bluuebunny/crossref_metadata_2025 huggingface dataset:
Proteomic analysis of human brain identifies α‐enolase as a novel autoantigen in Hashimoto's encephalopathy
Authors: Ochi Hirofumi , Horiuchi Izumi , Araki Norie , Toda Tosifusa , Araki Tomohiro , Sato Kaori , Murai Hiroyuki , Osoegawa Manabu , Yamada Takeshi , Okamura Ken , Ogino Tomoaki , Mizumoto Kiyohisa , Yamashita Hirohumi , Saya Hideyuki , Kira Jun-ichi
Published: October 2002

Hashimoto's encephalopathy (HE) is a rare autoimmune disease associated with Hashimoto's thyroiditis (HT). To identify the HE‐related autoantigens, we developed a human brain proteome map using two‐dimensional electrophoresis and applied it to the immuno‐screening of brain proteins that react with autoantibodies in HE patients. After sequential MALDI‐TOF‐MASS analysis, immuno‐positive spots of 48 kDa (pI 7.3–7.8) detected from HE patient sera were identified as a novel autoimmuno‐antigen, α‐enolase, harboring several modifications. Specific high reactivities against human α‐enolase were significant in HE patients with excellent corticosteroid sensitivity, whereas the patients with fair or poor sensitivity to the corticosteroid treatment showed less reactivities than cut‐off level. Although a few HT patients showed faint reactions to α‐enolase, 95% of HT patients, patients with other neurological disorders, and healthy subjects tested were all negative. These results suggest that the detection of anti‐α‐enolase antibody is useful for defining HE‐related pathology, and this proteomic strategy is a powerful method for identifying autoantigens of various central nervous system diseases with unknown autoimmune etiologies.
NMR studies of the hydrogen bonds involving the catalytic triad of Escherichia coli thioesterase/protease I
Authors: Tyukhtenko Sergiy I , Litvinchuk Alexandra V , Chang Chi-Fon , Leu Ruey-Jyh , Shaw Jei-Fu , Huang Tai-Huang
Published: October 2002

Escherichia coli thioesterase/protease I (TEP‐I) is a lipolytic enzyme of the serine protease superfamily with Ser10, Asp154 and His157 as the catalytic triad residues. Based on comparison of the low‐field 1H nuclear magnetic resonance spectra of two mutants (S10G and S12G) and two transition state analogue complexes we have assigned the exchangeable proton resonances at 16.3 ppm, 14.3 ppm, and 12.8 ppm at pH 3.5 to His157‐Nδ1H, Ser10‐OγH and His157‐Nϵ2H, respectively. Thus, the presence of a strong Asp154–His157 hydrogen bond in free TEP‐I was observed. However, Ser10‐OγH was shown to form a H‐bond with a residue other than His157‐Nϵ2.
Reasoning under uncertainty in deluded schizophrenic patients: a longitudinal study
Authors: Brankovic S.B. , Paunovic V.R.
Published: October 2002

Several current hypotheses consider the process of attribution of importance to stimuli and the integration of actually perceived reality with experience as a cognitive base for the genesis of delusions. We tested these models by a comparison of deluded schizophrenics, healthy controls, and anxious patients on reasoning under uncertainty. Reasoning under uncertainty was examined in currently deluded schizophrenics (n = 29), in 16 of them also in remission, in normal control groups (n = 35), and in anxious patients (n = 31) using a probabilistic inference task. Acutely psychotic schizophrenics were less ready than normal subjects, anxious patients, and schizophrenics, in remission to modify their judgement in probabilistic situation confronted with potentially disconfirmatory data. They were also less prone than anxious patients and schizophrenics in remission to correct their estimate confronted with confirmatory data. The data support the hypothesis of a weaker influence of incoming stimuli on reasoning under uncertainty as a cognitive base of the maintenance of delusions.
Dissociation between hemodynamic changes and symptom improvement in patients with advanced congestive heart failure
Authors: Shah Monica R. , Hasselblad Vic , Stinnett Sandra S. , Kramer Judith M. , Grossman Steven , Gheorghiade Mihai , Adams Kirkwood F. , Swedberg Karl , Califf Robert M. , O'Connor Christopher M.
Published: October 2002

Background:

Changes in hemodynamic measures often serve as surrogate end points in efficacy trials for advanced heart failure, although there are few objective data to support this practice.

Aims:

We compared changes in hemodynamic variables vs. changes in symptoms of decompensated heart failure in patients enrolled in a randomized trial.

Methods:

We studied 201 patients with New York Heart Association (NYHA) class IIIb or IV heart failure and ejection fraction ≤25% for ≥3 months. Patients underwent continuous monitoring by pulmonary‐artery catheter during inpatient drug administration. We assessed the relations of changes in hemodynamic variables (baseline minus final measure) to changes at 2 weeks in congestive heart failure symptoms, NYHA class, Yale Dyspnea‐Fatigue Index (YDFI) score, and distance achieved in a 6‐min walk.

Results:

No hemodynamic measure significantly predicted either symptom score or NYHA classification. Mean pulmonary artery pressure and pulmonary capillary wedge pressure did show some relation to change in YDFI score in univariable, but not multivariable, analysis. No hemodynamic measure correlated significantly with changes in distance achieved in the 6‐min walk test.

