bluuebunny/crossref_metadata_2025 huggingface dataset:
Rovibrational spectra of the N2–HF complex at the vHF=3 level
Authors: Medley Patrick , Yu Zhenhong , Connors Brendan , Klemperer William , Tsang Susy N. , Chuang Cheng-Chi
Published: June 2006

We report the analyses of the three intermolecular combination bands of the hydrogen-bonded N2–HF complex at vHF=3, observed by molecular beam intracavity laser induced fluorescence. The origin of the HF intermolecular bending combination band, (300110)←(00000), is 11548.45(3)cm−1, 328.2cm−1 higher than that of the (30000)←(00000) transition with an origin at 11220.250(1)cm−1. The average rotational constant of the (300110) level is 0.10363(1)cm−1, a 4.8% reduction from B(30000)=0.10921(1)cm−1. Perturbations are observed as line splittings, increased line widths, and reduced peak intensities of a number of lines of the e and f components of (300110). In addition, the centrifugal distortion coefficients of both components are large, negative, and different. The N2 intermolecular bend transition (300011)←(00000) has an origin at 11288.706(1)cm−1, 68.456(2)cm−1 above that of the (30000)←(00000) transition. This is the lowest combination state at vHF=3 level. It is unperturbed, yielding B(300011)=0.110.10(1)cm−1. The transition to the intermolecular stretching state, (30100)←(00000), has an origin at 11318.858(1)cm−1 with B(30100)=0.10584(1)cm−1. Both the (30100) and (30000) levels show an isolated perturbation at J=4. The Lorentzian component of the line widths, which show considerable variation with soft mode, are ΓL(30000)=490(30)MHz, ΓL(30100)=630(30)MHz, ΓL(300110)=250(30)MHz, and ΓL(300011)=500(50)MHz.
Competition between cation-π interactions and intermolecular hydrogen bonds in alkali metal ion-phenol clusters. II. Phenol trimer
Authors: Vaden Timothy D. , Lisy James M.
Published: June 2006

The competition between ion-molecule and molecule-molecule interactions was investigated in M+(phenol)3 cluster ions for M=Li, Na, K, and Cs. Infrared predissociation spectroscopy in the O–H stretch region was used to characterize the structure of the cluster ions. By adjusting the experimental conditions, it was possible to generate species where argon was additionally bound in order to investigate cold cluster ions. From a comparison of the M+(phenol)3 spectra with the M+(phenol)3Ar spectra, it is clear that the relative populations of hydrogen-bonded configurations are significantly higher in the colder (argon-bearing) species. For the cold species, the IR spectra were compared with minimum energy ab initio calculations to elucidate the hydrogen-bonded structures. The experimental spectra are most consistent with a cyclic hydrogen-bonded configuration for Cs+(phenol)3 in which the ion binds to the phenol molecules via cation-π interactions, and noncyclic configurations for Li+, Na+, and K+.
Rotational excitation of water by hydrogen molecules: Comparison of results from classical and quantum mechanics
Authors: Faure Alexandre , Wiesenfeld Laurent , Wernli Michael , Valiron Pierre
Published: June 2006

Quasiclassical trajectory calculations are carried out for rotational excitation of water by hydrogen molecules. State-to-state rate coefficients are determined at 100K and are compared to available quantum results. A good agreement between classical and quantum rates is observed for downward transitions, with an average accuracy of classical results better than a factor of 2. It is thus found that the ambiguities described by Faure and Wiesenfeld [J. Chem. Phys. 121, 6771 (2004)] can be solved in the particular case of waterlike asymmetric-top molecules.
Photoionization cross section and angular distribution calculations of carbon tetrafluoride
Authors: Toffoli D. , Stener M. , Fronzoni G. , Decleva P.
Published: June 2006

Correlation in the photoionization dynamics of carbon tetrafluoride is studied in the framework of the time-dependent density-functional theory (TDDFT) approach by employing a multicentric basis set expansion of the scattering wave function linear combination of atomic orbitals (LCAO) TDDFT. Results obtained with the statistical average of orbital potentials and LB94 exchange-correlation (xc) potentials are compared with photoabsorption, photoionization, and electron-scattering experiments as well as with past theoretical calculations. Inadequacies in both the Vxc parametrizations employed have been suggested from the analysis of the intensity plots for the D̃A12 ionization. The formation of resonant scattering states in selected continuum channels has been studied through the analysis of the dipole-prepared scattering wave function; our findings are then compared with results of electron-scattering calculations. Overall, the LCAO-TDDFT results highlight the effectiveness of the approach for the calculation of the unbound spectrum of fairly large molecules.
Thickness management in three-dimensional laser manufacturing of suspended structures in a single SU-8 layer
Authors: Li Biao , Gueit Aurelien , Sharon Andre
Published: June 2006

Cantilevers, embedded channels, microcavities, and other high-aspect-ratio geometries requiring gaps between layers are essential to microfluidic components used for biotech/biomedical applications. Intensive efforts have been expanded in the development of novel approaches for efficiently manufacturing suspended structures. We have recently demonstrated a three-dimensional (3D) fabrication technique for rapid processing of microfluidic structures using a scanning laser system [B. Li et al. Appl. Phys. Lett. 85, 2426 (2004)]. This technique enables spot-by-spot laser pulsing for both in-plane and in-depth (parallel to film thickness) processing. Its maskless feature allows rapid prototyping of multilevel microfluidic structures at low cost. This article describes our latest results in thickness management using the 3D laser manufacturing technique. Suspended beams of various thicknesses have been fabricated by modifying grid size, laser energy, and degree of focus. Towards this end, we have demonstrated a microfluidic system with a functional microvalve in a single SU-8 layer.
Differences between the internal energy depositions induced by collisional activation and by electron transfer of W(CO)62+ ions on collision with Ar and K targets
Authors: Hayakawa Shigeo , Kitaguchi Akihiro , Kameoka Satoko , Toyoda Michisato , Ichihara Toshio
Published: June 2006

