bluuebunny/crossref_metadata_2025 huggingface dataset:
Magnetic-field-induced localization of electrons in InGaN/GaN multiple quantum wells
Authors: Arnaudov B. , Paskova T. , Valassiades O. , Paskov P. P. , Evtimova S. , Monemar B. , Heuken M.
Published: September 2003

We study longitudinal electron transport in InGaN/GaN multiple quantum wells (MQWs) at moderate magnetic fields. We observe a stepwise behavior of both the Hall coefficient and magnetoresistivity. The peculiarities are explained by a magnetic-field-induced localization of electrons in a two-dimensional (2D) potential relief of the InGaN MQW due to composition fluctuations. We extend the model for a magnetic localization of electrons, treating every QW like a quasi-2D system with a cylindrical potential relief. The calculated values of the decrease of the sheet electron concentrations in a magnetic field based on such an assumption for 2D density of states in a InGaN MQW system are in good accordance with the experimentally obtained values.
Rayleigh type behavior of the Young's modulus of unpoled ferroelectric ceramics and its dependence on temperature
Authors: Algueró M. , Jiménez B. , Pardo L.
Published: September 2003

The dependence on stress of the low frequency Young's modulus and mechanical losses of unpoled ferroelectric ceramics has been studied as a function of temperature. The Young's modulus of unpoled Pb(Zr,Ti)O3 (PZT) showed a Rayleigh type dependence, analogous to the one already described for the longitudinal piezoelectric coefficient. This has been associated to ferroelectric/ferroelastic domain wall movements across, and their pinning/depinning on, randomly distributed defects. The Rayleigh coefficient was found to increase with temperature. The activation energy of the Rayleigh process was obtained, which must be related to the pinning energy. The Young's modulus of Mn doped 0.65Pb(Mg1/3Nb2/3)O3–0.35PbTiO3 showed no stress dependence.
Characterization of the optical loss of an integrated silicon oxynitride optical switch structure
Authors: Zhang Ailing , Chan Kam Tai
Published: September 2003

An optical switch structure based on total internal reflection effects in intersecting silicon oxynitride waveguides has been designed and successfully fabricated. The optical reflection losses of the waveguides have been analyzed and compared with experimental results. It was shown that, apart from materials and scattering losses, the major factors contributing to the reflection losses are waveguide width, reflection facet displacement, and reflection facet tilt angle, with the last factor being the most critical in deciding the overall loss of the device.
Properties of Bulk AlN grown by thermodecomposition of AlCl3⋅NH3
Authors: Freitas J. A. , Braga G. C. B. , Silveira E. , Tischler J. G. , Fatemi M.
Published: September 2003

Self-nucleated bulk AlN crystals were grown by thermodecomposition of AlCl3⋅NH3 vaporized in the low-temperature zone of a two-zone furnace. X-ray diffraction of the AlN crystals show single lines with a small linewidth indicating high single-crystalline quality. Polarized Raman scattering experiments of these samples confirm the x-ray results based on the detection of a small linewidth for all allowed optical phonons. Low-temperature cathodoluminescence spectra show very sharp emission bands close to the optical band gap, which have been assigned to free-excitons A and B, and exciton-bound to shallow neutral impurity. The latter has a full width at half maximum smaller than 1.0 meV.
Metallic glass ingots based on yttrium
Authors: Guo Faqiang , Poon S. Joseph , Shiflet Gary J.
Published: September 2003

We report a family of yttrium metallic alloys that are able to form glassy ingots directly from the liquid, as well as forming bulk-sized amorphous rods with diameters over 2 cm by water cooling of the alloy melt sealed in quartz tubes. It is apparent that, in addition to the strong chemical interaction among the components, the simultaneous occurrence of well-distributed atom sizes and a strongly depressed liquidus temperature in multicomponent metallic alloys is responsible for the formation of glassy ingots.
Vacuum breakdown of carbon-nanotube field emitters on a silicon tip
Authors: She J. C. , Xu N. S. , Deng S. Z. , Chen Jun , Bishop H. , Huq S. E. , Wang L. , Zhong D. Y. , Wang E. G.
Published: September 2003

Findings are given from the experimental observation of the vacuum breakdown of carbon-nanotube (CNT) field emitters on a Si tip. The CNTs were grown on the apex of a Si microtip by microwave plasma-enhanced chemical vapor deposition. The electrical contact of the CNT-Si junction was shown to be of ohmic type. A fine tungsten microprobe in combination with a scanning electron microscopy (SEM) system was employed for both the field emission and the contact conductivity measurements. This arrangement allows to precisely measure the characteristics of individual CNT and to in situ inspect the morphology of the CNT emitters on Si tips before and after vacuum breakdown events. An upper limit in emission current density of ∼103 A/m2 from the CNT emitters was recorded before a vacuum breakdown event is initiated. Clear evidence was found to show that the vacuum breakdown of the CNTs results in melting of the Si tip. These findings enhance the understanding of the failure mechanism of CNT emitters. It also has important technical implication to the development of ultrabright electron source.
Calculation of effective dielectric constants for advanced interconnect structures with low-k dielectrics
Authors: Rhee Seung-Hyun , Radwin Martin D. , Ng Man Fai , Martin Jeremy I. , Erb Darrell
Published: September 2003