Conclusion:

We noted no significant association between improved hemodynamics and improved symptoms in patients with advanced heart failure. Other measures may need to be evaluated as surrogate end points in future trials.
Photodissociation of the methane–argon complex. I. Ab initio intermolecular potential depending on the methane vibrational coordinates
Authors: Geleijns Michel , Wormer Paul E. S. , van der Avoird Ad
Published: October 2002

We calculated the intermolecular potential for the complex methane–Ar in which the methane is deformed along the ν1 and the ν3 vibrational normal modes. We present a fit of the potential energy surface as a function of the three argon coordinates and the four normal mode coordinates qν3x, qν3y, qν3z, and qν1. This potential is used in the following paper [J. Chem. Phys. 117, 7562 (2002)] dealing with the calculation of the lifetimes of the quasibound states of the dimer with the methane monomer in the vibrationally excited ν3 state.
Photodissociation of the methane–argon complex. II. Vibrational predissociation dynamics, spectral linewidths and fragment state distributions
Authors: Geleijns Michel , van der Avoird Ad , Wormer Paul E. S. , Halberstadt Nadine
Published: October 2002

We calculated the cross sections for vibrational predissociation of methane–Ar induced by excitation of the methane ν3 mode. We used the ab initio CH4–Ar potential depending explicitly on the ν3 and ν1 normal coordinates of the CH4 monomer that is presented in the preceding paper. It was found that dissociation into CH4 fragments excited in the ν1 mode—a V→V′ process with very low kinetic energy release—strongly dominates over direct dissociation into Ar and ground state CH4, and is responsible for the line broadening observed experimentally. The strong variation of the linewidths, observed as well as calculated, for the van der Waals levels excited in combination with the ν3 mode is related to the opening up of appropriate ν1 dissociation channels and the occurrence of rotational resonances in the ν1 continuum in the energy range of the quasibound ν3 levels. The rotational state distributions of the emerging ν1 excited methane fragment are predicted.
Two-electron pseudopotential investigation of the electronic structure of the CaAr molecule
Authors: Spiegelman F. , Maron L. , Breckenridge W. H. , Mestdagh J.-M. , Visticot J.-P.
Published: October 2002

The electronic structure of the Ca-Ar molecule is investigated using [Ca2+] and [Ar] core pseudopotentials complemented by core polarization operators on both atoms, considering the molecule to be a two-electron system. The electronic two-body problem is solved by achieving a full configuration interaction with extensive Gaussian basis sets. The potential energy curves and the molecular constants of all CaAr states dissociating into atomic configurations ranging between the ground state 4s2 1S and the doubly excited state 4p2 3P are determined. Spin–orbit coupling is also included in an atom-in-molecule scheme for states dissociating into the 4s4p and 4s3d configurations. The present theoretical results show good overall agreement with experimental data. They also help to clarify the very complicated spectroscopy of the CaAr system in the 38 000 cm−1 energy range where many states correlated with the 4s4d, 3d4p, and 4p2 atomic configurations interact with or cross one another. As a by-product of the present investigation and with the purpose of checking the pseudopotential accuracy on a simpler related system, low-lying potential energy curves of the single active electron CaAr+ ion are also reported and the corresponding molecular constants are compared with the existing literature.
Surface relaxation in liquid water and methanol studied by x-ray absorption spectroscopy
Authors: Wilson Kevin R. , Schaller R. D. , Co D. T. , Saykally R. J. , Rude Bruce S. , Catalano T. , Bozek J. D.
Published: October 2002

X-ray absorption spectroscopy is a powerful probe of local electronic structure in disordered media. By employing extended x-ray absorption fine structure spectroscopy of liquid microjets, the intermolecular O–O distance has been observed to undergo a 5.9% expansion at the liquid water interface, in contrast to liquid methanol for which there is a 4.6% surface contraction. Despite the similar properties of liquid water and methanol (e.g., abnormal heats of vaporization, boiling points, dipole moments, etc.), this result implies dramatic differences in the surface hydrogen bond structure, which is evidenced by the difference in surface tension of these liquids. This result is consistent with surface vibrational spectroscopy, which indicates both stronger hydrogen bonding and polar ordering at the methanol surface as a consequence of “hydrophobic packing” of the methyl group.
Tilting phase transition of amphiphile monolayers at the air–water interface: Physically reasoning phase portion in a phase diagram
Authors: Iwamoto Mitsumasa , Ou-Yang Zhong-can
Published: October 2002

The untilting to tilting (U→t) phase transition of amphiphile monolayers at the water–air interface is studied as a distortion of the orthogonally hexagonal orientation of molecules by a competition among entropy, Lennard-Jones potential, and the work done by surface and bulk pressures (Π,P). The U/t phase portion in the Π–T diagram is derived as an approximately linear van der Waals equation Π=kT/2A0−Pl0 with A0, l0 being the molecular area and chain length, respectively, at the U phase. A comparison with experiment in monolayers of C14–C24 acids [see, e.g., Peterson et al., Langmuir 8, 2995 (1992)] shows quantitative agreement. Besides two optimal tilting directions, i.e., in the direction to a nearest neighbor (NN) and to a next-nearest neighbor (NNN), an intermediate tilt at the NN→NNN transition is shown to be physically possible based on Selinger–Nelson theory [Phys. Rev. Lett. 61, 416 (1988)].
Effect of shape on the critical nucleus size in a three-dimensional Ising model: Energetic and kinetic approaches
Authors: Berim Gersh O. , Ruckenstein Eli
Published: October 2002

