bluuebunny/crossref_metadata_2025 huggingface dataset:
Biochemical dysfunction in heart mitochondria exposed to ischaemia and reperfusion
Authors: Solaini Giancarlo , Harris David A.
Published: August 2005

Heart tissue is remarkably sensitive to oxygen deprivation. Although heart cells, like those of most tissues, rapidly adapt to anoxic conditions, relatively short periods of ischaemia and subsequent reperfusion lead to extensive tissue death during cardiac infarction. Heart tissue is not readily regenerated, and permanent heart damage is the result. Although mitochondria maintain normal heart function by providing virtually all of the heart's ATP, they are also implicated in the development of ischaemic damage. While mitochondria do provide some mechanisms that protect against ischaemic damage (such as an endogenous inhibitor of the F1Fo-ATPase and antioxidant enzymes), they also possess a range of elements that exacerbate it, including ROS (reactive oxygen species) generators, the mitochondrial permeability transition pore, and their ability to release apoptotic factors. This review considers the process of ischaemic damage from a mitochondrial viewpoint. It considers ischaemic changes in the inner membrane complexes I–V, and how this might affect formation of ROS and high-energy phosphate production/degradation. We discuss the contribution of various mitochondrial cation channels to ionic imbalances which seem to be a major cause of reperfusion injury. The different roles of the H+, Ca2+ and the various K+ channel transporters are considered, particularly the K+ATP (ATP-dependent K+) channels. A possible role for the mitochondrial permeability transition pore in ischaemic damage is assessed. Finally, we summarize the metabolic and pharmacological interventions that have been used to alleviate the effects of ischaemic injury, highlighting the value of these or related interventions in possible therapeutics.
Characterization of the ATPase activity of topoisomerase II from Leishmania donovani and identification of residues conferring resistance to etoposide
Authors: Sengupta Tanushri , Mukherjee Mandira , Das Aditi , Mandal Chhabinath , Das Rakhee , Mukherjee Tanmoy , Majumder Hemanta K.
Published: August 2005

We have cloned and expressed the 43 kDa N-terminal domain of Leishmania donovani topoisomerase II. This protein has an intrinsic ATPase activity and obeys Michaelis–Menten kinetics. Cross-linking studies indicate that the N-terminal domain exists as a dimer both in the presence and absence of nucleotides. Etoposide, an effective antitumour drug, traps eukaryotic DNA topoisomerase II in a covalent complex with DNA. In the present study, we report for the first time that etoposide inhibits the ATPase activity of the recombinant N-terminal domain of L. donovani topoisomerase II. We have modelled the structure of this 43 kDa protein and performed molecular docking analysis with the drug. Mutagenesis of critical amino acids in the vicinity of the ligand-binding pocket reveals less efficient inhibition of the ATPase activity of the enzyme by etoposide. Taken together, these results provide an insight for the development of newer therapeutic agents with specific selectivity.
HIV-1 Nef regulates the release of superoxide anions from human macrophages
Authors: Olivetta Eleonora , Pietraforte Donatella , Schiavoni Ilaria , Minetti Maurizio , Federico Maurizio , Sanchez Massimo
Published: August 2005

The NADPH oxidase enzymatic complex participates in the oxidative burst by producing ROS (reactive oxygen species). Altered levels of ROS production may have pathogenetic implications due to the loss of some innate immune functions such as oxidative burst and phagocytosis. Considering that HIV-1 Nef protein plays a primary role in AIDS pathogenesis, by affecting the immune system, we sought to dissect possible effects of Nef on the release of superoxide anions. We show here that the inducible expression of Nef in human phagocytic cells modulates the superoxide release in a biphasic manner. In particular, an early Nef-induced increase of the superoxide release was followed by a dramatic decrease starting from 10 h after the Nef induction. This was observed whatever the presence of cell activators such as GM-CSF (granulocyte/macrophage colony-stimulating factor) or fMLP (N-formyl-L-methionyl-L-leucyl-L-phenylalanine). Whereas the early increase in superoxide release is probably the result of the already described Nef-dependent activation of PAK-2 (p21-activated kinase 2)–Rac2, we were interested in investigating the mechanisms underlying the late inhibition of superoxide release observed originally. In this regard, we individuated at least three independent requirements for the Nef-induced blockade of superoxide release: (i) the active protein synthesis; (ii) both the membrane localization and the interaction with endocytotic machinery of Nef; and (iii) the release of soluble factor(s). Moreover, we observed that IL-10 (interleukin-10) inhibits superoxide release, whereas its depletion restored NADPH oxidase activity. We propose that the cell membrane-to-lysosome Nef transit leads to the synthesis and release of soluble factor(s) and, among them, IL-10 might significantly contribute to the inhibition of NAPDH oxidase activity.
Cytoprotection by glycine against ATP-depletion-induced injury is mediated by glycine receptor in renal cells
Authors: Pan Chao , Bai Xiaoming , Fan Leming , Ji Yong , Li Xiaoyu , Chen Qi
Published: August 2005

