bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterization of n uricase from Bacillus fastidious A.T.C.C. 26904 and its application to serum uric acid assay by a patented kinetic uricase method
Authors: Zhao Yunsheng , Zhao Lina , Yang Gengqing , Tao Jia , Bu Youquan , Liao Fei
Published: August 2006

An intracellular uricase from Bacillus fastidious A.T.C.C. 26904 was characterized and evaluated for serum uric acid assay by a patented kinetic uricase method. The active uricase was 151 kDa by gel filtration through Sephadex G‐200. Both SDS/PAGE and matrix‐assisted laser‐desorption ionization–time‐of‐flight MS resolved a single polypeptide with a molecular mass of approx. 36.0 kDa. The N‐terminal sequence was AERTMFYGKGDV. The optimum pH for this uricase ranged from 9.0 to 10.5. At pH 9.2, the Km (Michaelis–Menten constant) was 204±14 μmol/l (n=8) and the Ki (inhibition constant) for xanthine was 41±7 μmol/l (n=5). By analysing the data monitored within 5 min at 0.03 unit/ml uricase, this kinetic uricase method gave linear response to uric acid in reaction solution from 1.3 to 60 μmol/l. Aside from other common errors, 30 μmol/l xanthine in the reaction solution caused no error in this kinetic uricase method, while it caused negative error in the indirect equilibrium method by peroxidase‐coupled assay of H2O2. Uric acid in clinical sera by this kinetic uricase method (Ck) closely and positively correlated with that from the indirect equilibrium method (Ce) (Ck=0.008+1.081× Ce, r>0.990, n=99). However, Bland–Altman analysis suggested inconsistency between Ck and Ce. These results indicated that this kinetic uricase method using this uricase was reliable for serum uric acid assay with enhanced resistance to xanthine besides other common errors.
Fabrication and detection of tissue‐engineered bones with bio‐derived scaffolds in a rotating bioreactor
Authors: Song Kedong , Yang Zhiming , Liu Tianqing , Zhi Wei , Li Xiangqin , Deng Li , Cui Zhanfeng , Ma Xuehu
Published: August 2006

In order to explore the methods for commercialized bone tissue engineering, engineered bones should be cultivated in bioreactors to realize three‐dimensional culture under well‐defined culture conditions. In the present paper, osteoblasts isolated from the cranium of 1‐month‐old Zelanian rabbits were inoculated on to the BDBS (bio‐derived bone scaffolds) to investigate the three‐dimensional fabrication of engineered bone in an RWVB (rotating‐wall vessel bioreactor). The osteoblasts, after being transfected with green fluorescent protein, were respectively seeded at 2×106 and 1×106 cells·ml−1 on to the BDBS and then cultured in a T‐flask and an RWVB for 1 week. The morphologies and structure of the fabricated bone were investigated by using an inverted microscope, a scanning electron microscope and a laser confocal microscope using the stains haematoxylin/eosin and Toluidine Blue. After being digested from the scaffolds, the cells were assayed with ALP (alkaline phosphatase) stain, von‐Kossa staining on mineralized nodules, type I collagen and bone morphogenetic protein‐2 expression, and the cell expansion and growth curves using different culture methods were quantitatively determined with MTT (3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyl‐2H‐tetrazolium bromide). Furthermore, cell cycle and apoptosis were detected by using a flow cytometer, and total DNA was also assayed. For a comparative study, cell‐seeded constructs were also cultured under static conditions. The results show that the cell number cultured in the RWVB was five times that in the T‐flask. Bone tissues cultured in the RWVB with two different densities grew well, and the osteoblasts maintained their normal cycle and DNA content. The result demonstrates that, with the stress stimulation in the fluid in the RWVB, the active expression of ALP can be increased, rapid proliferation and differentiation of osteoblasts are possible and the three‐dimensional fabrication of engineered bone could be realized.
Immobilized protein ZZ, an affinity tool for immunoglobulin isolation and immunological experimentation
Authors: Chen Cheng , Huang Qi‐Lai , Jiang Shu‐Han , Pan Xiao , Hua Zi‐Chun
Published: August 2006

At present, the common tool for affinity purification of IgG is immobilized Protein A, which is separated from native cell‐wall components of Staphylococcus aureus. It is complicated and costly to prepare natural Protein A. ZZ protein is a synthetic Fc region‐binding domain originated from B domain of Protein A. In the present study, recombinant ZZ protein with a hexahistidine tag at the N‐terminus was expressed in BL21 (DE3) under the control of T7 promoter. The protein was purified through one‐step Ni2+ chelating affinity chromatography at a yield of 50 mg of protein/litre of culture. Then it was covalently coupled with Sepharose 4B with butane‐1,4‐diol diglycidyl ether. The protein ZZ–Sepharose 4B resin exhibited good performance in affinity purification of IgG, as well as in capturing the protein‐interacting complexes in immunoprecipitation experiments. Compared with natural Protein A, the expression and purification of ZZ protein at high yield are very simple and low‐cost. At this point, extensive applications of protein ZZ in immunoassays are practicable and to be anticipated.
Enzymatic C‐4 deacetylation of 10‐deacetylbaccatin III
Authors: Hanson Ronald L. , Parker William L. , Patel Ramesh N.
Published: August 2006