The initial growth rate and the excitation energy of spin clusters of different shapes (cubic, stair-like, pyramidal) on a three-dimensional cubic lattice were calculated, assuming Ising-type interactions between spins and the Glauber-type spin dynamics. Using energetic and kinetic approaches, the critical cluster size was obtained and compared with existing Monte Carlo “experiments.” It was shown that in most cases the kinetic approach fits better the “experimental” results than the energetic one. A shape independent kinetic criterium for a critical cluster size was also formulated on the basis of an analysis of all possible configurations of a cluster with a given number of spins.
Dimensional changes as a function of charge injection for trans-polyacetylene: A density functional theory study
Authors: Sun Guangyu , Kürti Jenő , Kertesz Miklos , Baughman Ray H.
Published: October 2002

Charge-induced dimensional changes allow conducting polymers and single walled carbon nanotubes to function as electromechanical actuators. The unit cell of the prototypical conducting polymer, trans-polyacetylene, was calculated as a function of charge injection using density functional theory in combination with ultrasoft pseudopotentials using the solid-state Vienna ab initio simulation package. Test calculations on the charged pyridinium molecular ion give results in good agreement with the experimental geometry. Strain versus charge relationships are predicted from dimensional changes calculated using a uniform background charge (“jellium”) for representing the counterions, which we show provides results consistent with experiment for doped polyacetylenes. These jellium calculations are consistent with further presented calculations that include specific counterions, showing that hybridization between the guest dopant ions and the host polyacetylene chains is unimportant. The lack of guest–host orbital hybridization allows a qualitative rigid band interpretation of the amount of charge transfer for both acceptor and donor doping. For polyacetylene, asymmetry of strain along the chain with respect to the sign of the charge is predicted: negative charge elongates and positive charge shortens the polymer. For charge less than 0.05e per carbon, an approximately linear dependence is obtained for the dependence of chain-direction strain on the amount of injected charge.
Optimal series representations for numerical path integral simulations
Authors: Predescu Cristian , Doll J. D.
Published: October 2002

By means of the Ito-Nisio theorem, we introduce and discuss a general approach to series representations of path integrals. We then argue that the optimal basis for both “primitive” and partially averaged approaches is the Wiener sine-Fourier basis. The present analysis also suggests a new approach to improving the convergence of primitive path integral methods. Current work indicates that this new technique, the “reweighted” method, converges as the cube of the number of path variables for “smooth” potentials. The technique is based on a special way of approximating the Brownian bridge which enters the Feynman-Kaç formula and it does not require the Gaussian transform of the potential for its implementation.
Universal simulation method to compute surface and interfacial free energies of disordered solids
Authors: Grochola Gregory , Russo Salvy P. , Snook Ian K. , Yarovsky Irene
Published: October 2002

Previously we studied λ-integration paths for the calculation of “exact” surface and interfacial free energies that were limited to simulation methods where atomic interactions can be scaled using a multiplicative parameter λ, as is the case for analytical empirical potentials. Here we develop new reversible paths and associated λ-integration methodology to find exact surface and interfacial free energies of solids, that could potentially be used in conjunction with any intermolecular potential function and/or methods such as ab initio simulations, where one cannot trivially scale and sum the slab interactions as is done with “simple” classical intermolecular potentials. As a first step we test our paths and methodology on the (100), (110), and (111) faces of α-iron using embedded atom method interactions. We find accurate agreement with our previous surface free energy calculations for all faces, including the highly disordered (111) face.
Study of dynamics of anisotropic vibrational energy migration in dendrimer macromolecule by using a classical oscillator model
Authors: Nishioka Keita , Suzuki Masato
Published: October 2002

Dendrimers are nanometer size macromolecules with a regular tree-like array of branch units. For these macromolecules, it has been confirmed by various experiments that the phonon energy which is supplied by the infrared light irradiation at the periphery of these molecules migrates to the core efficiently. In order to clarify such an anisotropic migration of phonons in the dendrimer, we investigate the dynamical natures of the phonon in this molecule using a classical oscillator model which approximates complicated vibrations of the dendrimer as simple oscillators. We calculate the time developments of migration of photoexcited phonons solving the Newton equation for the classical oscillator model. From our calculated results, it is clarified that the phonon has a tendency to migrate efficiently from the outside to the core of this molecule through anharmonic vibrations between composition units of the dendrimer, and its energy is trapped in the inner region for a long time. We conclude that the characteristic tree-like structure of the dendrimer, wherein the composition units crowd toward the outside from the inside, plays an essential role in the anisotropic migration of phonons.
Interactions of functionalized carbon nanotubes with tethered pyrenes in solution
Authors: Qu Liangwei , Martin Robert B. , Huang Weijie , Fu Kefu , Zweifel Daniel , Lin Yi , Sun Ya-Ping , Bunker Christopher E. , Harruff Barbara A. , Gord James R. , Allard Lawrence F.
Published: October 2002

Single-wall carbon nanotubes (SWNTs) were functionalized by oligomeric species containing derivatized pyrenes. Absorption and emission properties of the pyrene moieties tethered to the functionalized SWNTs were studied in homogeneous solution. The absorption spectra suggest no significant ground-state complexation between the pyrenes and nanotubes. The fluorescence and fluorescence excitation results show that the tethered pyrenes form “intramolecular” (intra-nanotube) excimers and that the excimer formation is predominantly dynamic in nature. The time-resolved fluorescence results show that the pyrene monomer and excimer emissions are significantly quenched by the attached SWNTs. The quenching is explained in terms of a mechanism in which carbon nanotubes serve as acceptors for excited-state energy transfers from the tethered pyrene moieties.
Hall effect and hole densities in Ga1−xMnxAs
Authors: Edmonds K. W. , Wang K. Y. , Campion R. P. , Neumann A. C. , Foxon C. T. , Gallagher B. L. , Main P. C.
Published: October 2002