Doubly charged tungsten hexacarbonyl W(CO)62+ ions were made to collide with Ar and K targets to give singly and doubly charged positive ions by collision-induced dissociation (CID). The resulting ions were analyzed and detected by using a spherical electrostatic analyzer. Whereas the doubly charged fragment ions resulting from collisional activation (CA) were dominant with the Ar target, singly charged fragment ions resulting from electron transfer were dominant with the K target. The internal energy deposition in collisionally activated dissociation (CAD) evaluated with the Ar target was broad and decreased with increasing internal energy. The predominant peaks observed with the K target were associated with singly charged W(CO)2+ and W(CO)3+ ions: these ions were not the result of CA, but arose from dissociation induced by electron transfer (DIET). The internal energy deposition resulting from the electron transfer was very narrow and centered at a particular energy, 7.8eV below the energy level of the W(CO)62+ ion. This narrow internal energy distribution was explained in terms of electron transfer by Landau-Zener [Z. Phys. Soviet 2, 46 (1932); Proc. R. Soc. London, Ser. A 137, 646 (1952)] potential crossing at a separation of 5.9×10−8cm between a W(CO)62+ ion and a K atom, and the coulombic repulsion between singly charged ions in the exit channel. A large cross section of 1.1×10−14cm2 was estimated for electron capture of the doubly charged W(CO)62+ ion from the alkali metal target, whose ionization energy is very low. The term “collision-induced dissociation,” taken literally, includes all dissociation processes induced by collision, and therefore encompasses both CAD and DIET processes in the present work. Although the terms CID and CAD have been defined similarly, we would like to propose that they should not be used interchangeably, on the basis that there are differences in the observed ions and in their intensities with Ar and K targets.
Portable instrument that integrates irradiation with fluorescence and reflectance spectroscopies during clinical photodynamic therapy of cutaneous disease
Authors: Cottrell W. J. , Oseroff A. R. , Foster T. H.
Published: June 2006

We report a portable clinical instrument for delivering photodynamic therapy (PDT) while performing noninvasive spectroscopic monitoring in vivo. Using an off-surface probe, the instrument delivers the treatment beam to a user-defined field on the skin and performs reflectance and fluorescence spectroscopies at two regions within this field. The instrument is being used to monitor photosensitizer fluorescence photobleaching, fluorescent photoproduct kinetics, blood volume, and hemoglobin oxygen saturation during a pilot clinical trial of 5-aminolevulinic acid-PDT treatment of superficial basal cell carcinoma (BCC). Protoporphyrin IX and photoproduct fluorescence excited by the 633nm PDT treatment laser is collected between 655 and 800nm. During a series of brief treatment interruptions at programable time points, white light reflectance spectra between 475 and 800nm are acquired. Fluorescence spectra are corrected for the effects of absorption and scattering, informed by the reflectance measurements, and then decomposed into known fluorophore contributions in real time using a robust singular value decomposition fitting routine. Reflectance spectra additionally provide information on blood volume and hemoglobin oxygen saturation. Monitoring blood oxygenation and implicit dose metrics such as photosensitizer photobleaching during PDT allows the improved interpretation of clinical results and is helping to guide the treatment protocol for an anticipated low-irradiance PDT clinical trial of BCC.
The rotational spectrum of the NiI radical in the XΔ5∕22 and AΠ3∕22 states
Authors: Miyazawa Toru , Okabayashi Emi Y. , Koto Fumi , Tanimoto Mitsutoshi , Okabayashi Toshiaki
Published: June 2006

The millimeter- and submillimeter-wave spectra of the NiI radical in the XΔ5∕22 and AΠ3∕22 states were observed by a source-modulated microwave spectrometer. The NiI radical was generated by a dc glow discharge in the mixture of CH3I vapor and Ar gas through the sputtering reaction with a Ni cathode. Observed transition frequencies for each electronic state were independently analyzed using a polynomial energy expression based on Hund’s case (c) approximation. The deperturbed rotational constants were also estimated by the perturbation analysis including interaction terms between the ground state and the lowest excited state.
Evaluation of external Q of the superconducting cavity using Kroll-Yu method
Authors: Dhavale A. S. , Mittal K. C.
Published: June 2006

Design and development of superconducting (SC) cavity having βg>0.42 has been taken up as a part of the accelerator driven subcritical system project. An input coupler is designed for the SC, elliptical cavity operating at 1.056GHz, using the Kroll-Yu method. The evaluation procedure is optimized and the method has been successfully implemented for the evaluation of high Q external. The effect of beam pipe radius, coupler dimensions, penetration depth, and the position of the coupler on the external Q has also been studied.
High resolution frequency standard dissemination via optical fiber metropolitan network
Authors: Narbonneau F. , Lours M. , Bize S. , Clairon A. , Santarelli G. , Lopez O. , Daussy Ch. , Amy-Klein A. , Chardonnet Ch.
Published: June 2006