Second‐generation paclitaxel analogues that require replacement of the C‐4 acetate by other substituents are in development. An enzyme able to specifically remove the C‐4 acetate from paclitaxel could simplify preparation of the analogues. Several strains were isolated from soil samples that contain enzyme activities able to 4‐deacetylate 10‐DAB (10‐deacetylbaccatin III). Selection was made using plates containing 10‐DAB as the sole carbon source and screening colonies for deacetylation of 10‐DAB. Two strains initially isolated were identified as Rhodococcus sp. and deposited with the A.T.C.C. (Manassas, VA, U.S.A.) as strains 202191 and 202192. Whole cells were able to convert 10‐DAB into 4,10‐DDAB (4‐deacetyl‐10‐deacetylbaccatin III) in 90% yield. The enzyme activity in these strains was not effective with paclitaxel and 10‐deacetylpaclitaxel, although 4,10‐DDAB was produced from baccatin III. The activity in these strains was associated with an insoluble fraction of cell extracts. Several additional isolates were obtained that were identified as variants of Stenotrophomonas maltophilia, and a soluble C‐4 deacetylase was purified approx. 218‐fold from one of them. The activity of this enzyme was limited to 10‐DAB, and the enzyme was not effective with paclitaxel or baccatin III.
Effect of the silk protein sericin on the production of adenovirus‐based gene‐therapy vectors
Authors: Yanagihara Kana , Terada Satoshi , Miki Masao , Sasaki Masahiro , Yamada Hideyuki
Published: August 2006

Adenoviral vectors are extensively used as gene‐delivery vehicles in gene therapy. They are usually produced by HEK‐293 cell (human embryonic kidney‐293 cell) culture, which requires specially formulated serum‐free medium, the cost of which is considerable or by supplementation with FBS (fetal bovine serum). The risk of infectious diseases such as BSE (bovine spongiform encephalopathy) and endogenous retrovirus derived from cattle is a serious concern. The present study reports the use of sericin protein derived from silkworm (Bombyx mori) as an effective supplement instead of FBS. Without FBS, HEK‐293 cells significantly proliferated in the presence of 0.025–0.4% sericin, especially at 0.1%, but the effect was inferior to that of FBS. When a lower titre [MOI (multiplicity of infection) 0.03] of adenoviral vector pAxCAiLacZ was used as the inoculum, HEK‐293 cells in the presence of 0.1% sericin produced a nearly 3‐fold higher vector titre than culture in the presence of 5% (v/v) FBS. However, when a higher vector titre (MOI 3.7) was used as the inoculum, HEK‐293 cells in the presence of sericin produced a slightly higher vector titre than in the presence of FBS, which might suggest that HEK‐293 cells produce a maximum amount when a higher vector titre is used as the inoculum. These increases in vector production with sericin were confirmed by LacZ (β‐galactosidase reporter gene) activity assay. Supplementation with sericin decreased lactate dehydrogenase activity, an indicator of cell death, suggesting that sericin improved cell survival; hence, prolonging the culture period might be one of the reasons for increased vector production. On the basis of these results, sericin peptide seems to be a potent and effective alternative supplement for production of adenoviral vectors without such risks as BSE and retrovirus.
Positioning centrosomes and spindle poles: looking at the periphery to find the centre
Authors: Manneville Jean‐Baptiste , Etienne‐Manneville Sandrine
Published: August 2006

Centrosome positioning is tightly controlled throughout the cell cycle and probably shares common regulatory mechanisms with spindle‐pole positioning. In this article, we detail the possible mechanisms controlling centrosome and spindle positioning in various organisms both in interphase and mitotic cells, and discuss recent findings showing how microtubule plus‐end‐associated proteins interact with the cell cortex. We suggest that microtubule plus‐end complexes simultaneously regulate microtubule dynamics and microtubule anchoring at the cell periphery to allow proper centrosome and spindle‐pole positioning.
Integrin signalling in directed cell migration
Authors: Moissoglu Konstandinos , Schwartz Martin Alexander
Published: August 2006

Migrating cells tend to continue moving in the same direction, a property called persistence. During migration, cells, by definition, form new adhesions at their front and break old adhesions at the rear. We hypothesize that the distinction between new adhesions at the front and older adhesions at the rear plays a major role in directional persistence. We propose specific mechanisms of persistence on the basis of known properties of integrin signals, in hope of stimulating investigation of these ideas.
Id‐1 modulates senescence and TGF‐β1 sensitivity in prostate epithelial cells
Authors: Di Kaijun , Ling Ming‐tat , Tsao Sai Wah , Wong Yong Chuan , Wang Xianghong
Published: August 2006

Background information. Loss of sensitivity to TGF‐β1 (transforming growth factor β1)‐induced growth arrest is an important step towards malignant transformation in human epithelial cells, and Id‐1 (inhibitor of differentiation or DNA binding‐1) has been associated with cell proliferation and cell‐cycle progression. Here, we investigated the role of Id‐1 in cellular sensitivity to TGF‐β1.

Results. Using an immortalized prostate epithelial cell line, NPTX cells, we suppressed Id‐1 expression through antisense strategy. We found that inhibition of Id‐1 expression suppressed cell proliferation and at the same time induced cellular senescence and G2/M cell‐cycle arrest. In addition, inactivation of Id‐1 made cells more vulnerable to TGF‐β1‐induced growth arrest. The sensitization effect on TGF‐β1 was associated with up‐regulation of two downstream effectors of the TGF‐β1 pathway, p21WAF1/Cip1 and p27KIP1.