It is known that glycine protects mammalian cells against ischaemic cell injury by preventing cellular membrane leakage. However, the molecular mechanisms have not yet been clearly elucidated. The purpose of the present study was to clarify whether GlyR (glycine receptor) acts as a key mediator in cytoprotection of glycine. cDNA encoding human GlyRα1 (α1-subunit of glycine receptor) was transfected into HEK-293 cells. The membrane integrity of the cells with or without GlyRα1 was examined by the uptake of marker compounds, the release of LDH (lactate dehydrogenase) and the exclusion of Trypan Blue. Glycine prevented the permeability of 70 kDa dextrans and 140 kDa LDH in the cells in which GlyR was expressed under conditions of ATP depletion. The inhibition of endogenous GlyR expression by RNA interference attenuated the cytoprotection by glycine. Furthermore, the mutation of Tyr202 to phenylalanine in GlyRα1 blocked the glycine-mediated cytoprotection, while the mutation of Tyr202 to leucine abolished the cytoprotection by strychnine. Our results suggested that the cytoprotection of glycine against ATP-depletion-induced injury might be mediated by GlyR.
The human D-glucuronyl C5-epimerase gene is transcriptionally activated through the β-catenin–TCF4 pathway
Authors: Ghiselli Giancarlo , Agrawal Amit
Published: August 2005

Heparan sulphate (HS) is a ubiquitous constituent of the extracellular matrix that is required for the biological activity of circulating soluble and insoluble extracellular ligands. GLCE (D-glucuronyl C5-epimerase), an enzyme responsible for the epimerization of D-glucuronic acid into L-iduronic acid of HS, endows the nascent polysaccharide chain with the ability to bind to growth factors and cytokines. In order to examine the mechanism of regulation of GLCE expression, the functional organization of the human GLCE gene promoter has been investigated. Studies utilizing stepwise deleted and site-directed mutagenized promoter constructs have shed light on the functional relevance of two cis-acting binding elements for the β-catenin–TCF4 complex (where TCF4 stands for T-cell factor 4) that are located in the enhancer region of the promoter. The ability of the putative binding sequences to bind the β-catenin–TCF4 complex has been confirmed through electrophoretic mobility-shift and supershift analyses. We have found that, in a set of human colon carcinoma cell lines, the expression of GLCE correlates with the degree of activation of the β-catenin–TCF4 transactivation complex. Furthermore, the ectopic expression of β-catenin–TCF4 in cells that constitutively express low levels of the transactivation complex produces a significant increase of GLCE transcript level and, at the same time, enhances the rate of D-glucuronic acid epimerization in HS. The data obtained are consistent with the idea that the β-catenin–TCF4 transactivation pathway plays a major role in modulating GLCE expression, thus contributing to the regulation of HS biosynthesis and its structural organization.
Effect of Na+ binding on the conformation, stability and molecular recognition properties of thrombin
Authors: De Filippis Vincenzo , De Dea Elisa , Lucatello Filippo , Frasson Roberta
Published: August 2005

In the present work, the effect of Na+ binding on the conformational, stability and molecular recognition properties of thrombin was investigated. The binding of Na+ reduces the CD signal in the far-UV region, while increasing the intensity of the near-UV CD and fluorescence spectra. These spectroscopic changes have been assigned to perturbations in the environment of aromatic residues at the level of the S2 and S3 sites, as a result of global rigidification of the thrombin molecule. Indeed, the Na+-bound form is more stable to urea denaturation than the Na+-free form by ∼2 kcal/mol (1 cal≡4.184 J). Notably, the effects of cation binding on thrombin conformation and stability are specific to Na+ and parallel the affinity order of univalent cations for the enzyme. The Na+-bound form is even more resistant to limited proteolysis by subtilisin, at the level of the 148-loop, which is suggestive of the more rigid conformation this segment assumes in the ‘fast’ form. Finally, we have used hirudin fragment 1–47 as a molecular probe of the conformation of thrombin recognition sites in the fast and ‘slow’ form. From the effects of amino acid substitutions on the affinity of fragment 1–47 for the enzyme allosteric forms, we concluded that the specificity sites of thrombin in the Na+-bound form are in a more open and permissible conformation, compared with the more closed structure they assume in the slow form. Taken together, our results indicate that the binding of Na+ to thrombin serves to stabilize the enzyme into a more open and rigid conformation.
A role for tumour necrosis factor α in human small bowel iron transport
Authors: Sharma Naveen , Laftah Abas H. , Brookes Matthew J. , Cooper Brian , Iqbal Tariq , Tselepis Chris
Published: August 2005

Cytokines are integral to the development of anaemia of chronic inflammation. Cytokines modulate hepcidin expression and iron sequestration by the reticuloendothelial system but their direct effects on small bowel iron transport are not well characterized. The aim of the present study was to examine the local effects of TNFα (tumour necrosis factor α) on small bowel iron transport and on iron transporter expression in the absence of hepcidin. The effects of TNFα on iron transport were determined using radiolabelled iron in an established Caco-2 cell model. The effect of TNFα on the expression and localization of the enterocyte iron transporters DMT-1 (divalent metal transporter 1), IREG-1 (iron-regulated transporter 1) and ferritin was determined utilizing Caco-2 cells and in a human ex vivo small bowel culture system. TNFα mediated an early induction in both iron import and iron export, which were associated with increased DMT-1 and IREG-1 mRNA and protein expression (P<0.05). However, by 24 h, both iron import and iron export were significantly inhibited, coinciding with an induction of ferritin heavy chain (P<0.05) and a decrease in DMT-1 and IREG-1 to baseline levels. In addition, there was a relocalization of IREG-1 away from the basolateral cell border and increased iron deposition in villous enterocytes. In conclusion, TNFα has a direct effect on small bowel iron transporter expression and function, leading to an inhibition of iron transport.
Cloning and characterization of the human glutathione synthetase 5′-flanking region
Authors: Lee Taunia D. , Yang Heping , Whang Janet , Lu Shelly C.
Published: August 2005

