bluuebunny/crossref_metadata_2025 huggingface dataset:
Deletion of the mouse Slc30a8 gene encoding zinc transporter-8 results in impaired insulin secretion
Authors: Pound Lynley D. , Sarkar Suparna A. , Benninger Richard K. P. , Wang Yingda , Suwanichkul Adisak , Shadoan Melanie K. , Printz Richard L. , Oeser James K. , Lee Catherine E. , Piston David W. , McGuinness Owen P. , Hutton John C. , Powell David R. , O'Brien Richard M.
Published: May 2009

The Slc30a8 gene encodes the islet-specific zinc transporter ZnT-8, which provides zinc for insulin-hexamer formation. Polymorphic variants in amino acid residue 325 of human ZnT-8 are associated with altered susceptibility to Type 2 diabetes and ZnT-8 autoantibody epitope specificity changes in Type 1 diabetes. To assess the physiological importance of ZnT-8, mice carrying a Slc30a8 exon 3 deletion were analysed histologically and phenotyped for energy metabolism and pancreatic hormone secretion. No gross anatomical or behavioural changes or differences in body weight were observed between wild-type and ZnT-8−/− mice, and ZnT-8−/− mouse islets were indistinguishable from wild-type in terms of their numbers, size and cellular composition. However, total zinc content was markedly reduced in ZnT-8−/− mouse islets, as evaluated both by Timm's histochemical staining of pancreatic sections and direct measurements in isolated islets. Blood glucose levels were unchanged in 16-week-old, 6 h fasted animals of either gender; however, plasma insulin concentrations were reduced in both female (∼31%) and male (∼47%) ZnT-8−/− mice. Intraperitoneal glucose tolerance tests demonstrated no impairment in glucose clearance in male ZnT-8−/− mice, but glucose-stimulated insulin secretion from isolated islets was reduced ∼33% relative to wild-type littermates. In summary, Slc30a8 gene deletion is accompanied by a modest impairment in insulin secretion without major alterations in glucose metabolism.
Direct measurements of the α-ϵ transition stress and kinetics for shocked iron
Authors: Jensen B. J. , Gray G. T. , Hixson R. S.
Published: May 2009

Iron undergoes a polymorphic phase transformation from the α-phase (bcc) to the ϵ-phase (hcp) when compressed to stresses exceeding 13 GPa. Because the epsilon phase is denser than the alpha phase, a single shock wave is unstable and breaks up into an elastic wave, a plastic wave, and a phase transition wave. Examination of this structured wave coupled with various phase transformation models has been used to indirectly examine the transition kinetics. Recently, multimillion-atom molecular dynamics (MD) simulations have been used to examine the shock-induced transition in single crystal iron illustrating an orientation dependence of the transition stress, mechanisms, and kinetics. The objective of the current work was to perform plate impact experiments to examine the shock response of polycrystalline and single crystal iron with nanosecond resolution for impact stresses spanning the α-ϵ transition. The current data reveal an orientation dependence of the transition stress coupled with a transition time that is nonlinearly dependent on the impact stress with a duration ranging from picoseconds to hundreds of nanoseconds. The higher transition stress for iron shocked along the [100] direction is in agreement with the predictions from MD calculations that describe an orientation dependence of the transition stress. However, MD calculations do not capture the complexity of the continuum states achieved or the transition kinetics. Further results and implications are discussed in this paper.
Multimodal optical imaging and spectroscopy for the intraoperative mapping of nonmelanoma skin cancer
Authors: Salomatina Elena , Muzikansky Alona , Neel Victor , Yaroslavsky Anna N.
Published: May 2009

Basal cell carcinoma (BCC) is the most common human malignancy, and its incidence increases yearly. In this contribution we investigate the feasibility of combining multimodal reflectance and fluorescence polarization imaging (RFPI) with spectroscopic analysis of the reflectance images for facilitating intraoperative delineation of BCCs. Twenty fresh thick BCC specimens were obtained within 1 h after Mohs micrographic surgeries. The samples were soaked for up to 2 min in an aqueous 0.2 mg/ml solution of methylene blue, briefly rinsed in saline solution, and imaged. Reflectance images were acquired in the range from 395 to 735 nm, with steps of 10 nm. Fluorescence polarization images were excited at 630 nm and registered in the range between 660 and 750 nm. The results yielded by RFPI were qualitatively compared to each other and to histopathology. From the copolarized reflectance images the spectral responses including the optical densities and their wavelength derivatives were calculated. The differences in the spectral responses of the benign and malignant stained skin structures were assessed. Statistical analysis, i.e., Student’s t-test, was employed to verify the significance of the discovered differences. Both reflectance and fluorescence polarization images correlated well with histopathology in all the cases. Reflectance polarization images provided more detailed information on skin morphology, with the appearance of skin structures resembling that of histopathology. Fluorescence polarization images exhibited higher contrast of cancerous tissue as compared to reflectance imaging. The analysis of the optical densities and their wavelength derivatives for tumor and normal tissues has confirmed statistical significance of the differences that can be used for intraoperative cancer delineation. The results of the study indicate that spectral analysis is a useful adjunct to RFPI for facilitating skin cancer delineation.
An easy cell-based microchip assay method for a CYP1A1-mediated drug metabolism using adhesive cells, HepG2
Authors: Kato Masaru , Yamamoto Tatsuhiro , Sekimoto Masashi , Degawa Masakuni , Toyo’oka Toshimasa
Published: May 2009

