities of electron transport chain complexes were measured at various ages in mitochondria isolated from thoraces of the fruit fly, Drosophila melanogaster, which consist primarily of flight muscles. The rates of state 3 respiration (ADP-stimulated), RCRs (respiratory control ratios) and uncoupled respiration rates decreased significantly as a function of age, using either NAD+- or FAD-linked substrates; however, there were no differences in state 4 respiration (ADP-depleted) rates. There was also a significant age-related decline in the activity of cytochrome c oxidase (complex IV), but not of the other mitochondrial oxidoreductases examined. Exposure of mitochondria isolated from young flies to low doses of KCN or NaAz (sodium azide), complex IV inhibitors, decreased cytochrome c oxidase activity and increased the production of H2O2. Collectively, these results support the hypothesis that impairment of mitochondrial respiration may be a causal factor in the aging process, and that such impairment may result from and contribute to increased H2O2 production in vivo.
The signal peptide of the rat corticotropin-releasing factor receptor 1 promotes receptor expression but is not essential for establishing a functional receptor
Authors: Alken Martina , Rutz Claudia , Köchl Robert , Donalies Ute , Oueslati Morad , Furkert Jens , Wietfeld Doreen , Hermosilla Ricardo , Scholz Anne , Beyermann Michael , Rosenthal Walter , Schülein Ralf
Published: August 2005

Approximately 5–10% of the GPCRs (G-protein-coupled receptors) contain N-terminal signal peptides that are cleaved off during receptor insertion into the ER (endoplasmic reticulum) membrane by the signal peptidases of the ER. The reason as to why only a subset of GPCRs requires these additional signal peptides is not known. We have recently shown that the signal peptide of the human ETB-R (endothelin B receptor) does not influence receptor expression but is necessary for the translocation of the receptor's N-tail across the ER membrane and thus for the establishment of a functional receptor [Köchl, Alken, Rutz, Krause, Oksche, Rosenthal and Schülein (2002) J. Biol. Chem. 277, 16131–16138]. In the present study, we show that the signal peptide of the rat CRF-R1 (corticotropin-releasing factor receptor 1) has a different function: a mutant of the CRF-R1 lacking the signal peptide was functional and displayed wild-type properties with respect to ligand binding and activation of adenylate cyclase. However, immunoblot analysis and confocal laser scanning microscopy revealed that the mutant receptor was expressed at 10-fold lower levels than the wild-type receptor. Northern-blot and in vitro transcription translation analyses precluded the possibility that the reduced receptor expression is due to decreased transcription or translation levels. Thus the signal peptide of the CRF-R1 promotes an early step of receptor biogenesis, such as targeting of the nascent chain to the ER membrane and/or the gating of the protein-conducting translocon of the ER membrane.
Mapping leptin-interacting sites in recombinant leptin-binding domain (LBD) subcloned from chicken leptin receptor
Authors: Niv-Spector L. , Raver N. , Friedman-Einat M. , Grosclaude J. , Gussakovsky E. E. , Livnah O. , Gertler A.
Published: August 2005

The binding domain of the chicken leptin receptor [chLBD (chicken leptin-binding domain)], subcloned from the full-size chicken leptin receptor and prepared in an Escherichia coli system, was subjected to site-directed mutagenesis to identify the amino acids involved in leptin binding. A total of 22 electrophoretically pure, >90% monomer-containing mutants were expressed, refolded and purified. The effects of the mutations were tested by the ability to form complexes with ovine leptin, and the kinetic parameters of interaction were determined by surface plasmon resonance. Six mutants were used to determine whether mutations of several amino acids that differ between chLBD and mammalian LBDs will affect affinity: none showed any such effect, except the mutant A105D (Ala105→Asp), which exhibited some decrease in affinity. Surface plasmon resonance analysis identified six mutants in which binding activity was totally abolished (F73A, Y14A/F73A, V76A/F77A, L78A/L79A, V76A/F77A/L78A/L79A and A105D/D106V) and six mutants (Y14A, R41A, R41A/S42A/K43A, V103A, V135A/F136A and F136A) in which affinity for the hormone was reduced, mainly by increased dissociation rates. Gel-filtration experiments indicated the formation of a 1:1 ovine or human leptin–chLBD complex with a molecular mass of approx. 41 kDa. Gel-filtration experiments yielded 1:1 complexes with those mutants in which affinity had decreased, but not with the six mutants, which had totally lost their binding capacity. Modelling the leptin–chLBD complex indicated that the binding domain of the latter is located mainly in the L3 loop, which contributes nine amino acid residues interacting with leptin. Contact-surface analysis identified the residues having the highest contribution to the recognition site to be Phe73, Phe77 and Leu79.
NPC1 late endosomes contain elevated levels of non-esterified (‘free’) fatty acids and an abnormally glycosylated form of the NPC2 protein
Authors: Chen Fannie W. , Gordon Ronald E. , Ioannou Yiannis A.
Published: August 2005