Effective dielectric constants of advanced interconnects with low-k and ultra-low-k dielectrics were evaluated by two-dimensional capacitance analysis. The analysis was performed for interconnect design rules proposed for 65 nm node high-performance integration. Interconnects with various pitches and integration schemes were examined, and the effects of supporting dielectric layers including cap layer, chemical mechanical polishing stop layer, and etch stop layer were evaluated. The results indicated that the use of the supporting layers greatly affects the effective dielectric constant of interconnect structures. The impacts of the supporting dielectric layers on the effective dielectric constant were evaluated quantitatively, and the implications on back-end-of-line integration schemes were discussed.
Nonuniformities in GaN/AlN quantum wells
Authors: Mkhoyan K. A. , Silcox J. , Wu H. , Schaff W. J. , Eastman L. F.
Published: September 2003

Composition sensitive annular dark field imaging and electron energy-loss spectroscopy were used to determine long-range uniformities of GaN quantum wells and the sharpness of their interfaces grown in AlN matrix by molecular beam epitaxy. Low magnification annular dark field images reveal waviness along the growth plane with a period of ∼50 nm and a height ∼20 nm in one sample and significant changes of the long-range uniformity in the other. Measurements of the changes in energy-loss spectra of the Al L2,3, Ga L2,3, and N K edge across quantum well indicate that the interfaces between the quantum wells and the barriers are in most cases almost atomically sharp.
Theoretical analysis of spectral gain in a terahertz quantum-cascade laser: Prospects for gain at 1 THz
Authors: Lee S.-C. , Wacker A.
Published: September 2003

In a recent letter [B. S. Williams et al. Appl. Phys. Lett. 82, 1015 (2003)], Williams et al. reported the development of a terahertz quantum-cascade laser operating at 3.4 THz or 14.2 meV. We have calculated and analyzed the gain spectra of the quantum-cascade structure described in their work, and in addition to gain at the reported lasing energy of ≃14 meV, we have discovered substantial gain at a much lower energy of around 5 meV or just over 1 THz. This suggests an avenue for the development of a terahertz laser at this lower energy, or of a two-color terahertz laser.
Characteristics of erbium-silicided n-type Schottky barrier tunnel transistors
Authors: Jang Moongyu , Oh Jihun , Maeng Sunglyul , Cho Wonju , Lee Seongjae , Kang Kicheon , Park Kyoungwan
Published: September 2003

The current–voltage characteristics of erbium-silicided n-type Schottky barrier tunnel transistors (SBTTs) are discussed. The n-type SBTTs with 60 nm gate lengths shows typical transistor behaviors in drain current to drain voltage characteristics. The drain current on/off ratio is about 105 at low drain voltage regime in drain current to gate voltage characteristics. However, the on/off ratio tends to decrease as the drain voltage increases. From the numerical simulation results, the increase of off-current is mainly attributed to the thermionic current and the increase of drain current is mainly attributed to the tunneling current, respectively. This phenomenon is explained by using drain induced Schottky barrier thickness thinning effect.
Nonlinear refraction in potassium gadolinium tungstate: An efficient Raman crystal and laser host
Authors: Dharmadhikari J. A. , Dharmadhikari A. K. , Kumar G. R.
Published: September 2003

Third order nonlinear optical properties of a promising laser host and Raman shifting crystal—potassium gadolium tungstate are reported. The intensity dependent refractive index, n2, measured at 1064 and 532 nm are 8.76×10−16 and 43.1×10−16 cm2 W−1, respectively, using 35 ps pulses by the z-scan technique. The two-photon absorption (TPA) coefficient β at 532 nm is 0.29 cm GW−1. Furthermore, we examine the behavior of self-focusing and nonlinear lens inside a laser resonator and discuss its influence on laser performance.
Time-resolved dynamics in single InGaN quantum dots
Authors: Robinson James W. , Rice James H. , Jarjour Anas , Smith Jonathan D. , Taylor Robert A. , Oliver Rachel A. , Briggs G. Andrew D. , Kappers Menno J. , Humphreys Colin J. , Arakawa Yasuhiko
Published: September 2003

We present measurements of photoluminescence decay dynamics for single InGaN quantum dots. The recombination is shown to be characterized by a single exponential decay, in contrast to the nonexponential recombination dynamics seen in the two-dimensional wetting layer. The lifetimes of single dots in the temperature range 4 to 60 K decrease with increasing temperature.
Seventy-fold enhancement of light extraction from a defectless photonic crystal made on silicon-on-insulator
Authors: Zelsmann M. , Picard E. , Charvolin T. , Hadji E. , Heitzmann M. , Dal’zotto B. , Nier M. E. , Seassal C. , Rojo-Romeo P. , Letartre X.
Published: September 2003

Very high photoluminescence extraction is observed from defectless two-dimensional photonic crystals etched in the upper 200-nm-thick silicon layer of a silicon-on-insulator (SOI) substrate. Predicted very low group velocity modes near the Γ point of the band structure lying above the light line are used to extract light from the photonic crystal slab into the free space. It is found that light is extracted on a 80-nm-wide band along directions near to the perpendicular to the slab, with an extraction enhancement up to 70 compared to an unpatterned SOI.
Role of yttrium in glass formation of Fe-based bulk metallic glasses
Authors: Lu Z. P. , Liu C. T. , Porter W. D.
Published: September 2003

