bluuebunny/crossref_metadata_2025 huggingface dataset:
Predicting DNA–intercalator binding: the development of an arene–arene stacking parameter from SAPT analysis of benzene‐substituted benzene complexes
Authors: Hardebeck Laura K. E. , Johnson Charles A. , Hudson Graham A. , Ren Yi , Watt Michelle , Kirkpatrick Charles C. , Znosko Brent M. , Lewis Michael
Published: August 2013

A series of substituted naphthalimides were synthesized and intercalated into the DNA sequence d(GCGCGCGC)2, and an experimental ΔTm value was obtained. Two‐parameter QSAR analyses were performed to generate a theoretical ΔTm value. Although by no means exhaustive in terms of parameter selection, the correlations did not yield statistics that indicated the models met the threshold for significance at the 95% confidence level. Rather than continue with an exhaustive search of all possible QSAR parameters, a one‐parameter QSAR analysis was performed utilizing a novel arene–arene stacking parameter, designated Ππ, developed from Symmetry‐Adapted Perturbation Theory (SAPT) energy decomposition studies of calculated benzene‐substituted benzene dimer binding energies. The QSAR analysis using the Ππ stacking parameter yielded statistics suggesting the model was significant at the 95% confidence level. The approach of developing a novel QSAR parameter via SAPT calculations, rather than exhaustively searching all traditional QSAR parameters, is presented both as a new approach for QSAR studies and as a unique application of SAPT. Copyright © 2013 John Wiley & Sons, Ltd.
Isotope dilution assay in peptide quantification: The challenge of microheterogeneity of internal standard
Authors: Stoyanov Alexander V. , Rogatsky Eduard , Stein Daniel , Connolly Shawn , Rohlfing Curt L. , Little Randie R.
Published: August 2013

Isotope dilution analysis allows quantitation of elements and different compounds in complex mixtures. The quantitation is based on a known amount of reference material (internal standard, IS) added to a sample that makes the result critically dependent on the value assigned to the standard. In the case of peptides, IS concentration is determined by nitrogen and amino acid analysis while purity is normally assessed by methods such as chromatography or electrophoresis that might not be able to detect many possible amino acid modifications, either naturally occurring or chemically induced. Microheterogeneity of the IS, if it is not accounted for when assigning a reference value to the standard, results in highly overestimated values in target analyte quantitation. In this viewpoint article, we illustrate the problem of internal standard microheterogeneity by analyzing synthetic human C‐peptide labeled analogs.
Identification of small peptides inhibiting the integrase‐LEDGF/p75 interaction through targeting the cellular co‐factor
Authors: Cavalluzzo Claudia , Christ Frauke , Voet Arnout , Sharma Ajendra , Singh Brajendra Kumar , Zhang Kam Y.J. , Lescrinier Eveline , De Maeyer Marc , Debyser Zeger , Van der Eycken Erik
Published: August 2013

The integration of the viral DNA into the host genome is one of the essential steps in the HIV replication cycle. This process is mediated by the viral enzyme integrase (IN) and lens epithelium‐derived growth factor (LEDGF/p75). LEDGF/p75 has been identified as a crucial cellular co‐factor of integration that acts by tethering IN to the cellular chromatin. Recently, circular peptides were identified that bind to the C‐terminal domain of IN and disrupt the interaction with LEDGF/p75. Starting from the circular peptides, we identified a short peptidic sequence able to inhibit the LEDGF/p75‐IN interaction at low μM concentration through its binding to the IN binding site of LEDGF/p75. This discovery can lead to the synthesis of peptidomimetics with high anti‐HIV activity targeting the cellular co‐factor LEDGF/p75 and not the viral protein IN. Copyright © 2013 European Peptide Society and John Wiley & Sons, Ltd.
Robust‐decentralized tracking control for a class of uncertain MIMO nonlinear systems with time‐varying delays
Authors: Yu Yao , Sun Chang‐Yin , Jiao Zhuang
Published: August 2013

A new control design method based on signal compensation is proposed for a class of uncertain multi‐input multi‐output (MIMO) nonlinear systems in block‐triangular form with nonlinear uncertainties, unknown virtual control coefficients, strongly coupled interconnections, time‐varying delays, and external disturbances. By this method, the controller design is performed in a backstepping manner. At each step of backstepping procedure, a nominal virtual controller is first designed to get desired output tracking for the nominal disturbance‐free subsystem, and then a robust virtual compensator is designed to restrain the effect of the uncertainties, delays involved in the subsystem, and the couplings among the subsystems. The designed controller is linear and time‐invariant, so the explosion of complexity in the control law is avoid. It is proved that robust stability and robust practical tracking property of the closed‐loop system can be ensured, and the tracking errors can be made as small as desired. Copyright © 2013 John Wiley & Sons, Ltd.
Engineering the pH‐Responsive Catalytic Behavior of AuNPs by DNA
Authors: Zhan Pengfei , Wang Jinye , Wang Zhen‐Gang , Ding Baoquan
Published: August 2013