Conclusion. Our results indicate that endogenous Id‐1 levels might be a crucial factor in the development of resistance to TGF‐β1‐induced growth suppression in human prostate epithelial cells.
New comprehension of the apicoplast of Sarcocystis by transmission electron tomography
Authors: Tomova Cveta , Geerts Willie J.C. , Müller‐Reichert Thomas , Entzeroth Rolf , Humbel Bruno M.
Published: August 2006

Background information. Apicomplexan parasites (like Plasmodium, Toxoplasma, Eimeria and Sarcocystis) contain a distinctive organelle, the apicoplast, acquired by a secondary endosymbiotic process analogous to chloroplasts and mitochondria. The apicoplast is essential for long‐term survival of the parasite. This prokaryotic origin implies that molecular and metabolic processes in the apicoplast differ from those of the eukaryotic host cells and therefore offer options for specific chemotherapeutic treatment. We studied the apicoplast in high‐pressure frozen and freeze‐substituted cysts of Sarcocystis sp. from roe deer (Capreolus capreolus) to get better insight in apicoplast morphology.

Results and conclusions. We observed that the apicoplast contains four continuous membranes. The two inner membranes have a circular shape with a constant distance from each other and large‐sized protein complexes are located between them. The two outer membranes have irregular shapes. The periplastid membrane also contains large‐sized protein complexes, while the outer membrane displays protuberances into the parasite cytoplasm. In addition, it is closely associated with the endoplasmic reticulum by ‘contact sites’.
Origin of the enhancement of the second hyperpolarizability of singlet diradical systems with intermediate diradical character
Authors: Nakano Masayoshi , Kishi Ryohei , Ohta Suguru , Takebe Akihito , Takahashi Hideaki , Furukawa Shin-ichi , Kubo Takashi , Morita Yasushi , Nakasuji Kazuhiro , Yamaguchi Kizashi , Kamada Kenji , Ohta Koji , Champagne Benoît , Botek Edith
Published: August 2006

The origin of the diradical character dependence of the second hyperpolarizability (γ) of neutral singlet diradical systems is clarified based on the perturbation formula of γ using the simplest diradical molecular model with different diradical characters, i.e., H2 under bond dissociation. The enhancement of γ in the intermediate diradical character region turns out to originate from the increasing magnitude of the transition moment between the first and second excited states and the decrease of that between the ground and first excited states, respectively, with the increase in diradical character. This feature confirms that open-shell singlet conjugated molecules with intermediate diradical characters constitute a new class of third-order nonlinear optical systems, whose γ values can be controlled by the diradical character in addition to the conjugation length.
Calculating fifth-order Raman signals for various molecular liquids by equilibrium and nonequilibrium hybrid molecular dynamics simulation algorithms
Authors: Hasegawa Taisuke , Tanimura Yoshitaka
Published: August 2006

The fifth-order two-dimensional (2D) Raman signals have been calculated from the equilibrium and nonequilibrium (finite field) molecular dynamics simulations. The equilibrium method evaluates response functions with equilibrium trajectories, while the nonequilibrium method calculates a molecular polarizability from nonequilibrium trajectories for different pulse configurations and sequences. In this paper, we introduce an efficient algorithm which hybridizes the existing two methods to avoid the time-consuming calculations of the stability matrices which are inherent in the equilibrium method. Using nonequilibrium trajectories for a single laser excitation, we are able to dramatically simplify the sampling process. With this approach, the 2D Raman signals for liquid xenon, carbon disulfide, water, acetonitrile, and formamide are calculated and discussed. Intensities of 2D Raman signals are also estimated and the peak strength of formamide is found to be only five times smaller than that of carbon disulfide.
Extended treatment of charge response kernel comprising the density functional theory and charge regulation procedures
Authors: Ishida Tateki , Morita Akihiro
Published: August 2006

We propose an extended treatment of the charge response kernel (CRK), (∂Qa∕∂Vb), which describes the response of partial charges on atomic sites to external electrostatic potential, on the basis of the density functional theory (DFT) via the coupled perturbed Kohn-Sham equations. The present CRK theory incorporates regulation procedures in the definition of partial charges to avoid unphysical large fluctuation of the CRK on “buried” sites. The CRKs of some alcohol and organic molecules, methanol, ethanol, propanol, butanol, dimethylsulfoxide (DMSO), and tetrahydrofuran (THF) were calculated, demonstrating that the new CRK model at the DFT level has greatly improved the performance of accuracy in comparison with that at the Hartree-Fock level previously proposed. The CRK model was also applied to investigate spatial nonlocality of the charge response through alkyl chain sequences. The CRK model at the DFT level enables us to construct a nonempirical strategy for polarizable molecular modeling, with practical reliability and robustness.
Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics
Authors: Jayachandran Guha , Shirts Michael R. , Park Sanghyun , Pande Vijay S.
Published: August 2006

We present a technique for biomolecular free energy calculations that exploits highly parallelized sampling to significantly reduce the time to results. The technique combines free energies for multiple, nonoverlapping configurational macrostates and is naturally suited to distributed computing. We describe a methodology that uses this technique with docking, molecular dynamics, and free energy perturbation to compute absolute free energies of binding quickly compared to previous methods. The method does not require a priori knowledge of the binding pose as long as the docking technique used can generate reasonable binding modes. We demonstrate the method on the protein FKBP12 and eight of its inhibitors.
On the use of orientational restraints and symmetry corrections in alchemical free energy calculations
Authors: Mobley David L. , Chodera John D. , Dill Ken A.
Published: August 2006