NPC (Niemann–Pick type C) disease is a rare lipidosis characterized by the accumulation of LDL (low-density lipoprotein)-derived non-esterified cholesterol in the E/L (endosomal/lysosomal) system. The gene products that are responsible for the two NPC complementation groups are distinct and dissimilar, yet their cellular and disease phenotypes are virtually indistinguishable. To investigate the relationship between NPC1 and NPC2 and their potential role in NPC disease pathogenesis, we have developed a method for the rapid and efficient isolation of late endocytic vesicles from mouse liver by magnetic chromatography. Late endosomes from Wt (wild-type) and NPC1 mice were found to differ not only in their cholesterol and sphingomyelin content, as expected, but also in their non-esterified (‘free’) fatty acid content, with NPC1 vesicles showing an approx. 7-fold increase in non-esterified fatty acid levels compared with Wt vesicles. Furthermore, we show that the NPC2 protein is in an incompletely deglycosylated form in NPC1 late endosomes by a mechanism that is specific to the NPC2 protein and not a global aberration of protein glycosylation/deglycosylation or trafficking, since NPC2 secreted from NPC1 cells is indistinguishable from that secreted from Wt cells. Also, a greater proportion of the normally soluble cellular NPC2 protein partitions with detergent-insoluble late endosomal internal membrane domains in NPC1 vesicles. In addition, we show that, although a small amount of the NPC2 protein associates with these membranes in Wt vesicles, this localization becomes much more pronounced in NPC1 vesicles. These results suggest that the function of the NPC2 protein may be compromised as well in NPC1 endosomes, which might explain the paradoxical phenotypic similarities of the two NPC disease complementation groups.
Bacillus subtilis 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase revisited: resolution of two long-standing enigmas
Authors: Wu Jing , Sheflyan Galina Ya. , Woodard Ronald W.
Published: August 2005

The mono/bifunctional and metallo/non-metallo properties of Bacillus subtilis DAHPS (3-deoxy-D-arabino-heptulosonate 7-phosphate synthase) have been controversial for several decades. The present study investigated the DAHPSs from both the B. subtilis parent Marburg strain and the derivative strain 168 in detail and clarified the above two long-standing questions. The DAHPSs from the parent and the derivative 168 strains have identical sequence and are both bifunctional enzymes with a CM (chorismate mutase) activity and a DAHPS activity. The parent strain expresses a second independent monofunctional CM, encoded by aroH, that is highly active, while the 168 strain expresses an aroH containing a single residue mutation (A112V) that is significantly less active thus leading to previous confusion regarding the mono/bifunctionality of DAHPS. Metal analysis showed that B. subtilis DAHPS as isolated contained iron and zinc and is inactivated by dipicolinic acid; the inactive apoenzyme can be reactivated by bivalent metal ions, indicating that the enzyme is a metalloenzyme. The enzyme-bound metal is insensitive to EDTA treatment, leading to the previous conclusion that this DAHPS does not require a metal. The enzyme displays a homotetrameric structure in solution and appears to follow Michaelis–Menten kinetics with KmPEP=139±11.4 μM for phosphoenolpyruvate, KmE4P=1760±110 μM for D-erythrose 4-phosphate, kcat=4.6±0.1 s−1 for DAHPS activity and Kmchorismate=850±97 μM, kcat=0.41±0.01 s−1 for CM activity. B. subtilis DAHPS is inhibited by the Shikimate pathway intermediates prephenate and chorismate.
Novel human-derived cell-penetrating peptides for specific subcellular delivery of therapeutic biomolecules
Authors: de Coupade Catherine , Fittipaldi Antonio , Chagnas Vanessa , Michel Matthieu , Carlier Sophie , Tasciotti Ennio , Darmon Audrey , Ravel Denis , Kearsey Jonathan , Giacca Mauro , Cailler Françoise
Published: August 2005

Short peptide sequences that are able to transport molecules across the cell membrane have been developed as tools for intracellular delivery of therapeutic molecules. This work describes a novel family of cell-penetrating peptides named Vectocell® peptides [also termed DPVs (Diatos peptide vectors)]. These peptides, originating from human heparin binding proteins and/or anti-DNA antibodies, once conjugated to a therapeutic molecule, can deliver the molecule to either the cytoplasm or the nucleus of mammalian cells. Vectocell® peptides can drive intracellular delivery of molecules of varying molecular mass, including full-length active immunoglobulins, with efficiency often greater than that of the well-characterized cell-penetrating peptide Tat. The internalization of Vectocell® peptides has been demonstrated to occur in both adherent and suspension cell lines as well as in primary cells through an energy-dependent endocytosis process, involving cell-membrane lipid rafts. This endocytosis occurs after binding of the cell-penetrating peptides to extracellular heparan sulphate proteoglycans, except for one particular peptide (DPV1047) that partially originates from an anti-DNA antibody and is internalized in a caveolar independent manner. These new therapeutic tools are currently being developed for intracellular delivery of a number of active molecules and their potentiality for in vivo transduction investigated.
Biochemical characterization of the chondroitinase ABC I active site
Authors: Prabhakar Vikas , Raman Rahul , Capila Ishan , Bosques Carlos J. , Pojasek Kevin , Sasisekharan Ram
Published: August 2005