GSH synthesis occurs through a two-step enzymatic reaction driven by GCL (glutamate–cysteine ligase; made up of catalytic and modifying subunits) and GSS (glutathione synthetase). In humans, oxidative stress regulates GCL expression in an antioxidant response element-dependent manner via Nrf2 [NFE (nuclear factor erythroid)-related factor 2]. In the rat, GSS and GCL are regulated co-ordinately by oxidative stress, and induction of GSS further increases GSH synthetic capacity. Transcriptional regulation of the human GSS has not been examined. To address this, we have cloned and characterized a 2.2 kb 5′-flanking region of the human GSS. The transcriptional start site is located 80 nt upstream of the translation start site. The human GSS promoter efficiently drove luciferase expression in Chang cells. Overexpression of either Nrf1 or Nrf2 induced the GSS promoter activity by 130 and 168% respectively. Two regions homologous to the NFE2 motif are demonstrated to be important for basal expression of human GSS, as mutation of these sites reduced the promoter activity by 66%. Nrf1, Nrf2 and c-Jun binding to these NFE2 sites under basal conditions was demonstrated using chromatin immunoprecipitation assays. In summary, two NFE2 sites in the human GSS promoter play important roles in the basal expression of GSS and, similar to the GCL subunits, the human GSS gene expression is also regulated by Nrf2.
Effects of nitroglycerin/L-cysteine on soluble guanylate cyclase: evidence for an activation/inactivation equilibrium controlled by nitric oxide binding and haem oxidation
Authors: Gorren Antonius C. F. , Russwurm Michael , Kollau Alexander , Koesling Doris , Schmidt Kurt , Mayer Bernd
Published: August 2005

GTN (nitroglycerin; glycerol trinitrate) causes dilation of blood vessels via activation of nitric oxide (NO)-sensitive sGC (soluble guanylate cyclase), a heterodimeric haem protein that catalyses the conversion of GTP into cGMP. Activation of sGC by GTN requires enzymatic or non-enzymatic bioactivation of the nitrate. Based on insufficient NO release and lack of spectroscopic evidence for formation of NO–sGC, the cysteine (Cys)-dependent activation of sGC by GTN was proposed to occur in an NO-independent manner. This extraordinary claim is questioned by the present findings. First, the effect of GTN/Cys was blocked by the NO scavenger oxyhaemoglobin, the superoxide-generating compound flavin mononucleotide and the haem-site sGC inhibitor ODQ (1H-[1,2,4]oxadiazolo[4,3-a]quinoxalin-1-one). Secondly, at equi-effective concentrations, GTN/Cys and the NO donor 2,2-diethyl-1-nitroso-oxyhydrazine released identical amounts of NO. Finally, at sufficiently high rates of NO release, activation of sGC by GTN/Cys was accompanied by a shift of the Soret band from 431 to 399 nm, indicating formation of NO–sGC. In the absence of Cys, GTN caused haem oxidation, apparent as a shift of the Soret band to 392 nm, which was accompanied by inactivation of the NO-stimulated enzyme. These results suggest that the effect of GTN/Cys is the result of an activation/inactivation equilibrium that is controlled by the rate of NO release and haem oxidation.
Reconstitution of the mammalian PI3K/PTEN/Akt pathway in yeast
Authors: Rodríguez-Escudero Isabel , Roelants Françoise M. , Thorner Jeremy , Nombela César , Molina María , Cid Víctor J.
Published: August 2005

The mammalian signalling pathway involving class I PI3K (phosphoinositide 3-kinase), PTEN (phosphatidylinositol 3-phosphatase) and PKB (protein kinase B)/c-Akt has roles in multiple processes, including cell proliferation and apoptosis. To facilitate novel approaches for genetic, molecular and pharmacological analyses of these proteins, we have reconstituted this signalling pathway by heterologous expression in the unicellular eukaryote, Saccharomyces cerevisiae (yeast). High-level expression of the p110 catalytic subunit of mammalian PI3K dramatically inhibits yeast cell growth. This effect depends on PI3K kinase activity and is reversed partially by a PI3K inhibitor (LY294002) and reversed fully by co-expression of catalytically active PTEN (but not its purported yeast orthologue, Tep1). Growth arrest by PI3K correlates with loss of PIP2 (phosphatidylinositol 4,5-bisphosphate) and its conversion into PIP3 (phosphatidylinositol 3,4,5-trisphosphate). PIP2 depletion causes severe rearrangements of actin and septin architecture, defects in secretion and endocytosis, and activation of the mitogen-activated protein kinase, Slt2. In yeast producing PIP3, PKB/c-Akt localizes to the plasma membrane and its phosphorylation is enhanced. Phospho-specific antibodies show that both active and kinase-dead PKB/c-Akt are phosphorylated at Thr308 and Ser473. Thr308 phosphorylation, but not Ser473 phosphorylation, requires the yeast orthologues of mammalian PDK1 (3-phosphoinositide-dependent protein kinase-1): Pkh1 and Pkh2. Elimination of yeast Tor1 and Tor2 function, or of the related kinases (Tel1, Mec1 and Tra1), did not block Ser473 phosphorylation, implicating another kinase(s). Reconstruction of the PI3K/PTEN/Akt pathway in yeast permits incisive study of these enzymes and analysis of their functional interactions in a simplified context, establishes a new tool to screen for novel agonists and antagonists and provides a method to deplete PIP2 uniquely in the yeast cell.
On the mechanisms of the internalization of S413-PV cell-penetrating peptide
Authors: Mano Miguel , Teodósio Cristina , Paiva Artur , Simões Sérgio , Pedroso de Lima Maria C.
Published: August 2005

