bluuebunny/crossref_metadata_2025 huggingface dataset:
Spin‐density functional theory: Some open problems and application to inhomogeneous Heisenberg models
Authors: Capelle K. , Líbero Valter L.
Published: August 2005

Spin‐density functional theory (SDFT) is the most widely implemented and applied formulation of density functional theory. However, it is still finding novel applications, and occasionally encounters unexpected problems. In this article, we first briefly describe a few of the latter, related to issues such as nonuniqueness, noncollinearity, and currents. We then turn to an example of the former, namely SDFT for the Heisenberg model. It is shown that time‐honored concepts of Coulomb DFT, such as the local‐density approximation, can be applied to this (and other) model Hamiltonians, as well, once the concept of “density” has been suitably reinterpreted. Local‐density‐type approximations for the inhomogeneous Heisenberg model are constructed. Numerical applications to finite‐size and impurity systems demonstrate that DFT is a computationally efficient and reasonably accurate alternative to conventional methods of statistical mechanics for the Heisenberg model. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
Image retrieval with principal component analysis for breast cancer diagnosis on various ultrasonic systems
Authors: Huang Y.‐L. , Kuo S.‐J. , Chang C.‐S. , Liu Y.‐K. , Moon W. K. , Chen D.‐R.
Published: August 2005

Objectives

We present a computer‐aided diagnostic (CAD) system with textural features and image retrieval strategies for classifying benign and malignant breast tumors on various ultrasonic systems. Effective applications of CAD have used different types of texture analysis. Nevertheless, most approaches performed in a specific ultrasonic machine do not indicate whether the technique functions satisfactorily for other ultrasonic systems. This study evaluated a series of pathologically proven breast tumors using various ultrasonic systems.

Methods

Altogether, 600 ultrasound images of solid breast nodules comprising 230 malignant and 370 benign tumors were investigated. All ultrasound images were acquired from four diverse ultrasonic systems. The suspicious tumor area in the ultrasound image was manually chosen as the region‐of‐interest (ROI) subimage. Textural features extracted from the ROI subimage are supported in classifying the breast tumor as benign or malignant. However, the textural feature always behaves as a high‐dimensional vector. In practice, high‐dimensional vectors are unsatisfactory at differentiating breast tumors. This study applied the principal component analysis (PCA) to project the original textural features into a lower dimensional principal vector that summarized the original textural information. The image retrieval techniques were employed to differentiate breast tumors, according to the similarities of the principal vectors. The query ROI subimages were identified as malignant or benign tumors according to characteristics of retrieved images from the ultrasound image database.

Results

Using the proposed CAD system, historical cases could be directly added into the database without a retraining program. The area under the receiver–operating characteristics curve for the system was 0.970 ± 0.006.

Conclusion

The CAD system identified solid breast nodules with comparatively high accuracy in the different ultrasound systems investigated. Copyright © 2005 ISUOG. Published by John Wiley & Sons, Ltd.
The nuclear actin‐related protein Act3p/Arp4p is involved in the dynamics of chromatin‐modulating complexes
Authors: Sunada Rie , Görzer Irene , Oma Yukako , Yoshida Takahito , Suka Noriyuki , Wintersberger Ulrike , Harata Masahiko
Published: August 2005

Chromatin remodelling and histone‐modifying complexes govern the modulation of chromatin structure. While components of these complexes are diverse, nuclear actin‐related proteins (Arps) have been repeatedly found in these complexes from yeast to mammals. In most cases, Arps are required for functioning of the complexes, but the molecular mechanisms of nuclear Arps have as yet been largely unknown. The Arps and actin, sharing a common ancestor, are supposed to be highly similar in the three‐dimensional structure of their core regions, including the ATP‐binding pocket. The Arp Act3p/Arp4p of Saccharomyces cerevisiae exists within the nucleus, partly as a component of several high molecular mass complexes, including the NuA4 histone acetyltransferase (HAT) complex, and partly as uncomplexed molecules. We observed that mutations in the putative ATP‐binding pocket of Act3p/Arp4p increased its concentration in the high molecular mass complexes and, conversely, that an excess of ATP or ATPγS led to the release of wild‐type Act3p/Arp4p from the complexes. These results suggest a requirement of ATP binding by Act3p/Arp4p for its dissociation from the complexes. In accordance, a mutation in the putative ATP binding site of Act3p/Arp4p inhibited the conversion of the NuA4 complex into the smaller piccoloNuA4, which does not contain Act3p/Arp4p and exhibits HAT activity distinct from that of NuA4. Although the in vitro binding activity of ATP by recombinant Act3p/Arp4p was found to be rather weak, our observations, taken together, suggest that the ATP‐binding pocket of Act3p/Arp4p is involved in the function of chromatin modulating complexes by regulating their dynamics. Copyright © 2005 John Wiley & Sons, Ltd.
Cloning, sequencing and application of the LEU2 gene from the sour dough yeast Candida milleri
Authors: Turakainen Hilkka , Korhola Matti
Published: August 2005