Noble metal nanoparticles have attracted much interest in the heterogeneous catalysis. Particularly, efficient manipulation of the responsive catalytic properties of the metal nanoparticles is an interesting topic. In this work, a simple and efficient strategy is developed to regulate the pH‐responsive catalytic activities of glucose oxidase (GOx)‐mimicking gold nanoparticles (AuNPs). Four DNA strands (regulating strands) that differ slightly in sequences are used to interact non‐covalently with citrate‐capped AuNPs, resulting in markedly distinct pH‐dependent catalytic behavior of AuNPs. This is ascribed to the characteristic pH‐induced conformational change of the DNA strands that leads to the different adsorption capability to the NPs surface, as demonstrated by pH‐CD profiles of the respective DNA molecules. The pH‐dependent catalysis of AuNPs is also encoded with structural information of the double‐stranded DNA (including regulating strands and their complementary strands) that has conformation resistant or responsive to pH change. As a result, the catalysis can be programmed into an AND gate, a XNOR gate or a NOT gate, using pH and complementary strand as the inputs, the nanoparticle activity as the output and the regulating strands as the programs. This work can be expanded by engineering the catalytic behavior of noble metal nanoparticles to respond smartly to a variety of environmental stimuli, such as metal ions or light wavelengths. These results may provide insight into understanding ligand‐regulated nanometallic catalysis.
Early Cretaceous sedimentation and orogeny on the active margin of Eurasia: Southern Central Pontides, Turkey
Authors: Okay Aral I. , Sunal Gürsel , Sherlock Sarah , Alt��ner Demir , Tüysüz Okan , Kylander‐Clark Andrew R. C. , Aygül Mesut
Published: August 2013

The Pontides in northern Turkey constituted part of the southern active margin of Eurasia during the Mesozoic. In the Early Cretaceous, a large submarine turbidite fan covered most of the Central Pontides. New U‐Pb detrital zircon data imply that the major source of the turbidites was the East European Craton‐Scythian Platform in the north. This implies that there was no thoroughgoing Black Sea basin between the Pontides and the East European Craton during the Early Cretaceous. The Lower Cretaceous turbidites are bounded in the south by a large metamorphic area, the Central Pontide Supercomplex (CPS). New geological mapping, petrology, and U‐Pb zircon and Ar‐Ar muscovite ages indicate that the northern part of the CPS consists of Lower Cretaceous distal turbidites deformed and metamorphosed in a subduction zone in the Albian. The rest of the CPS is made of Middle Jurassic, Lower Cretaceous, and middle Cretaceous (Albian) metamorphic belts, each constituting distinct subduction‐accretion units. They represent episodes of collision of oceanic volcanic arcs and oceanic plateaus with the Eurasian margin and are marked in the stratigraphy of the hinterland by periods of uplift and erosion. The accretionary complexes are overlain by Upper Cretaceous (Turonian‐Santonian) volcano‐sedimentary sequences deposited in a fore‐arc setting. The detrital zircon data, middle Cretaceous (Albian) metamorphism, and widespread Albian uplift of the Black Sea region suggest that Early Cretaceous (Barremian‐Aptian) nonvolcanic rifting and Late Cretaceous (Turonian‐Santonian) opening of the Black Sea by the splitting of the arc are unrelated events.
The power of coarse graining in biomolecular simulations
Authors: Ingólfsson Helgi I. , Lopez Cesar A. , Uusitalo Jaakko J. , de Jong Djurre H. , Gopal Srinivasa M. , Periole Xavier , Marrink Siewert J.
Published: August 2013

Computational modeling of biological systems is challenging because of the multitude of spatial and temporal scales involved. Replacing atomistic detail with lower resolution, coarse grained (CG), beads has opened the way to simulate large‐scale biomolecular processes on time scales inaccessible to all‐atom models. We provide an overview of some of the more popular CG models used in biomolecular applications to date, focusing on models that retain chemical specificity. A few state‐of‐the‐art examples of protein folding, membrane protein gating and self‐assembly, DNA hybridization, and modeling of carbohydrate fibers are used to illustrate the power and diversity of current CG modeling.

This article is categorized under:

Molecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods
Prediction of pathological mutations in proteins: the challenge of integrating sequence conservation and structure stability principles
Authors: Riera Casandra , Lois Sergio , de la Cruz Xavier
Published: August 2013

The recent drop in genome sequencing costs has created a promising horizon for the development of genomic medicine. Within the biomedical environment, sequencing data are increasingly used for disease diagnosis and prognosis, treatment development, counseling, and so on. Many of these applications rely on the identification of disease causing variants. This is a particularly challenging problem because of the large number and wide variety of sequence variants identified in sequencing projects, and also because we only have a limited understanding of the physicochemical/biochemical properties that differentiate neutral from pathologic variants. Nonetheless, these last years have witnessed important methodological advances for one class of variants, those corresponding to changes in the amino‐acid sequence of proteins. Proteins are a main constituent of living systems. We know that although their biological properties are essentially determined by the amino‐acid sequence, not all the changes in this sequence have the same impact. Some are neutral, but others affect protein function and lead to disease. A large body of evidence shows that whether one or the other is the case that depends on properties such as mutation location in the protein structure, interspecies conservation, and so on. Mutation prediction methods based on these features have good success rates, in the 70–90% range, although representation over time suggests there is a performance plateau that would limit their applicability. In light of the most recent advances in the field, and after reviewing the foundations of prediction methods, we discuss the existence of this performance threshold and how it can be overcomed.