Cell-penetrating peptides have been shown to translocate across eukaryotic cell membranes through a temperature-insensitive and energy-independent mechanism that does not involve membrane receptors or transporters. Although cell-penetrating peptides have been successfully used to mediate the intracellular delivery of a wide variety of molecules of pharmacological interest both in vitro and in vivo, the mechanisms by which cellular uptake occurs remain unclear. In the face of recent reports demonstrating that uptake of cell-penetrating peptides occurs through previously described endocytic pathways, or is a consequence of fixation artifacts, we conducted a critical re-evaluation of the mechanism responsible for the cellular uptake of the S413-PV karyophilic cell-penetrating peptide. We report that the S413-PV peptide is able to accumulate inside live cells very efficiently through a rapid, dose-dependent and non-toxic process, providing clear evidence that the cellular uptake of this peptide cannot be attributed to fixation artifacts. Comparative analysis of peptide uptake into mutant cells lacking heparan sulphate proteoglycans demonstrates that their presence at the cell surface facilitates the cellular uptake of the S413-PV peptide, particularly at low peptide concentrations. Most importantly, our results clearly demonstrate that, in addition to endocytosis, which is only evident at low peptide concentrations, the efficient cellular uptake of the S413-PV cell-penetrating peptide occurs mainly through an alternative, non-endocytic mechanism, most likely involving direct penetration across cell membranes.
Role of chirality in peptide-induced formation of cholesterol-rich domains
Authors: Epand Richard M. , Rychnovsky Scott D. , Belani Jitendra D. , Epand Raquel F.
Published: August 2005

The chiral specificity of the interactions of peptides that induce the formation of cholesterol-rich domains has not been extensively investigated. Both the peptide and most lipids are chiral, so there is a possibility that interactions between peptide and lipid could require chiral recognition. On the other hand, in our models with small peptides, the extent of folding of the peptide to form a specific binding pocket is limited. We have determined that replacing cholesterol with its enantiomer, ent-cholesterol, alters the modulation of lipid organization by peptides. The phase-transition properties of SOPC (1-stearoyl-2-oleoylphosphatidylcholine):cholesterol [in a 6:4 ratio with 0.2 mol% PtdIns(4,5)P2] are not significantly altered when ent-cholesterol replaces cholesterol. However, in the presence of 10 mol% of a 19-amino-acid, N-terminally myristoylated fragment (myristoyl-GGKLSKKKKGYNVNDEKAK-amide) of the protein NAP-22 (neuronal axonal membrane protein), the lipid mixture containing cholesterol undergoes separation into cholesterol-rich and cholesterol-depleted domains. This does not occur when ent-cholesterol replaces cholesterol. In another example, when N-acetyl-Leu-Trp-Tyr-Ile-Lys-amide (N-acetyl-LWYIK-amide) is added to SOPC:cholesterol (7:3 ratio), there is a marked increase in the transition enthalpy of the phospholipid, indicating separation of a cholesterol-depleted domain of SOPC. This phenomenon completely disappears when ent-cholesterol replaces cholesterol. The all-D-isomer of N-acetyl-LWYIK-amide also induces the formation of cholesterol-rich domains with natural cholesterol, but does so to a lesser extent with ent-cholesterol. Thus specific peptide chirality is not required for interaction with cholesterol-containing membranes. However, a specific chirality of membrane lipids is required for peptide-induced formation of cholesterol-rich domains.
Slow thrombin in solution
Authors: Huntington James A.
Published: August 2005

As a tool for understanding biological mechanisms, X-ray crystallography possesses unparalleled power to enlighten, resolve controversy and shift a field of study on to a secure new paradigm. Thanks largely to developments in crystallographic methods, the technique has become accessible to the general biochemist and we have thus witnessed an exponential increase in the number of protein structures deposited every year. It is now commonplace for several structures to be published of the same protein under different crystallization conditions, sometimes resulting in conflicting mechanistic interpretations. Such a controversy has arisen over thrombin's conformational response to Na+ co-ordination, and in this issue of Biochemical Journal, De Filippis and colleagues put the two structural models of thrombin allostery to the test by returning to the techniques of solution biochemistry.
What we Never have, we Never Miss? Decision Error and the Risks of Premature Termination
Authors: Drummond Helga
Published: August 2005

The history of IT systems construction contains many examples of large-scale failures that were compounded by undue persistence - a phenomenon known as escalation of commitment. Yet organizations also need to guard against erring in the opposite direction, that is, terminating (or never starting) a project that, on economic grounds, ought to be completed. This paper highlights the notion of premature termination, suggests why such errors are possible and discusses the implications for practice.
Vortex dynamics associated with the collision of a sphere with a wall
Authors: Leweke Thomas , Thompson Mark C. , Hourigan Kerry
Published: August 2005