We have cloned by complementation in Saccharomyces cerevisiae and sequenced a LEU2 gene from the sour dough yeast Candida milleri CBS 8195 and studied its chromosomal location. The LEU2 coding sequence was 1092 nt long encoding a putative β‐isopropylmalate dehydrogenase protein of 363 amino acids. The nucleotide sequence in the coding region had 71.6% identity to S. cerevisiae LEU2 sequence. On the protein level, the identity of C. milleri Leu2p to S. cerevisiae Leu2p was 84.1%. The DNA sequence of the C. milleri LEU2 gene was submitted to GenBank and assigned Accession No. AY571337. The CmLEU2 DNA probe hybridized to one to three chromosomal bands and two or three BamHI restriction fragments in C. milleri but did not give any signal to chromosomes or restriction fragments of C. albicans, S. cerevisiae, S. exiguus or Torulaspora delbrueckii. Using CmLEU2 probe for DNA hybridization makes it easy to quickly identify C. milleri among other sour dough yeasts. Copyright © 2005 John Wiley & Sons, Ltd.
A rapid and simple procedure for high‐efficiency lithium acetate transformation of cryopreserved Schizosaccharomyces pombe cells
Authors: Suga Minoru , Hatakeyama Toyomasa
Published: August 2005

A rapid, simple, convenient, and highly efficient transformation of the fission yeast Schizosaccharomyces pombe has been developed. Freezing fission yeast cells in glycerol, a permeating cryoprotectant, with lithium acetate improved remarkably the transformation efficiency by one to two orders of magnitude. The optimum concentration of glycerol was found to be 30%, which is higher than that (10–15%) in the conventional cryopreservation of yeast cells. Glycerol not only played a role in cryopreserving the competent cells but also improved the transformation efficiency of the process. The thawed cell suspension with glycerol and lithium acetate was immediately mixed with carrier DNA, plasmid DNA and polyethylene glycol. Next, the mixture was heat shocked and directly spread on a selection plate. This simple procedure yielded more than 106 transformants/µg plasmid DNA, reducing the time required to only 20 min in total, including the thawing time. Furthermore, the frozen competent cells were stored long‐term for more than 3 months without any significant loss of efficiency. Copyright © 2005 John Wiley & Sons, Ltd.
Hepatectomy as Treatment of Choice for Hepatocellular Carcinoma in Elderly Cirrhotic Patients
Authors: Ferrero Alessandro , Viganò Luca , Polastri Roberto , Ribero Dario , Tesoriere Roberto Lo , Muratore Andrea , Capussotti Lorenzo
Published: August 2005

In recent decades liver resection has become a safe procedure; however, the outcome of hepatectomies in aged cirrhotic patients is often uncertain. To elucidate early and long‐term outcomes of hepatectomy for HCC in the elderly, we studied 241 cirrhotic patients who underwent liver resection for HCC between 1985 and 2003. According to their age at the time of surgery, patients were divided into two groups: aged > 70 years (64 patients) and aged ≤ 70 years (177 patients). Operative mortality was 3.1% in the elderly and 9.6% in the younger group (p = 0.113). Postoperative morbidity and liver failure rates were higher in the younger group (42.4% versus 23.4%, p = 0.0073; 12.9% versus l.6%, p = 0.0065). Five‐year survival rates are 48.6% in the elderly group and 32.3% in the younger group (p = 0.081). Considering only radical resections in Child‐Pugh A patients, survival remains similar in the two groups (p = 0.072). Disease‐free survival is not different in the two groups. A survival analysis performed according to the tumor diameter shows a better survival for elderly Child‐Pugh A patients with HCC larger than 5 cm radically resected (50.8% versus 16.1% 5‐year survival, p = 0.034). In univariate analysis, tumor size is not a prognostic factor in the elderly, whereas younger patients with large tumors have a worse outcome. Age by itself is not a contraindication for surgery, and selected cirrhotic patients with HCC who are 70 years of age or older could benefit from resection, even in the presence of large tumors. Long‐term results of liver resections for HCC in the elderly may be even better than in younger patients.
Prevalence of Thyroid Nodules and Carcinomas in Patients Operated on for Renal Hyperparathyroidism: Experience with 339 Consecutive Patients and Review of the Literature
Authors: Seehofer Daniel , Rayes Nada , Klupp Jochen , Nüssler Natascha C. , Ulrich Frank , Graef Klaus‐Jürgen , Schindler Ralph , Steinmüller Thomas , Frei Ulrich , Neuhaus Peter
Published: August 2005

The association between renal hyperparathyroidism (HPT) and differentiated thyroid carcinoma is discussed. To determine the prevalence and potential risk factors, we performed a retrospective analysis of our patients (1998–2004) and compared the data with the data from other surgical and autopsy studies. At our hospital, a total of 347 parathyroidectomies in 339 patients with renal HPT were performed. Most patients underwent preoperative ultrasound investigation of the thyroid gland and, if indicate, thyroid scintigraphy. Intraoperatively, both thyroid lobes were mobilized and palpated. Detected thyroid nodules were adequately resected and investigated histologically. A systematic analysis of the international literature was performed using the PubMed/MEDLINE system to identify publications on the prevalence of papillary thyroid carcinoma (PTC) in patients with renal HPT and in the overall population. Altogether, 133 patients (39.2%) underwent simultaneous thyroid surgery. The initial operation was hemithyroidectomy in 55 (16.2%), Dunhill operation in 36 (10.6%), unilateral subtotal resection in 17 (5.0%), bilateral subtotal resection in 5 (1.5%), and enucleation of a thyroid nodule in 18 (5.3%). A PTC was found in 8 of 339 patients (2.4%) and a follicular thyroid carcinoma in 1. Among 311 patients with primary cervical operation, 6 (1.9%) had a papillary thyroid carcinoma. All papillary tumors were classified as pT1 with a diameter of 1 to 12 mm; three were bifocal, and only one patient had positive lymph nodes. None of the analyzed factors showed a significant correlation with the occurrence of thyroid carcinoma. Depending on the screening method, the prevalence of occult PTC in European autopsy studies ranged from 5% to 9% and was markedly higher in almost all studies than in the present one. The prevalence of PTC in the present study makes an etiologic association between renal HPT and PTC unlikely. The clinical significance of these tumors remains unclear becauses all incidental tumors were small. However, if easily and safely feasible, relevant thyroid nodules should be removed during parathyroid surgery.
Prospective Randomized Comparison between a New Mattress Technique and Cattell (duct‐to‐mucosa) Pancreaticojejunostomy for Pancreatic Resection
Authors: Langrehr Jan M. , Bahra Marcus , Jacob Dietmar , Glanemann Matthias , Neuhaus Peter
Published: August 2005