This article is categorized under:

Computer and Information Science > Databases and Expert Systems
Hepatic Artery Reconstruction in Living Donor Liver Transplantation: Risk Factor Analysis of Complication and a Role of MDCT Scan for Detecting Anastomotic Stricture
Authors: Marubashi Shigeru , Kobayashi Shogo , Wada Hiroshi , Kawamoto Koichi , Eguchi Hidetoshi , Doki Yuichiro , Mori Masaki , Nagano Hiroaki
Published: August 2013

Background

In partial liver transplantation, reconstruction of the hepatic artery is technically highly demanding and the incidence of arterial complications is high. We attempted to identify the risk factors for anastomotic complications after hepatic artery reconstruction and examined the role of multidetector‐row computed tomography (MDCT) in the evaluation of the reconstructed hepatic artery in liver transplant recipients.

Methods

A total of 109 adult‐to‐adult living donor liver transplantations (LDLT) were performed at our institute between 1999 and July 2011. Hepatic artery reconstruction was performed under a surgical microscope (MS group, n = 84), until we began to adopt surgical loupes (4.5×) for arterial reconstructions in all cases after January 2009 (SL group, n = 25). A dynamic MDCT study was prospectively carried out on postoperative days 7, 14, and 28, and at postoperative month 3, 6, and 12 after April 2005 (n = 60).

Results

There were no cases of hepatic artery thrombosis and six cases (5.5 %) of interventional radiology‐confirmed hepatic artery stenosis (HAS). Risk factor analysis for HAS showed that ABO‐incompatible LDLT was associated with HAS. Use of surgical loupes provided superior results as compared to anastomosis under a surgical microscope, and it also provided the advantage of reduced operative time. The MDCT procedure was useful for detecting HAS; however, the false positive rate was relatively high until 3 months after the LDLT (100 % sensitivity and 72.8 % specificity at 3 months).

Conclusions

Hepatic arterial anastomosis using surgical loupes tended to be time‐saving and to yield similar or better results than traditional microscope‐anastomosis. The use of MDCT aided the diagnosis of HAS, although the substantial false positive rate should be borne in mind in clinical practice.
Airtight Tracheocutaneostomy After Window Resection of the Trachea for Invasive Papillary Thyroid Carcinoma: Experience of 109 Cases
Authors: Ito Yasuhiro , Miyauchi Akira , Kihara Minoru , Higashiyama Takuya , Kobayashi Kaoru , Miya Akihiro
Published: August 2013

Background

There are some tracheal surgeries for invasive papillary thyroid carcinoma (PTC) requiring tracheal resection. We create an airtight tracheocutaneostomy (TCS) by suturing the tracheal hole to the skin when window resection of the trachea is required. Here, we present the outcomes of PTC patients who underwent surgery with airtight TCS.

Methods

We enrolled 109 patients (18 males and 91 females) who underwent initial surgery for PTC and TCS after partial window resection of the trachea between 1987 and 2010. The average patient age was 61 and the average follow‐up was 99 months. The TCS was closed using a local skin flap 3–6 months after surgery in 78 patients, and it closed spontaneously in 13 patients. The TCS of the remaining 18 patients was not closed for various reasons, such as a poor general condition, permanent bilateral vocal cord paralysis, and loss to follow‐up.

Results

None of the 109 patients showed any serious complications of TCS. Minor wound infection, partial skin necrosis, granulation, and air leakage were observed in 12 (11 %), 2 (2 %), 7 (6 %), and 4 (4 %) patients, respectively. Infection was more likely to occur in patients whose cricoid cartilage was resected (p = 0.0456). Although macroscopically curative surgery was performed for all patients, 38 patients (35 %) had a suspiciously positive margin in the resected tracheal mucosa. Five margin‐positive (13 %) and five margin‐negative (7 %) patients showed excision site recurrence, but the margin status did not directly affect the prognosis. External beam radiation therapy (EBRT) (50–60 Gy) was administered to nine patients, none of whom showed excision site recurrence, although eight were microscopically margin‐positive. Among various clinicopathological features, tumor size > 4 cm and age ≥ 60 years were significant (p = 0.0281) and marginal (p = 0.0771) predictors of excision site recurrence on univariate analysis. On multivariate analysis, age ≥ 60 years (p = 0.0484) and tumor size > 4 cm (p = 0.0763) were independent and marginal predictors of excision site recurrence, respectively. To date, 14 and 17 patients have shown lymph node and distant recurrence, respectively, and nine have died of PTC.

Conclusions

Tracheocutaneostomy is a safe surgical technique after partial window resection of the trachea, although we have to be careful of infection when resecting the cricoid cartilage. Large tumor size and old age are risk factors for excision site recurrence. EBRT may be useful to prevent excision site recurrence, especially in patients with a suspected positive margin.
Broadband light trapping in thin organic photovoltaic cells using plasmonic resonant antennas
Authors: Le Khai Q.
Published: August 2013

A numerical investigation of plasmonic resonant antennas influence on optical absorption efficiency of organic photovoltaic (PV) cells with thin active layers is reported. Integrating cylindrical Ag antennas on PV cells can enhance absorption efficiency by up to 22%, over a broad bandwidth of operation. This corresponds to an increase in integrated AM1.5G absorption at normal incidence from 48 to 58.5%. Broadband enhancement is observed for transverse-electric and transverse-magnetic polarized incident light, over a wide angle range. It is attributed to plasmonic antennas converting incident sunlight to surface plasmon resonant modes, localized around the antenna/polymer active layer interface. This results in a strong field enhancement in the active layer and enhances absorption efficiency.
Reorientational dynamics in molecular liquids as revealed by dynamic light scattering: From boiling point to glass transition temperature
Authors: Schmidtke B. , Petzold N. , Kahlau R. , Rössler E. A.
Published: August 2013