We present in this article results on a new dissemination system of an ultrastable reference signal at 100MHz on a standard fiber network. The 100MHz signal is simply transferred by amplitude modulation of an optical carrier. Two different approaches for compensating the noise introduced by the link have been implemented. The limits of the two systems are analyzed and several solutions are suggested in order to improve the frequency stability and to further extend the distribution distance. Nevertheless, our system is a good tool for the best cold atom fountains comparison between laboratories, up to 100km, with a relative frequency resolution of 10−14 at 1s integration time and 10−17 for 1day of measurement. The distribution system may be upgraded to fulfill the stringent distribution requirements for the future optical clocks.
Nonexponential relaxation and fragility in a model system and in supercooled liquids
Authors: Halpern V.
Published: June 2006

Among the outstanding problems in the theory of supercooled liquids are the reasons for the rapid increase in their viscosity and relaxation times as the temperature is lowered towards the glass transition temperature Tg, the nonexponential time dependence of the relaxation, and the possible connection between these two properties. The ferromagnetic Potts model on a square latice is a simple system that is found to exhibit these properties. Our calculations show that in this system the connection between them is associated with the dependence on temperature and time of the average environment of the sites. Some of the consequences of this for understanding the behavior of supercooled liquids are discussed.
Anisotropic rupture of polymer strips driven by Rayleigh instability
Authors: Park Jeong-yong , Suh Kahp Y. , Seo Soon-min , Lee Hong H.
Published: June 2006

We demonstrate that the separated polymer strips of micro- and sub-micro-length-scales rupture anisotropically along the strip direction, resulting in the formation of distinctly observable, regularly spaced polymer drops. The wavelength of the polymer drops and the surface tension dependence of the rupture behavior are found to be well represented by a relationship derived on the basis of Rayleigh instability. The period is proportional to the square root of the cross-sectional area of the strip and the proportionality constant depends on the contact angle. The rupture of polymer strips into polymer blocks instead of drops, which result when annealed with physically confining walls in place, is found to be well described by the same relationship.
Modeling the influence of a laser pulse on the potential energy surface in optimal molecular control theory
Authors: Farnum John D. , Gidofalvi Gergely , Mazziotti David A.
Published: June 2006

Understanding and modeling the interaction between light and matter is essential to the theory of optical molecular control. While the effect of the electric field on a molecule’s electronic structure is often not included in control theory, it can be modeled in an optimal control algorithm by a set or toolkit of potential energy surfaces indexed by discrete values of the electric field strength where the surfaces are generated by Born-Oppenheimer electronic structure calculations that directly include the electric field. Using a new optimal control algorithm with a trigonometric mapping to limit the maximum field strength explicitly, we apply the surface-toolkit method to control the hydrogen fluoride molecule. Potential energy surfaces in the presence and absence of the electric field are created with two-electron reduced-density-matrix techniques. The population dynamics show that adjusting for changes in the electronic structure of the molecule beyond the static dipole approximation can be significant for designing a field that drives a realistic quantum system to its target observable.
On scattering trajectories of dynamical systems
Authors: Díaz-Cano A. , González-Gascón F. , Peralta-Salas D.
Published: June 2006

Dynamical systems on Rn presenting geometric chaos, i.e., open domains where bounded and unbounded orbits are intermingled, have been constructed. The opposite situation (open scattering) has been studied for integrable Hamiltonian and non-Hamiltonian vector fields and for equations of type ẍ=−∇V(x) when the potential has the form V=a(r)+b(r)F(θ) in spherical coordinates.
Exchange energy gradients with respect to atomic positions and cell parameters within the Hartree-Fock Γ-point approximation
Authors: Weber Valéry , Daul Claude , Challacombe Matt
Published: June 2006

Recently, linear scaling construction of the periodic exact Hartree-Fock exchange matrix within the Γ-point approximation has been introduced [J. Chem. Phys. 122, 124105 (2005)]. In this article, a formalism for evaluation of analytical Hartree-Fock exchange energy gradients with respect to atomic positions and cell parameters at the Γ-point approximation is presented. While the evaluation of exchange gradients with respect to atomic positions is similar to those in the gas phase limit, the gradients with respect to cell parameters involve the accumulation of atomic gradients multiplied by appropriate factors and a modified electron repulsion integral (ERI). This latter integral arises from use of the minimum image convention in the definition of the Γ-point Hartree-Fock approximation. We demonstrate how this new ERI can be computed with the help of a modified vertical recurrence relation in the frame of the Obara-Saika and Head-Gordon-Pople algorithm. As an illustration, the analytical gradients have been used in conjunction with the QUICCA algorithm [K. Németh and M. Challacombe, J. Chem. Phys. 121, 2877 (2004)] to optimize periodic systems at the Hartree-Fock level of theory.
The mechanical properties of crystalline cyclopentyl polyhedral oligomeric silsesquioxane
Authors: Capaldi Franco M. , Boyce Mary C. , Rutledge Gregory C.
Published: June 2006

The anisotropic elastic constants of crystalline octacyclopentyl polyhedral oligomeric silsesquioxane (CpPOSS) were determined using molecular dynamics. The force field used for these calculations was shown to model accurately the rhombohedral and triclinic crystal structures of octasilsesquioxane and CpPOSS, respectively, as well as the vibrational frequencies of octasilsesquioxane. The moduli for CpPOSS are anisotropic, with a Reuss-averaged bulk modulus of 7.5GPa, an isotropic averaged Young’s modulus of 11.78GPa, and an isotropic averaged shear modulus of 4.75GPa. These isotropic averages or, alternatively, the full anisotropic stiffness tensor of the crystal can be used with micromechanical composite models to calculate the effective elastic properties of polymer nanocomposites that contain crystalline aggregates of CpPOSS.
Organic light-emitting devices with a mixture emitting layer of tris-(8-hydroxyquinoline) aluminum and 4,4′-bis(carbazol-9-yl)-biphenyl
Authors: Chen B. J. , Sun X. W. , Sarma K. R.
Published: June 2006