In this study, we discovered that a small addition of Y is very effective in improving glass-forming ability of Fe-based alloys. As-cast bulk amorphous alloys containing 2 at. % Y showed large thermal stability, with glass transition temperatures above 900 K and supercooled liquid regions above 55 K, and high strength, with Vickers hardnesses larger than HV 1200. The beneficial effect of Y on glass formation is twofold: (1) Y adjusted the compositions closer to the eutectic and thus lowered their liquidus temperatures, and (2) Y improved the manufacturability of these alloys by scavenging the oxygen impurity from it via the formation of innocuous yttrium oxides.
Amplified spontaneous emission and distributed feedback lasing from a conjugated compound in various polymer matrices
Authors: Tsutsumi Naoto , Kawahira Tetsuya , Sakai Wataru
Published: September 2003

This letter presents amplified spontaneous emission (ASE) and distributed feedback (DFB) lasing of the conjugated compound, 1,4-bis[2-[4-[N,N-di(p-tolyl)amino]phenyl] vinyl]benzene, in various polymer matrices of poly(methylmethacrylate), poly(styrene) (PS), poly(vinyl butyral), poly(N-vinyl carbazole), and poly(methyl phenylsilane). Effective and large ASE intensity, lowest threshold, and maximum optical gain were measured in the PS matrix. Sharp DFB lasing with full width at half-maximum=0.6 nm was measured at 490 nm. The lasing wavelength of 490 nm was fitted well by the theoretically calculated value of 491 nm.
GaN/AlGaN multiple quantum wells on a-plane GaN pillars for stripe-geometry nonpolar ultraviolet light-emitting devices
Authors: Sun W. H. , Yang J. W. , Chen C. Q. , Zhang J. P. , Gaevski M. E. , Kuokstis E. , Adivarahan V. , Wang H. M. , Gong Z. , Su M. , Khan M. Asif
Published: September 2003

We investigated the growth of GaN/Al0.20Ga0.80N multiple quantum wells (MQWs) on selective-area-grown a-plane GaN pillars over r-plane sapphire. In contrast to the MQWs grown on planar a-plane GaN templates, these GaN/Al0.20Ga0.8N MQWs on the pillars exhibited pit-free and atomically smooth surface morphology. Their structural quality and their UV emission (at 357 nm) increased with the underlying pillar height. The epitaxy of GaN/AlGaN MQWs on the selective-area-grown pillars is thus a promising and simple approach for fabricating stripe-geometry, high-efficiency, nonpolar UV emitters.
Kelvin probe spectroscopy of a two-dimensional electron gas below 300 mK
Authors: Vančura T. , Kičin S. , Ihn T. , Ensslin K. , Bichler M. , Wegscheider W.
Published: September 2003

A scanning force microscope with a base temperature below 300 mK is used for measuring the local electron density of a two-dimensional electron gas embedded in a Ga[Al]As heterostructure. At different separations between atomic force microscope tip and sample, a dc voltage is applied between the tip and the electron gas while simultaneously recording the frequency shift of the oscillating tip. Using a plate capacitor model, the local electron density can be extracted from the data. The result coincides within 10% with the data obtained from transport measurements.
Inelastic electron tunneling spectroscopy study of ultrathin HfO2 and HfAlO
Authors: He Wei , Ma T. P.
Published: September 2003

We have studied inelastic electron tunneling spectroscopy (IETS) in silicon metal-oxide-semiconductor systems with HfO2 and aluminum-doped HfO2 (HfAlO) as gate dielectrics. Samples with a thermal SiO2 layer (∼2 nm) were used to obtain reference spectra for the study. Information on chemical bonding structures and compositions of ultrathin HfO2 and HfAlO has been revealed by the IETS data. The bias polarity dependence of IETS has enabled differentiation of microstructures either near the gate electrode interface or near the silicon substrate interface.
Deep traps in unpassivated and Sc2O3-passivated AlGaN/GaN high electron mobility transistors
Authors: Polyakov A. Y. , Smirnov N. B. , Govorkov A. V. , Danilin V. N. , Zhukova T. A. , Luo B. , Ren F. , Gila B. P. , Onstine A. H. , Abernathy C. R. , Pearton S. J.
Published: September 2003

Sc 2 O 3 thin-film layers deposited by rf plasma-assisted molecular-beam epitaxy were found to significantly reduce the concentration of prominent surface traps with activation energies of 1 and 0.9 eV on AlGaN/GaN high electron mobility transistors (HEMTs). The surface passivation is accompanied by effective mitigation of the current collapse observed under rf conditions in HEMTs without Sc2O3. The passivation is stable to post-deposition annealing temperatures of 400 °C and device degradation at higher temperatures is due to reaction of the gate metal with the AlGaN.
Enhanced dynamic response of the photoinduced nematic–isotropic transition in a polymer matrix
Authors: Sandhya K. L. , Prasad S. Krishna , Nair Geetha G.
Published: September 2003

We have investigated the dynamic response of the photoinduced nematic–isotropic transition and the thermal back relaxation process of a liquid crystal with photoactive molecules embedded in a polymer matrix. The results show that the presence of the polymer matrix leads to a dramatic improvement in the response time. Possible causes for this finding have been discussed.
Single-electron AND/NAND logic circuits based on a self-organized dot network
Authors: Nakajima F. , Miyoshi Y. , Motohisa J. , Fukui T.
Published: September 2003

