bluuebunny/crossref_metadata_2025 huggingface dataset:
Semiclassical extension of the Landau-Teller theory of collisional energy transfer
Authors: Dashevskaya E. I. , Litvin I. , Nikitin E. E. , Troe J.
Published: October 2006

A semiclassical version of the quantum coupled-states approximation for the vibrational relaxation of diatomic molecules in collisions with monatomic bath gases is presented. It is based on the effective mass approximation and a recovery of the semiclassical Landau exponent from the classical Landau-Teller collision time. For an interaction with small anisotropy, the Landau exponent includes first order corrections with respect to the orientational dependence of the collision time and the effective mass. The relaxation N2(v=1)→N2(v=0) in He is discussed as an example. Employing the available vibrationally elastic potential, the semiclassical approach describes the temperature dependence of the rate constant k10(T) over seven orders of magnitude across the temperature range of 70–3000K in agreement with experimental data and quantum coupled-states calculations. For this system, the hierarchy of corrections to the Landau-Teller conventional treatment in the order of importance is the following: quantum effects in the energy release, dynamical contributions of the rotation of N2 to the vibrational transition, and deviations of the interaction potential from a purely repulsive form. The described treatment provides significant simplifications over complete coupled-states calculations such that applications to more complex situations appear promising.
Light absorption during alkali atom-noble gas atom interactions at thermal energies: A quantum dynamics treatment
Authors: Pacheco Alexander B. , Reyes Andrés , Micha David A.
Published: October 2006

The absorption of light during atomic collisions is treated by coupling electronic excitations, treated quantum mechanically, to the motion of the nuclei described within a short de Broglie wavelength approximation, using a density matrix approach. The time-dependent electric dipole of the system provides the intensity of light absorption in a treatment valid for transient phenomena, and the Fourier transform of time-dependent intensities gives absorption spectra that are very sensitive to details of the interaction potentials of excited diatomic states. We consider several sets of atomic expansion functions and atomic pseudopotentials, and introduce new parametrizations to provide light absorption spectra in good agreement with experimentally measured and ab initio calculated spectra. To this end, we describe the electronic excitation of the valence electron of excited alkali atoms in collisions with noble gas atoms with a procedure that combines l-dependent atomic pseudopotentials, including two- and three-body polarization terms, and a treatment of the dynamics based on the eikonal approximation of atomic motions and time-dependent molecular orbitals. We present results for the collision induced absorption spectra in the Li–He system at 720K, which display both atomic and molecular transition intensities.
Periodic arrays of epitaxial self-assembled SiGe quantum dot molecules grown on patterned Si substrates
Authors: Gray J. L. , Hull R. , Floro J. A.
Published: October 2006

Ex situ focused ion-beam (FIB) patterning of arrays of holes on Si (001) substrates results in the subsequent formation of SiGe quantum dot molecules at each of the patterned sites during heteroepitaxial growth under kinetically limited growth conditions where island formation is constrained. These quantum dot molecules are fourfold self-assembled island nanostructures bound by a central pit. During growth, material is ejected from the patterned sites forming the pits that in turn provide favorable sites for the cooperative nucleation of {105} faceted islands. The degree of order and quality of the resulting structures depend on many factors including growth temperature, ion-beam milling depth, Si buffer thickness, and spacings between FIB exposed sites. This technique provides a method for controlling the lateral placement of semiconductor nanostructures, which could be used in applications such as complex nanoelectronic architectures.
Densification of silica glass at ambient pressure
Authors: Zheng Lianqing , An Qi , Fu Rongshan , Ni Sidao , Luo Sheng-Nian
Published: October 2006