Organic light-emitting devices with a mixture of tris-(8-hydroxyqunoline) aluminum (Alq3) and 4,4′-bis(carbazol-9-yl)-biphenyl (CBP) as the emitting layer have been fabricated. The devices were fabricated in the same run with a standard device without CBP for comparison, with an identical structure of indium tin oxide (ITO)∕m-MTDATA (80nm)∕NPB (20nm)∕CBP:Alq3 (40nm)∕BCP (10nm)∕Alq3 (60nm)∕Mg:Ag (200nm), where m-MTDATA is 4,4′,4″-tris(N-3-methylphenyl-N-phenyl-amino) triphenylamine, which is used to improve hole injection; NPB is N,N′-di(naphth-2-yl)-N,N′-diphenyl-benzidine; and BCP is 2,9-Dimethyl-4,7-diphenyl-1,110-phenanthorline. The ratio of CBP to Alq3 in mixture was varied from 0 to 2. For device with a ratio of 0.5, the current efficiency and power efficiency were significantly improved by 35% and 32%, respectively, compared to the standard device with Alq3 only as emitting layer. By increasing the ratio to 2, the current efficiency and power efficiency were dropped by 20% and 11%, respectively. The electroluminescence spectra showed a slight blueshift with the increase of CBP to Alq3 ratio.
Control of single-wall-nanotube field-effect transistors via indirect long-range optically induced processes
Authors: Narayan K. S. , Rao Manohar , Zhang R. , Maniar P.
Published: June 2006

We observe significant changes in the response of single-wall-carbon-nanotube-based field-effect transistors upon photoexcitation in the presence of optically active conjugated polymer network. The primary features observed are in the form of an increase in the current in the depletion mode upon photoexcitation. Pulsed measurements indicate that the transistor enters the depleted state prior to the rise in current brought about by the transfer of the photogenerated carriers from the semiconducting polymer to the nanotube under depletion bias.
Laser-induced air ionization microscopy
Authors: Zhao Y. , Zhang N. , Yang J. , Zhu X.
Published: June 2006

A nonlinear scanning imaging method is introduced that uses the highly localized air ionization initiated by photoelectrons from the sample surface under irradiation of femtosecond laser pulses as the microprobe. This type of microscopy with realizable subdiffraction spatial resolution has the unique advantages of being highly sensitive to both elemental and topographical properties of the samples of interest. Microscopic images of a femtosecond laser ablated micropattern, the cross section and the side view profile of an optical fiber, and a fresh mulberry leaf are obtained with this imaging technique, which demonstrate this technique’s broad applicability in microscopic studies of different materials.
Terahertz frequency comb by multifrequency-heterodyning photoconductive detection for high-accuracy, high-resolution terahertz spectroscopy
Authors: Yasui Takeshi , Kabetani Yasuhiro , Saneyoshi Eisuke , Yokoyama Shuko , Araki Tsutomu
Published: June 2006

We report a terahertz spectroscopy technique based on a stable terahertz frequency comb from a photoconductive terahertz emitter driven by a stabilized femtosecond laser. To this end, a photocurrent frequency comb is induced in a photoconductive terahertz detector by instantaneous photogating with another detuned femtosecond laser and is applied to read out the terahertz frequency comb. The detailed structure of the terahertz frequency comb was clearly observed with frequency accuracy of 2.5×10−7 and resolution of 81.8MHz using multifrequency-heterodyning photoconductive detection, which in turn is caused by the slightly mismatched frequency spacing between terahertz and photocurrent frequency combs.
Photoluminescence properties peculiar to the Mn-related transition in a lightly alloyed ZnMnO thin film grown by pulsed laser deposition
Authors: Nakayama M. , Tanaka H. , Masuko K. , Fukushima T. , Ashida A. , Fujimura N.
Published: June 2006

We have investigated photoluminescence properties of ZnO and Zn0.95Mn0.05O thin films at 10K grown on a (0001¯) ZnO crystal substrate by pulsed laser deposition. The structural characterization with x-ray diffraction and atomic force microscopy demonstrates the pseudomorphic growth of the Zn0.95Mn0.05O thin film and the atomically smooth surface. It has been found that a photoluminescence band originating from the d-d transition of Mn2+ in the Zn0.95Mn0.05O thin film appears in the energy region of deep-level transitions in a ZnO crystal: The photoluminescence-decay time is in the order of sub-milliseconds. The photoluminescence-excitation spectrum of the Mn-related transition exhibits a peaky structure with a broad profile at the energy lower than the A-exciton energy by ∼100meV. This indicates that the light incorporation of Mn to ZnO leads to a negative energy shift of the band-gap energy. The broad profile of the band-edge transition observed in the photoluminescence-excitation spectrum suggests that the incorporation of Mn produces remarkable random-potential fluctuations.
Subpicosecond pulse generation at 134GHz using a quantum-dash-based Fabry-Perot laser emitting at 1.56μm
Authors: Gosset C. , Merghem K. , Martinez A. , Moreau G. , Patriarche G. , Aubin G. , Ramdane A. , Landreau J. , Lelarge F.
Published: June 2006

We demonstrate passive mode locking in one-section monolithic semiconductor laser diodes based on quantum-dash active layer at very high repetition rate in the 1.5μm window. Transform-limited pulses are generated at 134GHz with subpicosecond width, without any pulse compression scheme. A 50kHz linewidth of the radio-frequency spectrum is also demonstrated at 42GHz, the lowest value reported for any passively mode-locked semiconductor laser. We further show that the saturable absorption section in two-section devices has no significant impact on the mode-locking behavior.
Effect of temperature on the Hurst and growth exponents of CdTe polycrystalline films
Authors: Ferreira S. O. , Ribeiro I. R. B. , Suela J. , Menezes-Sobrinho I. L. , Ferreira S. C. , Alves S. G.
Published: June 2006