We experimentally demonstrated single-electron operations of an AND/NAND logic circuit based on a self-organized GaAs quantum-dot (QD) network fabricated by applying a selective-area metalorganic vapor-phase epitaxy technique. Single-electron logic operations using four cooperating single-electron tunneling (SET) transistors has been tested. This logic circuit has an architecture based on a binary decision diagram (BDD) using a Coulomb blockade (CB) in GaAs QDs, which is a representation of digital logic functions using directed graphs. BDD node devices consisting of two SET transistors achieved a two-way path switching operation in single-electron mode due to the CB effects which appeared complementarily in the two SET transistors at 1.9 K. We also demonstrated an AND/NAND operation in a logic circuit by integrating two BDD nodes.
Guided mode lasing in a double-layered square microcavity
Authors: Moon Hee-Jong , Sun Sang-Pil , Lee Jai-Hyung , An Kyungwon
Published: September 2003

We investigated the lasing characteristics of guided modes in a double-layered square microcavity made of a fused-silica hollow square capillary, in which the modes were formed by the total internal reflections off the inner and outer boundaries. Periodically peaked spectra of guided modes were observed when a dye-doped dielectric was coated on the outer boundary for a laser gain. By reducing the distance between the outer and the inner boundaries, we could achieve even a lasing of single closed guided modes with multiple reflections at each side of the inner boundary. Our double-layered square cavity can be adapted for various applications, particularly in the photonic integrated circuits.
ZnSe nanowires epitaxially grown on GaP(111) substrates by molecular-beam epitaxy
Authors: Chan Y. F. , Duan X. F. , Chan S. K. , Sou I. K. , Zhang X. X. , Wang N.
Published: September 2003

We report molecular-beam epitaxy growth of single crystalline ZnSe nanowires with uniform diameters (∼10 nm) on GaP(111) substrates. The growth process was based on the Au-catalyzed vapor-liquid-solid deposition. As determined by electron microdiffraction and high-resolution transmission electron microscopy, ZnSe nanowires grew generally along the 〈110〉 and 〈112〉 directions with the orientation relationship of (111)ZnSe wire//(111)GaP and 〈11̄0〉ZnSe wire//〈11̄0〉GaP. The dominant defects were found to be twins at the interface between the substrate and the nanowires along the (111) plane.
Spectral narrowing of the emission from rhodamine 6G infiltrated in synthetic opals enhanced by the surface plasmon resonance
Authors: Ishikawa Keiji , Okubo Tatsuya
Published: September 2003

We report on the observation of spectrally narrowed emission (SNE) from rhodamine 6G infiltrated in synthetic opals, and the enhancement of the spectral narrowing by the surface plasmon resonance effect of Ag particles anchored on the internal surface of the opals. With Ag particles, SNE is observed at a lower pump intensity, and the threshold of the spectral narrowing is one-tenth lower than that without Ag. It was clarified that enhancement is not caused by the light scattering of the Ag particles, but by the surface plasmon resonance.
Anode sheath in Hall thrusters
Authors: Dorf L. , Semenov V. , Raitses Y.
Published: September 2003

A set of hydrodynamic equations is used to describe quasineutral plasma in ionization and acceleration regions of a Hall thruster. The electron distribution function and Poisson equation are invoked for description of a near-anode region. Numerical solutions suggest that steady-state operation of a Hall thruster can be achieved at different anode sheath regimes. It is shown that the anode sheath depends on the thruster operating conditions, namely the discharge voltage and the mass flow rate.
Ultrafast three-dimensional tunable photonic crystal
Authors: Hu Xiaoyong , Zhang Qi , Liu Yuanhao , Cheng Bingying , Zhang Daozhong
Published: September 2003

We demonstrate a continuously tunable photonic crystal with several picoseconds response, which is fabricated through a self-assembly formation method of polystyrene spheres. The large optical nonlinearity originates from the delocalization of the conjugated π-electron along polymer chains. The pump and probe scheme is adopted to measure the transmission changes based on the optical Kerr effect. The dynamic shift of the photonic band gap is studied. It is found that the band gap shifts about 13 nm when the input peak intensity is 40.4 GW/cm2, which is in agreement with the theoretical predictions.
Long-wavelength strain-compensated GaAsSb quantum-well heterostructures laser grown by metalorganic chemical vapor deposition
Authors: Noh M. S. , Dupuis R. D. , Bour D. P. , Walter G. , Holonyak N.
Published: September 2003

We report data on strain-compensated GaAsSb double-quantum-well lasers having a type-I band alignment and grown by metalorganic chemical vapor deposition on GaAs substrates. In order to compensate for strain effects and to establish a type-I band alignment, tensile-strained higher-band-gap GaAsP quantum-well barriers have been employed. A lasing wavelength of λ∼1.200 μm from a 500 μm long device at 1.15Ith has been achieved at room temperature in pulsed-mode operation. The maximum output power was 20 mW for the same device. A low threshold current density of 608.0 A/cm2 was obtained for 1370 μm long and 60 μm stripe lasers. The calculated internal quantum efficiency and internal loss were 33.8% and 8.4 cm−1, respectively. We also calculated an infinite cavity length threshold current density of 265 A/cm2. From these data, a gain constant G0∼1728 cm−1 and transparency current density of 135 A/cm2 were calculated. The result showed that the strain-compensated GaAsSb quantum wells are promising active materials for 1.3 μm vertical-cavity surface-emitting lasers.
Multiple negative differential resistance of InP/InGaAs superlattice-emitter resonant-tunneling bipolar transistor at room temperature
Authors: Tsai Jung-Hui
Published: September 2003