For moderate Reynolds numbers, a sphere striking a wall in the normal direction leads to the trailing recirculating wake threading over the sphere and developing into a complex vortex ring system as it interacts with the wall. The primary vortex ring, which consists of vorticity from the wake, persists and convects slowly outwards away from the sphere due to the motion induced from its image. The structure and evolution of this vortex system is quantified through a combined experimental and numerical study. At higher Reynolds numbers a non-axisymmetric instability develops, which leads to rapid dispersion of the ring system. A comparison of the wavelength and growth rate, predicted from both linear stability theory and direct simulations, with idealized models indicates that the mechanism is dominated by a centrifugal instability at the edge of the primary vortex core.
Polymer drag reduction in exact coherent structures of plane shear flow
Authors: Stone Philip A. , Roy Anshuman , Larson Ronald G. , Waleffe Fabian , Graham Michael D.
Published: August 2005

Recently discovered traveling-wave solutions to the Navier–Stokes equations in plane shear geometries provide model flows for the study of turbulent drag reduction by polymer additives. These solutions, or “exact coherent states” (ECS), qualitatively capture the dominant structure of the near-wall buffer region of shear turbulence, i.e., counter-rotating pairs of streamwise-aligned vortices flanking a low-speed streak in the streamwise velocity. The optimum length scales for the ECS match well the length scales of the turbulent coherent structures and evidence suggests that the ECS underlie the dynamics of these structures. We study here the effect of viscoelasticity on these states. The changes to the velocity field for the viscoelastic ECS, where the FENE-P model calculates the polymer stress, mirror the modifications seen in experiments of fully turbulent flows of polymer solutions at low to moderate levels of drag reduction: drag is reduced, streamwise velocity fluctuations increase while wall-normal fluctuations decrease, and smaller wavelength structures are suppressed. These modifications to the ECS are due to the suppression of the streamwise vortices. The polymer molecules become highly stretched in the wavy, streamwise streaks, where the flow is predominately elongational, then relax as they move from the streaks into and around the streamwise vortices, where the flow is predominately rotational. This relaxation of the polymer molecules produces a force that directly opposes the fluid motion in the vortices, weakening them. Since the pressure fluctuations have their greatest magnitude (i.e., they are most negative) in the cores of the vortices, a reduction in vortex strength leads to a decrease in the magnitude of the pressure fluctuations. The pressure fluctuations redistribute energy from the streamwise velocity fluctuations to the Reynolds shear stress, so a decrease in their magnitude leads to a reduction in turbulent drag. For the viscoelastic ECS, we also find that after the onset of drag reduction (at Weissenberg number, We≈7) there is a dramatic increase in the critical wall-normal length scale at which the ECS can exist. This sharp increase in length scale mirrors experimental observations and is also consistent with the observed shift to higher Reynolds numbers of the transition to turbulence in polymer solutions.
Toward a description of contact line motion at higher capillary numbers
Authors: Eggers Jens
Published: August 2005

The surface of a liquid near a moving contact line is highly curved owing to diverging viscous forces. Thus, microscopic physics must be invoked at the contact line and matched to the hydrodynamic solution farther away. This matching has already been done for a variety of models, but always assuming the limit of vanishing speed. This excludes phenomena of the greatest current interest, in particular the stability of contact lines. Here we extend perturbation theory to arbitrary order and compute finite speed corrections to existing results. We also investigate the impact of different contact line models on the large-scale shape of the interface.
On the axisymmetric vortex breakdown of a swirling jet entering a sudden expansion pipe
Authors: Revuelta Antonio
Published: August 2005

This Brief Communication investigates the onset and bifurcation structure of vortex breakdown in a laminar sudden expansion flow. Bifurcation diagrams for variable inlet swirl levels are determined by integration of the time dependent, incompressible, axisymmetric, Navier–Stokes equations in a sudden expansion with expansion ratio λ=2.0 and for moderately large values of the Reynolds number. As in the case of swirling flows in pipes, vortex breakdown is seen to occur associated with the emergence of a stagnation point when the Reynolds number is sufficiently small (Re≲125 for λ=2), while for larger values it appears as a fold in the solution space. The standing wave analysis for the stream tube emerging from the inlet orifice rim indicates that the local criticality of the flow is a necessary condition for the appearance of the vortex breakdown. The axisymmetric computations also reveal the unsteadiness of the nonslender solutions above Re≳400.
Electronic and geometric structure of the 3d-transition metal monocarbonyls MCO, M=Sc, Ti, V, and Cr
Authors: Koukounas Constantine , Kardahakis Stavros , Mavridis Aristides
Published: August 2005

The electronic and geometric structure of the 3d-transition metal monocarbonyls MCO, M=Sc, Ti, V, and Cr was investigated through coupled cluster (CC) and multireference variational methods (MRCI) combined with large basis sets. For the ground and a few low-lying excited states complete potential energy profiles were constructed at the CC-level of theory. The M–CO dissociation energies of the ground states X̃Σ−4,X̃Δ5,X̃Σ+6, and X̃A′7 are calculated to be 36, 27, 18, and 2kcal∕mol for ScCO, TiCO, VCO, and CrCO, with respect to Sc(F4),Ti(F5),V(D6),Cr(S7)+CO(XΣ+1). The bonding is rather complicated and could be attributed mainly to π-conjugation effects between the M and CO π-electrons, along with weak σ-charge transfer from CO to M atoms. Almost in all cases the metal atoms appear to be slightly positively charged, at least according to the direction of the dipole moment vectors and the MRCI population densities.
Controlled erbium incorporation and photoluminescence of Er-doped Y2O3
Authors: Van Trinh Tu , Chang Jane P.
Published: August 2005