cABC I (chondroitinase ABC I) from Proteus vulgaris is a GalAG (galactosaminoglycan) depolymerizing lyase that cleaves its substrates at the glycosidic bond via β-elimination. cABC I cleaves a particularly broad range of GalAG substrates, including CS (chondroitin sulphate), DS (dermatan sulphate) and hyaluronic acid. We recently cloned and recombinantly expressed cABC I in Escherichia coli, and completed a preliminary biochemical characterization of the enzyme. In the present study, we have coupled site-directed mutagenesis of the recombinant cABC I with a structural model of the enzyme–substrate complex in order to investigate in detail the roles of active site amino acids in the catalytic action of the enzyme. The putative catalytic residues His-501, Tyr-508, Arg-560 and Glu-653 were probed systematically via mutagenesis. Assessment of these mutants in kinetic and end-point assays provided direct evidence on the catalytic roles of these active-site residues. The crystal structure of the native enzyme provided a framework for molecular docking of representative CS and DS substrates. This enabled us to construct recombinant enzyme–substrate structural complexes. These studies together provided structural insights into the effects of the mutations on the catalytic mechanism of cABC I and the differences in its processing of CS and DS substrates. All His-501 mutants were essentially inactive and thereby implicating this amino acid to play the critical role of proton abstraction during catalysis. The kinetic data for Glu-653 mutants indicated that it is involved in a hydrogen bonding network in the active site. The proximity of Tyr-508 to the glycosidic oxygen of the substrate at the site of cleavage suggested its potential role in protonating the leaving group. Arg-560 was proximal to the uronic acid C-5 proton, suggesting its possible role in the stabilization of the carbanion intermediate formed during catalysis.
An experimental investigation of the angular dependence of diffusion-driven flow
Authors: Peacock Thomas , Stocker Roman , Aristoff Jeff M.
Published: August 2005

We present experimental results on diffusion-driven flow along an inclined wall in a stably stratified fluid. The experiments focus on the dependence of the velocity in the buoyancy layer on the angle of inclination. The increase of velocity with decreasing angle is in agreement with theory for larger angles. For small angles, where current theory breaks down, the velocity tends to zero and an angle of maximum velocity exists.
Observations of flow repeatability and secondary circulation in an oscillating grid-stirred tank
Authors: McKenna Sean P. , McGillis Wade R.
Published: August 2005

An oscillating grid-stirred tank was studied for flow repeatability and the existence of secondary circulations. For the particular tank studied, results indicate that mean flow values may vary by up to 25% and turbulent fluctuations may vary by up to 15% from one run to another. This result was observed to exhibit a potential grid geometry dependence. More importantly, there is evidence of significant flow field sensitivity to initial conditions. Particle image velocimetry results were used to reveal secondary mean flows in the grid-stirred tank. Because these characteristics are believed to be intrinsic to grid-stirred tanks, studies using such tanks must recognize and consider these effects.
Enhanced diffusion due to motile bacteria
Authors: Kim Min Jun , Breuer Kenneth S.
Published: August 2005

The effect of bacterial motion on the diffusion of a molecule of high molecular weight is studied by observing the mixing of two streams of fluid in a microfluidic flow cell. We show that the presence of motile E. coli bacteria in one of the streams results in a marked increase in the effective diffusion coefficient of Dextran, which rises linearly with the concentration of bacteria from a baseline value of 0.2×10−7 to 0.8×10−7 (cm2/s) at a concentration of 2.1×109/ml (approximately 0.5% by volume). Furthermore, we observe that the diffusion process is also observed to undergo a change from standard Fickian diffusion to a superdiffusive behavior in which the diffusion exponent rises from 0.5 to 0.55 as the concentration of bacteria rises from 0 to 2.1×109/ml.
Diffusion studies and critical current in superconducting Nb–Ti–Ta artificial pinning center wire
Authors: Bormio-Nunes C. , Gomes P. M. N. , Tirelli M. A. , Ghivelder L.
Published: August 2005

The diffusion between Nb–20%Ta (wt %) and pure Ti is studied at temperatures of 973, 1023, and 1073K, for duration times among 25 and 121h in an artificial pinning center (APC) wire composed of a Ti core surrounded by a Nb–20%Ta layer. The produced diffusion layer is a ternary alloy with superconducting properties, such as critical field Bc2 and critical current density JC, which intrinsically depend on the layer composition. Measurements of layer morphology and composition were performed, and the results show a preferential diffusion of Nb and Ta into Ti. There is a slight diffusion of Ti into Nb through grain boundaries. The presence of Ta also slows down the diffusion of Nb in Ti if compared to the couple formed by pure Nb and Ti. Regarding the mechanical properties of the composite wire, the use of lower temperatures to form the ternary phase is desirable in order to avoid a larger portion of the diffusion layer rich in Ti that favorites α-Ti precipitations that are detrimental to the wire ductility. The best JC value was obtained for the sample heat treated at 973K. The improvement of the flux-line pinning was associated with a sharp change of the diffusion layer composition rather than pinning by normal layer interfaces, suggesting a new source of pinning in this kind of material. Nb–Ti–Ta ternary alloys have the potential to be used in superconducting magnets when fields above 12T are required.
Electrical and field-emission properties of chemically anchored single-walled carbon nanotube patterns
Authors: Jung Myung-Sup , Ko Young Koan , Jung Dae-Hwan , Choi Do Hwan , Jung Hee-Tae , Heo Jung Na , Sohn Byung Hee , Jin Yong Wan , Kim Jongmin
Published: August 2005

Well-defined and high-density single-walled carbon nanotube (SWNT) patterns were fabricated using a combination of photolithographic and chemical assembling processes. Unlike the patterned SWNT arrays reported thus far, these SWNT patterned layers have high-density multilayer structures and excellent surface adhesion due to their direct chemical bonding to their substrates, which results in high electrical conductivity. We found that the high-density multilayer SWNT patterns emit electrons under an applied electrical field. The electrical resistivities of the SWNT layers were found to be 5–10Ωcm, with a turn-on electric field of about 3V∕μm at an emission current density of 10μA∕cm2. This technique for fabricating SWNT patterns can be used in the production of field-emission displays and in future device integration requiring carbon nanotubes (CNTs), because it provides large-area patterning of SWNTs with high stability and uniformity.
Transient observation of extended x-ray absorption fine structure in laser-melted Si by using femtosecond laser-produced-plasma soft x ray
Authors: Oguri Katsuya , Okano Yasuaki , Nishikawa Tadashi , Nakano Hidetoshi
Published: August 2005