Alchemical free energy calculations are becoming a useful tool for calculating absolute binding free energies of small molecule ligands to proteins. Here, we find that the presence of multiple metastable ligand orientations can cause convergence problems when distance restraints alone are used. We demonstrate that the use of orientational restraints can greatly accelerate the convergence of these calculations. However, even with this acceleration, we find that sufficient sampling requires substantially longer simulations than are used in many published protocols. To further accelerate convergence, we introduce a new method of configuration space decomposition by orientation which reduces required simulation lengths by at least a factor of 5 in the cases examined. Our method is easily parallelizable, well suited for cases where a ligand cocrystal structure is not available, and can utilize initial orientations generated by docking packages.
Photodissociation dynamics of the NO dimer. I. Theoretical overview of the ultraviolet singlet excited states
Authors: Levchenko Sergey V. , Reisler Hanna , Krylov Anna I. , Gessner Oliver , Stolow Albert , Shi Huancong , East Allan L. L.
Published: August 2006

Molecular orbital theory and calculations are used to describe the ultraviolet singlet excited states of NO dimer. Qualitatively, we derive and catalog the dimer states by correlating them with monomer states, and provide illustrative complete active space self-consistent field calculations. Quantitatively, we provide computational estimates of vertical transition energies and absorption intensities with multireference configuration interaction and equations-of-motion coupled-cluster methods, and examine an important avoided crossing between a Rydberg and a valence state along the intermonomer and intramonomer stretching coordinates. The calculations are challenging, due to the high density of electronic states of various types (valence and Rydberg, excimer and charge transfer) in the 6–8eV region, and the multiconfigurational nature of the ground state. We have identified a bright charge-transfer (charge-resonance) state as responsible for the broadband seen in UV absorption experiments. We also use our results to facilitate the interpretation of UV photodissociation experiments, including the time-resolved 6eV photodissociation experiments to be presented in the next two papers of this series.
Analytic plane wave solutions for the quaternionic potential step
Authors: De Leo Stefano , Ducati Gisele C. , Madureira Tiago M.
Published: August 2006

By using the recent mathematical tools developed in quaternionic differential operator theory, we solve the Schrödinger equation in the presence of a quaternionic step potential. The analytic solution for the stationary states allows one to explicitly show the qualitative and quantitative differences between this quaternionic quantum dynamical system and its complex counterpart. A brief discussion on reflected and transmitted times, performed by using the stationary phase method, and its implication on the experimental evidence for deviations of standard quantum mechanics is also presented. The analytic solution given in this paper represents a fundamental mathematical tool to find an analytic approximation to the quaternionic barrier problem (up to now solved by numerical method).
Characterization of spectral diffusion from two-dimensional line shapes
Authors: Roberts Sean T. , Loparo Joseph J. , Tokmakoff Andrei
Published: August 2006

The analysis of line shapes in two-dimensional optical and infrared spectroscopies is a powerful approach to characterizing the dynamics of molecules in the condensed phase. Changes in line shape from diagonally elongated to symmetric as a function of waiting time arise from evolution of the transition frequency. We describe a number of quantitative measures of frequency fluctuations and spectral diffusion through the analysis of two-dimensional (2D) line shapes. These metrics are identical to the system’s frequency correlation function and independent of population relaxation in the limit of a short time approximation for the 2D response. We also test the broader applicability of these expressions for analyzing three-level vibrational systems and experiments with finite pulses.
Structure and stability of the Al14 halides Al14In− (n=1–11): Can we regard the Al14 core as an alkaline earthlike superatom?
Authors: Han Young-Kyu , Jung Jaehoon
Published: August 2006

We have studied the structures and stabilities of Al14In− (n=1–11) clusters at the density functional level of theory. The experimentally observed Al14In− (n=3, 5, 7, 9, and 11) [Bergeron et al., Science 307, 231 (2005)] are found to be stable both kinetically and thermodynamically. Al14I3−, not Al14I−, is the first member of the Al14In− series in the mass spectrometric experiment, which is ascribable to the low kinetic stability of the Al14I− cluster. The Al14 core in Al14I3− is close to neutral Al14, both electronically and structurally. Population analysis shows that charge transfer occurs from the Al cluster to the I atoms, where the populations for Al14 vary from −0.70(Al14I−) to +0.96(Al14I11−). The Al14I5− and Al14I7− clusters have the structure of Al14I3− as a core framework, but, for n=9 and 11, we found many more stable isomers than the isomers having the Al14I3− core. In particular, the shape of Al14 in the Al14I11− cluster is a hexagonal wheel-shaped form, which was observed in the x-ray experiment for the metalloid complex [Al14{N(SiMe3)2}6I6Li(OEt2)2]−[Li(OEt2)4]+∙toluene [Köhnlein et al., Angew. Chem., Int. Ed. 39, 799 (2000)]. We have demonstrated that a simple jellium model cannot describe the structure and stability of the iodine-doped aluminum clusters, although it is successful for describing those of aluminum clusters. The electronic and geometric changes of the Al14− cluster due to the presence of iodines are very similar to the case of a magic cluster Al13−. It can be concluded from our electronic and structural analysis that one cannot regard the Al14 core as an alkaline earthlike superatom in the Al14 iodide clusters.
Vibrational spectrum of cyclic TiC3 in solid Ar
Authors: Kinzer R. E. , Rittby C. M. L. , Graham W. R. M.
Published: August 2006