We determine the reorientational correlation time τ of a series of molecular liquids by performing depolarized light scattering experiments (double monochromator, Fabry-Perot interferometry, and photon correlation spectroscopy). Correlation times in the range 10−12 s–100 s are compiled, i.e., the full temperature interval between the boiling point and the glass transition temperature Tg is covered. We focus on low-Tg liquids for which the high-temperature limit τ ≅ 10−12 s is easily accessed by standard spectroscopic equipment (up to 440 K). Regarding the temperature dependence three interpolation formulae of τ(T) with three parameters each are tested: (i) Vogel-Fulcher-Tammann equation, (ii) the approach recently discussed by Mauro et al. [Proc. Natl. Acad. Sci. U.S.A. 106, 19780 (2009)], and (iii) our approach decomposing the activation energy E(T) in a constant high temperature value E∞ and a “cooperative part” Ecoop(T) depending exponentially on temperature [Schmidtke et al., Phys. Rev. E 86, 041507 (2012)]10.1103/PhysRevE.86.041507. On the basis of the present data, approaches (i) and (ii) are insufficient as they do not provide the correct crossover to the high-temperature Arrhenius law clearly identified in the experimental data while approach (iii) reproduces the salient features of τ(T). It allows to discuss the temperature dependence of the liquid's dynamics in terms of a Ecoop(T)/E∞ vs. T/E∞ plot and suggests that E∞ controls the energy scale of the glass transition phenomenon.
Strain driven migration of In during the growth of InAs/GaAs quantum posts
Authors: Alonso-Álvarez D. , Alén B. , Ripalda J. M. , Rivera A. , Taboada A. G. , Llorens J. M. , González Y. , González L. , Briones F.
Published: August 2013

Using the mechano-optical stress sensor technique, we observe a counter-intuitive reduction of the compressive stress when InAs is deposited on GaAs (001) during the growth of quantum posts. Through modelling of the strain fields, we find that such anomalous behaviour can be related to the strain-driven detachment of In atoms from the crystal and their surface diffusion towards the self-assembled nanostructures.
Multiphysics of ionic polymer–metal composite actuator
Authors: Zhu Zicai , Asaka Kinji , Chang Longfei , Takagi Kentaro , Chen Hualing
Published: August 2013

Water-based ionic polymer–metal composites (IPMCs) exhibit complex deformation properties, especially with decreasing water content. Based on our experimental understanding, we developed a systemic actuation mechanism for IPMCs in which the water swelling was taken as the basic cause of deformation. We focused on Nafion-IPMC, and formulated a multiphysical model to describe the complicated deformation properties. The model emphasizes pressure-induced convection fluxes and the significance of the water distribution on deformation. It shows that there are three eigen stresses activated by the migration of ions and water, namely, osmotic pressure, electrostatic stress, and capillary pressure. The model also provides a convenient way of simultaneously handling the internal eigen stresses and the external mechanical load. In this paper, we used a fundamental model, which only considered the hydrostatic pressure in the multiphysical model, to analyze the general transport properties of cations and water by numerical methods. Three effects were investigated: (1) the inter-coupling effects between cations and water, which slow down cation migration and attenuate the back-diffusion of water; (2) the pressure effect, which rarely influences the electric field and the cation distribution, but greatly changes the profile of the water concentration and then the deformation behavior; and (3) the hydration effect, which has a significant impact on the distribution profiles of the cations and the electrical potential. In contrast to the findings of traditional studies, the water concentration displays an almost uniform gradient across the thickness in the bulk, and the cation concentration at the cathode is greatly reduced by the volume effect of the hydrated cations.
Simulation of the electronic properties of InxGa1−xAs quantum dots and their wetting layer under the influence of indium segregation
Authors: Maia A. D. B. , da Silva E. C. F. , Quivy A. A. , Bindilatti V. , de Aquino V. M. , Dias I. F. L.
Published: August 2013

We present anisotropic nonparabolic position-dependent effective-mass calculations of the bound energy levels of electrons confined in lens-shaped InxGa1−xAs quantum dots embedded in a GaAs matrix. The strain and In gradient inside the quantum dots and their wetting layer (due to the strong In segregation effect present in the InxGa1−xAs/GaAs system) were taken into account. The bound eigenstates and eigenenergies of electrons in a finite 3D confinement potential were determined by the full numerical diagonalization of the Hamiltonian. The quantum dots and their wetting layer were sliced into a finite number of monolayers parallel to the substrate surface, each one with a specific In concentration, in order to be able to reproduce any composition profile along the growth direction. A comparison between the eigenenergies of the “pure” InAs quantum dots and the quantum dots with an inhomogeneous In content indicates that In segregation dramatically affects their electronic structure and must be taken into account if one wishes to accurately simulate the real optoelectronic properties of such nanostructures.
Low-frequency Landau–Zener–Stückelberg interference in dissipative superconducting qubits
Authors: Du Lingjie , Lan Dong , Yu Yang
Published: August 2013