By studying the Hall effect in a series of low resistivity Ga1−xMnxAs samples, accurate values for the hole density p, Mn concentration x, and Curie temperature TC are obtained over the range 0.015⩽x⩽0.08. The hole density corresponds to 90% of the Mn concentration at low x, and has a maximum value of 1.0×1027 m−3 when TC=125 K. These data allow the first meaningful comparison of mean field predicted Curie temperatures with experiment over a wide range of x. The theory is in qualitative agreement with experiment, but overestimates TC at large x and underestimates TC at low x.
Site-specific growth of Zno nanorods using catalysis-driven molecular-beam epitaxy
Authors: Heo Y. W. , Varadarajan V. , Kaufman M. , Kim K. , Norton D. P. , Ren F. , Fleming P. H.
Published: October 2002

We report on catalyst-driven molecular beam epitaxy of ZnO nanorods. The process is site specific, as single crystal ZnO nanorod growth is realized via nucleation on Ag films or islands that are deposited on a SiO2-terminated Si substrate surface. Growth occurs at substrate temperatures on the order of 300–500 °C. The nanorods are uniform cylinders, exhibiting diameters of 15–40 nm and lengths in excess of 1 μm. With this approach, nanorod placement can be predefined via location of metal catalyst islands or particles. This, coupled with the relatively low growth temperatures needed, suggests that ZnO nanorods could be integrated on device platforms for numerous applications, including chemical sensors and nanoelectronics.
Influence of stacking faults on the performance of 4H–SiC Schottky barrier diodes fabricated on (112̄0) face
Authors: Kojima K. , Ohno T. , Fujimoto T. , Katsuno M. , Ohtani N. , Nishio J. , Suzuki T. , Tanaka T. , Ishida Y. , Takahashi T. , Arai K.
Published: October 2002

The influence of stacking faults (SFs) on the performance of 4H–SiC (112̄0) Schottky barrier diodes fabricated on the epilayer grown on the substrate which was grown in [112̄0] direction by the sublimation method was investigated. The number of SFs under the Schottky electrode was determined by KOH etching of (11̄00) face cross section. SFs were found to have a severe influence on the leakage current of reverse characteristic and Schottky barrier height. The leakage current is increased even though a few SFs exist under the electrode. The Schottky barrier height is also affected by the SF under the electrode.
Decreasing giant splitting of longitudinal and transverse optical phonons in PbxSr1−xTiO3 due to Pb covalency
Authors: Kuo Shou-Yi , Li Chung-Ting , Hsieh Wen-Feng
Published: October 2002

In contrast to the increase of giant splitting of longitudinal optical (LO) and transverse optical (TO) phonons in polycrystalline BaxSr1−xTiO3 [Phys. Rev. B. 64, 224103-1 (2001)], a decreasing splitting of the softest A1(1TO) and the hardest A1(3LO) was observed in PbxSr1−xTiO3. A similar structure but anomalous discrepancies in lattice dynamics of ABO3 perovskite are related to the diverse electronic states of Pb2+ and Ba2+ ions. In this article, Pb–O interaction is proposed to be more hybridized than Ba–O, and thus the change of effective charge to the LO–TO splitting may be the dominant mechanism in PbxSr1−xTiO3, while unit-cell volume change is in the BaxSr1−xTiO3 systems.
Periodic array of intramolecular junctions of silicon nanowires
Authors: Ma D. D. D. , Lee C. S. , Lifshitz Y. , Lee S. T.
Published: October 2002

The formation of periodic arrays of intramolecular junctions in silicon nanowires from a single growth process is reported. Scanning tunneling microscopic images show intramolecular junctions formed by fusing together two straight wire segments (∼3 nm in diameter) 5 and 10 nm long, respectively, at an angle of ∼30° with respect to each other. The junction repeats itself in a regular pattern along a nanowire, forming a striking superlattice ∼3 nm in diameter and at least several microns long. Scanning tunneling spectroscopic measurements reveal distinctly different current–voltage curves for the two different segments changing sharply across each junction. The segments are most probably formed by a periodic change of growth direction while the different electronic properties of the two segments forming the junction are attributed to the differences in surface structure and segment diameter.
Carrier profiling of Al-doped 4H-SiC by scanning spreading resistance microscopy
Authors: Osterman J. , Hallén A. , Anand S.
Published: October 2002

Epitaxially-grown Al-doped 4H-SiC has been studied by scanning spreading resistance microscopy. The measured current shows good quantitative agreement with the chemical Al concentration in the range 2×1016 to 2×1020 atoms cm−3. Simulations of the sample temperature distribution using finite element calculations predict a maximum temperature exceeding 750 K within 100 nm of the contact region at 7.5 V dc bias for an Al doping of 1020 cm−3. The heating causes a significant increase in the ionization of the dopants relative to that at room temperature. Due to the strong voltage dependence, the effect can be avoided by operating below 5 V dc bias where the temperature rise is shown to be negligible for all dopant concentrations.
Integrity of hafnium silicate/silicon dioxide ultrathin films on Si
Authors: Morais J. , Miotti L. , Soares G. V. , Teixeira S. R. , Pezzi R. , Bastos K. P. , Baumvol I. J. R. , Rotondaro A. L. P. , Chambers J. J. , Visokay M. R. , Colombo L.
Published: October 2002