The majority of lethal complications after pancreatic head resection are due to septic complications after leakage from the pancreatojejunostomy. Especially the smooth pancreatic remnant is prone to develop parenchymal leaks from shear forces applied during tying of the sutures. We developed a new mattress technique that avoids such shear forces, and we compared this method to the standard Cattell (duct‐to‐mucosa) technique. A total of 113 patients undergoing standard pancreatic head resection were prospectively randomized to receive either the standard Cattell anastomosis (n = 56) or the new mattress technique (n = 57). All patients were evaluated for surgical and medical complications until discharge. Primary diagnosis and further demographic data compared well between the groups. The time to perform the mattress anastomosis was significantly shorter (15 vs. 22 minutes; p < 0.0001). The incidence of complications at the pancreatojejunostomy, and the length of hospital stay and survival were not significantly different between the two groups; however, a trend toward more reoperations was noted in the Cattell group (10 vs. 5; p < 0.097). The new mattress technique is simple, and our data show that the two techniques yield similar incidences of complications. Therefore the mattress technique for pancreatojejunostomy seems to be safe and is, in our opinion, well suitable for training schedules in pancreatic surgery.
What is the Role of Magnetic Resonance Imaging in the Evaluation of Total Hip Arthroplasty?
Authors: Potter Hollis G. , Foo Li F. , Nestor Bryan J.
Published: August 2005

MRI has been shown to be an extremely effective instrument in the management of painful hip arthroplasty. Its superior soft tissue contrast and direct multiplanar acquisition compared to computerized tomography (CT) and radiographs allows for reproducible visualization of periacetabular osteolysis, demonstrating compression of neurovascular bundles by extracapsular synovial deposits. In addition, MRI can often elucidate etiology of neuropathy in the perioperative period and is further helpful in evaluating the soft tissue envelope, including the attachment of the hip abductors, short external rotators and iliopsoas tendon. A further advantage of MRI over CT is its lack of ionizing radiation. Most importantly, MRI can disclose intracapsular synovial deposits that precede osteoclastic resorption of bone.
Analgesic efficacy and safety of intravenous paracetamol (acetaminophen) administered as a 2 g starting dose following third molar surgery
Authors: Juhl Gitte I. , Norholt Sven E. , Tonnesen Else , Hiesse‐Provost Odile , Jensen Troels S.
Published: August 2005

Background The recommended dose for intravenous (IV) paracetamol injection in adults is 1 g, however pharmacokinetic and pharmacodynamic findings suggest that a better analgesia could be obtained with a 2 g starting dose.

Methods A single‐centre, randomised, double‐blind, placebo‐controlled, 3‐parallel group study was performed to demonstrate the analgesic efficacy and safety of IV paracetamol 2 g. Following third molar surgery, patients reporting moderate to severe pain received a single 15‐min infusion of either IV paracetamol 2 g, IV paracetamol 1 g or placebo. Efficacy and safety were evaluated over 8 h. Laboratory tests were performed before and 48 h after drug administration.

Results Two hundred and ninety seven patients (132 = IV paracetamol 2 g; 132 = IV paracetamol 1 g; 33 = placebo) were randomised and completed the study. The summed pain relief over 6 h (TOTPAR6) was significantly superior with IV paracetamol 2 g as compared to IV paracetamol 1 g and placebo (p < 0.0001). Pain relief scores of IV paracetamol 2 g were significantly superior to IV paracetamol 1 g and to placebo from T30′ to T8h (p < 0.0001). Median duration of analgesia was significantly longer following IV paracetamol 2 g compared to IV paracetamol 1 g and placebo (p < 0.0001). Adverse events occurred with the same frequency in the 3 treatment groups. No clinically significant changes from baseline were observed for vital signs or laboratory tests.

Conclusion The analgesic efficacy of a 2 g starting dose of IV paracetamol was superior over the recommended dose of 1 g in terms of magnitude and duration of analgesic effect for postoperative pain following third molar surgery, with no significant difference between groups regarding safety.
Changes in linkage pattern of glucan products induced by substitution of Lys residues in the dextransucrase
Authors: Funane Kazumi , Ishii Tadashi , Ono Hiroshi , Kobayashi Mikihiko
Published: August 2005

Dextransucrase S (DSRS) is the only active glucansucrase that has been found in Leuconostoc mesenteroides NRRL B‐512F strain. Native DSRS produces mainly 6‐linked glucopyranosyl residue (Glcp), while Escherichia coli recombinant DSRS was observed to produce a glucan consisting of 70% 6‐linked Glcp and 15% 3,6‐Glcp. Lys residues were introduced at the N‐terminal end of the core domain by site‐directed mutagenesis. In glucans produced by the one‐point mutants T350K and S455K, the amount of 6‐linked Glcp was increased to about 85% of the total glucan produced, more similar in structure to native B‐512F dextran. The double mutant T350K/S455K produced adhesive, water‐insoluble glucan with 77% 6‐linked Glcp, 8% 3,6‐linked Glcp and 4% 2,6‐linked Glcp. The T350K/S455K mutant exhibited a 10‐fold increase in glucosyltransferase activity over those of the parental DSRS‐His6 and its T350K and S455K mutants. This is the first report demonstrating a change in the properties of a dextransucrase or a related glucosyltransferase through simple site‐directed mutagenesis to create 2,6‐linked Glcp.
Extreme total electron content along satellite‐to‐satellite ray paths
Authors: Kersley L. , Bailey G. J.
Published: August 2005