We have studied the influence of substrate temperature on the Hurst and growth exponents of CdTe thin films grown on glass substrates covered by fluorine doped tin oxide. The sample roughness profile was measured with a stylus profiler at different growth times and substrate temperatures in order to determine the critical exponents. The Hurst exponent increases linearly from 0.72 to 0.8, whereas the growth exponent increases exponentially from 0.14 to 0.62, for temperatures between 150 and 300°C. The global roughness also increases with growth temperature, which turns to be a very good parameter for roughness control.
Diels - Alder Reactions of 3-Furylamines in Organic and Aqueous Solvents
Authors: Lingham Anthony R. , Hügel Helmut M. , Rook Trevor J.
Published: June 2006

Various 5-methyl-3-aminofurans have been shown to undergo facile Diels–Alder reactions with methyl acrylate in aqueous media. Reactions proceeded with exclusive regiochemistry, and enamine cycloadducts were readily hydrolyzed to afford 7-oxabicyclo[2.2.1]heptanones in high yields.
Molecular Recognition in Proton-Transfer Compounds of Brucine with Achiral Substituted Salicylic Acid Analogues
Authors: Smith Graham , Wermuth Urs D. , Healy Peter C. , White Jonathan M.
Published: June 2006

The 1:1 proton-transfer brucinium compounds from the reaction of the alkaloid brucine with 5-nitrosalicylic acid, 3,5-dinitrosalicylic acid, and 5-sulfosalicylic acid, namely anhydrous brucinium 5-nitrosalicylate (1), brucinium 3,5-dinitrosalicylate monohydrate (2), and brucinium 5-sulfosalicylate trihydrate (3) have been prepared and their crystal structures determined by X-ray crystallography. All structures further demonstrate the selectivity of brucine for meta-substituted benzoic acids and comprise three-dimensional hydrogen-bonded framework polymers. Two of the compounds (1 and 3) have the previously described undulating brucine sheet host-substructures which incorporate interstitially hydrogen-bonded salicylate anion guest species and additionally in 3 the water molecules of solvation. The structure of 2 differs in having a three-centre brucinium–salicylate anion bidentate N+–H···O(carboxyl) hydrogen-bonding association linking the species through interstitial associations involving also the water molecules of solvation. A review of the crystallographic structural literature on strychnine and brucine is also given.
Open Source Research — the Power of Us
Authors: Kepler Thomas B. , Marti-Renom Marc A. , Maurer Stephen M. , Rai Arti K. , Taylor Ginger , Todd Matthew H.
Published: June 2006

Academic and industrial scientific research operate on powerful and complementary models, consisting of some mix of competitive funding, peer review, and limited inter-laboratory collaboration. Enormous successes have arisen from both models. Yet there are clear failures to deliver results in certain areas, such as the provision of drugs for some of the most prevalent of human diseases. Is there a mechanism of research that is not wholly dependent on funding for its operation nor on traditional peer-reviewed articles for its propagation? Open source methods have delivered tangible benefits in the computer science community. We describe here efforts to extend these principles to science generally, and in particular biomedical research. Open source research holds great promise for solving complex problems in areas where profit-driven research is seen to have failed. We illustrate this with a specific problem in organic chemistry that we think will be solved substantially faster with an open source approach.
Synthesis of NTA3-DTDA — A Chelator-Lipid that Promotes Stable Binding of His-Tagged Proteins to Membranes
Authors: Altin Joseph G. , Banwell Martin G. , Coghlan Phillip A. , Easton Christopher J. , Nairn Michael R. , Offermann Daniel A.
Published: June 2006

A six-step reaction sequence is described for the preparation of compound 1 (NTA3-DTDA), a membrane-penetrating and potent chelator that can be incorporated into liposomes and plasma membrane vesicles containing antigens and thus allowing targeted delivery of such assemblies to a variety of cells for the purposes of eliciting anti-tumour responses. Full spectroscopic characterization of this dendritic-type compound as well as certain of its precursors is reported.
The Silver - Alkene Interaction as a Supramolecular Synthon: Divinylbenzene-Based Assemblies
Authors: Burgess Jennifer , Cottam Justine R. A. , Steel Peter J.
Published: June 2006

The interaction of silver(i) salts with alkenes is shown to be a useful synthon for the assembly of both discrete and polymeric metallosupramolecular architectures. The three isomers of divinylbenzene lead to a diverse range of adducts, seven of which have been structurally characterized by X-ray crystallography.
Design of metal cofactors activated by a protein–protein electron transfer system
Authors: Ueno Takafumi , Yokoi Norihiko , Unno Masaki , Matsui Toshitaka , Tokita Yuichi , Yamada Masako , Ikeda-Saito Masao , Nakajima Hiroshi , Watanabe Yoshihito
Published: June 2006