We have developed a convenient cell-based assay method using a microchip. In the method, adhesive cells, HepG2, were cultured in the conventional culture dish containing glass disks and then the disks covered with the HepG2 were transferred to the microchip for cell assay. Activity of ethoxyresorufin O-deethylation (EROD), which is mainly mediated by cytochrome P4501A1 (CYP1A1), in HepG2 was measured. Treatment of HepG2 with 3-methylcholanthrene, a CYP1A1 inducer, resulted in significant increase in EROD activity.
Theoretical analysis of coupled diffuse-photon-density and thermal-wave field depth profiles photothermally generated in layered turbid dental structures
Authors: Matvienko Anna , Mandelis Andreas , Jeon Raymond J. , Abrams Stephen H.
Published: May 2009

A coupled diffuse-photon-density and thermal-wave model is developed for theoretical analysis of the photothermal field in demineralized teeth. Intact and demineralized layers of enamel, as well as dentin, are described as a layered one-dimensional system. The solution of the radiative transport equation in the limit of diffuse-photon-density field is considered as a source term in the thermal-wave field equation. The influence of optical parameters (absorption and scattering coefficients) and thermal parameters (thermal diffusivity and conductivity) of each layer on the diffuse-photon-density and thermal-wave depth profiles is analyzed using computer simulations, allowing the verification of accuracy and validity of the developed theory. The proposed model and simulations are intended for identifying the parameters most affecting the diffuse-photon-density and thermal-wave fields in turbid media, which leads to optimization of the fitting process of thermal and optical properties of teeth from experimental data obtained by frequency-domain photothermal radiometry.
Polarimetry in turbid, birefringent, optically active media: A Monte Carlo study of Mueller matrix decomposition in the backscattering geometry
Authors: Ghosh Nirmalya , Wood Michael F. G. , Vitkin I. Alex
Published: May 2009

Determination of the intrinsic polarization properties of a complex turbid medium such as biological tissue in the backscattering geometry (a geometry that is convenient for in situ applications) is complicated due to the confounding influence of scattering, and due to simultaneous occurrence of several polarization effects. We have investigated the polar decomposition approach of Mueller matrices to delineate individual intrinsic polarization parameters (specifically linear retardance δ and optical rotation ψ) of a birefringent, chiral, turbid medium in the backscattering geometry, using Mueller matrices generated with polarization-sensitive Monte Carlo simulations. The results show that near the exact backscattering direction, the interplay of the scattering-induced linear retardance and diattenuation on the intrinsic values for δ and ψ is coupled in a complex interrelated way, due to contribution of the backscattered photons. In contrast, these effects were significantly reduced for detection positions at distances larger than a transport length away from the point of illumination. Simultaneous determination of the intrinsic values for δ and ψ of a birefringent, chiral, turbid medium in the backward detection geometry can thus be accomplished by decomposing the Mueller matrices recorded at distances larger than a transport length away from the point of illumination. Determination of the intrinsic values for these polarization parameters in backscattering geometry could be significant in, for example, for quantification of tissue structural anisotropy and for noninvasive blood glucose measurements of diabetic patients.
Spectral distortion in diffuse molecular luminescence tomography in turbid media
Authors: Davis Scott C. , Pogue Brian W. , Tuttle Stephen B. , Dehghani Hamid , Paulsen Keith D.
Published: May 2009

The influence of tissue optical properties on the shape of near-infrared (NIR) fluorescence emission spectra propagating through multiple centimeters of tissue-like media was investigated. Fluorescence emission spectra measured from 6 cm homogeneous tissue-simulating phantoms show dramatic spectral distortion which results in emission peak shifts of up to 60 nm in wavelength. Measured spectral shapes are highly dependent on the photon path length and the scattered photon field in the NIR amplifies the wavelength-dependent absorption of the fluorescence spectra. Simulations of the peak propagation using diffusion modeling describe the experimental observations and confirm the path length dependence of fluorescence emission spectra. Spectral changes are largest for long path length measurements and thus will be most important in human tomography studies in the NIR. Spectrally resolved detection strategies are required to detect and interpret these effects which may otherwise produce erroneous intensity measurements. This observed phenomenon is analogous to beam hardening in x-ray tomography, which can lead to image artifacts without appropriate compensation. The peak shift toward longer wavelengths, and therefore lower energy photons, observed for NIR luminescent signals propagating through tissue may readily be described as a beam softening phenomenon.
Noninvasive, in vivo imaging of the mouse brain using photoacoustic microscopy
Authors: Stein Erich W. , Maslov Konstantin , Wang Lihong V.
Published: May 2009

Noninvasive, high resolution imaging of mouse brain activity is poised to provide clinically translatable insights into human neurological disease progression. Toward noninvasive imaging of brain activity through the hemodynamic response, the dark-field photoacoustic microscopy (PAM) technique was enhanced to image the cortex vasculature of the mouse brain in vivo using endogenous hemoglobin contrast. Specifically, the PAM system was redesigned to efficiently collect photoacoustic waves originating from cortical vessels, providing high (70 μm lateral and 54 μm axial) resolution images of the mouse brain vasculature with a contrast-to-noise ratio of 25 dB. These findings confirm the efficacy of PAM to noninvasively image vascular structures in the mouse brain and the potential to image mouse brain function by tracking the hemodynamic response.
Quantified light-induced fluorescence, review of a diagnostic tool in prevention of oral disease
Authors: de Josselin de Jong Elbert , Higham Susan M. , Smith Philip W. , van Daelen Catherina J. , van der Veen Monique H.
Published: May 2009