Sequential resonant-tunneling behavior of a resonant-tunneling bipolar transistor with five-period i-InP/n-InGaAs superlattice emitter has been demonstrated. An interesting multiple negative differential resistance (NDR) phenomena resulting from the creation and extension of the high-field domain in a superlattice is observed at room temperature. Furthermore, the employing of a thin n-InGaAs emitter layer between an InP/InGaAs superlattice and p+-InGaAs base layer helps to lower the potential spike at the base–emitter junction and the reduce neutral–emitter recombination current. Experimentally, transistor performance, incorporating multiple NDR, with a relatively large current gain of 454 and an offset voltage as low as 80 mV, is achieved.
Raman scattering and anti-Stokes emission from a single spherical microcavity with a CdTe quantum dot monolayer
Authors: Rakovich Yu. P. , Donegan J. F. , Gaponik N. , Rogach A. L.
Published: September 2003

We have studied the Raman and luminescence spectra of a microcavity–quantum dot system consisting of a melamine formaldehyde latex microsphere coated by CdTe colloidal quantum dots. The cavity-induced enhancement of the Raman scattering allows the observation of Raman spectra from only a monolayer of CdTe quantum dots. Periodic structure with very narrow peaks in the luminescence spectra of a single microsphere was detected arising from the coupling between the emission from quantum dots and spherical cavity modes. Strong anti-Stokes emission from CdTe quantum dots coupled to the cavity modes was observed using low intensity below band-gap excitation and attributed to the strong field enhancement at the microcavity resonances.
Effect of microstructural evolution on magnetic property of Mn-implanted p-type GaN
Authors: Baik Jeong Min , Kim Hyung Seok , Park Chan Gyung , Lee Jong-Lam
Published: September 2003

The microstructural evolution of Mn-implanted p-type GaN has been studied using cross-sectional transmission electron microscopy. As Mn3Ga nanoclusters (3–7 nm) with a hexagonal structure were produced by annealing (⩽800 °C), the weak ferromagnetic property emerged. Higher-temperature annealing (⩾900 °C) reduced the ferromagnetic signal and produced antiferromagnetic Mn-nitride nanoclusters, such as Mn6N2.58 and Mn3N2. This provides evidence that the ferromagnetic property was deeply related to microstructural changes of nanoclusters.
Giant Goos-Hänchen effect at the reflection from left-handed metamaterials
Authors: Shadrivov Ilya V. , Zharov Alexander A. , Kivshar Yuri S.
Published: September 2003

We study the beam reflection from a layered structure with a left-handed metamaterial. We predict a giant lateral (Goos-Hänchen) shift and splitting of the beam due to the resonant excitation of surface polaritons with a vortexlike energy flow between the right- and left-handed materials.
Nanoparticle-assisted microwave absorption by single-wall carbon nanotubes
Authors: Wadhawan A. , Garrett D. , Perez J. M.
Published: September 2003

We report the effects of microwave irradiation on both unpurified and purified iron-catalyzed high-pressure disproportionation (HiPco)-grown single-walled carbon nanotubes (SWNTs) in ultrahigh vacuum. Under microwave irradiation, we observe that unpurified HiPco SWNTs quickly reach temperatures of approximately 1850 °C. As a result, H2, H2O, CO, CO2, and CH4 gases are observed, and the Fe catalyst nanoparticles melt and coalesce into larger crystallites approximately four times their original diameter. In contrast, carbon black and purified HiPco SWNTs heat up to temperatures of 500–650 °C. We propose that the significant heating of unpurified HiPco SWNTs is due to the Fe catalysts.
Magneto-optical properties of GaAsSb/GaAs quantum wells
Authors: Senger R. T. , Bajaj K. K. , Jones E. D. , Modine N. A. , Waldrip K. E. , Jalali F. , Klem J. F. , Peake G. M. , Wei X. , Tozer S. W.
Published: September 2003

We have measured the diamagnetic shift of a heavy-hole exciton in a single 60 Å wide GaAs0.7Sb0.3/GaAs quantum well as a function of magnetic field up to 32 T at 1.3 K using photoluminescence spectroscopy. The sample was grown on (001)-oriented GaAs substrate using solid-source molecular beam epitaxy. We have calculated the variation of the diamagnetic shift as a function of magnetic field using a variational approach and a free exciton model. We assumed a weak type-I conduction-band lineup in our calculations. We found that the values thus obtained are more than twice as large as the observed values. A similar calculation assuming a complete localization of the heavy hole leads to the values of the diamagnetic shift which agree very well with the experimental data. Our study suggests that the excitons are strongly localized in GaAs0.7Sb0.3/GaAs quantum well structures at low temperatures, and that this heterostructure has a weak type-I conduction-band lineup.
Mode control by nanoengineering light emitters in spherical microcavities
Authors: Möller B. , Woggon U. , Artemyev M. V. , Wannemacher R.
Published: September 2003

Quantum-confined semiconductor nanorods are used as highly polarized nanoemitters to actively control the polarization state of microcavity photons. A wet-chemical method to tangentially align CdSe nanorods on a polymer surface is applied to a spherical R≈2λ-microcavity. The cavity emission is studied by imaging spectroscopy and polarization-sensitive mode mapping. The efficient confinement of photons spontaneously emitted by nanorods into single transverse electric (TE) cavity modes is achieved while transverse magnetic modes are suppressed. A microscopic tricolor TE-emitter operating at room temperature in the visible spectral range is demonstrated.
High-contrast optical modulation by surface acoustic waves
Authors: Krishnamurthy Srinivasan , Santos P. V.
Published: September 2003