We show that densification of silica glass at ambient pressure as observed in irradiation experiments can be attributed to defect generation and subsequent structure relaxation. In our molecular dynamics simulations, defects are created by randomly removing atoms, by displacing atoms from their nominal positions in an otherwise intact glass, and by assigning certain atom excess kinetic energy (simulated ion implantation). The former forms vacancies; displacing atoms and ion implantation produce both vacancies and “interstitials.” Appreciable densification is induced by these defects after equilibration of the defective glasses. The structural and vibrational properties of the densified glasses are characterized, displaying resembling features regardless of the means of densification. These results indicate that relaxation of high free-energy defects into metastable amorphous structures enriched in atomic coordination serves as a common mechanism for densification of silica glass at ambient pressure.
Optical properties of the interband transitions of layered gallium sulfide
Authors: Ho C. H. , Lin S. L.
Published: October 2006

Optical properties of GaS layered semiconductor have been characterized using temperature-dependent absorption and piezoreflectance (PzR) measurements in the temperature range between 15 and 300K. From the comparison of optical-absorption and PzR spectra at low temperature, the gallium sulfide layer was confirmed to be an indirect semiconductor. The band gap of GaS was determined to be 2.53±0.03eV at room temperature. PzR measurements of GaS were carried out in the energy range between 2 and 5eV. The low-temperature PzR spectrum obviously shows three doublet-excitonic structures (denoted as series A, B, and C) presented at the energies around 3, 4, and 4.5eV, respectively. The Rydberg constant and threshold energy of the excitonic series A, B, and C were determined. Transition origins of the A, B, and C series were examined. Temperature dependences of the interband transitions of the gallium sulfide are analyzed. The parameters that describe temperature variations of the transition energies of GaS are evaluated and discussed.
Third-order interactions in symmetry-adapted perturbation theory
Authors: Patkowski Konrad , Szalewicz Krzysztof , Jeziorski Bogumił
Published: October 2006

We present an extension of many-body symmetry-adapted perturbation theory (SAPT) by including all third-order polarization and exchange contributions obtained with the neglect of intramonomer correlation effects. The third-order polarization energy, which naturally decomposes into the induction, dispersion, and mixed, induction-dispersion components, is significantly quenched at short range by electron exchange effects. We propose a decomposition of the total third-order exchange energy into the exchange-induction, exchange-dispersion, and exchange-induction-dispersion contributions which provide the quenching for the corresponding individual polarization contributions. All components of the third-order energy have been expressed in terms of molecular integrals and orbital energies. The obtained formulas, valid for both dimer- and monomer-centered basis sets, have been implemented within the general closed-shell many-electron SAPT program. Test calculations for several small dimers have been performed and their results are presented. For dispersion-bound dimers, the inclusion of the third-order effects eliminates the need for a hybrid SAPT approach, involving supermolecular Hartree-Fock calculations. For dimers consisting of strongly polar monomers, the hybrid approach remains more accurate. It is shown that, due to the extent of the quenching, the third-order polarization effects should be included only together with their exchange counterparts. Furthermore, the latter have to be calculated exactly, rather than estimated by scaling the second-order values.
Characterization of hydrogen passivated defects in strain-engineered semiconductor quantum dot structures
Authors: Gurioli M. , Zamfirescu M. , Vinattieri A. , Sanguinetti S. , Grilli E. , Guzzi M. , Mazzucato S. , Polimeni A. , Capizzi M. , Seravalli L. , Frigeri P. , Franchi S.
Published: October 2006

The effects of hydrogen incorporation on carrier relaxation and recombination efficiencies in a large series of InAs self-assembled quantum dot structures deposited on InGaAs lower confining layers with different thicknesses and compositions have been addressed. With increasing H dose we observe an improvement in the radiative efficiency. By comparing steady state and time resolved photoluminescence measurements, it is established that the H passivation does not enhance the relaxation and capture efficiencies, but instead directly improves the emission yield from carriers in the dots. We therefore conclude that the H-passivated defects are located nearby, or even inside, the dots.
Absorption intensities and emission cross sections of Tb3+ (4f8) in TbAlO3
Authors: Sardar Dhiraj K. , Nash Kelly L. , Yow Raylon M. , Gruber John B. , Valiev Uygun V. , Kokanyan Edvard P.
Published: October 2006