Diagnostic methods for the use in preventive dentistry are being developed continuously. Few of these find their way into general practice. Although the general trend in medicine is to focus on disease prevention and early diagnostics, in dentistry this is still not the case. Nevertheless, in dental research some of these methods seem to be promising for near future use by the general dental professional. In this paper an overview is given of a method called quantitative light-induced fluorescence or (QLF) in which visible and harmless light excites the teeth in the patient's mouth to produce fluorescent images, which can be stored on disk and computer analyzed. White spots (early dental caries) are detected and quantified as well as bacterial metabolites on and in the teeth. An overview of research to validate the technique and modeling to further the understanding of the technique by Monte Carlo simulation is given and it is shown that the fluorescence phenomena can be described by the simulation model in a qualitative way. A model describing the visibility of red fluorescence from within the dental tissue is added, as this was still lacking in current literature. An overview is given of the clinical images made with the system and of the extensive research which has been done. The QLF™ technology has been shown to be of importance when used in clinical trials with respect to the testing of toothpastes and preventive treatments. It is expected that the QLF™ technology will soon find its way into the general dental practice.
In situ real-time monitoring of biomolecular interactions by using surface infrared spectroscopy
Authors: Hirano-Iwata Ayumi , Yamaguchi Ryo-taro , Miyamoto Ko-ichiro , Kimura Yasuo , Niwano Michio
Published: May 2009

This paper reviews our recent approaches for in situ label-free detection of biomolecules and their interactions by using infrared absorption spectroscopy (IRAS) in the multiple internal reflection (MIR) geometry. Biomolecular interactions, such as DNA hybridization, DNA hydration, protein-protein interaction, cell growth and cell death, were characterized and monitored in situ both in D2O and H2O media. Combination of MIR-IRAS and various sensing platforms, such as Si, GaAs, porous Si, and porous amunina, was also discussed in terms of sensitivity and applicability to chip analysis. It is demonstrated that MIR-IRAS is a promising tool not only for the label-free detection of biomolecules but also for the accurate discrimination between specific and nonspecific interactions, which is critically important when we are monitoring complex and dynamic biological samples.
Electric-field-induced interaction between biological cells or colloidal particles
Authors: Tian W. J. , Huang J. P. , Yu K. W.
Published: May 2009

Biological cells can be treated as an inhomogeneous particle. In addition to biomaterials, inhomogeneous particles are also important in more traditional colloidal science. By using two energy methods that are based on Legendre polynomials and Green’s function, respectively, we investigate the interaction between biological cells or colloidal particles in the presence of an external electric field, in an attempt to investigate the effect of inhomogeneity on crossover frequencies across which the interaction force changes from attraction to repulsion or vice versa. The predictions by the two methods agree with each other very well. It is shown that there exist two kinds of crossover frequencies ωp, one from attraction to repulsion and the other from repulsion to attraction as external frequencies increase. The first ωp strongly depends on the degree of inhomogeneity, while the second ωp does not. This work has relevance to manipulation of biological cells or colloidal particles.
Photoemission study of C60-induced barrier reduction for hole injection at N, N′-bis(naphthalene-1-y1)-N, N′-bis(phenyl) benzidine/Al
Authors: Xie Z. T. , Ding B. F. , Gao X. D. , You Y. T. , Sun Z. Y. , Zhang W. H. , Ding X. M. , Hou X. Y.
Published: May 2009

Synchrotron radiation photoemission study showed that the energy level alignment at the interface between N, N′-bis(naphthalene-1-y1)-N, N′-bis(phenyl) benzidine (NPB), a typical hole transport material, and Al could be adjusted by precovering a thin C60 layer on Al. The interface dipoles so formed could shift both the highest occupied molecular orbital level of NPB and the secondary electron cutoff measured at the early stage of the NPB deposition. The barrier height for hole injection from Al to NPB could thus be lowered by as much as 0.98 eV, and the optimal thickness of the inserted C60 layer was found to be 8–12 Å.
Thermal stability of Ba(Zr0.8−xCexY0.2)O2.9 ceramics in carbon dioxide
Authors: Tu C.-S. , Chien R. R. , Schmidt V. H. , Lee S.-C. , Huang C.-C. , Tsai C.-L.
Published: May 2009

In situ x-ray diffraction spectra (25–1000 °C) have been measured as a function of temperature for proton-conducting Ba(Zr0.8−xCexY0.2)O2.9 (x=0.0–0.4) ceramics in CO2 atmosphere. Atomic vibrations before and after exposure to CO2 were obtained by using the micro-Raman scattering (150–1600 cm−1). Ba(Zr0.8Y0.2)O2.9 and Ba(Zr0.6Ce0.2Y0.2)O2.9 reveal a promising thermal stability in CO2 without apparent decomposition up to 1000 °C. However, Ba(Zr0.5Ce0.3Y0.2)O2.9 and Ba(Zr0.4Ce0.4Y0.2)O2.9 exhibit thermally stable below 550 °C and then proceed an obvious chemical decomposition of BaCO3 and Zr0.8−xCexY0.2O2 above 550 °C, which were clearly evidenced by the Raman vibrations of 1057 and 466 cm−1, respectively. A first-order orthorhombic-hexagonal structure transition was confirmed in BaCO3 in the region of 810–850 °C upon heating. This study suggests that the Ba(Zr0.8−xCexY0.2)O2.9 ceramics with x≤0.2 are promising candidates for proton-conducting applications in CO2-containing environment.
Thermoelectric properties of electron doped SrO(SrTiO3)n (n=1,2) ceramics
Authors: Wang Yifeng , Lee Kyu Hyoung , Ohta Hiromichi , Koumoto Kunihito
Published: May 2009