We have demonstrated the time-resolved measurement of the extended x-ray absorption fine structure (EXAFS) in laser-melted Si foil by using a pump-probe absorption spectroscopy system that utilizes a femtosecond laser-produced-plasma soft x-ray source. By using 100-fs laser irradiation, we observed the transient change in the Si L-edge EXAFS, that is, a slight shortening of its oscillation period and a decrease in its oscillation amplitude. This result suggests that the Si-Si atomic distance expanded and structural disordering occurred as a result of the production of liquid Si.
Tensile strained Ge p-i-n photodetectors on Si platform for C and L band telecommunications
Authors: Liu Jifeng , Cannon Douglas D. , Wada Kazumi , Ishikawa Yasuhiko , Jongthammanurak Samerkhae , Danielson David T. , Michel Jurgen , Kimerling Lionel C.
Published: August 2005

We demonstrate a 0.25% tensile strained Ge p-i-n photodetector on Si platform that effectively covers both C and L bands in telecommunications. The direct band edge of the Ge film has been pushed from 1550 to 1623 nm with 0.25% tensile strain, enabling effective photon detection in the whole L band. The responsivities of the device at 1310, 1550, and 1620 nm are 600, 520, and 100mA∕W under 0 V bias, which can be further improved to 980, 810, and 150mA∕W with antireflection coating based on calculations. Therefore, the device covers the whole wavelength range used in telecommunications. The responsivities at 1310 and 1550 nm are comparable to InGaAs photodetectors currently used in telecommunications. In the spectrum range of 1300–1650 nm, maximum responsivity was already achieved at 0 V bias because carrier transit time is much shorter than carrier recombination life time, leading to ∼100% collection efficiency even at 0 V bias. This is a desirable feature for low voltage operation. The absorption coefficients of 0.25% tensile strained Ge in the L band have been derived to be nearly an order of magnitude higher than bulk Ge. The presented device is compatible with conventional Si processing, which enables monolithic integration with Si circuitry.
Reactions on cell membranes: Comparison of continuum theory and Brownian dynamics simulations
Authors: Monine Michael I. , Haugh Jason M.
Published: August 2005

Biochemical transduction of signals received by living cells typically involves molecular interactions and enzyme-mediated reactions at the cell membrane, a problem that is analogous to reacting species on a catalyst surface or interface. We have developed an efficient Brownian dynamics algorithm that is especially suited for such systems and have compared the simulation results with various continuum theories through prediction of effective enzymatic rate constant values. We specifically consider reaction versus diffusion limitation, the effect of increasing enzyme density, and the spontaneous membrane association/dissociation of enzyme molecules. In all cases, we find the theory and simulations to be in quantitative agreement. This algorithm may be readily adapted for the stochastic simulation of more complex cell signaling systems.
Absolute solvation free energy of Li+ and Na+ ions in dimethyl sulfoxide solution: A theoretical ab initio and cluster-continuum model study
Authors: Westphal Eduard , Pliego Josefredo R.
Published: August 2005

The solvation of the lithium and sodium ions in dimethyl sulfoxide solution was theoretically investigated using ab initio calculations coupled with the hybrid cluster-continuum model, a quasichemical theory of solvation. We have investigated clusters of ions with up to five dimethyl sulfoxide (DMSO) molecules, and the bulk solvent was described by a dielectric continuum model. Our results show that the lithium and sodium ions have four and five DMSO molecules into the first coordination shell, and the calculated solvation free energies are −135.5 and −108.6kcalmol−1, respectively. These data suggest a solvation free energy value of −273.2kcalmol−1 for the proton in dimethyl sulfoxide solution, a value that is more negative than the present uncertain experimental value. This and previous studies on the solvation of ions in water solution indicate that the tetraphenylarsonium tetraphenylborate assumption is flawed and the absolute value of the free energy of transfer of ions from water to DMSO solution is higher than the present experimental values.
A density-functional approach to polarizable models: A Kim-Gordon response density interaction potential for molecular simulations
Authors: Tabacchi Gloria , Hutter Jürg , Mundy Christopher J.
Published: August 2005

A combined linear-response–frozen electron-density model has been implemented in a molecular-dynamics scheme derived from an extended Lagrangian formalism. This approach is based on a partition of the electronic charge distribution into a frozen region described by Kim-Gordon theory [J. Chem. Phys. 56, 3122 (1972); J. Chem. Phys. 60, 1842 (1974)] and a response contribution determined by the instantaneous ionic configuration of the system. The method is free from empirical pair potentials and the parametrization protocol involves only calculations on properly chosen subsystems. We apply this method to a series of alkali halides in different physical phases and are able to reproduce experimental structural and thermodynamic properties with an accuracy comparable to Kohn-Sham density-functional calculations.
Theoretical formalism and experimental verification of line shapes of NMR intermolecular multiple-quantum coherence spectra
Authors: Zheng Bingwen , Chen Zhong , Cai Shuhui , Zhong Jianhui , Ye Chaohui
Published: August 2005