The Fourier transform infrared spectrum of TiC3 was observed by trapping the vapor produced during dual Nd:YAG laser ablation of Ti and C rods in solid Ar at ∼9K. Measurements of frequencies and C13 isotopic shifts have enabled the identification of the fanlike (C2v) isomer of TiC3 with fundamental vibrations ν3(a1)=624.3 and ν5(b2)=1484.2cm−1. A third fundamental ν4(b1) has been tentatively identified at 573.8cm−1. The results are in good agreement with the predictions of density functional theory calculations at the B3LYP∕6-311G(3df,3pd) level. The observed C2v structure and the observed ν3 metal-carbon stretching mode are also consistent with earlier results from photoelectron spectroscopy.
Vlasov simulations of plasma-wall interactions in a magnetized and weakly collisional plasma
Authors: Devaux S. , Manfredi G.
Published: August 2006

A Vlasov code is used to model the transition region between an equilibrium plasma and an absorbing wall in the presence of a tilted magnetic field, for the case of a weakly collisional plasma (λmfp≫ρi, where λmfp is the ion-neutral mean-free path and ρi is the ion Larmor radius). The phase space structure of the plasma-wall transition is analyzed in detail and theoretical estimates of the magnetic presheath width are tested numerically. It is shown that the distribution near the wall is far from Maxwellian, so that temperature measurements should be interpreted with care. Particular attention is devoted to the angular distribution of ions impinging on the wall, which is an important parameter to determine the level of wall erosion and sputtering.
Femtosecond pump/probe photoelectron spectroscopy of isolated C60 negative ions
Authors: Ehrler Oli T. , Yang Ji Ping , Hättig Christof , Unterreiner Andreas-N. , Hippler Horst , Kappes Manfred M.
Published: August 2006

We have measured pump/probe photoelectron spectra of mass-selected, near room temperature C60− in the gas phase. The lifetime of the vibrationally excited B̃−(Eg2) state at a calculated energy of 1.26eV was found to be τ=2.2±0.2ps. The dominant decay process corresponds to intramolecular radiationless transitions into ground state C60−. This is in contrast to C60 for which pumping at the absorption onset (1.95eV) leads to predominantly intersystem crossing.
Modeling vibrational dephasing and energy relaxation of intramolecular anharmonic modes for multidimensional infrared spectroscopies
Authors: Ishizaki Akihito , Tanimura Yoshitaka
Published: August 2006

Starting from a system-bath Hamiltonian in a molecular coordinate representation, we examine an applicability of a stochastic multilevel model for vibrational dephasing and energy relaxation in multidimensional infrared spectroscopy. We consider an intramolecular anharmonic mode nonlinearly coupled to a colored noise bath at finite temperature. The system-bath interaction is assumed linear plus square in the system coordinate, but linear in the bath coordinates. The square-linear system-bath interaction leads to dephasing due to the frequency fluctuation of system vibration, while the linear-linear interaction contributes to energy relaxation and a part of dephasing arises from anharmonicity. To clarify the role and origin of vibrational dephasing and energy relaxation in the stochastic model, the system part is then transformed into an energy eigenstate representation without using the rotating wave approximation. Two-dimensional (2D) infrared spectra are then calculated by solving a low-temperature corrected quantum Fokker-Planck (LTC-QFP) equation for a colored noise bath and by the stochastic theory. In motional narrowing regime, the spectra from the stochastic model are quite different from those from the LTC-QFP. In spectral diffusion regime, however, the 2D line shapes from the stochastic model resemble those from the LTC-QFP besides the blueshifts caused by the dissipation from the colored noise bath. The preconditions for validity of the stochastic theory for molecular vibrational motion are also discussed.
Higher-order equation-of-motion coupled-cluster methods for ionization processes
Authors: Kamiya Muneaki , Hirata So
Published: August 2006

Compact algebraic equations defining the equation-of-motion coupled-cluster (EOM-CC) methods for ionization potentials (IP-EOM-CC) have been derived and computer implemented by virtue of a symbolic algebra system largely automating these processes. Models with connected cluster excitation operators truncated after double, triple, or quadruple level and with linear ionization operators truncated after two-hole-one-particle (2h1p), three-hole-two-particle (3h2p), or four-hole-three-particle (4h3p) level (abbreviated as IP-EOM-CCSD, CCSDT, and CCSDTQ, respectively) have been realized into parallel algorithms taking advantage of spin, spatial, and permutation symmetries with optimal size dependence of the computational costs. They are based on spin-orbital formalisms and can describe both α and β ionizations from open-shell (doublet, triplet, etc.) reference states into ionized states with various spin magnetic quantum numbers. The application of these methods to Koopmans and satellite ionizations of N2 and CO (with the ambiguity due to finite basis sets eliminated by extrapolation) has shown that IP-EOM-CCSD frequently accounts for orbital relaxation inadequately and displays errors exceeding a couple of eV. However, these errors can be systematically reduced to tenths or even hundredths of an eV by IP-EOM-CCSDT or CCSDTQ. Comparison of spectroscopic parameters of the FH+ and NH+ radicals between IP-EOM-CC and experiments has also underscored the importance of higher-order IP-EOM-CC treatments. For instance, the harmonic frequencies of the ÃΣ−2 state of NH+ are predicted to be 1285, 1723, and 1705cm−1 by IP-EOM-CCSD, CCSDT, and CCSDTQ, respectively, as compared to the observed value of 1707cm−1. The small adiabatic energy separation (observed 0.04eV) between the X̃Π2 and ãΣ−4 states of NH+ also requires IP-EOM-CCSDTQ for a quantitative prediction (0.06eV) when the ãΣ−4 state has the low-spin magnetic quantum number (sz=1∕2). When the state with sz=3∕2 is sought, the energy separations converge much more rapidly with the IP-EOM-CCSD value (0.03eV) already being close to the observed (0.04eV).
q
stars in scalar-tensor gravitational theories in extra dimensions
Authors: Prikas Athanasios
Published: August 2006