Rapid thermal annealing at 1000 °C of (HfO2)1−x(SiO2)x pseudobinary alloy films deposited on Si were performed in N2 or O2 atmospheres. The effects on the atomic transport, structure, and composition were investigated using isotopic substitution of oxygen, high-resolution transmission electron microscopy, nuclear reaction analyses, narrow nuclear reaction resonance profiling, and grazing angle x-ray reflection.
Polymer—perylene diimide heterojunction solar cells
Authors: Breeze A. J. , Salomon A. , Ginley D. S. , Gregg B. A. , Tillmann H. , Hörhold H.-H.
Published: October 2002

Thin-film small molecule/polymer hybrid bilayer photovoltaic cells have been constructed, exhibiting power conversion efficiencies of 0.71% under 80 mW/cm2 white light illumination. The parameters influencing the photovoltage of these devices are explored by reversing the order of the photoactive layers while maintaining the same electrode configuration. It has been found that the properties of the organic photoactive layers play an important role in determining the direction of current flow and the photovoltage of the device. Comparison is made to analogous pure small molecule bilayer devices, and conclusions about some of the factors influencing device efficiency are drawn. It has been shown that ordering of the band offsets of the two organic materials plays an important role in determining the polarity of the photocurrent and the photovoltage of the device.
Ferromagnetism and interlayer exchange coupling in short-period (Ga,Mn)As/GaAs superlattices
Authors: Mathieu R. , Svedlindh P. , Sadowski J. , Światek K. , Karlsteen M. , Kanski J. , Ilver L.
Published: October 2002

Magnetic properties of (Ga,Mn)As/GaAs superlattices are investigated. The structures contain magnetic (Ga,Mn)As layers, separated by thin layers of nonmagnetic GaAs spacer. The short-period Ga0.93Mn0.07As/GaAs superlattices exhibit a paramagnetic-to-ferromagnetic phase transition close to 60 K, for thicknesses of (Ga,Mn)As down to 23 Å. For Ga0.96Mn0.04As/GaAs superlattices of similar dimensions, the Curie temperature associated with the ferromagnetic transition is found to oscillate with the thickness of nonmagnetic spacer. The observed oscillations are related to an interlayer exchange interaction mediated by the polarized holes of the (Ga,Mn)As layers.
Sub-picosecond electron relaxation of near-infrared intersubband transitions in n-doped (CdS/ZnSe)/BeTe quantum wells
Authors: Akimoto R. , Akita K. , Sasaki F. , Hasama T.
Published: October 2002

We report on intersubband (ISB) absorption and ultrafast ISB energy relaxation of carriers in n-type doped (CdS/ZnSe)/BeTe quantum wells (QWs), grown by molecular-beam epitaxy. The highly n-type doped QW samples were obtained by introducing a few monolayer CdS into a ZnSe/BeTe QW, and ISB absorption with a peak wavelength as short as 1.62 μm, covering 1.55 μm within its absorption bandwidth, was achieved. The ISB carrier relaxation was investigated by means of femtosecond (∼150 fs) one-color pump and probe technique at the ISB absorption peak. The ISB carrier relaxation time of 270 fs was observed in the sample with the absorption peak at 1.82 μm. The slow decay component with a time constant of a few ps, which has been observed in ZnSe/BeTe QWs, was not observed in the (CdS/ZnSe)/BeTe QWs, indicating that the Γ(ZnSe)–X(BeTe) electron transfer is suppressed, as expected from the band alignment.
Born–Oppenheimer invariants along nuclear configuration paths
Authors: Baer Roi
Published: October 2002

Whenever a quantum chemist extracts the eigenstate of an electronic Hamiltonian, he makes, consciously or not, a decision concerning the phase of the wave function. This is done for each calculated state at each nuclear position. Thus he defines a Born–Oppenheimer (BO) frame of reference. There is no absolute phase just as there is no absolute position or time in mechanics. This leads naturally to the question: What are the quantities which do not depend on the arbitrary phases, i.e., what are the BO invariants? In this article we identify BO invariants with respect to an arbitrary path in nuclear configuration space. We identify invariant electronic states along these paths and their Aharonov–Anandan geometric phases. For closed loops not passing through electronic energy degeneracies these invariant states are the BO adiabatic wave functions and the phases are the Berry phases. The results establish rigorous relations between the full nonadiabatic couplings matrix and the geometric phases.
X-ray diffuse scattering study of the kinetics of stacking fault growth and annihilation in boron-implanted silicon
Authors: Luebbert D. , Arthur J. , Sztucki M. , Metzger T. H. , Griffin P. B. , Patel J. R.
Published: October 2002

Stacking faults in boron-implanted silicon give rise to streaks or rods of scattered x-ray intensity normal to the stacking fault plane. We have used the diffuse scattering rods to follow the growth of faults as a function of time when boron-implanted silicon is annealed in the range of 925 to 1025 °C. From the growth kinetics we obtain an activation energy for interstitial migration in silicon: EI=1.98±0.06 eV. Fault intensity and size versus time results indicate that faults do not shrink and disappear, but rather are annihilated by a dislocation reaction mechanism.
Possible solution of the grain-boundary problem for applications of high-Tc superconductors
Authors: Hammerl G. , Herrnberger A. , Schmehl A. , Weber A. , Wiedenmann K. , Schneider C. W. , Mannhart J.
Published: October 2002