Landau–Zener–Stückelberg (LZS) interference of continuously driven superconducting qubits is studied. Going beyond the second order perturbation expansion, we find a time dependent stationary population evolution as well as unsymmetrical microwave driven Landau–Zener transitions, resulting from the nonresonant terms which are neglected in rotating-wave approximation. For the low-frequency driving, the qubit population at equilibrium is a periodical function of time, owing to the contribution of the nonresonant terms. In order to obtain the average population, it is found that the average approximation based on the perturbation approach can be applied to the low-frequency region. For the extremely low frequency which is much smaller than the decoherence rate, we develop noncoherence approximation by dividing the evolution into discrete time steps during which the coherence is lost totally. These approximations present comprehensive analytical descriptions of LZS interference in most of parameter space of frequency and decoherence rate, agreeing well with those of the numerical simulations and providing a simple but integrated understanding to system dynamics. The application of our models to microwave cooling can obtain the minimal frequency to realize effective microwave cooling.
Structure and magnetism of copper-substituted cobalt ludwigite Co3O2BO3
Authors: Ivanova N. B. , Kazak N. V. , Knyazev Yu. V. , Velikanov D. A. , Vasiliev A. D. , Bezmaternykh L. N. , Platunov M. S.
Published: August 2013

Single crystals of Co3O2BO3 with partial (4%) substitution of Co by Cu ions were synthesized by the flux technique. X-ray diffraction and magnetic studies were carried out. The x-ray diffraction measurements show clearly that Cu preferentially occupies only one of the four nonequivalent crystallographic positions, the one with the smallest electric field gradient. The ferrimagnetic ordering near TN = 43 K and the high magnetic hardness in this magnetic phase are similar to those of Co3O2BO3. Copper substitution causes a small reduction in the effective magnetic moment.
Transformation of cryovacuum condensates of ethanol near the glass transition temperature
Authors: Drobyshev A. , Aldiyarov A. , Katpaeva K. , Korshikov E. , Kurnosov V. , Sokolov D.
Published: August 2013

Thin films of cryovacuum condensates of ethanol formed by condensation of the gas on a cooled metal substrate are studied by infrared spectrometry and thermal desorption techniques. The main purpose was to examine dynamic relaxation processes near the glass transition temperature and the transition from orientationally disordered to orders states in thin ethanol cryocondensate films. It was found that ethanol cryocondensate films formed by condensation at T = 16 K are in an amorphous state (ASE). Increasing the sample temperature to T = 80 K leads to the transformation of the ASE into a structural glass. With further heating to T = 97 K, the structural glass is converted into a supercooled liquid and at T = 105 K, a plastic crystal is formed.
On the applicability of the standard approaches for evaluating a neoclassical radial electric field in a tokamak edge region
Authors: Dorf M. A. , Cohen R. H. , Simakov A. N. , Joseph I.
Published: August 2013

The use of the standard approaches for evaluating a neoclassical radial electric field Er, i.e., the Ampere (or gyro-Poisson) equation, requires accurate calculation of the difference between the gyroaveraged electron and ion particle fluxes (or densities). In the core of a tokamak, the nontrivial difference appears only in high-order corrections to a local Maxwellian distribution due to the intrinsic ambipolarity of particle transport. The evaluation of such high-order corrections may be inconsistent with the accuracy of the standard long wavelength gyrokinetic equation (GKE), thus imposing limitations on the applicability of the standard approaches. However, in the edge of a tokamak, charge-exchange collisions with neutrals and prompt ion orbit losses can drive non-intrinsically ambipolar particle fluxes for which a nontrivial (Er-dependent) difference between the electron and ion fluxes appears already in a low order and can be accurately predicted by the long wavelength GKE. The parameter regimes, where the radial electric field dynamics in the tokamak edge region is dominated by the non-intrinsically ambipolar processes, thus allowing for the use of the standard approaches, are discussed.
Unusual persistence of superconductivity against high magnetic fields in the strongly-correlated iron-chalcogenide film FeTe:Ox
Authors: Dimitrov I. K. , Si W. D. , Ku W. , Han S. J. , Jaroszynski J.
Published: August 2013

We report an unusual persistence of superconductivity against high magnetic fields in the iron-chalcogenide film FeTe:Ox below ≈ 2.5 K. Instead of saturating, like mean-field behavior with a single order parameter, the measured low-temperature upper critical field increases progressively, suggesting a large supply of superconducting states accessible via magnetic field or low-energy thermal fluctuations. We demonstrate that superconducting states of finite momenta can be realized within the conventional theory, despite its questionable applicability. Our findings reveal a fundamental characteristic of superconductivity and electronic structure in the strongly correlated iron-based superconductors.
Manifestation of polaronic effects in Josephson currents
Authors: Parafilo A. V. , Krive I. V. , Shekhter R. I. , Park Y. W. , Jonson M.
Published: August 2013

Polaronic effects on the Josephson current through a vibrating quantum dot are considered. In the regime of strong electron–vibron interactions they lead to a power-law suppression of the critical current. This is manifested in an anomalous temperature dependence of the critical current at temperatures of the order of the polaronic energy shift.
Anomalous conductivity in Hall thrusters: Effects of the non-linear coupling of the electron-cyclotron drift instability with secondary electron emission of the walls
Authors: Héron A. , Adam J. C.
Published: August 2013