Protein-to-protein electron transfer (ET) is a critical process in biological chemistry for which fundamental understanding is expected to provide a wealth of applications in biotechnology. Investigations of protein–protein ET systems in reductive activation of artificial cofactors introduced into proteins remains particularly challenging because of the complexity of interactions between the cofactor and the system contributing to ET. In this work, we construct an artificial protein–protein ET system, using heme oxygenase (HO), which is known to catalyze the conversion of heme to biliverdin. HO uses electrons provided from NADPH/cytochrome P450 reductase (CPR) through protein–protein complex formation during the enzymatic reaction. We report that a Fe
III
(Schiff-base), in the place of the active-site heme prosthetic group of HO, can be reduced by NADPH/CPR. The crystal structure of the Fe(10-CH
2
CH
2
COOH-Schiff-base)·HO composite indicates the presence of a hydrogen bond between the propionic acid carboxyl group and Arg-177 of HO. Furthermore, the ET rate from NADPH/CPR to the composite is 3.5-fold faster than that of Fe(Schiff-base)·HO, although the redox potential of Fe(10-CH
2
CH
2
COOH-Schiff-base)·HO (−79 mV vs. NHE) is lower than that of Fe(Schiff-base)·HO (+15 mV vs. NHE), where NHE is normal hydrogen electrode. This work describes a synthetic metal complex activated by means of a protein–protein ET system, which has not previously been reported. Moreover, the result suggests the importance of the hydrogen bond for the ET reaction of HO. Our Fe(Schiff-base)·HO composite model system may provide insights with regard to design of ET biosystems for sensors, catalysts, and electronics devices.
Melanosomal sequestration of cytotoxic drugs contributes to the intractability of malignant melanomas
Authors: Chen Kevin G. , Valencia Julio C. , Lai Barry , Zhang Guofeng , Paterson Jill K. , Rouzaud François , Berens Werner , Wincovitch Stephen M. , Garfield Susan H. , Leapman Richard D. , Hearing Vincent J. , Gottesman Michael M.
Published: June 2006

Multidrug resistance mechanisms underlying the intractability of malignant melanomas remain largely unknown. In this study, we demonstrate that the development of multidrug resistance in melanomas involves subcellular sequestration of intracellular cytotoxic drugs such as
cis
-diaminedichloroplatinum II (cisplatin; CDDP). CDDP is initially sequestered in subcellular organelles such as melanosomes, which significantly reduces its nuclear localization when compared with nonmelanoma/KB-3-1 epidermoid carcinoma cells. The melanosomal accumulation of CDDP remarkably modulates melanogenesis through a pronounced increase in tyrosinase activity. The altered melanogenesis manifested an ≈8-fold increase in both intracellular pigmentation and extracellular transport of melanosomes containing CDDP. Thus, our experiments provide evidence that melanosomes contribute to the refractory properties of melanoma cells by sequestering cytotoxic drugs and increasing melanosome-mediated drug export. Preventing melanosomal sequestration of cytotoxic drugs by inhibiting the functions of melanosomes may have great potential as an approach to improving the chemosensitivity of melanoma cells.
Chlamydial ribonucleotide reductase: Tyrosyl radical function in catalysis replaced by the Fe
III
-Fe
IV
cluster
Authors: Voevodskaya N. , Narvaez A.-J. , Domkin V. , Torrents E. , Thelander L. , Gräslund A.
Published: June 2006

Ribonucleotide reductase (RNR) from
Chlamydia trachomatis
is a class I RNR composed of proteins R1 and R2. In protein R2, the tyrosine residue harboring the radical that is necessary for catalysis in other class I RNRs is replaced by a phenylalanine. Active
C. trachomatis
RNR instead uses the Fe
III
-Fe
IV
state of the iron cluster in R2 as an initiator of catalysis. The paramagnetic Fe
III
-Fe
IV
state, identified by
57
Fe substitution, becomes electron spin resonance detectable in samples that are frozen during conditions of ongoing catalysis. Its amount depends on the conditions for catalysis, such as incubation temperature and the R1/R2 ratio. The results link induction of the Fe
III
-Fe
IV
state with enzyme activity of chlamydial RNR. Based on these observations, a reaction scheme is proposed for the iron site. This scheme includes (
i
) an activation cycle involving reduction and an oxygen reaction in R2 and (
ii
) a catalysis cycle involving substrate binding and turnover in R1.
Nonviral Aβ DNA vaccine therapy against Alzheimer’s disease: Long-term effects and safety
Authors: Okura Yoshio , Miyakoshi Akira , Kohyama Kuniko , Park Il-Kwon , Staufenbiel Matthias , Matsumoto Yoh
Published: June 2006

It was recently demonstrated that amyloid β (Aβ) peptide vaccination was effective in reducing the Aβ burden in Alzheimer model mice. However, the clinical trial was halted because of the development of meningoencephalitis in some patients. To overcome this problem, anti-Aβ antibody therapy and other types of vaccination are now in trial. In this study, we have developed safe and effective nonviral Aβ DNA vaccines against Alzheimer’s disease. We administered these vaccines to model (APP23) mice and evaluated Aβ burden reduction. Prophylactic treatments started before Aβ deposition reduced Aβ burden to 15.5% and 38.5% of that found in untreated mice at 7 and 18 months of age, respectively. Therapeutic treatment started after Aβ deposition reduced Aβ burden to≈50% at the age of 18 months. Importantly, this therapy induced neither neuroinflammation nor T cell responses to Aβ peptide in both APP23 and wild-type B6 mice, even after long-term vaccination. Although it is reported that other anti-Aβ therapies have pharmacological and∕or technical difficulties, nonviral DNA vaccines are highly secure and easily controllable and are promising for the treatment of Alzheimer’s disease.
Selective identification of newly synthesized proteins in mammalian cells using bioorthogonal noncanonical amino acid tagging (BONCAT)
Authors: Dieterich Daniela C. , Link A. James , Graumann Johannes , Tirrell David A. , Schuman Erin M.
Published: June 2006