It is shown that the critical current density of high-Tc wires can be greatly enhanced by using a three-fold approach, which consists of grain alignment, doping, and optimization of the grain architecture. According to model calculations, current densities of 4×106 A/cm2 can be achieved for an average grain alignment of 10° at 77 K. Based on this approach, a road to competitive high-Tc cables is proposed.
Coexistence of the Cu3Au type ordered structure and the fine modulation in CdxZn1−xTe epilayers grown on GaAs substrates
Authors: Lee H. S. , Lee J. Y. , Kim T. W. , Choo D. C. , Park H. L.
Published: October 2002

Selected-area electron diffraction pattern (SADP) and transmission electron microscopy (TEM) measurements were carried out to investigate the spontaneously ordered structure in CdxZn1−xTe epitaxial layers grown on (001) GaAs substrates. The SADP showed superstructure reflections with symmetrical intensity, and the high-resolution TEM (HRTEM) image showed doublet periodicity in the contrast of the {100} and {110} lattice planes. The results of the SADP and HRTEM measurements showed that Cu3Au type ordered structures were formed in the CdxZn1−xTe epitaxial layers. The dark-field TEM image showed that the size of the Cu3Au type ordered domains with a rectangular-like shape was approximately 15∼30 nm thick, with widths ranging from 30 to 200 nm. Fine modulations in the ordered domains were also observed. These results provide important information on the microstructural properties for enhancing the efficiencies of CdxZn1−xTe-based optoelectronic devices operating at the blue-green region of the spectrum.
Optimal algorithms for local vertex quartet cleaning
Authors: Della Vedova Gianluca , Wareham H. Todd
Published: October 2002

Motivation: Reconstructing evolutionary trees is an important problem in biology. A response to the computational intractability of most of the traditional criteria for inferring evolutionary trees has been a focus on new criteria, particularly quartet-based methods that seek to merge trees derived on subsets of four species from a given species-set into a tree for that entire set. Unfortunately, most of these methods are very sensitive to errors in the reconstruction of the trees for individual quartets of species. A recently developed technique called quartet cleaning can alleviate this difficulty in certain cases by using redundant information in the complete set of quartet topologies for a given species-set to correct such errors.

Results: In this paper, we describe two new local vertex quartet cleaning algorithms which have optimal time complexity and error-correction bound, respectively. These are the first known local vertex quartet cleaning algorithms that are optimal with respect to either of these attributes.

Contact: gianluca.dellavedova@unimib.itharold@cs.mun.ca

* To whom correspondence should be addressed.
Threading Using Neural nEtwork (TUNE): the measure of
protein sequence—structure compatibility
Authors: Lin Kuang , May Alex C.W. , Taylor William R.
Published: October 2002

Motivation: Fold recognition programs align a probe protein sequence onto protein three-dimensional (3D) structure templates. The alignment between the probe sequence and the most suitable template can be used to predict the 3D structure and often biological function of the probe. Here we present a new threading scoring function of protein sequence–structure compatibility. An artificial neural network model is trained to predict compatibility of amino acid side-chains with structural environments. Log-odds scores of predicted probabilities from this model can then be used to construct protein sequence–structure alignments.

Results: Our model is tested on discrimination of native and decoy protein 3D structures. With a residue level structural description, its performance is comparable to those of pseudo-energy functions with atom level structural descriptions, better than the two functions with residue level structural descriptions.

Availability: The C++ source code of our neural network model is available at http://mathbio.nimr.mrc.ac.uk/~kxlin.

Contact: wtaylor@nimr.mrc.ac.uk

* To whom correspondence should be addressed.
Data mining of sequences and 3D structures of allergenic proteins
Authors: Ivanciuc Ovidiu , Schein Catherine H. , Braun Werner
Published: October 2002

Motivation: Many sequences, and in some cases structures, of proteins that induce an allergic response in atopic individuals have been determined in recent years. This data indicates that allergens, regardless of source, fall into discreet protein families. Similarities in the sequence may explain clinically observed cross-reactivities between different biological triggers. However, previously available allergy databases group allergens according to their biological sources, or observed clinical cross-reactivities, without providing data about the proteins. A computer-aided data mining system is needed to compare the sequential and structural details of known allergens. This information will aid in predicting allergenic cross-responses and eventually in determining possible common characteristics of IgE recognition.

Results: The new web-based Structural Database of Allergenic Proteins (SDAP) permits the user to quickly compare the sequence and structure of allergenic proteins. Data from literature sources and previously existing lists of allergens are combined in a MySQL interactive database with a wide selection of bioinformatics applications. SDAP can be used to rapidly determine the relationship between allergens and to screen novel proteins for the presence of IgE or T-cell epitopes they may share with known allergens. Further, our novel similarity search method, based on five dimensional descriptors of amino acid properties, can be used to scan the SDAP entries with a peptide sequence. For example, when a known IgE binding epitope from shrimp tropomyosin was used as a query, the method rapidly identified a similar sequence in known shellfish and insect allergens. This prediction of cross-reactivity between allergens is consistent with clinical observations.

Availability: SDAP is available on the web at http://fermi.utmb.edu/SDAP/index.html

Contact: werner@newton.utmb.edu

* To whom correspondence should be addressed.
Finding motifs in the twilight zone
Authors: Keich U. , Pevzner P.A.
Published: October 2002

Motivation: Gene activity is often affected by binding transcription factors to short fragments in DNA sequences called motifs. Identification of subtle regulatory motifs in a DNA sequence is a difficult pattern recognition problem. In this paper we design a new motif finding algorithm that can detect very subtle motifs.