With the help of an implicit particle-in-cell code, we have shown in a previous paper that the electron-cyclotron drift instability was able to induce anomalous conductivity as well as anomalous heating. As such it can be a major actor among the mechanisms involved in the operation of Hall thrusters. However, experimental results show that the nature of wall material has a significant effect on the behavior of the thruster. The purpose of this paper is to study the plasma-wall interaction in the case where the plasma is heated self-consistently by electrostatic fluctuations induced by the electron-cyclotron drift instability.
Nature of metastable amorphous-to-crystalline reversible phase transformations in GaSb
Authors: Kalkan B. , Edwards T. G. , Raoux S. , Sen S.
Published: August 2013

The structural, thermodynamic, and kinetic aspects of the transformations between the metastable amorphous and crystalline phases of GaSb are investigated as a function of pressure at ambient temperature using synchrotron x-ray diffraction experiments in a diamond anvil cell. The results are consistent with the hypothesis that the pressure induced crystallization of amorphous GaSb into the β-Sn crystal structure near ∼5 GPa is possibly a manifestation of an underlying polyamorphic phase transition between a semiconducting, low density and a metallic, high density amorphous (LDA and HDA, respectively) phases. In this scenario, the large differences in the thermal crystallization kinetics between amorphous GaSb deposited in thin film form by sputtering and that prepared by laser melt quenching may be related to the relative location of the glass transition temperature of the latter in the pressure-temperature (P-T) space with respect to the location of the critical point that terminate the LDA ↔ HDA transition. The amorphous → β-Sn phase transition is found to be hysteretically reversible as the β-Sn phase undergoes decompressive amorphization near ∼2 GPa due to the lattice instabilities that give rise to density fluctuations in the crystal upon decompression.
A standalone perfusion platform for drug testing and target validation in micro-vessel networks
Authors: Zhang Boyang , Peticone Carlotta , Murthy Shashi K. , Radisic Milica
Published: August 2013

Studying the effects of pharmacological agents on human endothelium includes the routine use of cell monolayers cultivated in multi-well plates. This configuration fails to recapitulate the complex architecture of vascular networks in vivo and does not capture the relationship between shear stress (i.e. flow) experienced by the cells and dose of the applied pharmacological agents. Microfluidic platforms have been applied extensively to create vascular systems in vitro; however, they rely on bulky external hardware to operate, which hinders the wide application of microfluidic chips by non-microfluidic experts. Here, we have developed a standalone perfusion platform where multiple devices were perfused at a time with a single miniaturized peristaltic pump. Using the platform, multiple micro-vessel networks, that contained three levels of branching structures, were created by culturing endothelial cells within circular micro-channel networks mimicking the geometrical configuration of natural blood vessels. To demonstrate the feasibility of our platform for drug testing and validation assays, a drug induced nitric oxide assay was performed on the engineered micro-vessel network using a panel of vaso-active drugs (acetylcholine, phenylephrine, atorvastatin, and sildenafil), showing both flow and drug dose dependent responses. The interactive effects between flow and drug dose for sildenafil could not be captured by a simple straight rectangular channel coated with endothelial cells, but it was captured in a more physiological branching circular network. A monocyte adhesion assay was also demonstrated with and without stimulation by an inflammatory cytokine, tumor necrosis factor-α.
The time correlation function perspective of NMR relaxation in proteins
Authors: Shapiro Yury E. , Meirovitch Eva
Published: August 2013

We applied over a decade ago the two-body coupled-rotator slowly relaxing local structure (SRLS) approach to NMR relaxation in proteins. One rotator is the globally moving protein and the other rotator is the locally moving probe (spin-bearing moiety, typically the 15N−1H bond). So far we applied SRLS to 15N−H relaxation from seven different proteins within the scope of the commonly used data-fitting paradigm. Here, we solve the SRLS Smoluchowski equation using typical best-fit parameters as input, to obtain the corresponding generic time correlation functions (TCFs). The following new information is obtained. For actual rhombic local ordering and main ordering axis pointing along ${\rm C}_{{\rm i} - {\rm 1}}^\alpha - {\rm C}_{\rm i}^\alpha$Ci−1α−Ciα, the measurable TCF is dominated by the (K,K′) = (−2,2), (2,2), and (0,2) components (K is the order of the rank 2 local ordering tensor), determined largely by the local motion. Global diffusion axiality affects the analysis significantly when the ratio between the parallel and perpendicular components exceeds approximately 1.5. Local diffusion axiality has a large and intricate effect on the analysis. Mode-coupling becomes important when the ratio between the global and local motional rates falls below 0.01. The traditional method of analysis − model-free (MF) − represents a simple limit of SRLS. The conditions under which the MF and SRLS TCFs are the same are specified. The validity ranges of wobble-in-a-cone and rotation on the surface of a cone as local motions are determined. The evolution of the intricate Smoluchowski operator from the simple diffusion operator for a sphere reorienting in isotropic medium is delineated. This highlights the fact that SRLS is an extension of the established stochastic theories for treating restricted motions. This study lays the groundwork for TCF-based comparison between mesoscopic SRLS and atomistic molecular dynamics.
On the adiabatic ionization energy of the propargyl radical
Authors: Jacovella U. , Gans B. , Merkt F.
Published: August 2013