Although the theories and potential applications of intermolecular multiple-quantum coherences (iMQCs) have been under active investigations for over a decade, discussion of iMQC NMR signal formation was mainly confined in the time domain. In this paper, a full line-shape theory was developed to describe iMQC signals in the frequency domain. Relevant features of the line shape, such as peak height, linewidth, and phase, were investigated in detail. Predictions based on the theory agree well with experimental and simulated results. Since radiation-damping effects always couple with iMQCs in highly polarized liquid-state NMR systems, and strongly radiation-damped signals have many spectral characteristics similar to those of iMQCs, a detailed comparison was also made between them from different spectral aspects. With detailed comparison of peak height, linewidth, and phase, this work demonstrates that the iMQC and radiation-damping phenomena result from two completely different physical mechanisms despite that both present similar signal features and coexist in highly polarized liquid-state NMR systems.
Active-space coupled-cluster study of electronic states of Be3
Authors: Kowalski Karol , Hirata So , Włoch Marta , Piecuch Piotr , Windus Theresa L.
Published: August 2005

The active-space coupled-cluster (CC) and equation-of-motion (EOM) CC methods with all single and double excitations with triple excitations defined via active orbitals (CCSDt, EOMCCSDt), as implemented with TENSOR CONTRACTION ENGINE, are applied to the challenging Be3 system, which is characterized by a large number of low-lying excited states dominated by two-electron transitions and significant high-order correlation effects in the ground electronic state. It is demonstrated that the CCSDt and EOMCCSDt methods provide an excellent description of complicated electronic quasidegeneracies present in the Be3 cluster. Different strategies for defining triple excitations within the CCSDt∕EOMCCSDt approach are discussed.
Intraband relaxation in CdSe nanocrystals and the strong influence of the surface ligands
Authors: Guyot-Sionnest Philippe , Wehrenberg Brian , Yu Dong
Published: August 2005

The intraband relaxation between the 1Pe and 1Se state of CdSe colloidal quantum dots is studied by pump-probe time-resolved spectroscopy. Infrared pump-probe measurements with ∼6-ps pulses show identical relaxation whether the electron has been placed in the 1Se state by above band-gap photoexcitation or by electrochemical charging. This indicates that the intraband relaxation of the electrons is not affected by the photogenerated holes which have been trapped. However, the surface ligands are found to strongly affect the rate of relaxation in colloid solutions. Faster relaxation (<8ps) is obtained with phosphonic acid and oleic acid ligands. Alkylamines lead to longer relaxation times of ∼10ps and the slowest relaxation is observed for dodecanethiol ligands with relaxation times ∼30ps. It is concluded that, in the absence of holes or when the holes are trapped, the intraband relaxation is dominated by the surface and faster relaxation correlates with larger interfacial polarity. Energy transfer to the ligand vibrations may be sufficiently effective to account for the intraband relaxation rate.
Infrared spectra of O2−∙(CO2)n clusters (n=1–6): Asymmetric docking at the π* orbital
Authors: Schneider Holger , Boese A. Daniel , Weber J. Mathias
Published: August 2005

Isolated superoxide ions solvated by CO2 have been studied by infrared photodissociation spectroscopy and density-functional theory, using CO2 evaporation upon infrared excitation of the O2−∙(CO2)n (n=1–6) parent ions. We can assign the observed frequencies to the asymmetric stretch vibration and its combination bands with the symmetric stretch and the overtone of the bending vibration of CO2 in various binding situations. We interpret our findings with the help of density-functional theory. Our data suggest that only one CO2 moiety binds strongly to the O2−, whereas the rest of the CO2 molecules are weakly bound, which is consistent with the experimental spectra. The lobes of the π* orbital of O2− provide a template for the structure of the microsolvation environment.
Homonuclear transition-metal trimers
Authors: Papas Brian N. , Schaefer Henry F.
Published: August 2005

Density-functional theory has been used to determine the ground-state geometries and electronic states for homonuclear transition-metal trimers constrained to equilateral triangle geometries. This represents the first application of consistent theoretical methods to all of the ten 3d block transition-metal trimers, from scandium to zinc. A search of the potential surfaces yields the following electronic ground states and bond lengths: Sc3(A1′2,2.83Å), Ti3(E′7,2.32Å), V3(E″2,2.06Å), Cr3(E′17,2.92Å), Mn3(A2′16,2.73Å), Fe3(E″11,2.24Å), Co3(E″6,2.18Å), Ni3(A2″3,2.23Å), Cu3(E′2,2.37Å), and Zn3(A1′1,2.93Å). Vibrational frequencies, several low-lying electronic states, and trends in bond lengths and atomization energies are discussed. The predicted dissociation energies ΔE(M3→M2+M) are 49.4kcalmol−1(Sc3), 64.3kcalmol−1(Ti3), 60.7kcalmol−1(V3), 11.5kcalmol−1(Cr3), 32.4kcalmol−1(Mn3), 61.5kcalmol−1(Fe3), 78.0kcalmol−1(Co3), 86.1kcalmol−1(Ni3), 26.8kcalmol−1(Cu3), and 4.5kcalmol−1(Zn3).
Exit-channel dynamics in barrierless unimolecular reactions: Criteria of vibrational adiabaticity
Authors: Pavlov-Verevkin V. B. , Lorquet J. C.
Published: August 2005