Numerical calculations are employed to study the modulation of light by surface acoustic waves (SAWs) in photonic band gap (PBG) structures. The on/off contrast ratio in a PBG switch based on an optical cavity is determined as a function of the SAW-induced dielectric modulation. We show that these structures exhibit high-contrast ratios even for moderate acousto-optic coupling.
Jumping spider phylogeny (Araneae : Salticidae)
Authors: Maddison Wayne P. , Hedin Marshal C.
Published: September 2003

A phylogenetic analysis of five sequenced genes (28S, 16S, EF1-α, CO1, ND1) from 81 genera of jumping spiders (Salticidae) and five outgroups supports the monophyly of the Dendryphantinae and Euophryinae and refines the concepts of the Plexippinae and Pelleninae. The clade that excludes lyssomanines and spartaeines and contains the bulk of salticid species is formally named as the Salticoida. The previously proposed clade delimited by an embolus articulated and separated from the tegulum by a developed distal hematodocha (as opposed to fused immovably to the tegulum) is rejected, suggesting the 'free embolus' evolved independently several times. Three major clades are discovered, the Marpissoida (including Dendryphantinae, Marpissinae and smaller groups such as synagelines), the Plexippoida (plexippines plus pellenines) and the Amycoida (including Amycinae, Sitticinae, Hyetusseae, Hurieae, Synemosyninae). The amycoids form a large neotropical radiation from which only a single known group (Sitticus and Attulus) has reached the Old World. The marpissoids also constitute a major New World group with relatively few species in the Old World. In contrast, the Plexippoida is predominantly an Old World group (except for the spectacular radiation of Habronattus in North America), as is the Heliophaninae. These results suggest that much of salticid diversification occurred after the separation of the continents of the Old World and New World.
Molecular taxonomy of the Anadenobolus excisus (Diplopoda : Spirobolida : Rhinocricidae) species-group on the Caribbean island of Jamaica
Authors: Bond Jason E. , Sierwald Petra
Published: September 2003

This paper documents the mtDNA genealogy and molecular taxonomy of the Anadenobolus excisus millipede species-group on the island of Jamaica. This endemic species-group originally comprised two nominal species, A. excisus (Karsch) and A. holomelanus Pocock. However, the latter species was considered by Hoffman likely to be a subspecies of the former, owing to their overall morphological and gonopodal similarity (the secondary sexual features most commonly used to delineate millipede species). We summarise molecular and morphological data that paints a rather different picture of the diversity in this group. Based on the 16S rRNA gene of the mitochondrion and a comparative analysis of millipede size (reported here and elsewhere), we find that this species-group comprises at least three sibling species, one of which, A. dissimulans, sp. nov., is newly described. The study documents the first myriapod species diagnosed on the basis of molecular data.
Revision of the subgenus Marquesania (Acari : Atopomelidae : Listrophoroides)
Authors: Bochkov Andre V. , Fain Alex
Published: September 2003

The subgenus Marquesania Womersley (Acari : Atopomelidae : Listrophoroides) is revised. The species of this subgenus are permanent parasites living in the fur of rats (Rodentia : Murinae) in the Oriental region, Australia and New Guinea. Most of the type material has been examined. Two new species, Listrophoroides melomys, sp. nov. from Melomys moncktoni (Thomas) and L. mordax, sp. nov. from Rattus mordax (Thomas) are described from New Guinea. A new diagnosis of the subgenus Marquesania, detailed descriptions, and a key for all species is provided. The phylogenetic reconstruction of the subgenus Marquesania was effected by the method of parsimonius cladistics. The monophyly of the subgenus is strongly supported by this analysis, and most species from the Oriental region fall at the base of the cladogram. The distribution of Marquesania species on their hosts is discussed. It is suggested that these mites originated in the Oriental region and then migrated to Australia and New Guinea. The distribution of Marquesania species in the Australian and New Guinean regions is noticeably complicated, reflecting the complex settling history of their hosts.
Designing hardware for protein sequence analysis
Authors: Marongiu Alessandro , Palazzari Paolo , Rosato Vittorio
Published: September 2003

We present the architecture of PROSIDIS, a special purpose co-processor designed to search for the occurrence of substrings similar to a given ‘template string’ within a proteome. Actual tests show speed up figures ranging from 5 to 50 with respect to conventional general-purpose processors.

Availability: the PROSIDIS configuration file and the c code are available at http://www.enea.it/hpcn/php/rosato/
Disulfide by Design™: a computational method for the rational design of disulfide bonds in proteins
Authors: Dombkowski Alan A.
Published: September 2003

Summary: Disulfide by Design is a program for the design of novel disulfide bonds in proteins. Protein structure files in PDB format are analyzed to identify residue pairs that are likely to form a disulfide bond if the respective amino acids are mutated to cysteines. The output displays residue pairs having the appropriate geometric characteristics for disulfide formation and provides automated generation of modified PDB files including modeled disulfides. Validation demonstrates a high level of accuracy for the algorithm.

Availability: http://www.ehscenter.org/dbd/

Supplementary information:  http://www.ehscenter.org/dbd/
CLICK and EXPANDER: a system for clustering and visualizing gene expression data
Authors: Sharan Roded , Maron-Katz Adi , Shamir Ron
Published: September 2003

Motivation: Microarrays have become a central tool in biological research. Their applications range from functional annotation to tissue classification and genetic network inference. A key step in the analysis of gene expression data is the identification of groups of genes that manifest similar expression patterns. This translates to the algorithmic problem of clustering genes based on their expression patterns.