This paper reports results from an investigation into possible total electron content (TEC) on ray paths between GPS satellites and satellites in geostationary orbit. The Sheffield University Plasmasphere Ionosphere Model (SUPIM) has been used to estimate the TEC for conditions appropriate to solar maximum as a first step to assessing possible errors in the potential use of the navigation satellites for station keeping in the geostationary orbit. It has been found that in general, for paths through the plasmasphere, where the satellite‐to‐satellite geometry is far removed from eclipse by the Earth's horizon, the TEC is usually less than 20 TECU (total electron content units, 1 TECU = 1016 el m−2) with resultant errors in single‐frequency GPS positioning of a only a few meters. However, when the rays cross the equatorial F2 ionosphere at near‐grazing incidence close to the layer peak, TEC of up to some 2000 TECU have been found, with consequent potential single‐frequency GPS positioning uncertainties of hundreds of meters. The exact magnitudes of the TEC are very dependent on the precise geometry and vary significantly with time, so they would be difficult to simulate in any real‐time, model‐based mitigation system.
Clathrin‐independent internalization of the human histamine H1‐receptor in CHO‐K1 cells
Authors: Self Timothy J , Oakley Sarah M , Hill Stephen J
Published: August 2005

The aim of the present study was to investigate the cellular pathway involved in histamine‐stimulated internalization of the human H1‐receptor in CHO‐K1 cells expressing N‐terminal myc‐tagged H1‐receptor (Myc‐H1) or N‐terminal myc‐C‐terminal green fluorescent protein (Myc‐GFP H1) versions of the receptor.

Studies of3H‐mepyramine binding and histamine‐stimulated3H‐inositol phosphate accumulation in these cells showed that the Myc‐H1and Myc‐GFP H1‐receptors had identical pharmacology to the wild‐type H1‐receptor.

The Myc‐H1‐receptor was rapidly internalized in CHO‐K1 cells following stimulation with histamine (0.1 mM). This response occurred within 15 min, and could be prevented by the quaternary H1‐receptor antagonistα‐pirdonium. Similar data were obtained with the Myc‐GFP H1‐receptors.

Internalization of the Myc‐GFP H1‐receptor was maintained in the absence of extracellular calcium and was not inhibited by the CAM kinase II inhibitor KN‐62 (10 μM).

Phorbol dibutyrate, an activator of protein kinase C, was also able to stimulate internalization of the H1‐receptor. However, inhibition or downregulation of protein kinase C (which significantly modified histamine‐stimulated inositol phosphate responses) was without effect on the internalization of the H1‐receptor stimulated by histamine.

Hypertonic sucrose did not prevent histamine‐induced internalization of the Myc‐GFP H1‐receptor, but was able to attenuate internalization of transferrinviaclathrin‐mediated endocytosis in the same cells. In contrast, preincubation of cells with filipin or nystatin, which disrupts caveolae and lipid rafts, completely inhibited the histamine‐induced internalization of the Myc‐GFP H1‐receptor, but was without effect on the sequestration of transferrin.

The H1‐receptor and cholera toxin subunit B were colocalized under resting conditions at the cell surface. Immunohistochemical studies with an antibody to caveolin‐1 confirmed that this protein was also localized predominantly to the plasma membrane. However, following stimulation of CHO‐Myc‐GFP H1cells with histamine, there was no evidence for internalization of caveolin‐1 in parallel with the H1‐receptor.

These data provide strong evidence that the H1‐receptor is internalizedviaa clathrin‐independent mechanism and most likely involves lipid rafts.

British Journal of Pharmacology(2005)146, 612–624. doi:10.1038/sj.bjp.0706337
The role of p38 MAPK activation in auranofin‐induced apoptosis of human promyelocytic leukaemia HL‐60 cells
Authors: Park Seon‐Joo , Kim In‐Sook
Published: August 2005

In a previous study, we reported an antileukaemic activity of auranofin (AF), demonstrating its dual effects: on the induction of apoptotic cell death and its synergistic action with retinoic acid on cell differentiation. In this study, we investigated the downstream signalling events of AF‐induced apoptosis to determine the molecular mechanisms of AF activity.

Treatment of HL‐60 cells with AF induced apoptosis in a concentration‐ and time‐dependent manner. Western blot analysis showed that AF‐induced apoptosis was accompanied by the activation of caspase‐8, caspase‐9, and caspase‐3, and the release of cytochrome c from the mitochondria.

The phosphorylation and kinase activities of p38 mitogen‐activated protein kinase (p38 MAPK) increased gradually until 12 h after AF (2 μM) treatment, and p38 MAPK was also activated concentration‐dependently. Pretreatment with SB203580, a specific inhibitor of p38 MAPK, significantly blocked DNA fragmentation and the cleavage of procaspase‐8, procaspase‐3, and poly‐ADP‐ribose polymerase (PARP), whereas SB203580 alone had no effect.