The photoionization and pulsed-field-ionization zero-kinetic-energy photoelectron spectra of the propargyl radical have been recorded in the vicinity of the origin of the \documentclass[12pt]{minimal}\begin{document}$\tilde{\mathrm{X}}^+\; ^1\mathrm{A}_1 \leftarrow \tilde{\mathrm{X}}\; ^2\mathrm{B}_1$\end{document}X̃+A11←X̃B12 photoionizing transition. An internally cold sample of propargyl with a rotational temperature of ∼45 K was produced in a supersonic expansion of 1,3-butadiene in helium. Propargyl was generated by excimer laser (ArF, 193 nm) photolysis of 1,3-butadiene in a quartz capillary mounted at the exit of a pulsed valve. The rotational structure of the origin band of the photoelectron spectrum was partially resolved and an improved value of the adiabatic ionization energy of propargyl (EI/hc = 70174.5(20) cm−1) was determined.
Exploring surface photoreaction dynamics using pixel imaging mass spectrometry (PImMS)
Authors: Kershis Matthew D. , Wilson Daniel P. , White Michael G. , John Jaya John , Nomerotski Andrei , Brouard Mark , Lee Jason W. L. , Vallance Claire , Turchetta Renato
Published: August 2013

A new technique for studying surface photochemistry has been developed using an ion imaging time-of-flight mass spectrometer in conjunction with a fast camera capable of multimass imaging. This technique, called pixel imaging mass spectrometry (PImMS), has been applied to the study of butanone photooxidation on TiO2(110). In agreement with previous studies of this system, it was observed that the main photooxidation pathway for butanone involves ejection of an ethyl radical into vacuum which, as confirmed by our imaging experiment, undergoes fragmentation after ionization in the mass spectrometer. This proof-of-principle experiment illustrates the usefulness and applicability of PImMS technology to problems of interest within the surface science community.
Numerical study of thermocoalescence of microdroplets in a microfluidic chamber
Authors: Ho Peng Ching , Nguyen Nam-Trung
Published: August 2013

The present paper reports the numerical investigation of thermocoalescence of droplets in a microchannel network consisting of a droplet formation section connecting to a temperature-induced merging chamber. The numerical model is formulated as an incompressible immiscible two-phase flow problem with oil and water as the continuous and dispersed phase, respectively. The governing equations are solved using finite volume method on a staggered mesh. The interface is captured by a narrow-band particle level-set method. The paper examines the droplet formation process and droplet size at 4 different ratios of oil and water flow rate. The motion of the droplets from the formation section into and through the heat-induced merging chamber is analyzed. The numerical method is able to provide a visual presentation of the droplet movement in a heated environment under the influence of thermocapillarity. The relationship between the critical merging temperature and the fluid flow rate is also analyzed and discussed.
Quantum mechanical/molecular mechanical/continuum style solvation model: Time-dependent density functional theory
Authors: Thellamurege Nandun M. , Cui Fengchao , Li Hui
Published: August 2013

A combined quantum mechanical/molecular mechanical/continuum (QM/MMpol/C) style method is developed for time-dependent density functional theory (TDDFT, including long-range corrected TDDFT) method, induced dipole polarizable force field, and induced surface charge continuum model. Induced dipoles and induced charges are included in the TDDFT equations to solve for the transition energies, relaxed density, and transition density. Analytic gradient is derived and implemented for geometry optimization and molecular dynamics simulation. QM/MMpol/C style DFT and TDDFT methods are used to study the hydrogen bonding of the photoactive yellow protein chromopore in ground state and excited state.
Experimental study of the scintillation index of a radially polarized beam with controllable spatial coherence
Authors: Wang Fei , Liu Xianlong , Liu Lin , Yuan Yangsheng , Cai Yangjian
Published: August 2013

Radially polarized (RP) beam with controllable spatial coherence (i.e., partially coherent RP beam) was generated in experiment recently [Appl. Phys. Lett. 100, 051108 (2012)]. In this letter, we report experimental study of the scintillation index of a partially coherent RP beam propagating through thermally induced turbulence. Our results show that a partially coherent RP beam has advantage over a linearly polarized partially coherent beam for reducing turbulence-induced scintillation, which will be useful in free-space optical communications, remote sensing and laser radar systems.
Hybrid simulation of shock formation for super-Alfvénic expansion of laser ablated debris through an ambient, magnetized plasma
Authors: Clark S. E. , Winske D. , Schaeffer D. B. , Everson E. T. , Bondarenko A. S. , Constantin C. G. , Niemann C.
Published: August 2013

Two-dimensional hybrid simulations of perpendicular collisionless shocks are modeled after potential laboratory conditions that are attainable in the LArge Plasma Device (LAPD) at the University of California, Los Angeles Basic Plasma Science Facility. The kJ class 1053 nm Nd:Glass Raptor laser will be used to ablate carbon targets in the LAPD with on-target energies of 100-500 J. The ablated debris ions will expand into ambient, partially ionized hydrogen or helium. A parameter study is performed via hybrid simulation to determine possible conditions that could lead to shock formation in future LAPD experiments. Simulation results are presented along with a comparison to an analytical coupling parameter.
Feasibility study of endoscopic x-ray luminescence computed tomography: Simulation demonstration and phantom application
Authors: Chen Xueli , Liang Jimin , Cao Xin , Yang Defu , Chen Dongmei , Ripoll Jorge , Tian Jie
Published: August 2013