In both normal and pathological states, cells respond rapidly to environmental cues by synthesizing new proteins. The selective identification of a newly synthesized proteome has been hindered by the basic fact that all proteins, new and old, share the same pool of amino acids and thus are chemically indistinguishable. We describe here a technology, based on the cotranslational introduction of azide groups into proteins and the chemoselective tagging of azide-labeled proteins with an alkyne affinity tag, to separate and identify, specifically, the newly synthesized proteins in mammalian cells. Incorporation of the azide-bearing amino acid azidohomoalanine is unbiased, not toxic, and does not increase protein degradation. As a first demonstration of the method, we report the selective purification and identification of 195 metabolically labeled proteins with multidimensional liquid chromatography in-line with tandem MS. Furthermore, in combination with leucine-based mass tagging, candidates were immediately validated as newly synthesized proteins. The identified proteins, synthesized in a 2-h window, possess a broad range of biochemical properties and span most functional gene ontology categories. This technology makes it possible to address the temporal and spatial characteristics of newly synthesized proteomes in any cell type.
IRBIT, an inositol 1,4,5-trisphosphate receptor-binding protein, specifically binds to and activates pancreas-type Na
+
/HCO
3
−
cotransporter 1 (pNBC1)
Authors: Shirakabe Kyoko , Priori Giuseppina , Yamada Hideomi , Ando Hideaki , Horita Shoko , Fujita Toshiro , Fujimoto Ichiro , Mizutani Akihiro , Seki George , Mikoshiba Katsuhiko
Published: June 2006

Inositol 1,4,5-trisphosphate (IP
3
) receptors (IP
3
Rs) are IP
3
-gated Ca
2+
channels that are located on intracellular Ca
2+
stores. We previously identified an IP
3
R binding protein, termed IP
3
R binding protein released with IP
3
(IRBIT). Because IRBIT is released from IP
3
R by physiological concentrations of IP
3
, we hypothesized that IRBIT is a signaling molecule that is released from IP
3
R and regulates downstream target molecules in response to the production of IP
3
. Therefore, in this study, we attempted to identify the target molecules of IRBIT, and we succeeded in identifying Na
+
/HCO
3
−
cotransporter 1 (NBC1) as an IRBIT binding protein. Of the two major splicing variants of NBC1, pancreas-type NBC1 (pNBC1) and kidney-type NBC1 (kNBC1), IRBIT was found to bind specifically to pNBC1 and not to bind to kNBC1. IRBIT binds to the N-terminal pNBC1-specific domain, and its binding depends on the phosphorylation of multiple serine residues of IRBIT. Also, an electrophysiological analysis in
Xenopus
oocytes revealed that pNBC1 requires coexpression of IRBIT to manifest substantial activity comparable with that of kNBC1, which displays substantial activity independently of IRBIT. These results strongly suggest that pNBC1 is the target molecule of IRBIT and that IRBIT has an important role in pH regulation through pNBC1. Also, our findings raise the possibility that the regulation through IRBIT enables NBC1 variants to have different physiological roles.
Structural basis of catalysis by monometalated methionine aminopeptidase
Authors: Ye Qi-Zhuang , Xie Sheng-Xue , Ma Ze-Qiang , Huang Min , Hanzlik Robert P.
Published: June 2006

Methionine aminopeptidase (MetAP) removes the amino-terminal methionine residue from newly synthesized proteins, and it is a target for the development of antibacterial and anticancer agents. Available x-ray structures of MetAP, as well as other metalloaminopeptidases, show an active site containing two adjacent divalent metal ions bridged by a water molecule or hydroxide ion. The predominance of dimetalated structures leads naturally to proposed mechanisms of catalysis involving both metal ions. However, kinetic studies indicate that in many cases, only a single metal ion is required for full activity. By limiting the amount of metal ion present during crystal growth, we have now obtained a crystal structure for a complex of
Escherichia coli
MetAP with norleucine phosphonate, a transition-state analog, and only a single Mn(II) ion bound at the active site in the position designated M1, and three related structures of the same complex that show the transition from the mono-Mn(II) form to the di-Mn(II) form. An unliganded structure was also solved. In view of the full kinetic competence of the monometalated MetAP, the much weaker binding constant for occupancy of the M2 site compared with the M1 site, and the newly determined structures, we propose a revised mechanism of peptide bond hydrolysis by
E. coli
MetAP. We also suggest that the crystallization of dimetalated forms of metallohydrolases may, in some cases, be a misleading experimental artifact, and caution must be taken when structures are generated to aid in elucidation of reaction mechanisms or to support structure-aided drug design efforts.
Mechanics-based statistics of failure risk of quasibrittle structures and size effect on safety factors
Authors: Bažant Zdeněk P. , Pang Sze-Dai
Published: June 2006

In mechanical design as well as protection from various natural hazards, one must ensure an extremely low failure probability such as 10
−6
. How to achieve that goal is adequately understood only for the limiting cases of brittle or ductile structures. Here we present a theory to do that for the transitional class of quasibrittle structures, having brittle constituents and characterized by nonnegligible size of material inhomogeneities. We show that the probability distribution of strength of the representative volume element of material is governed by the Maxwell–Boltzmann distribution of atomic energies and the stress dependence of activation energy barriers; that it is statistically modeled by a hierarchy of series and parallel couplings; and that it consists of a broad Gaussian core having a grafted far-left power-law tail with zero threshold and amplitude depending on temperature and load duration. With increasing structure size, the Gaussian core shrinks and Weibull tail expands according to the weakest-link model for a finite chain of representative volume elements. The model captures experimentally observed deviations of the strength distribution from Weibull distribution and of the mean strength scaling law from a power law. These deviations can be exploited for verification and calibration. The proposed theory will increase the safety of concrete structures, composite parts of aircraft or ships, microelectronic components, microelectromechanical systems, prosthetic devices, etc. It also will improve protection against hazards such as landslides, avalanches, ice breaks, and rock or soil failures.
Calcium dependence of aequorin bioluminescence dissected by random mutagenesis
Authors: Tricoire Ludovic , Tsuzuki Keisuke , Courjean Olivier , Gibelin Nathalie , Bourout Gaëlle , Rossier Jean , Lambolez Bertrand
Published: June 2006