Reactive oxygen species (ROS) were also detected within 1 h after AF treatment, and the antioxidant N‐acetyl‐L‐cysteine (NAC) effectively protected the cells from apoptosis by inhibiting the phosphorylation of p38 MAPK and the activation of caspases.

These results suggest that ROS generation and the subsequent activation of p38 MAPK are essential for the proapoptotic effects of AF in human promyelocytic leukaemia HL‐60 cells.

British Journal of Pharmacology (2005) 146, 506–513. doi:10.1038/sj.bjp.0706360
The regulatory subunits of fission yeast protein phosphatase 2A (PP2A) affect cell morphogenesis, cell wall synthesis and cytokinesis
Authors: Kinoshita Kazuhisa , Nemoto Takeshi , Nabeshima Kentaro , Kondoh Hiroshi , Niwa Hajime , Yanagida Mitsuhiro
Published: August 2005

Background:  Protein phosphatase 2A (PP2A) holoenzymes have a trimeric structure, consisting of a catalytic subunit C and two regulatory subunits A (PR65) and B (PR55). In fission yeast the C subunits, being 80% identical to their mammalian counterparts, are essential for viability and negatively regulate the entry into mitosis. Genetic analyses in budding yeast and Drosophila show that the regulatory subunits are implicated in chromosome segregation, cell morphogenesis and/or cytokinesis.

Results:  We isolated fission yeast genes paa1+ and pab1+ encoding the regulatory subunits PR65 and PR55, respectively. Gene disruption showed that the paa1+ gene was essential for viability while pab1+ was not required at 26–33°C. Microtubule and actin distributions were anomalous in gene disrupted Δpaa1 cells which were incapable of forming a polarized cell shape. Gene disrupted Δpab1 cells were pear‐ or round‐shaped, and lost the polar distributions of actin and microtubules. In addition, Δpab1 cells were defective in cell wall synthesis and sporulation at permissive temperatures. At restrictive temperatures, Δpab1 cells showed an osmoremedial temperature‐sensitive phenotype and delayed in cytokinesis. However, chromosome segregation was normal.

Conclusion:  Fission yeast PPZA regulatory subunit plays a critical role in cell morphogenesis, probably through regulation of the cytoskeletal network and cell wall synthesis.
Probing correlated spectral motion: Two-color photon echo study of Nile blue
Authors: Prall Bradley S. , Parkinson Dilworth Y. , Fleming Graham R.
Published: August 2005

We performed two-color three-pulse photon echo peak shift experiments on Nile blue in ethylene glycol and acetonitrile to determine the role of solvent dynamics in correlated spectral motion. The system was pumped near the absorption maximum and the correlation between the initial state and the final state was probed at a number of wavelengths, from the absorption maximum to the fluorescence maximum. In addition to solvent dynamics, we found that strongly coupled intramolecular vibrations generated correlations between different spectral regions. The inertial solvent response was found for both solvents to have a time scale on the order of 100–145 fs. This response contributed half of the solvent interaction strength for acetonitrile, but less than a third for ethylene glycol. Several diffusive time scales were observed: 500 fs and 2.5 ps for acetonitrile, and 1, 15, and 100 ps for ethylene glycol. A single description of the solvation dynamics was insufficient to quantitatively describe the dynamics at all probe wavelengths, which could indicate different dynamics in the ground and excited states or the presence of an additional contribution to the signal from the excited-state absorption.
Spectroscopy of Ar–SH and Ar–SD. II. Determination of the three-dimensional intermolecular potential-energy surface
Authors: Sumiyoshi Yoshihiro , Endo Yasuki
Published: August 2005

All the pure rotational transitions reported in the previous studies [J. Chem. Phys. 113, 10121 (2000); J. Mol. Spectrosc. 222, 22 (2003)] and newly observed rotation-vibration transitions, P=1∕2←3∕2, for Ar–SH and Ar–SD [J. Chem. Phys. (2005), the preceding paper] have been simultaneously analyzed to determine a new intermolecular potential-energy surface of Ar–SH in the ground state. A Schrödinger equation considering the three-dimensional freedom of motion for an atom-diatom complex in the Jacobi coordinate, R, θ, and r, was numerically solved to obtain energies of the rovibrational levels using the discrete variable representation method. A three-dimensional potential-energy surface is determined by a least-squares fitting with initial values of the parameters for the potential obtained by ab initio calculations at the RCCSD(T)/aug-cc-pVTZ level of theory. The potential well reproduces all the observed data in the microwave and millimeter wave regions with parity doublings and hyperfine splittings. Several low-lying rovibrational energies are calculated using the new potential-energy surface. The dependence of the interaction energy between Ar and SH(Πi2) on the bond length of the SH monomer is discussed.
Miscibility of small colloidal spheres with large polymers in good solvent
Authors: Hennequin Y. , Evens M. , Angulo C. M. Quezada , van Duijneveldt J. S.
Published: August 2005

Nearly athermal colloid-polymer mixtures were studied in the “protein limit.” A fluid-fluid transition was observed in mixtures of stearyl-alcohol-coated silica particles and large polystyrene coils in toluene. The ratios of the polymer radius of gyration to the particle radii were q=4.1 and q=5.2. The binodal curves and the critical points were determined. Turbidity measurements and analysis for one set of particles allowed the systems to be mapped onto hard sphere-polymer mixtures. A comparison with recent predictions for the miscibility of model mixtures shows that the experimental binodals lie between the two extreme results for ideal and interacting polymers. The critical colloid volume fraction is also found to decrease with increasing size ratios.
Nonequilibrium molecular dynamics of the rheological and structural properties of linear and branched molecules. Simple shear and poiseuille flows; instabilities and slip
Authors: Castillo-Tejas Jorge , Alvarado Juan F. J. , González-Alatorre Guillermo , Luna-Bárcenas Gabriel , Sanchez Isaac C. , Macias-Salinas Ricardo , Manero Octavio
Published: August 2005