Trivalent terbium absorption intensities in single-crystal TbAlO3 are analyzed using the Judd-Ofelt model to assess the crystal’s potential as a solid state laser system. The standard Judd-Ofelt model was applied to the room temperature absorption intensities of Tb3+ (4f8) to determine the phenomenological intensity parameters Ω2, Ω4, and Ω6. Seven multiplet manifolds are identified and the absorption intensities of these manifolds are least-squares fitted to the calculated intensities to obtain the intensity parameters: Ω2=40.52×10−20cm2, Ω4=8.74×10−20cm2, and Ω6=2.26×10−20cm2 in TbAlO3. These intensity parameters are then applied to determine the radiative decay rates and branching ratios of Tb3+ transitions from the D45 to the FJ′7 multiplet manifolds. Based on the results, the radiative lifetime of the excited state manifold D45 is determined from the radiative decay rates and found to be 3.5ms. The calculated lifetime is longer than the measured lifetime, reflecting the nonradiative interactions between the Tb3+ ions and the lattice in the pure compound. The intensity parameters, radiative lifetime, and emission cross sections are then compared to those reported in other laser hosts. The quantum efficiency of the laser transition D45→F57 of Tb3+ is approximately 57.0% in TbAlO3.
Wavelength-resolved low-frequency noise of GaInN∕GaN green light emitting diodes
Authors: Rumyantsev S. L. , Wetzel C. , Shur M. S.
Published: October 2006

Light intensity low-frequency noise was studied in green GaInN∕GaN quantum well light emitting diodes. The light intensity noise was measured as a function of wavelength within the light emitting diode spectral emission line. The spectral noise density is found to increase with decreasing wavelength. Comparing the wavelength-resolved noise with the total light noise, we found that the emission intensity fluctuates synchronously across the entire linewidth. The source of this noise can be ascribed to nonradiative recombination centers.
Valence band structure of BaCuSF and BaCuSeF
Authors: Yanagi Hiroshi , Tate Janet , Park Sangmoon , Park Cheol-Hee , Keszler Douglas A. , Hirano Masahiro , Hosono Hideo
Published: October 2006

The origin of high hole conduction in BaCuQF (Q=S,Se) was investigated by photoemission measurements and full-potential linearized augmented plane wave band-structure calculations. In both compounds, the large dispersion near the top of the valence band is realized by admixed states of Cu 3d and S 3p or Se 4p orbitals, indicating that high hole mobility is possible. In addition, the valence band maxima of BaCuQF are much closer to the vacuum level than most p-type transparent oxides, which leads to high hole stability in the valence band. The high hole mobility and stability in BaCuQF relative to most oxides afford a significantly larger p-type conductivity.
Localization of electrons in multiple layers of self-assembled GeSi∕Si islands
Authors: Yakimov A. I. , Nikiforov A. I. , Dvurechenskii A. V.
Published: October 2006

Space-charge spectroscopy was employed to study the electronic structure of single and multiple layers of GeSi islands embedded in a n-type Si(001) matrix. For a multilayer sample, the evidence for an electron localization in strained Si in the vicinity of GeSi dots was found. From the admittance measurements the electron binding energy was determined to be 40–70meV. The electron accumulation was not observed in a sample with a single layer of GeSi islands. Existence of localized electronic states is explained by a modification of the conduction band alignment induced by inhomogeneous tensile strain in Si around the buried GeSi dots.
Nonlinear evolution of resistive wall mode in a cylindrical tokamak with poloidal rotation
Authors: Sato M. , Nakajima N.
Published: October 2006