Crystal structure and thermoelectric properties of Nb5+- and Ln3+-(rare earth: La3+, Nd3+, Sm3+, and Gd3+) doped SrO(SrTiO3)n (n=1,2) ceramics, which were fabricated by conventional hot-pressing, were measured to clarify the effects of Ti4+- and Sr2+-site substitution on the thermoelectric properties. The thermal conductivities are very close between the n=1 and 2 phases either doped with Nb5+ or Ln3+ and decreased by ∼60% at room temperature and ∼30% at 1000 K as compared to that of SrTiO3, which is likely due to an enhanced phonon scattering at the SrO/(SrTiO3)n (n=1,2) interfaces. The density of states effective mass md∗ (1.8–2.4 m0) and consequently the Seebeck coefficient |S| in Nb5+-doped samples are fairly smaller than those reported for SrTiO3, which probably resulted from a deterioration of DOS due to the formation of the singly degenerate a1g (Ti 3dxy) orbital as the conduction band bottom, which should be induced by the distortion of TiO6 octahedra in (SrTiO3)n layers. However, in the Ln3+-doped SrO(SrTiO3)2, the TiO6 octahedra were found to be restored, in contrast to the Nb5+-doped, with a gradually increasing O–Ti–O bond angle in the (100) plane at high temperatures, which would lead to the formation of triply degenerate Ti 3d-t2g (dxy, dyz, and dxz) orbitals to cause a significant enhancement in md∗ (∼7.5 m0 at 1000 K) and consequently in |S|. Accordingly, the maximum dimensionless figure of merit ZT∼0.24 obtained in 5%-Gd3+-doped SrO(SrTiO3)2 at 1000 K is about 70% larger than that of Nb-doped SrO(SrTiO3)2 (ZT1000 K∼0.14).
Solution-processed omnidirectional antireflection coatings on amorphous silicon solar cells
Authors: Wang Yuehui , Tummala Rajesh , Chen L. , Guo L. Qing , Zhou Weidong , Tao Meng
Published: May 2009

Solution-processed spherical surface textures are demonstrated on commercial amorphous silicon solar cells. The texture is formed with a monolayer of silica microspheres by convective coating, followed by a spin-on-glass film. It is found that the spherical texture reduces the reflectivity of the cells in the wavelength regime of 400–1200 nm, thus broad spectrum. It is also found that the spherical texture improves the efficiency of the cells at various incident angles from surface normal to at least 60°. The improvement in efficiency increases at larger incident angles to as high as 12% relative improvement, demonstrating its omnidirectionality. Current-voltage characteristics show that the efficiency improvement with coating is largely due to the increased short circuit current, while the open-circuit voltage remains the same. Therefore the efficiency improvement is attributed to more light coupled into the cells. This omnidirectional surface texture offers an attractive solution for antireflection in both polycrystalline silicon and thin-film solar cells.
Interface properties in sequence permutated Fe–B–Ag multilayers
Authors: Balogh J. , Bujdosó L. , Kaptás D. , Kemény T. , Vincze I. , Kovács A. , Tóth L.
Published: May 2009

Fe–B–Ag multilayers have been prepared in two different sequences of the layers in order to reveal distinctness of “top” and “bottom” interfaces of each element in relation to the other two elements. Transmission electron microscopy analysis showed a much larger interface roughness for the Fe/B/Ag (i.e., Fe at bottom, Ag on top of B) than for the B/Fe/Ag sequence, which is mainly due to the different growth processes of Ag. For both sequence Fe and B layers of 2 nm thickness are continuous and solid state amorphization—similar to that observed in Fe/B multilayers—takes place during sample growth. Mössbauer spectroscopy measurements indicate that the amorphous interface has a broad bimodal concentration distribution for both layer sequence, but intermixing is larger at the Fe/B than at the B/Fe interface.
Stress-driven formation of terraced hollow oxide nanorods during metal oxidation
Authors: Zhou Guangwen
Published: May 2009

We report the formation of terraced hollow Cu2O nanorods upon oxidation of Cu(100) thin films at ∼600 °C. Transmission electron microscopy and atomic force microscopy observations reveal that the oxide islands have an initially square pyramid shape that transits to an elongated nanorod shape and then to a terraced hollow nanorod morphology as the oxide growth proceeds. A mechanism based on the relaxation of interfacial epitaxial stress followed by the release of the bulk stress induced by the large volume expansion accompanying the conversion of metal into oxide is proposed to explain the pathway of the morphological evolution of this new oxide structure.
Self-assembled Gd silicide nanostructures grown on Si(001)
Authors: Ye Gangfeng , Crimp Martin A. , Nogami Jun
Published: May 2009