Nonequilibrium molecular-dynamics simulations are performed for linear and branched chain molecules to study their rheological and structural properties under simple shear and Poiseuille flows. Molecules are described by a spring-monomer model with a given intermolecular potential. The equations of motion are solved for shear and Poiseuille flows with Lees and Edward’s [A. W. Lees and S. F. Edwards, J. Phys. C 5, 1921 (1972)] periodic boundary conditions. A multiple time-scale algorithm extended to nonequilibrium situations is used as the integration method, and the simulations are performed at constant temperature using Nosé-Hoover [S. Nosé, J. Chem. Phys. 81, 511 (1984)] dynamics. In simple shear, molecules with flow-induced ellipsoidal shape, having significant segment concentrations along the gradient and neutral directions, exhibit substantial flow resistance. Linear molecules have larger zero-shear-rate viscosity than that of branched molecules, however, this behavior reverses as the shear rate is increased. The relaxation time of the molecules is associated with segment concentrations directed along the gradient and neutral directions, and hence it depends on structure and molecular weight. The results of this study are in qualitative agreement with other simulation studies and with experimental data. The pressure (Poiseuille) flow is induced by an external force Fe simulated by confining the molecules in the region between surfaces which have attractive forces. Conditions at the boundary strongly influence the type of the slip flow predicted. A parabolic velocity profile with apparent slip on the wall is predicted under weakly attractive wall conditions, independent of molecular structure. In the case of strongly attractive walls, a layer of adhered molecules to the wall produces an abrupt distortion of the velocity profile which leads to slip between fluid layers with magnitude that depends on the molecular structure. Finally, the molecular deformation under flow depends on the attractive force of the wall, in such a way that molecules are highly deformed in the case of strong attracting walls.
Molecular self-diffusion in nanoscale cylindrical pores and classical Fick’s law predictions
Authors: Cui S. T.
Published: August 2005

Molecular-dynamics calculations are carried out to study the self-diffusion of water molecules confined in cylindrical pores. It is found that the classical Fick’s law description provides a surprisingly accurate prediction for the general behaviors of self-diffusion even for pore size of a few molecular diameters. The diffusion coefficient in the axial direction is reduced relative to bulk fluids for pore size less than about ten molecular diameters. In the radial direction, the mean-square displacement accurately follows Fick’s law prediction, but with an average diffusion coefficient slightly lower than the bulk value. The origin of the diffusion behaviors is traced to the molecular motion in the restricted geometry of the cylindrical pores.
First-principles modeling of electronic transport in π-stacked molecular junctions
Authors: Liu X.-Y. , Raynolds J. E. , Wells C. , Welch J. , Cale T. S.
Published: August 2005

A fundamental theoretical understanding of transport in molecular systems and contacts will play an important role in interpreting and guiding the realization of molecular interconnects. We have performed local-orbital-basis density-functional theory and Green’s-function-based simulations to determine the electronic structure and transport properties of π-stacked molecular junctions, which closely complement ongoing experimental studies. Surface slabs are used to model electrode contacts with molecules. We have used simulations to study I-V characteristics, applied voltage effects, and band alignments. The I-V results of geometry-confined phenolate∕benzenediazonium pairs between Au(111) surfaces show a substantial increase in currents at low bias voltages, compared with that of benzene-based molecular wires.
Lifetime of C2Cl4− ions produced by nondissociative electron attachment to C2Cl4
Authors: Liu Y. , Suess L. , Dunning F. B.
Published: August 2005

The lifetimes of long-lived C2Cl4− ions formed by Rydberg electron transfer in K(np)∕C2Cl4 collisions are investigated using a Penning ion trap. Measurements at high n, n⩾30, show that low-energy electron attachment to C2Cl4 leads to the production of C2Cl4− ions with a broad range of lifetimes that extends up to at least 1ms. This is attributed to capture by molecules in different initial vibrational states. At low n, internal-to-translational energy transfer in postattachment interactions between the product K+ and C2Cl4− ions becomes important and leads to a substantial increase in ion lifetimes.
Hexagonal close-packing structure on a cubic cell
Authors: Almarza N. G.
Published: August 2005

It is shown how the simulation of crystalline phases with hexagonal close-packing structure can be performed using cubic simulation boxes.
Determination of the chemical potential using energy-biased sampling
Authors: Delgado-Buscalioni R. , De Fabritiis G. , Coveney P. V.
Published: August 2005

An energy-biased method to evaluate ensemble averages requiring test-particle insertion is presented. The method is based on biasing the sampling within the subdomains of the test-particle configurational space with energies smaller than a given value freely assigned. These energy wells are located via unbiased random insertion over the whole configurational space and are sampled using the so-called Hit-and-Run algorithm, which uniformly samples compact regions of any shape immersed in a space of arbitrary dimensions. Because the bias is defined in terms of the energy landscape it can be exactly corrected to obtain the unbiased distribution. The test-particle energy distribution is then combined with the Bennett relation for the evaluation of the chemical potential. We apply this protocol to a system with relatively small probability of low-energy test-particle insertion, liquid argon at high density and low temperature, and show that the energy-biased Bennett method is around five times more efficient than the standard Bennett method. A similar performance gain is observed in the reconstruction of the energy distribution.
Ultralow threshold current terahertz quantum cascade lasers based on double-metal buried strip waveguides
Authors: Dhillon Sukhdeep , Alton Jesse , Barbieri Stefano , Sirtori Carlo , de Rossi A. , Calligaro M. , Beere Harvey E. , Ritchie David
Published: August 2005