We present Jordan-Brans-Dicke and general scalar-tensor gravitational theory in extra dimensions in an asymptotically flat or anti de Sitter spacetime. We consider a special gravitating, boson field configuration, a q star, in three, four, five, and six dimensions, within the framework of the above gravitational theory, and find that the parameters of the stable stars are a few percent different from the case of General Relativity.
Information entropies for eigendensities of homogeneous potentials
Authors: Sen K. D. , Katriel Jacob
Published: August 2006

For homogeneous potentials, the sum ST, of position and momentum Shannon information entropies Sr and Sp is shown to be independent of the coupling strength scaling. The other commonly used uncertainty like products also follow similar behavior. The ramifications of this scaling property in the cases of hydrogenlike, harmonic oscillator, Morse, and Poeschl-Teller potentials are discussed with the example of ST.
Direct optical observation of magnetic domains in Ni–Mn–Ga martensite
Authors: Ge Y. , Heczko O. , Söderberg O. , Hannula S.-P.
Published: August 2006

This letter reports the direct optical observation, i.e., without polarization, of the magnetic domain structure explained by a large surface relief in Ni–Mn–Ga martensite. The authors suggest that the relief is due to the different straining of the surface and the bulk caused by the internal stresses associated with the magnetic shape memory effect. As a result of the relief the projection of the (011) twin traces upon the (010) plane creates the observed zigzag pattern. The surface tilt angle calculated from the zigzag pattern is ∼3°.
Fractal growth mechanism of sp3-bonded 5H-BN microcones by plasma-assisted pulsed-laser chemical vapor deposition
Authors: Komatsu Shojiro , Kazami Daisuke , Tanaka Hironori , Moriyoshi Yusuke , Shiratani Masaharu , Okada Katsuyuki
Published: August 2006

Here we propose a repetitive photochemical reaction and diffusion model for the fractal pattern formation of sp3-bonded 5H-BN microcones in laser-assisted plasma chemical vapor deposition, which was observed experimentally and reported previously. This model describing the behavior of the surface density of precursor species gave explanations to (1) the “line-drawing” nature of the patterns, (2) the origin of the scale-invariant self-similarity (fractality) of the pattern, and (3) the temperature-dependent uniform to fractal transition. The results have implications for controlling the self-organized arrangements of electron-emitter cones at the micro-and nanoscale by adjusting macroscopically the boundary condition (LX,LY) for the deposition, which will be very effective in improving the electron field emission properties.
Hydrodynamic lubrication in nanoscale bearings under high shear velocity
Authors: Chen Yunfei , Li Deyu , Jiang Kai , Yang Juekuan , Wang Xiaohui , Wang Yujuan
Published: August 2006

The setting up process in a nanoscale bearing has been modeled by molecular dynamics simulation. Contrary to the prediction from the classical Reynolds’ theory, simulation results show that the load capacity of the nanoscale bearing does not increase monotonically with the operation speed. This is attributed to the change of the local shear rate, which will decrease with the shear velocity of the bearing as the shear velocity exceeds a critical value, i.e., the local shear rate has an upper limit. A simple nonlinear dynamic model indicates that the momentum exchange between the liquid and the solid wall is reduced with the shear velocity when the shear velocity is above a critical value. The weak momentum exchange results in a decrease of the local shear rate, which in turn causes a sharp increase of the slip length.
Ab initio determination of the ionization potentials of DNA and RNA nucleobases
Authors: Roca-Sanjuán Daniel , Rubio Mercedes , Merchán Manuela , Serrano-Andrés Luis
Published: August 2006

Quantum chemical high level ab initio coupled-cluster and multiconfigurational perturbation methods have been used to compute vertical and adiabatic ionization potentials of the five canonical DNA and RNA nucleobases: uracil, thymine, cytosine, adenine, and guanine. Several states of their cations have been also calculated. The present results represent a systematic compendium of these magnitudes, establishing theoretical reference values at a level not reported before, calibrating computational strategies, and guiding the assignment of the features in the experimental photoelectron spectra.
Temperature-dependent elastic properties of single-walled carbon nanotubes: Prediction from molecular dynamics simulation
Authors: Zhang Chen-Li , Shen Hui-Shen
Published: August 2006

The authors report here a method of determining the mechanical properties of single-walled carbon nanotubes by direct measurement from molecular dynamics simulation test. The authors find that single-walled carbon nanotubes exhibit obvious anisotropic, temperature-dependent properties. The value of Young’s modulus decreases with increase in temperature, whereas the shear modulus increases when the temperature is less than 700K and remains almost constant when the temperature is greater than 700K. By direct buckling measuring, the authors obtain the effective wall thickness of nanotubes and find that the effective wall thickness of zigzag nanotubes is larger than that of armchair nanotubes.
Thickness dependence of dielectric properties in bismuth layer-structured dielectrics
Authors: Takahashi Kenji , Suzuki Muneyasu , Kojima Takashi , Watanabe Takayuki , Sakashita Yukio , Kato Kazumi , Sakata Osami , Sumitani Kazushi , Funakubo Hiroshi
Published: August 2006

c -axis-oriented epitaxial SrBi4Ti4O15 and CaBi4Ti4O15 films having natural superlattice structure were grown on (001)cSrRuO3‖(001)SrTiO3 substrates by metal organic chemical vapor deposition. SrBi4Ti4O15 films suffer no degradation with a dielectric constant of 200 down to a film thickness of 15nm, which corresponds to four unit cells. Temperature coefficients of capacitance were low enough despite their high dielectric constant. They exhibited stable capacitance and superior insulating properties against applied electric field, irrespective of film thickness. These results open the door to designable size-effect-free materials with high dielectric constant having bias- and temperature-independent characteristics together with superior electrical insulation for high-density capacitor applications.
Efficient ultraviolet-blue polymer light-emitting diodes based on a fluorene-based non-conjugated polymer
Authors: Huang Fei , Niu Yu-Hua , Liu Michelle S. , Zhou Xing-Hua , Tian Yan-Qing , Jen Alex K.-Y.
Published: August 2006