Nonlinear simulations of resistive wall modes (RWMs) with a Doppler shift dominant equilibrium poloidal rotation have been carried out by using reduced magnetohydrodynamic equations in a low beta cylindrical tokamak, where the core plasma is surrounded by a cold plasma with a high resistivity. When the equilibrium poloidal rotation frequency is small and the Doppler shift is predominant, the wall mode becomes unstable, which is one of the RWMs nearly locked to the resistive wall. Since the slowing down torque increases with equilibrium poloidal rotation frequency and the poloidal rotation decreases to almost zero near the plasma surface before the saturation, the nonlinear saturation level does not depend on either the equilibrium poloidal rotation frequency or the density of the cold plasma. When the equilibrium poloidal rotation frequency becomes larger than a critical value, the plasma mode rotating to the resistive wall becomes unstable. When the cold plasma has the same density as that in the core plasma, neither the centrifugal force nor the Coriolis force has any effect. In such a case, as the equilibrium poloidal rotation frequency increases, the magnetic flux is so hard to diffuse into the resistive wall that the slowing down torque decreases and the rotation tends to survive in the nonlinear phase, which makes the saturation level decrease.
Optimal grids for generalized finite basis and discrete variable representations: Definition and method of calculation
Authors: Szalay Viktor
Published: October 2006

The method of optimal generalized finite basis and discrete variable representations (FBR and DVR) generalizes the standard, Gaussian quadrature grid-classical orthonormal polynomial basis-based FBR/DVR method to general sets of grid points and to general, nondirect product, and/or nonpolynomial bases. Here, it is shown how an optimal set of grid points can be obtained for an optimal generalized FBR/DVR calculation with a given truncated basis. Basis set optimized and potential optimized grids are defined. The optimized grids are shown to minimize a function of grid points derived by relating the optimal generalized FBR of a Hamiltonian operator to a non-Hermitian effective Hamiltonian matrix. Locating the global minimum of this function can be reduced to finding the zeros of a function in the case of one dimensional problems and to solving a system of D nonlinear equations repeatedly in the case of D>1 dimensional problems when there is an equal number of grid points and basis functions. Gaussian quadrature grids are shown to be basis optimized grids. It is demonstrated by a numerical example that an optimal generalized FBR/DVR calculation of the eigenvalues of a Hamiltonian operator with potential optimized grids can have orders of magnitude higher accuracy than a variational calculation employing the same truncated basis. Nevertheless, for numerical integration with the optimal generalized FBR quadrature rule basis optimized grids are the best among grids of the same number of points. The notions of Gaussian quadrature and Gaussian quadrature accuracy are extended to general, multivariable basis functions.
Effect of the surface coating on the magnetic nanoparticle smectic-A liquid crystal interaction
Authors: Martínez-Miranda L. J. , McCarthy Kevin , Kurihara L. K , Harry Jason J. , Noel Alexis
Published: October 2006

The behavior of smectic-A liquid crystals with magnetic particles has not been very well characterized. The authors have studied the interaction of a smectic-A liquid crystal with magnetic nanoparticles. They concentrate on the effect of the particles’ surface coating or functionalization compound. The surface coating in a nanoparticle is used to avoid phase separation and in biological applications to identify a particular cell or protein. Thus it is important to see how the surface coating interacts with the liquid crystal in conjunction with the magnetic nanoparticles. They have found out that depending on the surface coating the interaction of the nanoparticles with the liquid crystal varies. This variation is related to how the surface coating aligns the liquid crystal, how it contributes to the relative concentration of the nanoparticles in the liquid crystal-nanoparticle mixture, and how it affects the magnetic energy of the system.
Anomalous cross field electron transport in a Hall effect thruster
Authors: Boniface C. , Garrigues L. , Hagelaar G. J. M. , Boeuf J. P. , Gawron D. , Mazouffre S.
Published: October 2006

The origin of anomalous electron transport across the magnetic field in the channel of a Hall effect thruster has been the subject of controversy, and the relative importance of electron-wall collisions and plasma turbulence on anomalous transport is not clear. From comparisons between Fabry-Pérot measurements and hybrid model calculations of the ion velocity profile in a 5kW Hall effect thruster, we deduce that one and the same mechanism is responsible for anomalous electron transport inside and outside the Hall effect thruster channel. This suggests that the previous assumption that Bohm anomalous conductivity is dominant outside the thruster channel whereas electron-wall conductivity prevails inside the channel is not valid.
Hole-particle characterization of coupled-cluster singles and doubles and related models
Authors: Luzanov A. V. , Prezhdo O. V.
Published: October 2006