A high concentration of erbium doping was achieved in Y2O3 thin films on Si (100) by depositing Y2O3 alternatively with Er2O3 using radical-enhanced atomic layer deposition (ALD). Specifically, the erbium doping level was controlled by varying the ratio of Y2O3:Er2O3 cycles during deposition, and a 10:5 ratio yielded ∼9at.% erbium incorporation in Y2O3, confirmed by the compositional analysis using x-ray photoelectron spectroscopy. Room-temperature photoluminescence was observed in a 320-Å Er-doped (9 at. %) Y2O3 film deposited at 350 °C. This result is very promising, since the film was fairly thin and no annealing at high temperature was needed to activate the erbium ions. This suggests that radical-enhanced ALD was able to preserve the optically active trivalent state of the erbium ion from its precursor state. The effective absorption cross section for Er3+ ions incorporated in Y2O3 was estimated to be on the order of 10−18cm2, about three orders of magnitude larger than the direct optical absorption cross section reported for Er3+ ions in a stoichiometric SiO2 host. These results validate Y2O3 as a promising Er3+ host material and demonstrate that radical-enhanced ALD is a viable technique for synthesizing these materials.
Nondispersive dielectric component of ferroelectric thin films in the frequency range of 10−1–106Hz
Authors: Jiang A. Q. , Chu D. P. , Migliorato P. , Kijima T. , Natori E. , Shimoda T.
Published: August 2005

We show that there exists a nondispersive (or elastic) capacitance component Cnon which is independent of frequency f, ac amplitude VOSC, and dc bias voltage Vdc, in the frequency range of 0.063 Hz–1 MHz. It can be separated from the total capacitance Ct of ferroelectric thin films by using either the C(Vdc,f)-C[Vdc,f(r)](VOSC=const) or C(f,VOSC)-C[f,VOSC(r)](Vdc=const) plot, where f(r) and VOSC(r) are the referenced frequency and ac amplitude, respectively. Our results suggest that the dispersive and nondispersive capacitance components may originate from different dielectric relaxation mechanisms. The extracted nondispersive Cnon can be a useful physical parameter in evaluating maximum dielectric tunability for the phase-shift application of ferroelectric thin films in microwave devices and characterizing phase-transition temperature in a multilayered 0.2Pb(Zn1∕3Nb2∕3)O3–0.8BaTiO3∕Pb(Mg1∕3Nb2∕3)O3 relaxor.
Pulsed field-ionization photoelectron-photoion coincidence study of the process N2+hν→N++N+e−: Bond dissociation energies of N2 and N2+
Authors: Tang Xiaonan , Hou Yu , Ng C. Y. , Ruscic Branko
Published: August 2005

We have examined the dissociative photoionization reaction N2+hν→N++N+e− near its threshold using the pulsed field-ionization photoelectron-photoion coincidence (PFI-PEPICO) time-of-flight (TOF) method. By examining the kinetic-energy release based on the simulation of the N+ PFI-PEPICO TOF peak profile as a function of vacuum ultraviolet photon energy and by analyzing the breakdown curves of N+ and N2+, we have determined the 0-K threshold or appearance energy (AE) of this reaction to be 24.2884±0.0010eV. Using this 0-K AE, together with known ionization energies of N and N2, results in more precise values for the 0-K bond dissociation energies of N–N (9.7543±0.0010eV) and N–N+ (8.7076±0.0010eV) and the 0-K heats of formation for N (112.469±0.012kcal∕mol) and N+ (447.634±0.012kcal∕mol).
Correlation energies for He isoelectronic sequence with Z=2–116 from four-component relativistic configuration interactions
Authors: Watanabe Yoshihiro , Tatewaki Hiroshi
Published: August 2005

The relativistic correlation energies (CEs) for the He isoelectronic sequence from He2 to Uuh116 were investigated using configuration-interaction (CI) calculations. We used a large universal-type Gaussian basis set, which gives accurate Dirac-Fock total energies for the ions under consideration. In contrast to nonrelativistic CEs, the relativistic CEs decrease monotonically with increasing nuclear charge, but the p-, d-, and f-partial CEs have a hump like the relativistic Hylleraas CI.
Adsorption and scattering of H2 and D2 by NiAl(110)
Authors: Rivière P. , Busnengo H. F. , Martín F.
Published: August 2005

We present quasiclassical dynamics calculations of H2 and D2 scattering by the NiAl(110) surface using a recently proposed six-dimensional potential-energy surface (PES) obtained from density-functional theory calculations. The results for dissociative adsorption confirm several experimental predictions using (rotationally hot) D2 beams, namely, the existence of a dissociation barrier, the small isotopic effect, the importance of vibrational enhancement, and the existence of normal energy scaling. The latter conclusion shows that normal energy scaling is not necessarily associated with weak corrugated surfaces. The results for rotationally elastic and inelastic diffractions are also in reasonable agreement with experiment, but they show that many more diffractive transitions are responsible for the observed structures than previously assumed. This points to the validity of the PES recently proposed [P. Rivière, H. F. Busnengo, and F. Martín, J. Chem. Phys. 121, 751 (2004)] to describe dissociative adsorption as well as rotationally elastic and inelastic diffractions in the H2∕NiAl(110) system.
The convergence of complete active space self-consistent-field energies to the complete basis set limit
Authors: Petersson George A. , Malick David K. , Frisch Michael J. , Braunstein Matthew
Published: August 2005