Results: We present a novel clustering algorithm, called CLICK, and its applications to gene expression analysis. The algorithm utilizes graph-theoretic and statistical techniques to identify tight groups (kernels) of highly similar elements, which are likely to belong to the same true cluster. Several heuristic procedures are then used to expand the kernels into the full clusters. We report on the application of CLICK to a variety of gene expression data sets. In all those applications it outperformed extant algorithms according to several common figures of merit. We also point out that CLICK can be successfully used for the identification of common regulatory motifs in the upstream regions of co-regulated genes. Furthermore, we demonstrate how CLICK can be used to accurately classify tissue samples into disease types, based on their expression profiles. Finally, we present a new java-based graphical tool, called EXPANDER, for gene expression analysis and visualization, which incorporates CLICK and several other popular clustering algorithms.

Availability:  http://www.cs.tau.ac.il/~rshamir/expander/expander.html
DDBASE2.0: updated domain database with improved identification of structural domains
Authors: Vinayagam A. , Shi J. , Pugalenthi G. , Meenakshi B. , Blundell T.L. , Sowdhamini R.
Published: September 2003

Motivation: Although many methods are available for the identification of structural domains from protein three-dimensional structures, accurate definition of protein domains and the curation of such data for a large number of proteins are often possible only after manual intervention. The availability of domain definitions for protein structural entries is useful for the sequence analysis of aligned domains, structure comparison, fold recognition procedures and understanding protein folding, domain stability and flexibility.

Results: We have improved our method of domain identification starting from the concept of clustering secondary structural elements, but with an intention of reducing the number of discontinuous segments in identified domains. The results of our modified and automatic approach have been compared with the domain definitions from other databases. On a test data set of 55 proteins, this method acquires high agreement (88%) in the number of domains with the crystallographers' definition and resources such as SCOP, CATH, DALI, 3Dee and PDP databases. This method also obtains 98% overlap score with the other resources in the definition of domain boundaries of the 55 proteins. We have examined the domain arrangements of 4592 non-redundant protein chains using the improved method to include 5409 domains leading to an update of the structural domain database.

Availability: The latest version of the domain database and online domain identification methods are available from http://www.ncbs.res.in/~faculty/mini/ddbase/ddbase.html

Supplementary information:  http://www.ncbs.res.in/~faculty/mini/ddbase/supplementary/supplementary.html
Batch mode generation of residue-based diagrams of proteins
Authors: Campagne Fabien , Bettler Emmanuel , Vriend Gert , Weinstein Harel
Published: September 2003

Summary: Residue-based diagrams of proteins are graphical representations that can be used in protein information systems. These diagrams make it possible to visually integrate different types of biological information. The approach has been used successfully for membrane proteins. We developed the Residue-based diagram generator to (i) make it possible to generate residue-based diagrams of proteins in a batch mode that is compatible with the needs of information system curators, (ii) allow the generation of residue-based diagrams for families of soluble proteins or domains.

Availability: Licensed. Royalty free licenses are granted to non-profit institutions for educational and research purposes. http://icb.mssm.edu/crt/RbDg/index.xml
Characterizing proteolytic cleavage site activity using bio-basis function neural networks
Authors: Thomson Rebecca , Hodgman T. Charles , Yang Zheng Rong , Doyle Austin K.
Published: September 2003

Motivation: In protein chemistry, proteomics and biopharmaceutical development, there is a desire to know not only where a protein is cleaved by a protease, but also the susceptibility of its cleavage sites. The current tools for proteolytic cleavage prediction have often relied purely on regular expressions, or involve models that do not represent biological data well.

Results: A novel methodology for characterizing proteolytic cleavage site activities has been developed, which incorporates two fundamental features: activity class prediction and the use of an amino acid similarity matrix for (non-parametric) neural learning. The first solved the problem of predicting proteolytic efficiency. The second significantly improved the robustness in prediction and reduced the time complexity for learning. This study shows that activity class prediction is successful when applying this methodology to the prediction and characterization of Trypsin cleavage sites and the prediction of HIV protease cleavage sites.

Availability: Requests for software and data should be made respectively to Dr Zheng Rong Yang and Miss Rebecca Thomson.
New algorithms for multi-class cancer diagnosis using tumor gene expression signatures
Authors: Bagirov A. M. , Ferguson B. , Ivkovic S. , Saunders G. , Yearwood J.
Published: September 2003

Motivation: The increasing use of DNA microarray-based tumor gene expression profiles for cancer diagnosis requires mathematical methods with high accuracy for solving clustering, feature selection and classification problems of gene expression data.

Results: New algorithms are developed for solving clustering, feature selection and classification problems of gene expression data. The clustering algorithm is based on optimization techniques and allows the calculation of clusters step-by-step. This approach allows us to find as many clusters as a data set contains with respect to some tolerance. Feature selection is crucial for a gene expression database. Our feature selection algorithm is based on calculating overlaps of different genes. The database used, contains over 16 000 genes and this number is considerably reduced by feature selection. We propose a classification algorithm where each tissue sample is considered as the center of a cluster which is a ball. The results of numerical experiments confirm that the classification algorithm in combination with the feature selection algorithm perform slightly better than the published results for multi-class classifiers based on support vector machines for this data set.

Availability: Available on request from the authors.
Haplotype inference by maximum parsimony
Authors: Wang Lusheng , Xu Ying
Published: September 2003

Motivation: Haplotypes have been attracting increasing attention because of their importance in analysis of many fine-scale molecular-genetics data. Since direct sequencing of haplotype via experimental methods is both time-consuming and expensive, haplotype inference methods that infer haplotypes based on genotype samples become attractive alternatives.