The growth of self-assembled gadolinium silicide nanostructures on Si(001) was studied over a range of metal coverages and growth temperatures. Scanned probe microscopy was used to study the nanostructure morphology. The analyses of cross-sectional transmission electron microscopy images, plan view transmission electron microscopy moiré fringe patterns, and nanobeam electron diffraction patterns show that the Gd silicide nanostructures fall into two classes: elongated nanowires with hexagonal crystal structure and rectangular islands with orthorhombic (or tetragonal) crystal structure. These results indicate that the nanostructure morphology is controlled by the magnitude and direction of the lattice mismatch with respect to the substrate. Optimum growth conditions for preferential growth of either nanowires or islands are described. In addition, the phase transformation from hexagonal to the more stable orthorhombic (or tetragonal) phase is observed and discussed.
Damage profile and ion distribution of slow heavy ions in compounds
Authors: Zhang Yanwen , Bae In-Tae , Sun Kai , Wang Chongmin , Ishimaru Manabu , Zhu Zihua , Jiang Weilin , Weber William J.
Published: May 2009

Slow heavy ions inevitably produce a significant concentration of defects and lattice disorder in solids during their slowing-down process via ion-solid interactions. For irradiation effects research and many industrial applications, atomic defect production, ion range, and doping concentration are commonly estimated by the stopping and range of ions in matter (SRIM) code. In this study, ion-induced damage and projectile ranges of low energy Au ions in SiC are determined using complementary ion beam and microscopy techniques. Considerable errors in both disorder profile and ion range predicted by the SRIM code indicate an overestimation of the electronic stopping power, by a factor of 2 in most cases, in the energy region up to 25 keV/nucleon. Such large discrepancies are also observed for slow heavy ions, including Pt, Au, and Pb ions, in other compound materials, such as GaN, AlN, and SrTiO3. Due to the importance of these materials for advanced device and nuclear applications, better electronic stopping cross section predictions, based on a reciprocity principle developed by Sigmund, is suggested with fitting parameters for possible improvement.
Effects of mucosal loading on vocal fold vibration
Authors: Tao Chao , Jiang Jack J.
Published: May 2009

A chain model was proposed in this study to examine the effects of mucosal loading on vocal fold vibration. Mucosal loading was defined as the loading caused by the interaction between the vocal folds and the surrounding tissue. In the proposed model, the vocal folds and the surrounding tissue were represented by a series of oscillators connected by a coupling spring. The lumped masses, springs, and dampers of the oscillators modeled the tissue properties of mass, stiffness, and viscosity, respectively. The coupling spring exemplified the tissue interactions. By numerically solving this chain model, the effects of mucosal loading on the phonation threshold pressure, phonation instability pressure, and energy distribution in a voice production system were studied. It was found that when mucosal loading is small, phonation threshold pressure increases with the damping constant Rr, the mass constant Rm, and the coupling constant Rμ of mucosal loading but decreases with the stiffness constant Rk. Phonation instability pressure is also related to mucosal loading. It was found that phonation instability pressure increases with the coupling constant Rμ but decreases with the stiffness constant Rk of mucosal loading. Therefore, it was concluded that mucosal loading directly affects voice production.
Impact of ligands on CO2 adsorption in metal-organic frameworks: First principles study of the interaction of CO2 with functionalized benzenes. I. Inductive effects on the aromatic ring
Authors: Torrisi Antonio , Mellot-Draznieks Caroline , Bell Robert G.
Published: May 2009

Intermolecular interactions between the CO2 molecule and a range of functionalized aromatic molecules have been investigated using density functional theory. The work is directed toward the design of linker molecules which could form part of new metal-organic framework materials with enhanced affinity for CO2 adsorption at low pressure. Two classes of substituted benzene molecules were considered: (i) with halogen substituents (tetrafluoro-, chloro-, bromo-, and dibromobenzene) and (ii) with methyl substituents (mono-, di-, and tetramethylbenzene). In the benzene-CO2 complex, the main interaction is between the delocalized π aromatic system and the molecular quadrupole of CO2. Halogen substituents have an electron-withdrawing effect on the ring which destabilizes the π-quadrupole interaction. Weak “halogen-bond” and hydrogen bondlike interactions partially compensate for this, but not to the extent that any significant enhancement of the intermolecular binding energy is observed. Methyl groups, on the other hand, have a positive inductive effect which strengthens the CO2-aromatic interaction by up to 3 kJ mol−1 in the case of tetramethylbenzene. Weak hydrogen bondlike interactions with methyl H also contribute to the stability of the complexes.
On the applicability of centroid and ring polymer path integral molecular dynamics for vibrational spectroscopy
Authors: Witt Alexander , Ivanov Sergei D. , Shiga Motoyuki , Forbert Harald , Marx Dominik
Published: May 2009

Centroid molecular dynamics (CMD) and ring polymer molecular dynamics (RPMD) are two conceptually distinct extensions of path integral molecular dynamics that are able to generate approximate quantum dynamics of complex molecular systems. Both methods can be used to compute quasiclassical time correlation functions which have direct application in molecular spectroscopy; in particular, to infrared spectroscopy via dipole autocorrelation functions. The performance of both methods for computing vibrational spectra of several simple but representative molecular model systems is investigated systematically as a function of temperature and isotopic substitution. In this context both CMD and RPMD feature intrinsic problems which are quantified and investigated in detail. Based on the obtained results guidelines for using CMD and RPMD to compute infrared spectra of molecular systems are provided.
Time-dependent wave packet and quasiclassical trajectory study of the C(P3)+OH(X Π2)→CO(X Σ1+)+H(S2) reaction at the state-to-state level
Authors: Bulut Niyazi , Zanchet Alexandre , Honvault Pascal , Bussery-Honvault Béatrice , Bañares Luis
Published: May 2009