Examination of the convergence of full valence complete active space self-consistent-field energies with expansion of the one-electron basis set reveals a pattern very similar to the convergence of single determinant Hartree-Fock energies. Calculations on 26 molecular examples with the sequence of ntuple-ζ augmented polarized (nZaP) basis sets (n=2, 3, 4, 5, and 6) are used to evaluate complete basis set extrapolation schemes. The most effective extrapolation reduces the rms one-electron basis set truncation errors from 3.03, 0.58, and 0.12mhartree to 0.23, 0.05, and 0.014mhartree for the 3ZaP, 4ZaP, and 5ZaP basis sets, respectively.
Determination of the conditional dimerization constants from the sound velocity data in binary liquid mixtures containing an associating solute and a nonassociating solvent
Authors: Gliński Jacek
Published: August 2005

A new model of calculating the self-association constants in mixtures of two liquids, an associating solute and a nonassociating solvent, is proposed and analyzed. The model assumes additivity of the time of transmission of the acoustic signal with the volume fractions of the components of the mixture. The model was tested for different systems, showing that the results are reliable and close to expectations. The presented attempt seems to be an interesting alternative in interpreting the experimental results of sound velocity measurements in liquid mixtures.
A skewed-momenta method to efficiently generate conformational-transition trajectories
Authors: MacFadyen James , Andricioaei Ioan
Published: August 2005

We present a novel computational method, the skewed-momenta method (Skew’M), which applies a bias to the Maxwell distribution of initial momenta used to generate ensembles of trajectories. As a result, conformational transitions are accentuated and kinetic properties are calculated more effectively. The connection to the related puddle jumping method is discussed. A reweighting scheme permits the exact calculation of kinetic properties. Applications are presented for the rapid calculation of rate constants for molecular isomerization, and for the efficient reconstruction of free-energy profiles using a straightforward modification of the Jarzynski identity.
Crystal structure analysis under uniaxial strain at low temperature using a unique design of four-axis x-ray diffractometer with a fixed sample
Authors: Kondo Ryusuke , Kagoshima Seiichi , Harada Jimpei
Published: August 2005

For the purpose of crystal structure analysis under uniaxial strain at low temperatures, we developed a pressure cell for uniaxial compression and a unique design of an x-ray diffractometer wherein both the x-ray source and the detector are capable of two-axial rotation with a fixed sample. This arrangement is advantageous to crystal structure analyses under extreme conditions that require a large and heavy apparatus. Using the present diffractometer, we performed the crystal structure analyses of the organic conductor, α-(BEDT–TTF)2I3 (BEDT–TTF denotes bis(ethylene)dithio-tetrathiafulvalene), under uniaxial strain and ambient pressure, and at room and low temperatures, and obtained results that were qualitatively consistent with those of resistivity measurements.
Hydrogen-bonding interactions in acetic acid monohydrates and dihydrates by density-functional theory calculations
Authors: Gao Q. , Leung K. T.
Published: August 2005

Equilibrium structures and the respective binding energies of acetic acid monohydrates and dihydrates have been determined by density-functional theory calculations with different basis sets, including 6-31+G(3d,p), 6-311++G(d,p), and 6-311++G(3df,3pd). Given that the CO and OH groups in acetic acid provide the predominant hydrogen-bonding interactions with water, six stable conformer structures have been found each for the monohydrate and syn-dihydrate. Of the three syn- and three anti-conformers of acetic acid with water, the most stable monohydrate structure is found to be that of the syn-conformer bonding with water in a cyclic double H-bonded geometry. Similarly, the syn-conformer bonding with two water molecules in a cyclic double H-bonded geometry has also been determined to be the most stable among the six plausible structures for the syn-dihydrate. Frequency analysis of the stable conformers has been performed and the vibrational spectra of the most stable monohydrate and dihydrate structures are compared with the experimental gas-phase and matrix data. Furthermore, the calculated binding energies between an acetic acid and a water molecule for both monohydrate and dihydrate are larger than that between two water molecules, which supports our recent experimental observation of coevaporation of acetic acid with water upon annealing acetic acid on ice.
Convergence of approximate two-component Hamiltonians: How far is the Dirac limit
Authors: Kȩdziera Dariusz
Published: August 2005

A systematic elimination of the off-diagonal parts of the Dirac Hamiltonian is carried out in the spirit of the Douglas-Kroll [Ann. Phys. 82, 87 1974] approach and the recently proposed infinite-order two-component method. The present approach leads to a series of approximate two-component Hamiltonians which are exact through a certain order in the external potential. These Hamiltonians are used to study the convergence pattern of approximate two-component theories. It is shown that to achieve an acceptably high accuracy for low-lying one-electron levels in heavy and superheavy systems one needs to use approximate Hamiltonians of prohibitively high order in the external potential. One can conclude that the finite-order two-component Hamiltonians are of limited usefulness in accurate relativistic calculations for heavy and superheavy systems.
Shear thickening in a model colloidal suspension
Authors: Delhommelle Jerome , Petravic J.
Published: August 2005

We study the rheology of model colloidal suspensions using molecular-dynamics simulations. We relate the onset of shear thickening to the transition from a low-viscosity regime, in which the solvent facilitates the flow of colloids, to a high-viscosity regime associated with jamming of the colloids and the formation of chains of colloids. In the low-viscosity regime, the colloidal particles are, on average, surrounded by two layers of solvent particles. On the contrary, in the high-viscosity regime, the solvent is expelled from the interstice between the jammed colloids. The thickening in suspensions is shown to obey the same criterion as in simple fluids. This demonstrates that jamming, even without the divergence of lubrication interactions, is sufficient to observe shear thickening.
Interpreting closed-loop learning control of molecular fragmentation in terms of wave-packet dynamics and enhanced molecular ionization
Authors: Cardoza David , Baertschy Mark , Weinacht Thomas
Published: August 2005