Results: We introduce the notion of a multiprofile and use it for finding subtle motifs in DNA sequences. Multiprofiles generalize the notion of a profile and allow one to detect subtle patterns that escape detection by the standard profiles. Our MULTIPROFILER algorithm outperforms other leading motif finding algorithms in a number of synthetic models. Moreover, it can be shown that in some previously studied motif models, MULTIPROFILER is capable of pushing the performance envelope to its theoretical limits.

Availability: http://www-cse.ucsd.edu/groups/bioinformatics/software.html

Contact: keich@cs.ucsd.edu

* To whom correspondence should be addressed.
GENOTRACE: cDNA-based local GENOme assembly from TRACE archives
Authors: Berezikov Eugene , Plasterk Ronald H.A. , Cuppen Edwin
Published: October 2002

Summary: GENOTRACE identifies the genomic organization for a cDNA using raw data from genome sequencing projects in progress (trace archives). Local genomic contigs are generated, allowing for example the design of PCR primers in intronic sequences to amplify coding regions of a gene, needed for example for mutation or SNP detection.

Availability: The package and examples of output files can be downloaded from http://rat.niob.knaw.nl/GENOTRACE

Contact: ecuppen@niob.knaw.nl

* To whom correspondence should be addressed.
CINEMA-MX: a modular multiple alignment editor
Authors: Lord P.W. , Selley J.N. , Attwood T.K.
Published: October 2002

Summary: Analyzing and visualizing multiple sequence alignments is a common task in many areas of molecular biology and bioinformatics. Many tools exist for this purpose, but are not easily customizable for specific in-house uses. Here we report the development of an editor, CINEMA-MX, that addresses these issues. CINEMA-MX is highly modular and configurable, and we present examples to illustrate its extensibility.

Availability: The program and full source code, which are available from http://www.bioinf.man.ac.uk/dbbrowser/cinema-mx, are being released under a combination of the LGPL and GPL, for Unix or Windows platforms.

Contact: p.lord@russet.org.uk

* To whom correspondence should be addressed at Department of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PL, UK
Study on a condition for forming the high density of silicon needles with high aspect ratio
Authors: Kanechika Masakazu , Sugimoto Noriaki , Mitsushima Yasuichi
Published: October 2002

We have developed a process to fabricate needle-shaped silicon crystals (silicon needles) by highly selective anisotropic dry etching. The etching masks are fine SiOx clusters in the silicon substrate. Under high density of these clusters, side etching easily occurs at the silicon needles in the process of dry etching. This mechanism is as follows. As the dry etching proceeds, the etching area becomes smaller and smaller due to existing high density of silicon needles. This leads to reduction in the deposition rate of sidewall passivation film, because gas for this film comes from the etched silicon substrate. Accordingly, for forming high density of the silicon needles, the deposition rate must be kept higher than the etching rate of the sidewall passivation film during the dry etching. By adjusting the deposition rate, we confirmed this mechanism and obtained high density 3×108 cm−2 of the silicon needles with an aspect ratio of 5 without side etching. Such silicon needles can be expected to lead to high emission current density and electric field enhancement when applying the silicon needles to a field emitter array.
SiGe-on-insulator substrate fabricated by melt solidification for a strained-silicon complementary metal–oxide–semiconductor
Authors: Sugii Nobuyuki , Yamaguchi Shinya , Washio Katsuyoshi
Published: October 2002

We have developed a novel technique for fabricating completely strain-relaxed SiGe-on-insulator substrates. It features melt solidification to solve the problems of high defect density and a rough surface concerning SiGe substrates for a strained-silicon complementary metal–oxide–semiconductor. The technique involves three main steps: (1) growth of a SiGe layer on a silicon-on-insulator (SOI) substrate, (2) SiO2 capping to prevent germanium evaporation during annealing, and (3) melting and solidifying the SiGe layer accompanied with germanium diffusion into the SOI layer. The defect density of the fabricated substrate is less than 1000 cm−2 and its surface roughness is 0.39 nm (rms).
Comparative study of SiOCH low-k films with varied porosity interacting with etching and cleaning plasma
Authors: Shamiryan D. , Baklanov M. R. , Vanhaelemeersch S. , Maex K.
Published: October 2002

The interaction between conventional and highly porous SiOCH with CF4, O2, and H2 plasma has been investigated. The highly porous SiOCH film has porosity about 40% and a k value about 2.2. The pristine SiOCH film has 19% of porosity and k value of 2.7. All experiments were performed at room temperature in a downstream plasma reactor. It was found that (i) the CF4 plasma etches the SiOCH film without bulk material modification (however, the etch rate was higher in the case of the SiOCH film with increased porosity); (ii) the O2 plasma oxidizes the SiOCH film converting the top layer to a hydrophilic SiO2-like porous material, the SiOCH film with increased porosity suffers more severely from this kind of plasma; (iii) the CF4/O2 plasma mixture has an optimal O2 concentration at which the etch rate is maximal; and (iv) the H2 plasma does not interact with the SiOCH film and can be a promising candidate for the resist stripping.
Quantitative evaluation of local charge trapping in dielectric stacked gate structures using Kelvin probe force microscopy
Authors: Lubarsky G. , Shikler R. , Ashkenasy N. , Rosenwaks Y.
Published: October 2002