The first calculations of state-to-state reaction probabilities and product state-resolved integral cross sections at selected collision energies (0.05, 0.1, 0.5, and 1.0 eV) for the title reaction on the ab initio potential energy surface of [Zanchet et al. J. Phys. Chem. A 110, 12017 (2006)] with the OH reagent in selected rovibrational states (v=0–2, j=0–5) have been carried out by means of the real wave packet (RWP) and quasiclassical trajectory (QCT) methods. State-selected total reaction probabilities have been calculated for total angular momentum J=0 in a broad range of collision energies. Integral cross sections and state-specific rate coefficients have been obtained from the corresponding J=0 RWP reaction probabilities for initially selected rovibrational states by means of a capture model. The calculated RWP and QCT state-selected rate coefficients are practically temperature independent. Both RWP and QCT reaction probabilities, integral cross sections, and rate coefficients are almost independent of the initial rotational excitation. The RWP results are found to be in an overall good agreement with the corresponding QCT results. The present results have been compared with earlier wave packet calculations carried out on the same potential energy surface.
Effects of electron temperature and density on ion-dust bremsstrahlung spectrum in dusty plasmas
Authors: Jung Young-Dae , Murakami Izumi
Published: May 2009

The effects of electron temperature and density on the ion-dust grain bremsstrahlung process in dusty plasmas are studied. The ion-dust bremsstrahlung radiation cross section is obtained as a function of the dust charge, dust radius, Debye length, collision energy, radiation energy, electron density, and electron temperature by using the Born approximation. It is shown that the ion-dust bremsstrahlung radiation cross section decreases with an increase in the electron density in dusty plasmas. It is also shown that the electron temperature suppresses the bremsstrahlung radiation cross section. In addition, the effect of electron temperature on the ion-dust bremsstrahlung process is found to be more significant than the effect of electron density in dusty plasmas.
Titanium and germanium lined hohlraums and halfraums as multi-keV x-ray radiators
Authors: Girard F. , Primout M. , Villette B. , Stemmler Ph. , Jacquet L. , Babonneau D. , Fournier K. B.
Published: May 2009

As multi-keV x-ray radiators, hohlraums and halfraums with inner walls coated with metallic materials (called liner) have been tested for the first time with laser as the energy drive. For titanium, conversion efficiencies (CEs) are up to ∼14% for emission into 4π, integrating between 4.6 and 6.5 keV when a large diameter hohlraum is used. Germanium CE is ∼0.8% into 4π between 9 and 13 keV. The highest CEs have been obtained with a 1 ns squared pulse and phase plates giving laser absorption near 99%. These high CEs are due to long-lasting, good plasma conditions for multi-keV x-ray production maintained by plasma confinement inside the plastic cylinder and plasma collision leading to a burst of x rays at a time that depends on target size. As photon emitters at 4.7 keV, titanium-lined hohlraums are the most efficient solid targets and data are close to CEs for gas targets, which are considered as the upper limit for x-ray yields since their low density allows good laser absorption and low kinetics losses. As 10.3 keV x-ray emitters, exploded germanium foils give best results one order of magnitude more efficient than thick targets; doped aerogels and lined hohlraums give similar yields, about three times lower than those from exploded foils.
Detrended fluctuation analysis of the magnetic and electric field variations that precede rupture
Authors: Varotsos P. A. , Sarlis N. V. , Skordas E. S.
Published: May 2009

Magnetic field variations are detected before rupture in the form of “spikes” of alternating sign. The distinction of these spikes from random noise is of major practical importance since it is easier to conduct magnetic field measurements than electric field ones. Applying detrended fluctuation analysis (DFA), these spikes look to be random at short time lags. On the other hand, long-range correlations prevail at time lags larger than the average time interval between consecutive spikes with a scaling exponent α around 0.9. In addition, DFA is applied to recent preseismic electric field variations in long duration (several hours to a couple of days) and reveals a scale invariant feature with an exponent α≈1 over all scales available (around five orders of magnitude).
Nested variant of the method of moments of coupled cluster equations for vertical excitation energies and excited-state potential energy surfaces
Authors: Kowalski Karol
Published: May 2009

In this article we discuss the problem of proper balancing of the noniterative corrections to the ground- and excited-state energies obtained with approximate coupled cluster (CC) and equation-of-motion CC (EOMCC) approaches. It is demonstrated that for a class of excited states dominated by single excitations and for states with medium doubly excited component, the newly introduced nested variant of the method of moments of CC equations provides mathematically rigorous way of balancing the ground- and excited-state correlation effects. The resulting noniterative methodology accounting for the effect of triples is tested using its parallel implementation on the systems, for which iterative CC/EOMCC calculations with full inclusion of triply excited configurations or their most important subset are numerically feasible.
A study of cumulant approximations to n-electron valence multireference perturbation theory
Authors: Zgid Dominika , Ghosh Debashree , Neuscamman Eric , Chan Garnet Kin-Lic
Published: May 2009