Terahertz (THz) quantum cascade lasers based on a buried cavity geometry are demonstrated by combining double-metal waveguides with proton implantation. Devices are realized with emission at 2.8 THz, displaying ultralow threshold currents of 19 mA (127A∕cm2) at 4 K in both pulsed and continuous wave operation. Owing to the semiconductor material on both sides of the active region and to the narrow width of the top metal strip, the thermal properties of these devices have been greatly improved. A decrease of the thermal resistance by over a factor of two compared to standard ridge double-metal lasers of similar size has been measured.
Fast switching of bistable magnetic nanowires through collective spin reversal
Authors: Vindigni Alessandro , Rettori Angelo , Bogani Lapo , Caneschi Andrea , Gatteschi Dante , Sessoli Roberta , Novak Miguel A.
Published: August 2005

The use of magnetic nanowires as memory units is made possible by the exponential divergence of the characteristic time for magnetization reversal at low temperature, but the slow relaxation makes the manipulation of the frozen magnetic states difficult. We suggest that finite-size segments can show a fast switching if collective reversal of the spins is taken into account. This mechanism gives rise at low temperatures to a scaling law for the dynamic susceptibility that has been experimentally observed for the dilute molecular chain Co(hfac)2NitPhOMe. These results suggest a possible way of engineering nanowires for fast switching of the magnetization.
Critical current, pinning, and the resistive state of superconducting single-crystal niobium with various types of defect structure
Authors: Sokolenko V. I. , Starodubov Ya. D.
Published: August 2005

The critical current, pinning, and resistive state of single-crystal niobium of texture orientation are studied in various structural states obtained by rolling by 42% at 20 K and subsequent polishing of the surface layers. It is found that the heterogeneous structures typical of the strained sample have a lower current-carrying capacity even after thinning to ∼10% on account of the enhancement of the thermomagnetic instability in the parts with fragmented structure in the subsurface layers. For the case of a homogeneous defect structure of the mid-region of a sample with a uniformly distributed dislocation density of 1.3×1011 cm−2 in the resistive state a correlation between the component of the normal current and the critical current density is found, in accordance with the concepts of flux creep due to the scatter of the local values of Jc.
Dynamic behavior of Josephson-junction qubits: crossover between Rabi oscillations and Landau–Zener transitions
Authors: Shevchenko S. N. , Kiyko A. S. , Omelyanchouk A. N. , Krech W.
Published: August 2005

We study the dynamic behavior of a quantum two-level system with periodically varying parameters by solving numerically the master equation for the density matrix. Two limiting cases are considered: multiphoton Rabi oscillations and Landau–Zener transitions. The approach is applied to the description of the dynamics of superconducting qubits. In particular, the case of the interferometer-type charge qubit with periodically varying parameters (gate voltage or magnetic flux) is investigated. The time-averaged energy level populations are calculated as functions of the qubit’s control parameters.
Spectrum of nonlinear excitations of modulated nanoclusters
Authors: Bogdan M. M. , Kovalev A. S. , Malyuta E.
Published: August 2005

The nonlinear dynamics of a chain of four coupled anharmonic oscillators with alternating frequency parameters is investigated. This system is treated as an elementary fragment of a discrete modulated nonlinear medium, in particular, a medium of magnetic and elastic nanoclusters and coupled optical waveguides. The stationary monochromatic oscillations of the system are investigated analytically and numerically, and a complete classification of them is carried out. The bifurcation diagram for such a system is obtained: the spectral dependences of the oscillation frequencies on the integral of the number of states are found. A detailed investigation of the bifurcation process for the appearance of an excitation which is an analog of the gap soliton in a finite-size modulated medium is carried out.
On the sequence of quantum (meta)magnetic transitions in Ising antiferromagnets with single-ion anisotropy
Authors: Kalita V. M. , Loktev V. M.
Published: August 2005

A simple interpretation is proposed for the series of magnetization jumps observed in two-sublattice Ising antiferromagnets with single-ion anisotropy of the easy-plane type in a longitudinal external field.
Observation of mechanoelectric effect in He II
Authors: Rybalko A. S. , Rubets S. P.
Published: August 2005

An experimental study of the electrical response in He4 in the temperature interval 1.5–Tλ is investigated experimentally by the torsion generator technique. It is shown that the motion of the normal component of He II, entrained by the wall of the torsion oscillator, causes dynamic polarization of the liquid. It is established that the induction potential is proportional to the square of the linear velocity of the oscillator wall.
The superfluid vortex cooler
Authors: Tanaeva I. A. , de Waele A. T. A. M. , Lindemann U. , Jiang N. , Thummes G.
Published: August 2005

In this contribution a superfluid vortex cooler (SVC) is described. A SVC is a cooling device, the operation of which is based on the special properties of superfluid helium (HeII). The SVC is small, simple, has no moving parts, and is gravity independent. It is capable of reaching temperatures as low as 0.65K. First we have carried out a number of experiments, using a liquid-helium bath as a precooler for the SVC. Various geometries of the cooler components as well as the influence of the working pressure and the base temperature on the performance of the cooler have been investigated. Temperature below 1K have been reached with a base temperature of 1.4K. The next step has been combining the SVC with a pulse-tube refrigerator. In a preliminary experiment a lowest temperature of 1.19K has been reached. Several ways to improve the system are suggested.
Self-affine roughness influence on the pull-in voltage in capacitive electromechanical devices
Authors: Palasantzas G.
Published: August 2005