Even though endoscopic fluorescence diffuse optical tomography (eFDOT) exhibits significant potential, currently its application is limited due to the existence of strong autofluorescence and the imaging inaccuracy caused by a very short source-detector distance. Motivated by the emerging X-ray luminescence computed tomography (XLCT) technology, we presented an endoscopic XLCT (eXLCT) methodology. In the methodology, the aperture angle of the objective was incorporated into the forward model, providing a more accurate description of light propagation. Numerical simulation with a heterogeneous geometry and an imaging experiment with a physical phantom were illustrated to demonstrate the feasibility of the presented eXLCT methodology.
Low-temperature fabrication of fine structures on glass using electrical nanoimprint and chemical etching
Authors: Ikutame Naoki , Kawaguchi Keiga , Ikeda Hiroshi , Sakai Daisuke , Harada Kenji , Funatsu Shiro , Nishii Junji
Published: August 2013

Periodic structures were imprinted on a soda lime glass surface below its glass transition temperature (Tg) using a carbon-coated SiO2 mold under application of DC voltage. The structure height increased with the applied DC voltage, although no significant increase with pressure was found. At a temperature around Tg, the height reached saturation. Chemical etching using 55% KOH solution at 70 °C increased the structure height to eight times the height before etching. Noticeable alternating depression patterns and rapid chemical etching are closely related with the selective decrease in sodium concentration, which occurred only in the surface areas that were pressurized by the mold.
Spin mixing conductance at a well-controlled platinum/yttrium iron garnet interface
Authors: Qiu Z. , Ando K. , Uchida K. , Kajiwara Y. , Takahashi R. , Nakayama H. , An T. , Fujikawa Y. , Saitoh E.
Published: August 2013

A platinum (Pt)/yttrium iron garnet (YIG) bilayer system with a well-controlled interface has been developed; spin mixing conductance at the Pt/YIG interface has been studied. A clear interface with good crystal perfection is experimentally demonstrated to be one of the important factors for an ultimate spin mixing conductance. The spin mixing conductance is obtained to be 1.3 × 1018 m–2 at the well-controlled Pt/YIG interface, which is close to a theoretical prediction.
Assessment of solar and wind energy resources in Serbia
Authors: Gburčik Verica , Mastilović Sreten , Vučinić Željko
Published: August 2013

Serbia aims to improve the composition of its energy sources and increase the contribution of renewable and sustainable energies to meet its growing electricity production demand. Results of many studies and numerous measurement campaigns suggest that Serbia has a considerable potential for the solar and wind energy utilization for electricity generation. The objective of this article is to present a brief assessment of these solar and wind resources. Meteorological data from a network of meteorological stations covering a period of 30 yr are used to obtain annual energy density distributions from these two climatic sources. These results, summarizing in an abbreviated form comprehensive research efforts culminating in the last decade, are presented in an archival publication for the first time. This assessment indicates that southern and southeastern Serbia are very good regions for the solar energy utilization. Southern Banat, mountain ranges of eastern and southeastern Serbia, and the lower Danube river valley are the most promising regions for the wind power plant constructions. Final objective of this article is to show that the problem of individual intermittency of wind and solar power potentials could be compensated in Serbia by their complementary character.
Electrostatic attraction of charged drops of water inside dropwise cluster
Authors: Shavlov A. V. , Dzhumandzhi V. A.
Published: August 2013

Based on the analytical solution of the Poisson-Boltzmann equation, we demonstrate that inside the electrically neutral system of charges an electrostatic attraction can occur between the like-charged particles, where charge Z ≫ 1 (in terms of elementary charge) and radius R > 0, whereas according to the literature, only repulsion is possible inside non-electrically neutral systems. We calculate the free energy of the charged particles of water inside a cluster and demonstrate that its minimum is when the interdroplet distance equals several Debye radii defined based on the light plasma component. The deepest minimum depth is in a cluster with close spatial packing of drops by type, in a face-centered cubic lattice, if almost all the electric charge of one sign is concentrated on the drops and that of the other sign is concentrated on the light compensation carriers of charge, where the charge moved by equilibrium carriers is rather small.
Reformulation of solar cell physics to facilitate experimental separation of recombination pathways
Authors: Grover Sachit , Li Jian V. , Young David L. , Stradins Paul , Branz Howard M.
Published: August 2013

Experimentally identifying the spatial distribution of recombination in a solar cell is challenging, with only semi-quantitative information available from conventional characterization techniques. We develop a formulation of solar cell physics, based upon well-justified analytic approximations, to quantitatively extract information about recombination in different cell regions. We derive the dependence of VOC on light-intensity, temperature, and strength of recombination in the space-charge, quasi-neutral, and interface regions. Expanding the scope and utility of commonly used characterization techniques, we apply this formulation to evaluate the spatial distribution of recombination in exemplary crystalline silicon heterojunction and polycrystalline Cu(In,Ga)Se2 solar cells.
Fano resonances in ultracompact waveguide Fabry-Perot resonator side-coupled lossy nanobeam cavities
Authors: Yu Ping , Hu Ting , Qiu Huiye , Ge Fangfang , Yu Hui , Jiang Xiaoqing , Yang Jianyi
Published: August 2013

We propose and demonstrate experimentally an ultracompact resonant system exhibiting sharp asymmetric Fano-resonance, in which a tiny photonic crystal nanobeam cavity is laterally coupled to a waveguide Fabry-Perot resonator. Under the presence of cavity intrinsic loss, we find that the system produces sharper and higher extinction ratio Fano resonance spectra only if appropriate phase is selected. The whole device (∼6 μm2) is implemented on silicon on insulator platform, and experimentally we observe steep-slope Fano resonance with extinction ratio of 7.3 dB, slope above 5 dB/nm, and average insertion loss less than 1.8 dB.