Conversion of translational into vibrational energy during the last step of a unimolecular reaction is brought about by the curvature of the reaction path. The corresponding coupling is analyzed by an angle-action reaction path Hamiltonian (RPH). The accuracy of the vibrational adiabatic approximation is found to be completely independent of the shape of the potential energy V(s). Vibrations are adiabatic when two independent dimensionless parameters are small. The first one, denoted as σ, controls the dynamic coupling. The physical significance of the condition σ⪡1 is that the amplitude of the vibrations normal to the reaction path should be much smaller than the radius of curvature of the reaction path. The second parameter, denoted as μ, governs the static coupling. It results from the dependence of the vibrational frequency ω on the reaction coordinate s. The higher ω, the lower its derivative with respect to s and, more unexpectedly, the higher the translational energy ε, the lower μ is. A criterion for locating a particular dividing surface in barrierless reactions is proposed. This surface separates two regions of space: one where energy flows freely, and one where energy conversion between translation and vibration is hindered by adiabatic invariance. The nature of the dynamical constraint that prevents the product translational energy distribution from being fully statistical can be identified by a maximum entropy analysis. The constraint is found to bear on the translational momentum ps, i.e., on the square root of the translational energy ε1∕2. This can be understood by applying Jacobi’s form of the least action principle to the vibrationally adiabatic RPH.
Correlation between the performance of double-barrier quantum-well infrared photodetectors and their microstructure: On the origin of the photovoltaic effect
Authors: Luna E. , Trampert A. , Guzmán A. , Calleja E.
Published: August 2005

In this work we show clear evidences that silicon segregation out of quantum wells (QWs) is the mechanism responsible for the unexpected photovoltaic (PV) effect exhibited by AlGaAs∕AlAs∕GaAs double-barrier quantum-well infrared photodetectors. Our results are based on the combined analysis of the detectors’ microstructure [obtained by transmission electron microscopy (TEM)] and their electro-optical characteristics (dark current and responsivity versus bias). A TEM image intensity analysis yields the result of an unintentional asymmetry between the two AlAs barriers adjacent to the QW attributed to the presence of segregated Si at the interface. Moreover, we find that the higher this compositional asymmetry, the higher the asymmetries in the electro-optical response of the detector. Additionally we show here direct evidences of how the growth-induced nonequivalence of the AlAs tunnel barriers can be ruled out as the origin of the PV effect.
Monte Carlo simulation and self-consistent integral equation theory for polymers in quenched random media
Authors: Sung Bong June , Yethiraj Arun
Published: August 2005

The conformational properties and static structure of freely jointed hard-sphere chains in matrices composed of stationary hard spheres are studied using Monte Carlo simulations and integral equation theory. The simulations show that the chain size is a nonmonotonic function of the matrix density when the matrix spheres are the same size as the monomers. When the matrix spheres are of the order of the chain size the chain size decreases monotonically with increasing matrix volume fraction. The simulations are used to test the replica-symmetric polymer reference interaction site model (RSP) integral equation theory. When the simulation results for the intramolecular correlation functions are input into the theory, the agreement between theoretical predictions and simulation results for the pair-correlation functions is quantitative only at the highest fluid volume fractions and for small matrix sphere sizes. The RSP theory is also implemented in a self-consistent fashion, i.e., the intramolecular and intermolecular correlation functions are calculated self-consistently by combining a field theory with the integral equations. The theory captures qualitative trends observed in the simulations, such as the nonmonotonic dependence of the chain size on media fraction.
Structures and rearrangement reactions of 4-aminophenol(H2O)1+ and 3-aminophenol(H2O)1+ clusters
Authors: Gerhards M. , Jansen A. , Unterberg C. , Gerlach A.
Published: August 2005

In this paper the structures of 4-aminophenol(H2O)1+ and 3-aminophenol(H2O)1+ clusters are investigated in molecular beam experiments by different IR/UV-double resonance techniques as well as the mass analyzed threshold ionization spectroscopy yielding both inter- and intramolecular vibrations of the ionic and neutral species. Possible structures are extensively calculated at the level of density functional theory (DFT) or at the ab initio level of theory. From the experimental and theoretical investigations it can be concluded that in the case of 4-aminophenol(H2O)1 one OH⋯O hydrogen-bonded structure exists in the neutral cluster but two structures containing either an OH⋯O or a NH⋯O hydrogen-bonded arrangement are observed in the spectra of the ionic species. This observation is a result of an intramolecular rearrangement reaction within the ion which can only take place if high excess energies are used. A reaction path via the CH bonds is calculated and explains the experimental observations. In the case of 3-aminophenol(H2O)1+ only one OH⋯O bound structure is observed both in the neutral and ionic species. Ab initio and DFT calculations show that due to geometrical and energetical reasons a rearrangement cannot be observed in the 3-aminophenol(H2O)1+ cluster ion.
New all-fiber velocimeter
Authors: Weng Jidong , Tan Hua , Hu Shaolou , Ma Yun , Wang Xiang
Published: August 2005