Results: (1) We design and implement an algorithm for an important computational model of haplotype inference that has been suggested before in several places. The model finds a set of minimum number of haplotypes that explains the genotype samples. (2) Strong supports of this computational model are given based on the computational results on both real data and simulation data. (3) We also did some comparative study to show the strength and weakness of this computational model using our program.

Availability: The software HAPAR is free for non-commercial uses. Available upon request (lwang@cs.cityu.edu.hk).
Recognizing the fold of a protein structure
Authors: Harrison Andrew , Pearl Frances , Sillitoe Ian , Slidel Tim , Mott Richard , Thornton Janet , Orengo Christine
Published: September 2003

This paper reports a graph-theoretic program, GRATH, that rapidly, and accurately, matches a novel structure against a library of domain structures to find the most similar ones. GRATH generates distributions of scores by comparing the novel domain against the different types of folds that have been classified previously in the CATH database of structural domains.

GRATH uses a measure of similarity that details the geometric information, number of secondary structures and number of residues within secondary structures, that any two protein structures share. Although GRATH builds on well established approaches for secondary structure comparison, a novel scoring scheme has been introduced to allow ranking of any matches identified by the algorithm. More importantly, we have benchmarked the algorithm using a large dataset of 1702 non-redundant structures from the CATH database which have already been classified into fold groups, with manual validation. This has facilitated introduction of further constraints, optimization of parameters and identification of reliable thresholds for fold identification. Following these benchmarking trials, the correct fold can be identified with the top score with a frequency of 90%. It is identified within the ten most likely assignments with a frequency of 98%.

GRATH has been implemented to use via a server (http://www.biochem.ucl.ac.uk/cgi-bin/cath/Grath.pl). GRATH's speed and accuracy means that it can be used as a reliable front-end filter for the more accurate, but computationally expensive, residue based structure comparison algorithm SSAP, currently used to classify domain structures in the CATH database. With an increasing number of structures being solved by the structural genomics initiatives, the GRATH server also provides an essential resource for determining whether newly determined structures are related to any known structures from which functional properties may be inferred.
MutDB: annotating human variation with functionally relevant data
Authors: Mooney Sean D. , Altman Russ B.
Published: September 2003

Summary: We have developed a resource, MutDB (http://mutdb.org/), to aid in determining which single nucleotide polymorphisms (SNPs) are likely to alter the function of their associated protein product. MutDB contains protein structure annotations and comparative genomic annotations for 8000 disease-associated mutations and SNPs found in the UCSC Annotated Genome and the human RefSeq gene set. MutDB provides interactive mutation maps at the gene and protein levels, and allows for ranking of their predicted functional consequences based on conservation in multiple sequence alignments.

Availability:  http://mutdb.org/

Supplementary information:  http://mutdb.org/about/about.html
Controlling false-negative errors in microarray differential expression analysis: a PRIM approach
Authors: Cole Steve W. , Galic Zoran , Zack Jerome A.
Published: September 2003

Motivation: Theoretical considerations suggest that current microarray screening algorithms may fail to detect many true differences in gene expression (Type II analytic errors). We assessed ‘false negative’ error rates in differential expression analyses by conventional linear statistical models (e.g. t-test), microarray-adapted variants (e.g. SAM, Cyber-T), and a novel strategy based on hold-out cross-validation. The latter approach employs the machine-learning algorithm Patient Rule Induction Method (PRIM) to infer minimum thresholds for reliable change in gene expression from Boolean conjunctions of fold-induction and raw fluorescence measurements.

Results: Monte Carlo analyses based on four empirical data sets show that conventional statistical models and their microarray-adapted variants overlook more than 50% of genes showing significant up-regulation. Conjoint PRIM prediction rules recover approximately twice as many differentially expressed transcripts while maintaining strong control over false-positive (Type I) errors. As a result, experimental replication rates increase and total analytic error rates decline. RT-PCR studies confirm that gene inductions detected by PRIM but overlooked by other methods represent true changes in mRNA levels. PRIM-based conjoint inference rules thus represent an improved strategy for high-sensitivity screening of DNA microarrays.

Availability: Freestanding JAVA application at http://microarray.crump.ucla.edu/focus
Protein Ligand Database (PLD): additional understanding of the nature and specificity of protein–ligand complexes
Authors: Puvanendrampillai Dushyanthan , Mitchell John B. O.
Published: September 2003

Summary: The Protein Ligand Database (PLD) is a publicly available web-based database that aims to provide further understanding of protein–ligand interactions. The PLD contains biomolecular data including calculated binding energies, Tanimoto ligand similarity scores and protein percentage sequence similarities. The database has potential for application as a tool in molecular design.

Availability:  http://www-mitchell.ch.cam.ac.uk/pld/
Soap-HT-BLAST: high throughput BLAST based on Web services
Authors: Wang Jiren , Mu Qing
Published: September 2003

Summary: A high throughput Basic Local Alignment Search Tool (BLAST) system based on Web services is implemented. It provides an alternative BLAST service and allows users to perform multiple BLAST queries at one run in a distributed, parallel environment through the Internet.

Availability: It is available at http://mammoth.bii.a-star.edu.sg/webservices/htblast/index.html and at http://www.bii.a-star.edu.sg/jiren/download.html