We interpret a molecular fragmentation experiment using shaped, ultrafast laser pulses in terms of enhanced molecular ionization during dissociation. A closed-loop learning control experiment was performed to maximize the CF3+∕CH3+ production ratio in the dissociative ionization of CH3COCF3. Using ab inito molecular structure calculations and quasistatic molecular ionization calculations along with data from pump-probe experiments, we identify the primary control mechanism which is quite general and should be applicable to a broad class of molecules.
Electronic core levels of layered Li2xMn1−xPS3 film
Authors: Silipigni L. , Grasso V. , De Luca G. , Scolaro L. Monsù , Salvato G.
Published: August 2005

Lithium intercalate thin films have been obtained from MnPS3 starting material and characterized by the x-ray photoelectron spectroscopy technique. The regions of Mn 2p and 3p, P and S 2p, and Li 1s core levels have been investigated. The analysis of the spectra has revealed the lack of nonequivalent atoms of Mn, P and S, and Li. The presence of shake-up-type satellites at the Mn 2p and 3p core levels suggests that Li2xMn1−xPS3 is a large-gap insulating Mn compound analogously to the parent MnPS3. After lithium intercalation no remarkable shift has been observed in the binding energy positions of the investigated core levels in comparison with the corresponding MnPS3 pure compound. On these bases, we assume that only an ion transfer accompanies the lithium intercalation process.
Micro-Brillouin scattering study of ferroelectric relaxor Pb[(Zn1∕3Nb2∕3)0.91Ti0.09]O3 single crystals under the electric field along the [001] direction
Authors: Kim Do Han , Ko Jae-Hyeon , Feng C. D. , Kojima Seiji
Published: August 2005

Electric-field effects on structural phase transitions have been studied in ferroelectric relaxor Pb[(Zn1∕3Nb2∕3)1−xTix]O3 single crystals with x=0.09 by the high-resolution micro-Brillouin scattering. Sharp phase transitions from cubic-to-tetragonal and then from tetragonal-to-rhombohedral phases have been observed under zero-field-cooling (ZFC) condition. For two phase-transition temperatures a noticeable thermal hysteresis was clearly observed, consistent with dielectric measurements. The temperature range of a tetragonal phase has been markedly extended under the electric field of E=6.7kV∕cm along the [001] direction. A large difference of the LA-mode frequency and damping between the ZFC and field-cooling processes indicated that the multidomain structure induces the increase of the acoustic damping due to the elastic scattering. In addition, it was found that the elastic stiffness coefficient c33 in the tetragonal coordinates shows a slight decrease. The first-order character of the cubic-to-tetragonal phase transition has been gradually changed into a second-order one under the increase of the electric field along the [001] direction, reflecting a general trend of the first-order ferroelectric phase transition. Although a clear specification of the low-temperature symmetry could not be accomplished from Brillouin scattering itself, these results give new insights into an electric-field-temperature phase diagram containing phase boundaries among cubic, tetragonal, and low-temperature phases.
Model for the field effect from layers of biological macromolecules on the gates of metal-oxide-semiconductor transistors
Authors: Landheer D. , Aers G. , McKinnon W. R. , Deen M. J. , Ranuarez J. C.
Published: August 2005

The potential diagram for field-effect transistors used to detect charged biological macromolecules in an electrolyte is presented for the case where an insulating cover layer is used over a conventional eletrolyte-insulator metal-oxide-semiconductor (EIMOS) structure to tether or bind the biological molecules to a floating gate. The layer of macromolecules is modeled using the Poisson-Boltzmann equation for an ion-permeable membrane. Expressions are derived for the charges and potentials in the EIMOS and electrolyte-insulator-semiconductor structures, including the membrane and electrolyte. Exact solutions for the potentials and charges are calculated using numerical algorithms. Simple expressions for the response are presented for low solution potentials when the Donnan potential is approached in the bulk of the membrane. The implications of the model for the small-signal equivalent circuit and the noise analysis of these structures are discussed.
Annealing behavior between room temperature and 2000 °C of deep level defects in electron-irradiated n-type 4H silicon carbide
Authors: Alfieri G. , Monakhov E. V. , Svensson B. G. , Linnarsson M. K.
Published: August 2005

The annealing behavior of irradiation-induced defects in 4H-SiC epitaxial layers grown by chemical-vapor deposition has been systematically studied by means of deep level transient spectroscopy (DLTS). The nitrogen-doped epitaxial layers have been irradiated with 15-MeV electrons at room temperature and an isochronal annealing series from 100 to 2000 °C has been performed. The DLTS measurements, which have been carried out in the temperature range from 120 to 630 K after each annealing step, revealed the presence of six electron traps located in the energy range of 0.45–1.6 eV below the conduction-band edge (Ec). The most prominent and stable ones occur at Ec−0.70eV (labeled Z1∕2) and Ec−1.60eV(EH6∕7). After exhibiting a multistage annealing process over a wide temperature range, presumably caused by reactions with migrating defects, a significant fraction of both Z1∕2 and EH6∕7 (25%) still persists at 2000 °C and activation energies for dissociation in excess of 8 and ∼7.5eV are estimated for Z1∕2 and EH6∕7, respectively. On the basis of these results, the identity of Z1∕2 and EH6∕7 is discussed and related to previous assignments in the literature.