A new all-fiber velocity interferometer system for any reflector (AFVISAR) was developed. It was conceived and realized with the purpose of using it as the basic measuring element of a complete system for multiple point velocity measurements. Its main features are that it works at 532nm and partly adopts the multimode optical fiber. The velocimeter consists of only fibers or fiber coupled components and has no optic elements such as optic lenses or reflectors. It is therefore very compact and easy to operate. Unlike the conventional AFVISAR, which uses single-mode optic fiber components, the laser beam in this new interferometer system arrives at and reflects from the target surface through a multimode optical fiber component, and then enters and interferes in a [3×3] single-mode fiber coupler. Its working principle is elaborated on in this article. Preliminary experiments using a split Hopkins pressure bar (SHPB) device show that the new interferometer can successfully measure the velocity profiles of the metal specimen along the axial or radial direction. Further experiments on a one-stage gas gun are under consideration.
Evidence of a strong magnetic effect on the impedance of integrated piezoelectric resonators
Authors: Maglione M. , Zhu W. , Wang Z. H.
Published: August 2005

In the vicinity of their resonance frequency, piezoelectric resonators are highly sensitive to small perturbations. The present report is focused on the magnetic field as a perturbation source. Magnetocapacitance modulation of more than 5% is achieved at room temperature on both ferroelectric single crystals and quartz disks. Since such piezoelectric resonators are now available as membranes directly integrated on a silicon wafer, we have checked the magnetocapacitance modulation in such resonators. We show here that a moderate magnetic field of 2×104 Oersteds is able to efficiently tune the impedance of these resonators in their resonance window.
Swelling of Na∕Mg-montmorillonites and hydration of interlayer cations: A Monte Carlo study
Authors: Meleshyn Artur , Bunnenberg Claus
Published: August 2005

While the swelling behavior of laboratory-prepared homoionic montmorillonites has been studied extensively in numerous experimental and simulation works, far less attention has been given to much more abundant natural montmorillonites, containing a mix of monovalent and/or bivalent cations in interlayer spaces. We carried out a series of Monte Carlo simulations in order to investigate the reasons for the remarkable difference of experimental swelling patterns of a natural Na-rich/Mg-poor montmorillonite and a homoionic Na-montmorillonite. The simulations reproduced the swelling pattern of a natural montmorillonite, suggesting a mechanism of its hydration different from that of the homoionic montmorillonite. We also found that the differences in size and hydration energy of Mg2+ and Na+ ions have strong implications for the structure and the internal energy of interlayer water. This leads to a difference in the layer spacings of the simulated Mg- and Na-montmorillonites as large as ∼2.1Å at lower water contents.
Reactions and luminescence in passivated Si nanocrystallites induced by vacuum ultraviolet and soft-x-ray photons
Authors: Chao Y. , Krishnamurthy S. , Montalti M. , Lie L. H. , Houlton A. , Horrocks B. R. , Kjeldgaard L. , Dhanak V. R. , Hunt M. R. C. , Šiller L.
Published: August 2005

Alkyl-modified silicon nanocrystallites are efficient fluorophores which are of interest for fundamental spectroscopic studies and as luminescent probes in biology because of their stability in aqueous media. In this work we have investigated these particles using scanning tunneling microscopy, synchrotron-radiation excited photoemission, and x-ray excited optical luminescence (XEOL). During the course of illumination with 145-eV photons we have monitored the evolution of the Si2p core level and, in samples which have suffered prolonged atmospheric exposure, observed in real time the growth of an extra Si2p component attributed to in situ photoinduced oxidation of the Si nanocrystallites. XEOL reveals that two emission bands are active upon soft-x-ray photon excitation and that photoluminescence intensity decreases with photon exposure, which is attributed to charge trapping within the film.
Versatile low-temperature atomic force microscope with in situ piezomotor controls, charge-coupled device vision, and tip-gated transport measurement capability
Authors: Lee Jhinhwan , Chae Jungseok , Kim Chung Koo , Kim Hyunjin , Oh Seungeun , Kuk Young
Published: August 2005

A versatile cryogenic (5 K) ultrahigh-vacuum (UHV) atomic force microscope (AFM) with tip-gated transport measurement capability has been developed. Using high-resolution (<1.5μm) plan-view charge-coupled device (CCD) optics, and three planar piezomotors we achieved visually guided in situ alignments of a sample position with respect to the AFM tip, and the laser beam position with respect to the cantilever and the quadrant photodiode. We made optical fiber feedthroughs and a laser lens assembly to bring external laser light and CCD illuminating light onto the cantilever and the sample. A sample holder with an embedded temperature sensor and eight transport electrodes is detachably mounted on a piezotube scanner. The generic cantilever mount can be easily replaced with a tuning-fork mount or a piezoresistive cantilever mount for experiments where stray laser light should be avoided. To our knowledge, this is the first Dewar-immersion type cryogenic AFM with laser beam deflection sensing capability and high-resolution plan-view CCD optics.
Modulation transfer function and detective quantum efficiency of electron bombarded charge coupled device detector for low energy electrons
Authors: Horáček Miroslav
Published: August 2005

The use of a thinned back-side illuminated charge coupled device chip as two-dimensional sensor working in direct electron bombarded mode at optimum energy of the incident signal electrons is demonstrated and the measurements of the modulation transfer function (MTF) and detective quantum efficiency (DQE) are described. The MTF was measured for energy of electrons 4keV using an edge projection method and a stripe projection method. The decrease of the MTF for a maximum spatial frequency of 20.8cycles∕mm, corresponding to the pixel size 24×24μm, is 0.75≈−2.5dB, and it is approximately the same for both horizontal and vertical directions. DQE was measured using an empty image and the mixing factor method. Empty images were acquired for energies of electrons from 2to5keV and for various doses, ranging from nearly dark image to a nearly saturated one. DQE increases with increasing energy of bombarded electrons and reaches 0.92 for electron energy of 5keV. For this energy the detector will be used for the angle- and energy-selective detection of signal electrons in the scanning low energy electron microscope.
Characterization of remote inductively coupled CH4–N2 plasma for carbon nitride thin-film deposition
Authors: Seo Hyungtak , Kim Jung-Hyung , Chung Kwang-Hwa , Kim Ju Youn , Kim Seok Hoon , Jeon Hyeongtag
Published: August 2005