Efficient UV-blue polymer light-emitting diodes based on a fluorene-based nonconjugated polymer, poly[2,7-(9,9-dihexylfluorene)-alt-4,4′-phenylether] (PFPE), are fabricated. The device with PFPE as emitting layer shows a very narrow ultraviolet-blue electroluminescence emission with a peak at 397nm and a maximal external quantum efficiency of 1.07%. By blending PFPE into poly(N-vinylcarbazole) (PVK), the device performance can be further improved. A maximum external quantum efficiency of 1.81%, with a maximum irradiance power density of 1223μW∕cm2, was reached by using a blend of PVK and PFPE in the weight ratio of 95:5 as emitting layer.
Development of a new signal processor for tetralateral position sensitive detector based on single-chip microcomputer
Authors: Huang Mei-Zhen , Shi Long-Zhao , Wang Yu-Xing , Ni Yi , Li Zhen-Qing , Ding Hai-Feng
Published: August 2006

An inherently nonlinear relation between the output current of the tetralateral position sensitive detector (PSD) and the position of the incident light spot has been found theoretically. Based on single-chip microcomputer and the theoretical relation between output current and position, a new signal processor capable of correcting nonlinearity and reducing position measurement deviation of tetralateral PSD was developed. A tetralateral PSD (S1200, 13×13mm2, Hamamatsu Photonics K.K.) was measured with the new signal processor, a linear relation between the output position of the PSD, and the incident position of the light spot was obtained. In the 60% range of a 13×13mm2 active area, the position nonlinearity (rms) was 0.15% and the position measurement deviation (rms) was ±20μm. Compared with traditional analog signal processor, the new signal processor is of better compatibility, lower cost, higher precision, and easier to be interfaced.
Analysis of nucleation ability of cluster configurations with Monte Carlo simulations of argon
Authors: Merikanto Joonas , Zapadinsky Evgeni , Vehkamäki Hanna
Published: August 2006

We determine the nucleation ability of argon clusters from Monte Carlo simulations. The nucleation rate appears to be defined by a sole characteristic of the clusters, namely, the stability. The stability is calculated as the ratio of grand canonical growth and decay rates and can be assigned to individual cluster configurations. We study the connection between the stability of the cluster configurations and their volume and total potential energy. Neither the potential energy nor the volume of a cluster configuration has a clear relation to its stability, and thus to the nucleation ability. On the other hand, we show that it is possible to use a specific volume for each cluster size to calculate the work of the cluster formation. These clusters with a unique volume have the same average stability as the full set of clusters. Our simulation method allows us to study the effect of possible deviations from equilibrium in the cluster configuration distributions. We argue that the nucleation process itself can produce a source for such a deviation. We show that even a small deviation from equilibrium in the cluster configuration distribution can lead to a dramatic deceleration of the nucleation rate. Although our simulations may overestimate the magnitude of the effect, they give qualitative estimates for its importance.
Prediction of the thermal annealing of thick oxide metal-oxide-semiconductor dosimeters irradiated in a harsh radiation environment
Authors: Ravotti F. , Glaser M. , Saigné F. , Dusseau L. , Sarrabayrouse G.
Published: August 2006

Radiation-sensing metal-oxide-semiconductor field-effect transistors produced by the laboratory LAAS-CNRS were exposed to a harsh hadron field that represents the real radiation environment expected at the CERN Large Hadron Collider experiments. The long-term stability of the transistor’s Ids-Vgs characteristic was investigated using the isochronal annealing technique. In this work, devices exposed to high intensity hadron levels (Φ⩾1012neutrons∕cm2) show evidences of displacement damages in the Ids-Vgs annealing behavior. By comparing experimental and simulated results over 14months, the isochronal annealing method, originally devoted to oxide trapped charge, is shown to enable prediction of the recovery of silicon bulk defects.
Many-body effects of dispersion interaction
Authors: Donchev A. G.
Published: August 2006

The role of many-body (MB) dispersion forces have been analyzed for strands, films, and cubic lattices in the framework of a model Hamiltonian that allows exact solution of the multiparticle Shrödinger equation. For the systems investigated the MB contribution may be as large as 7% of specific dispersion energy and 11% of solvation energy. Nonadditivity becomes particularly important for aggregation in solution, where its effect may be several times larger than the pairwise contribution. For all systems considered, the three-body Axilrod-Teller approximation was insufficient to predict the magnitude and in some cases even the sign of the full MB effect.
High-temperature continuous wave operation of strain-balanced quantum cascade lasers grown by metal organic vapor-phase epitaxy
Authors: Diehl L. , Bour D. , Corzine S. , Zhu J. , Höfler G. , Lončar M. , Troccoli M. , Capasso Federico
Published: August 2006