We present a quantitative study of local charge injection into silicon nitride films inside dielectric stack gate structures. The charge is injected using atomic force microscope tips in direct contact with the dielectric layers. The charge distribution is imaged by measuring the contact potential difference between the atomic force microscope tip and the sample surface using Kelvin probe force microscopy. The trapped charge distribution and concentration is calculated using the two-dimensional Poisson equation. It is found that a peak trapped charge density of around 1×1012 cm−2 with a spreading of ∼250 nm is obtained using 15 V pulses of a few milliseconds in duration.
Copper sample analyzed with an n-doped silicon tip using conducting probe atomic force microscopy
Authors: Schneegans Olivier , Boyer Lionel , Houzé Frédéric , Meyer René , Chrétien Pascal
Published: October 2002

A study of the electrical properties of the nanocontact between a conducting tip made of n-doped silicon, and the surface of a cleaned copper sample has been carried out. Current–voltage (I–V) curves have been performed in order to clarify the electrical nature of the nanocontact. Apart from the breakdown phenomenon and the noticeable laser diode effect on the I–V curves, the nanocontact can be modeled by a Schottky diode, in series with a resistance of a few kΩ, which probably reflects the resistance of the semiconducting probe. This fact is partially confirmed by a simple calculation of the resistance of the tip/cantilever system using a rough model. Topographical and electrical images have also been recorded for a given tip/sample bias. For a positive sample–tip voltage, the copper surface appears uniformly conducting over 20×20 μm2, and remains stable during the whole period of study (three weeks). This study thus allows one to have a better understanding of the effects which must be kept in mind when using semiconducting tips to analyze conductive metal surfaces such as copper.
Interfacial reactions and Schottky barrier properties of composite patterned metal/GaN interfaces
Authors: Barinov A. , Gregoratti L. , Casalis L. , Kiskinova M.
Published: October 2002

Scanning photoelectron spectromicroscopy has been applied to study the interfacial chemistry and electronic properties of adjacent patterned Au and Ti/Au regions on GaN, fabricated by metal deposition at room temperature through appropriate masks. The lateral variations in the composition of the interfacial phases before and after annealing to 800 °C and their effect on local band bending are determined. The very small difference in the Schottky barrier heights measured in the adjacent Au/GaN and Ti/Au/GaN regions is identified as a property of the metal/GaN interfaces not predicted by the existing theoretical models.
Design of notched gate processes in high density plasmas
Authors: Foucher J. , Cunge G. , Vallier L. , Joubert O.
Published: October 2002

In less than ten years, we will be approaching the limits of the complementary metal-oxide-semiconductor technology with transistor gate length of between 10 and 30 nm. In the present article, we present a type of process allowing the design of gates having a bottom dimension smaller than the top dimension (the so-called “notched gate”). We discuss the design of the notched gate process with respect to a typical gate etch process and give some details on the sidewall passivation layer engineering. Finally, some results of critical dimension control across a 200-mm-diam wafer are shown and the potential implementation of the process in manufacturing is discussed.
Phase transformation of thin sputter-deposited tungsten films at room temperature
Authors: Rossnagel S. M. , Noyan I. C. , Cabral C.
Published: October 2002

Thin films of W have application in semiconductor interconnect structures as diffusion barriers and potentially as seed layers for electroplating. Thin W films have been deposited by sputtering [physical vapor deposition (PVD)] at near-room temperature, using Ar as the working gas, for evaluation of the electrical and structural properties of the films in the thickness range of 3 to 150 nm. Films deposited at 45 nm or greater thickness are composed of alpha (bcc) phase (only) with an electrical resistivity of 12 μΩ cm. Films deposited at thicknesses below 5 nm are mostly beta (A15 cubic) phase as-deposited with significantly higher resistivity, which is due partly to the phase and partly to electron-surface scattering (the “size effect”). In the thickness range of 5 to 45 nm, the as-deposited films are mostly beta phase and undergo transformation to the alpha phase at room temperature in tens of hours to several days. The resistivity also declines concurrently, as much as 70%. The exact mechanism driving the phase transformation is unclear, but is expected to be due to energy stored at grain boundaries and at the film–substrate interface coupled with the metastable nature of the beta phase. The transition is thermally driven and can be enhanced by heating or slowed by cooling. The effective activation energy for the phase transformation measured by the modified Kissenger method for the change in sheet resistance, the disappearance of the W-beta peaks, or the appearance of the W-alpha peaks has an average value of 1.1±0.2 eV. It does not appear that there is any critical thickness for the transition. However, since the deposition process for PVD-W is intrinsically hot, thicker films are effectively deposited at higher temperatures, which drives the beta-to-alpha transition to completion. Thicker films deposited cold (<20 °C) show beta-phase peaks, which then transform to alpha in 10–20 h at 25 °C. In addition, the scaling of the resistivity of the resultant alpha W with thickness suggests an electron scattering mean-free path of 10–12 nm, much below the reported 41 nm.
Positive resist for KrF excimer laser lithography
Authors: Park S. J. , Kim I. H. , Kang Y. J. , Lee H. , Lee S. H. , Choi S. J.
Published: October 2002

In order to develop a new positive-tone, chemically amplified photoresist for 248 nm lithography, a copolymer containing acrylic silicon moiety was synthesized. The copolymer of 1,3-bis(trimethylsilyl)isopropyl methacrylate and 4-hydroxystyrene was prepared by free radical polymerization. The polymer structure, properties and acid catalyzed deprotection were evaluated by H1 nuclear magnetic resonance, Fourier transform infrared, UV, thermogravimetric analysis and gel permeation chromatography. This polymer is thermally stable up to 150 °C and is suitably transparent at the KrF laser output wavelength (248 nm). The lithographic evaluation shows the capability of 0.28 μm resolution using a KrF excimer laser stepper.