We investigate the possibility of reducing the complexity of multireference perturbation theory through cumulant based approximations to the high-order density matrices that appear in such theories. Our test cases show that while the cumulant approximated forms are degraded in accuracy relative to the parent theory and exhibit intruder state problems that must be carefully handled, they may provide a route to a simple estimation of dynamic correlation when the parent perturbation theory is infeasible. Nonetheless, further work is clearly needed on better approximations to the denominators in the perturbation theory.
Propagation failures, breathing fronts, and nonannihilation collisions in the ferroin-bromate-pyrocatechol system
Authors: Harati Mohammad , Wang Jichang
Published: May 2009

The emergence of propagating pulses was investigated with the photosensitive ferroin-bromate-pyrocatechol reaction in capillary tubes, in which various interesting spatiotemporal behaviors such as propagation failure, breathing fronts, and transitions between propagating pulses and fronts have been observed. Rather than a mutual annihilation, the collision of a propagating pulse and a growing front forces the front to recede gradually. A phase diagram in the pyrocatechol-bromate concentration space shows that the pulse instabilities take place throughout the conditions at which the system generates wave activities, suggesting that the presence of coupled autocatalytic feedbacks may facilitate the onset of pulse instabilities.
Charge redistribution in core-shell nanoparticles to promote oxygen reduction
Authors: Tang Wenjie , Henkelman Graeme
Published: May 2009

Bimetallic core-shell nanoparticles are a class of near-surface alloy catalyst for which there is a high degree of control over size and composition. A challenge for theory is to understand the relationship between their structure and catalytic function and provide guidelines to design new catalysts that take advantage of material properties arising at the nanoscale. In this work, we use density functional theory to calculate the energetics of oxygen dissociative adsorption on 1 nm Pd-shell nanoparticles with a series of core metals. The barrier for this reaction and the binding energy of atomic oxygen is found to correlate well with the d-band level of the surface electrons. Noble metal cores lower the barrier and increase the binding, reducing the activity of the Pd-shell as compared to Pt. Reactive core metals such as Co and Mo, on the other hand, lower the d-band of the shell with respect to the Fermi level, giving the Pd-shelled particles oxygen reduction kinetics similar to that of Pt. While both ligand and strain effects determine the d-band center of the Pd shell, a greater surface relaxation reduces the strain in nanoparticles as compared to single-crystal near-surface alloys. Charge redistribution between core and shell then becomes an important factor for lowering the d-band center of Pd-shelled particles and increasing their activity for the oxygen reduction reaction.
Parallel computation of coupled-cluster hyperpolarizabilities
Authors: Hammond Jeff R. , Kowalski Karol
Published: May 2009

Static hyperpolarizabilities of molecules (water, acetonitrile, chloroform, and para-nitroaniline) are calculated with large basis sets using coupled-cluster response theory and compared to four common density functional theory methods. These results reveal which methods and basis sets are appropriate for nonlinear optical studies for different types of molecules and provide a means for estimating errors from the quantum chemical approximation when including vibrational contributions or solvent effects at the QM/MM level. The largest calculation reported, which was for 72 electrons in 812 functions at C2v symmetry, took only a few hours on 256 nodes demonstrating that even larger calculations are quite feasible using modern supercomputers.
Vacuum-UV negative photoion spectroscopy of CF3Cl, CF3Br, and CF3I
Authors: Simpson M. J. , Tuckett R. P. , Dunn K. F. , Hunniford C. A. , Latimer C. J.
Published: May 2009

Using synchrotron radiation, negative ions are detected by mass spectrometry following vacuum-UV photoexcitation of trifluorochloromethane (CF3Cl), trifluorobromomethane (CF3Br), and trifluoroiodomethane (CF3I). The anions F−, X−, F2−, FX−, CF−, CF2−, and CF3− are observed from all three molecules, where X=Cl, Br, or I, and their ion yields recorded in the range of 8–35 eV. With the exception of Br− and I−, the anions observed show a linear dependence of signal with pressure, showing that they arise from unimolecular ion-pair dissociation. Dissociative electron attachment, following photoionization of CF3Br and CF3I as the source of low-energy electrons, is shown to dominate the observed Br− and I− signals, respectively. Cross sections for ion-pair formation are put onto an absolute scale by calibrating the signal strengths with those of F− from both SF6 and CF4. These anion cross sections are normalized to vacuum-UV absorption cross sections, where available, and the resulting quantum yields are reported. Anion appearance energies are used to calculate upper limits to 298 K bond dissociation energies for Do(CF3−X), which are consistent with literature values. We report new data for Do(CF2I+–F)≤2.7±0.2 eV and ΔfH298o(CF2I+)≤(598±22) kJ mol−1. No ion-pair formation is observed below the ionization energy of the parent molecule for CF3Cl and CF3Br, and only weak signals (in both I− and F−) are detected for CF3I. These observations suggest that neutral photodissociation is the dominant exit channel to Rydberg state photoexcitation at these lower energies.
Ab initio molecular dynamics study of the static, dynamic, and electronic properties of liquid mercury at room temperature
Authors: Calderín L. , González L. E. , González D. J.
Published: May 2009