We investigated reaction characteristics in a CH4∕N2 plasma for deposition of amorphous CNx thin films (a-CNx) by evaluating the change in electron density using the wave cutoff method, and the behavior of ions and radicals with an optical emission spectroscopy (OES). An inductively coupled plasma source that was 30cm away from the substrate stage was used for the discharge. The change in electron density in the substrate region and OES spectra in the plasma-source region were evaluated to investigate both the reaction mechanism and the remote effect while varying process conditions such as rf power, pressure, and gas-mixing ratio. We found that the electron density in the remote CH4∕N2 plasma was closely related to recombination reactions of major ions such as N2+, CH4+, CH3+, and H2+ during diffusion from the plasma source to the substrate. The electron density and optical emission of major ions and radicals in the CH4∕N2 plasma increase at higher rf power. The ratio [N]∕([N]+[C]) in a-CNx films, as measured by auger electron spectroscopy, also increases with rf power since more excited N and C species are generated. For increasing pressure, the change in electron density and emission spectra showed different behavior, which arose from recombination of ions that generated more CH4, Nx (x=1,2), and CN radicals. The majority of positive ions generated from N2 species are greatly affected by the remote effect, while the majority of positive ions generated from CH4 species are not significantly influenced, since each species has different losses dependent on the pressure. A higher N2 gas fraction in the gas mixture generated more CN radicals, which resulted not only in more N incorporated into a-CNx films but also to a reduction of H passivation that retards formation of hybrid bonding between C and N in the films. These results suggest that efficient H abstraction is required to achieve more NC triple bonding in CH4∕N2 plasma deposition.
Breaking the diffraction limit with dynamic saturation optical microscopy
Authors: Enderlein Jörg
Published: August 2005

A scheme of fluorescence microscopy is proposed allowing the breaking of the diffraction limit of optical microscopy by a factor of four to five. It relies on fast temporal measurements of the fluorescence decay after sudden switch-on of the light excitation. The observed temporal dynamics of the fluorescence signal can be converted into information about the spatial distribution of fluorophores within the exciting laser focus. The proposed scheme is technically simple, allows resolution enhancement in three dimensions, and will be robust with respect to small optical aberrations as caused by refractive index variations in real samples.
p
-type conduction in wide-gap Zn1−xMgxO films grown by ultrasonic spray pyrolysis
Authors: Zhang X. , Li X. M. , Chen T. L. , Zhang C. Y. , Yu W. D.
Published: August 2005

p -type Zn1−xMgxO films doped with N and Al have been deposited by means of introducing Mg into p-type N- and Al-doped ZnO films using ultrasonic spray pyrolysis (USP) method. The structure of the films is confirmed by x-ray diffraction. Hall-effect measurements indicate that the p-type Zn1−xMgxO film shows a low resistivity of 6.4×10−2Ωcm, high mobility of 11.7cm2∕Vs and high carrier concentration of 8.31×1018cm−3 at room temperature. Furthermore, the optical absorption edge and photoluminescence (PL) peak of p-type Zn1−xMgxO film shift to a shorter wavelength of 356nm while maintaining excellent electrical performances. The blueshift extent of the film based on p-type ZnO film was not as distinct as compared to that of Zn1−xMgxO film based on pure ZnO film, perhaps owing to the variations in the effectiveness of Mg incorporation in the p-type Zn1−xMgxO film and in the Zn1−xMgxO film.
Characterization of oxide precipitates in epitaxial InN by transmission electron microscopy
Authors: Xu X. , Specht P. , Armitage R. , Ho J. C. , Weber E. R. , Kisielowski C.
Published: August 2005

InN thin films have been grown epitaxially on GaN-buffered sapphire substrates by molecular-beam epitaxy at 500°C. A high level of oxygen contamination in the growth chamber led to formation of In2O3 precipitates in the films. These precipitates were characterized in detail by transmission electron microscopy (TEM). The concentration of In2O3 was estimated to be less than 0.07vol% in the present samples of oxygen content ∼0.5at.%. Cross-sectional TEM investigations revealed that the precipitates adopt a preferred crystallographic orientation within the InN matrix, and show a characteristic diameter of ∼5nm with average distance of ∼500nm. These observations suggest the effective solubility of O in InN could be below 1at.% at 500°C.
Control of injected carriers in tetracyano-p-quinodimethane encapsulated carbon nanotube transistors
Authors: Shiraishi Masashi , Nakamura Shuichi , Fukao Tomohiro , Takenobu Taishi , Kataura Hiromichi , Iwasa Yoshihiro
Published: August 2005

We examined transistor characteristics of tetracyano-p-quinodimethane encapsulated single-walled carbon nanotubes (TCNQ@SWNTs). In device operations, a clear conversion to a p-type character was observed and the stability of carriers, previously doped into SWNTs, were simultaneously clarified. Because of an energy band shift, between the electrodes and the doped SWNTs induced by the doping, electron injection was achieved only by application of a high source-drain voltage, while holes were easily injected because of decrease in hole barrier height.