Aequorin bioluminescence is emitted as a rapidly decaying flash upon calcium binding. Random mutagenesis and functional screening were used to isolate aequorin mutants showing slow decay rate of luminescence. Calcium sensitivity curves were shifted in all mutants, and an intrinsic link between calcium sensitivity and decay rate was suggested by the position of all mutations in or near EF-hand calcium-binding sites. From these results, a low calcium affinity was assigned to the N-terminal EF hand and a high affinity to the C-terminal EF-hand pair. In WT aequorin, the increase of the decay rate with calcium occurred at constant total photon yield and thus determined a corresponding increase of light intensity. Increase of the decay rate was underlain by variations of a fast and a slow component and required the contribution of all three EF hands. Conversely, analyses of double EF-hand mutants suggested that single EF hands are sufficient to trigger luminescence at a slow rate. Finally, a model postulating that proportions of a fast and a slow light-emitting state depend on calcium concentration adequately described the calcium dependence of aequorin bioluminescence. Our results suggest that variations of luminescence kinetics, which depend on three EF hands endowed with different calcium affinities, critically determine the amplitude of aequorin responses to biological calcium signals.
Hydrogen chloride-induced surface disordering on ice
Authors: McNeill V. Faye , Loerting Thomas , Geiger Franz M. , Trout Bernhardt L. , Molina Mario J.
Published: June 2006

Characterizing the interaction of hydrogen chloride (HCl) with polar stratospheric cloud ice particles is essential for understanding the processes responsible for ozone depletion. We studied the interaction of gas-phase HCl with ice between 243 and 186 K by using (
i
) ellipsometry to monitor the ice surface and (
ii
) coated-wall flow tube experiments, both with chemical ionization mass spectrometry detection of the gas phase. We show that trace amounts of HCl induce formation of a disordered region, or quasi-liquid layer, at the ice surface at stratospheric temperatures. We also show that surface disordering enhances the chlorine activation reaction of HCl with chlorine nitrate (ClONO
2
) and also enhances acetic acid (CH
3
COOH) adsorption. These results impact our understanding of the chemistry and physics of ice particles in the atmosphere.
Flexible phenylalanine-glycine nucleoporins as entropic barriers to nucleocytoplasmic transport
Authors: Lim Roderick Y. H. , Huang Ning-Ping , Köser Joachim , Deng Jie , Lau K. H. Aaron , Schwarz-Herion Kyrill , Fahrenkrog Birthe , Aebi Ueli
Published: June 2006

Natively unfolded phenylalanine-glycine (FG)-repeat domains are alleged to form the physical constituents of the selective barrier-gate in nuclear pore complexes during nucleocytoplasmic transport. Presently, the biophysical mechanism behind the selective gate remains speculative because of a lack of information regarding the nanomechanical properties of the FG domains. In this work, we have applied the atomic force microscope to measure the mechanical response of individual and clusters of FG molecules. Single-molecule force spectroscopy reveals that FG molecules are unfolded and highly flexible. To provide insight into the selective gating mechanism, an experimental platform has been constructed to study the collective behavior of surface-tethered FG molecules at the nanoscale. Measurements indicate that the collective behavior of such FG molecules gives rise to an exponentially decaying long-range steric repulsive force. This finding indicates that the molecules are thermally mobile in an extended polymer brush-like conformation. This assertion is confirmed by observing that the brush-like conformation undergoes a reversible collapse transition in less polar solvent conditions. These findings reveal how FG-repeat domains may simultaneously function as an entropic barrier and a selective trap in the near-field interaction zone of nuclear pore complexes; i.e., selective gate.
Requirement of Nck adaptors for actin dynamics and cell migration stimulated by platelet-derived growth factor B
Authors: Rivera G. M. , Antoku S. , Gelkop S. , Shin N. Y. , Hanks S. K. , Pawson T. , Mayer B. J.
Published: June 2006

The Nck family of Src homology (SH) 2/SH3 domain adaptors functions to link tyrosine phosphorylation induced by extracellular signals with downstream regulators of actin dynamics. We investigated the role of mammalian Nck adaptors in signaling from the activated platelet-derived growth factor (PDGF) receptor (PDGFβR) to the actin cytoskeleton. We report here that Nck adaptors are required for cytoskeletal reorganization and chemotaxis stimulated by PDGF-B. Analysis of tyrosine-phosphorylated proteins demonstrated that Crk-associated substrate (p130
Cas
), not the activated PDGFβR itself, is the major Nck SH2 domain-binding protein in PDGF-B-stimulated cells. Both Nck- and p130
Cas
-deficient cells fail to display cytoskeletal rearrangements, including the formation of membrane ruffles and the disassembly of actin bundles, typically shown by their WT counterparts in response to PDGF-B. Furthermore, Nck and p130
Cas
colocalize in phosphotyrosine-enriched membrane ruffles induced by PDGF-B in NIH 3T3 cells. These results suggest that Nck adaptors play an essential role in linking the activated PDGFβR with actin dynamics through a pathway that involves p130
Cas
.