We report a study on several static, dynamic, and electronic properties of liquid Hg at room temperature. We have performed ab initio molecular dynamics simulations using Kohn–Sham density functional theory combined with a nonlocal ultrasoft pseudopotential. The calculated static structure shows good agreement with the available experimental data. We present results for the single-particle dynamics, and recent experimental data are analyzed. The calculated dynamic structure factors S(q,ω) fairly agree with their experimental counterparts as measured by inelastic x-ray (and neutron) scattering experiments. The dispersion relation exhibits a positive dispersion, which however is not so marked as suggested by the experiment; moreover, its slope at the long-wavelength limit provides a good estimate of the experimental sound velocity. We have also analyzed the dynamical processes behind the S(q,ω) in terms of a model including a relaxation mechanism with both fast and slow characteristic time scales.
Influence of subpicosecond laser pulse duration on proton acceleration
Authors: Carrié M. , Lefebvre E. , Flacco A. , Malka V.
Published: May 2009

The influence of pulse duration on proton acceleration using subpicosecond (30–300 fs), ultraintense (from 3.6×1018 to 3.6×1019 W/cm2), constant energy (0.14 J) laser pulses is studied using two-dimensional simulations. The entire pulse duration is modeled so that during the rising edge of the pulse a preplasma can naturally expand from the target front and rear surfaces into vacuum, altering respectively laser absorption and electrostatic field generation. In this paper, we study this effect for two target profiles (sharp-edge profile and smooth density gradient at the front side) and we point out the existence of a weak optimum pulse duration for proton acceleration. For the different pulse durations we consider, we first show that the maximum proton energy variations are similar to those of the rear side electrostatic field amplitude. The energy variations, however, are smaller than expected from the field variations, and we explain this effect by characteristic proton acceleration time.
Generation of controllable nondiffracting beams using multimode optical fibers
Authors: Zhu X. , Schülzgen A. , Li L. , Peyghambarian N.
Published: May 2009

A method of generating nondiffracting beams using multimode optical fibers is reported. When a large-core multimode fiber is spliced onto a piece of single-mode fiber, only linearly polarized (LP0,n) modes are excited inside the multimode fiber segment because of mode orthogonality and on-axis excitation. Since the excited LP0,n modes are actually Bessel fields with different transverse wave vectors truncated by the core of the multimode fiber, the beam exiting the multimode fiber facet can form a variety of readily controllable and nearly nondiffracting optical patterns resulting from interference of apertured Bessel fields.
Unusual energy shifts in resonant photoemission spectra of organic model molecules
Authors: Peisert H. , Biswas I. , Zhang L. , Schuster B.-E. , Casu M. B. , Haug A. , Batchelor D. , Knupfer M. , Chassé T.
Published: May 2009

We study the electronic structure of zinc phthalocyanine (ZnPc) and 1,4-octa-decyl substituted zinc phthalocyanine [(Dec)8PcZn] thin films (∼6–15 nm) using resonant photoemission spectroscopy and X-ray absorption spectroscopy (XAS) at room temperature and at liquid He temperature. From XAS we conclude that the probability amplitude of the lowest unoccupied molecular orbital is located predominantly at the inner C and N atoms of the molecules. Nonlinear energy shifts in resonant photoemission were observed; large shifts are explained by reduced electrical conductivity of inhomogeneously oriented molecules.
Chaotic mixing in electro-osmotic flows driven by spatiotemporal surface charge modulation
Authors: Chang Chih-Chang , Yang Ruey-Jen
Published: May 2009

This paper presents an investigation into chaotic mixing in an electro-osmotic flow through a microchannel. In the mixing system, the continuous throughput flow has the form of a pluglike electro-osmotic flow induced by a permanent surface charge on the wall surface, while electro-osmotic flows contributed by spatiotemporal surface charge variations act as a perturbed flow. The spatiotemporal surface charge variations are achieved using the field-effect control method. The analyses consider two different spatiotemporal surface charge modulation schemes, designated as “MS I” and “MS II,” respectively. It is shown that both modulation schemes prompt the crossing of the flow streamlines at different instances in time and produce a chaotic mixing effect. Utilizing the thin double layer assumption, the study commences by solving the biharmonic equation for the electro-osmotic flow fields analytically. The mixing phenomena induced by the two modulation schemes are then analyzed using the Lagrangian particle tracing method. Finally, the mixing performances of the two schemes are evaluated analytically using the Poincaré section method, the finite-time Lyapunov exponent (FTLE) technique, and a stretching value distribution analysis method, respectively. It is found that the mean FTLE combined with the coefficient of variance of the FTLE distribution provides the most suitable criterion for obtaining quantitative estimates of the mixing performance and therefore provides a feasible means of estimating the amplitude and time-switching period of the perturbed flows which optimize the mixing performance. The validity of the analytical results is confirmed via a comparison with the results obtained from the back-trace imaging method and direct numerical simulations based on a species convection-diffusion equation, respectively. In addition, the direct numerical simulation results show that the dimensionless mixing length and dimensionless mixing time required to achieve a 90% mixing both vary as a logarithmic function of the Péclet number when the mixing system is in a nearly fully chaotic state.
On Coulomb collisions in bi-Maxwellian plasmas
Authors: Hellinger Petr , Trávníček Pavel M.
Published: May 2009

Collisional momentum and energy transport in bi-Maxwellian plasmas with a drift velocity along the ambient magnetic field are calculated from both the Fokker–Planck and Boltzmann integral approximations. The transport coefficients obtained from the two approaches are identical to the leading order (proportional to the Coulomb logarithm) and are presented here in a closed form involving generalized double hypergeometric functions.