In this work we investigate the influence of self-affine roughness parameters on the pull-in voltage in capacitive microelectromechanical devices. The capacitor plate roughness is considered as self-affine type, which is described by the roughness amplitude w, the lateral correlation length ξ, and the roughness exponent H. By comparing the influence of the three parameters, we confirm that not only the long-wavelength roughness parameters w and ξ, but also the short-wavelength fine roughness details, as described by the roughness exponent H, play a major role. Therefore, the proper characterization of the involved surface roughness and its evolution at all relevant length scales are necessary to gauge properly the performance of associated devices.
High-temperature degradation of NiSi films: Agglomeration versus NiSi2 nucleation
Authors: Deduytsche D. , Detavernier C. , Van Meirhaeghe R. L. , Lavoie C.
Published: August 2005

The thermodynamical and morphological stability of NiSi thin films has been investigated for layers of thickness ranging from 10to60nm formed on either silicon-on-insulator (SOI), polycrystalline silicon, or preannealed polycrystalline silicon substrates. The stability of the films was evaluated using in situ x-ray-diffraction, sheet resistance, and laser light-scattering measurements. For NiSi films that are thinner than 20nm, agglomeration is the main degradation mechanism. For thicker films, the agglomeration of NiSi and nucleation of NiSi2 occur simultaneously, and both degradation mechanisms influence each other. Significant differences were observed in the degradation of the NiSi formed on different substrates. Surprisingly, agglomeration is worse on SOI substrates than on poly-Si substrates, suggesting that the texture of the NiSi film plays an important role in the agglomeration process. As expected, preannealing of the polycrystalline silicon substrate prior to metal deposition results in a significant improvement of the thermal stability of the NiSi layers.
Strain and composition profiles of self-assembled Ge∕Si(001) islands
Authors: Alonso M. I. , de la Calle M. , Ossó J. O. , Garriga M. , Goñi A. R.
Published: August 2005

Epitaxial growth of Ge∕Si(001) in the Stranski-Krastanow regime results in the formation of island ensembles with various sizes and morphologies. During formation there is generally a strain-driven Si diffusion into the Ge islands. We investigate this issue in an epilayer grown by molecular-beam epitaxy containing pyramids, domes, and superdomes. A series of samples obtained by wet chemical etching of the original layer for different times in diluted hydrogen peroxide was evaluated by atomic force microscopy, spectroscopic ellipsometry, and Raman scattering. The average island composition as etching proceeds becomes Si richer, changing from about Si0.2Ge0.8 to Si0.35Ge0.65, whereas the lattice strain increases, in particular, the material at the island summits is essentially relaxed. The composition of the wetting layer is nearly Si0.45Ge0.55. The results also reveal relatively Si-rich nuclei of a uniform size of ≃100nm for all domes and superdomes, in accordance with a dislocation-induced growth mechanism of superdomes.
Spin-enhanced magnetocaloric effect in molecular nanomagnets
Authors: Evangelisti Marco , Candini Andrea , Ghirri Alberto , Affronte Marco , Brechin Euan K. , McInnes Eric J. L.
Published: August 2005

An unusually large magnetocaloric effect for the temperature region below 10 K is found for the Fe14 molecular nanomagnet. This is to large extent caused by its extremely large spin S ground state combined with an excess of entropy arising from the presence of low-lying excited S states. We also show that the highly symmetric Fe14 cluster core, resulting in small cluster magnetic anisotropy, enables the occurrence of long-range antiferromagnetic order below TN=1.87K.
Excitation spectroscopy of two-electron shell structures in carbon nanotube quantum dots in magnetic fields
Authors: Moriyama S. , Fuse T. , Aoyagi Y. , Ishibashi K.
Published: August 2005

Single-quantum dots have been fabricated in an individual single-wall carbon nanotube, and the single-electron-transport measurements have been carried out at 40 mK. Coulomb diamonds showed an alternate change of the diamond size, an even-odd effect, indicating the two-electron shell filling. An excitation spectroscopy in which a Coulomb oscillation peak was measured in magnetic fields with a large source-drain bias voltage revealed the Zeeman splitting of single-particle states. The results suggest an important step for preparation of the spin two-level system.
Sidewalls contribution in integrated three-dimensional Sr0.8Bi2.2Ta2O9-based ferroelectric capacitors
Authors: Menou N. , Turquat Ch. , Madigou V. , Muller Ch. , Goux L. , Lisoni J. , Schwitters M. , Wouters D. J.
Published: August 2005

As compared to usual planar capacitors, three-dimensional (3D) ferroelectric capacitors display a large polarization increase due to the additional electrical contribution of the capacitor sidewalls. However, in 3D capacitors the polarization increase with respect to the planar geometry is lower than expected. To uncover the origin of this discrepancy, the microstructure of 3D Sr0.8Bi2.2Ta2O9-based (SBT) capacitors was studied. First, high-resolution synchrotron x-ray diffraction has found a unit cell expansion of the SBT phase in the capacitor sidewalls. From local chemical analyses, this lattice distortion has been correlated to composition variations in this region. These microstructural changes are due to the peculiar topography of the etched bottom electrode and to the variety of layers in contact with the SBT film, which can explain the nonoptimized polarization in 3D capacitors.