The authors report the fabrication of high-power strained quantum cascade lasers working in continuous mode above 370K. The devices, processed in narrow buried heterostructures, were grown by low-pressure metal organic vapor-phase epitaxy. Continuous wave output power as high as 312mW at 300K was obtained at a wavelength of 5.29μm from a 3.25mm long, 7.5μm wide laser with a high-reflectivity back facet coating. The slope efficiency was in excess of 1.5W∕A and the power conversion efficiency reached almost 5%.
Ni adsorption on Stone-Wales defect sites in single-wall carbon nanotubes
Authors: Yang Seong Ho , Shin Weon Ho , Kang Jeung Ku
Published: August 2006

Ni adsorption on Stone-Wales defect sites in (10,0) zigzag and (5,5) armchair single-wall carbon nanotubes was studied using the density functional theory. The stable adsorption sites and their binding energies on different Stone-Wales defect types were analyzed and compared to those on perfect side walls. It was determined that the sites formed via fusions of 7-7 and 6-7 rings are the most exothermic in the cases of (10,0) and (5,5) defective tubes. In addition C–C bonds associated with Stone-Wales defects are more reactive than the case for a perfect hexagon, thus enhancing the stability of the Ni adsorption. Moreover, the Ni adsorption was found to show a noticeable relationship to the orientation of the Stone-Wales defects with respect to the tube axis. The nature of the Ni adsorption on Stone-Wales defects that have the similar orientation is identical, in spite of the different chiralities.
Ba
0.9
Sr
0.1
Ti
O
3
-based Bragg reflectors fabricated from one single chemical solution
Authors: Hong X. K. , Hu G. J. , Chen J. , Chu J. H. , Dai N. , Wu H. Z.
Published: August 2006

Periodic ferroelectric multilayers consisting of alternating stack of the dense and porous Ba0.9Sr0.1TiO3 layers have been fabricated by spin-coating and annealing sol-gel techniques using one single precursor. With 16 periods, the Ba0.9Sr0.1TiO3 multilayers exhibit excellent performance as dielectric mirrors: symmetric peak reflectivities of above 95% and flattopped stop bands of about 75nm. The reflectance peak position is tunable through varying the spinning rate in the spin-coating process. The lead-free Ba0.9Sr0.1TiO3 multilayers show high stability.
Quantum dot intermixing using excimer laser irradiation
Authors: Djie H. S. , Ooi B. S , Gunawan O.
Published: August 2006

The authors report a spatial control of the band gap in InGaAs∕GaAs quantum dots (QDs) using the combined effects of pulsed excimer laser irradiation and impurity-free dielectric cap induced intermixing technique. A large band gap shift of up to 180meV has been obtained under laser irradiation of 480mJ∕cm2 and 150 pulses to the SiO2 capped shallow QD structure, while the nonirradiated SiO2 and SixNy capped QDs only exhibit band gap shifts of 18 and 91meV, respectively.
Tuning the wettability on La0.7Sr0.3MnO3 coatings from superhydrophilicity to superhydrophobicity by hierarchical microstructure
Authors: Xiao Wenjia , Huang Zhencheng , He Zhenhui
Published: August 2006

It is well known that surface roughness always enhances wetting for hydrophilic, but drying for hydrophobic surfaces. In this letter, the authors found that La0.7Sr0.3MnO3 coatings display distinct wettability from superhydrophilicity to superhydrophobictiy, which is tuned by their hierarchical microstructures obtained by annealing the coatings composed of nanopowder at different temperatures. This offers a strong support to Herminghaus’s model [Europhys. Lett. 52, 165 (2000)] which predicts that the material hierarchical structure determines its wettability and widens the range of raw materials for superhydrophobic surfaces.
Gate capacitance of back-gated nanowire field-effect transistors
Authors: Wunnicke Olaf
Published: August 2006

Gate capacitances of back-gated nanowire field-effect transistors (NW-FETs) are calculated by means of finite element methods and the results are compared with analytical results of the “metallic cylinder on an infinite metal plate model.” Completely embedded and nonembedded NW-FETs are considered. It is shown that the use of the analytical expressions also for nonembedded NW-FETs gives carrier mobilities that are nearly two times too small. Furthermore, the electric field amplification of nonembedded NW-FETs and the influence of the cross section shape of the nanowires are discussed.
Direct and heterodyne detection of microwaves in a metallic single wall carbon nanotube
Authors: Rodriguez-Morales F. , Zannoni R. , Nicholson J. , Fischetti M. , Yngvesson K. S. , Appenzeller J.
Published: August 2006

This letter reports measurements of microwave (up to 4.5GHz) detection in metallic single walled carbon nanotubes. The measured voltage responsivity was found to be 114V∕W at 77K. The authors also demonstrated heterodyne detection at 1GHz. The detection mechanism can be explained based on standard microwave detector theory and the nonlinearity of the dc IV curve. The authors discuss the possible causes of this nonlinearity. While the frequency response is limited by circuit parasitics in this measurement, the authors discuss evidence that indicates that the effect is much faster and that applications of carbon nanotubes as terahertz detectors are feasible.
Monolithic microspectrometer using tunable ferroelectric liquid crystals
Authors: McMurdy John W. , Crawford Gregory P. , Jay Gregory D.
Published: August 2006

A vertically aligned deformed helix ferroelectric liquid crystal is used to fabricate a thermally controllable monolithic microspectrometer using a single liquid crystal cell and a photodiode. The device has an active range over the entire visible spectrum from ∼400–720nm achieving an optimal resolution of 12nm in short wavelength regime to 20–25nm in the long wavelength regime. Operation is demonstrated through spectral reconstruction of the mercury emission spectra and a broadband white light emitting diode using a commercial spectrometer and the liquid crystal based spectrometer.