The hole-particle analysis introduced in the paper [J. Chem. Phys. 124, 224109 (2006)] is fully described and extended for coupled-cluster models of practical importance. Based on operator renormalization of the conventional amplitudes tai and tab,ij, we present a simplified method for estimating the hole-particle density matrices for coupled-cluster singles and doubles (CCSD). With this procedure we convert the first-order density matrix of the configuration interaction (CI) singles and doubles (CISD) model, which lacks size consistency, into an approximately size-consistent expression. This permits us to correctly estimate specific indices for CCSD, including the hole and particle occupation numbers for each atom, the total occupation of holes/particles, and the entropylike measure for effective unpaired geminals. Our calculations for simple diatomic and triatomic systems indicate reasonable agreement with the full CI values. For CCSD and CISD we derive special types of two-center indices, which are similar to the charge transfer analysis of excited states previously given within the CIS model. These new quantities, termed charge transfer correlation indices, reveal the concealed effects of atomic influence on electronic redistribution due to electron correlation.
Theoretical analysis for superprisming effect of photonic crystals composed of magnetic material
Authors: Yang S. Y. , Chang C. T.
Published: October 2006

In this work, we analyze theoretically the frequency-dependent phase index np(ω) of a guided mode in photonic crystals from the photonic band structures. The np(ω) reveals a promising possibility for fabricating a chromatic prism using photonic crystals. We then investigate the superprisming effect of a photonic-crystal prism for both guided continuous-wave TM and TE modes. In addition to dielectric intuition, the effects of magnetic permeability of a magnetic photonic crystal on the photonic band structure, the phase index, and the superprisming effect are examined. It was found that magnetic intuition could enhance the resolution of a photonic-crystal prism for dividing TE modes of various wavelengths, but reduce the resolution for dividing TM modes.
Locating hexagonal and cubic phases in boron nitride using wavelength-selective optically detected x-ray absorption spectroscopy
Authors: Evans D. A. , Vearey-Roberts A. R. , Poolton N. R. J.
Published: October 2006

Cubic and hexagonal phases of boron nitride (c-BN and h-BN) have been identified and located using optically detected x-ray absorption spectroscopy (ODXAS). Each phase was identified by distinct resonance features in the B K-edge absorption spectra. In a mixed-phase sample of predominantly c-BN, combined ODXAS and electron yield measurements suggested near-surface localization of h-BN. Using x-ray excited luminescence, emission bands due to each phase were identified and applied in wavelength-selective ODXAS to locate surface and bulk h-BN phases. These combined techniques provide a method of correlating the local structure and optical emission in these wide-gap semiconductors.
Dephasing of Bloch oscillating electrons in GaAs-based superlattices due to interface roughness scattering
Authors: Unuma T. , Sekine N. , Hirakawa K.
Published: October 2006

We have investigated dephasing mechanisms of Bloch oscillating electrons in GaAs-based superlattices (SLs) by time-domain terahertz electro-optic sampling method. It was found that dephasing time τr for GaAs∕AlAs SLs in the Wannier-Stark regime rapidly becomes shorter with decreasing well width Lw as τr∝Lw3−5. The observed strong Lw dependence of τr indicates that the dominant dephasing mechanism is interface roughness scattering, which was indeed confirmed by quantitative comparison between theory and experiment. It was also found that alloy disorder scattering is negligibly weak even in the case of GaAs∕Al0.3Ga0.7As SLs.
Grain size reduction in CoCrPt:SiO2 perpendicular recording media with oxide-based intermediate layers
Authors: Piramanayagam S. N. , Pock C. K. , Lu L. , Ong C. Y. , Shi J. Z. , Mah C. S.
Published: October 2006

Co Cr Pt – Si O 2 perpendicular recording media containing an oxide-based intermediate layer have been studied in order to minimize the grain size in the recording layer. A RuCr alloy thin film deposited in an argon and oxygen reactive atmosphere was found to produce finer grains in the intermediate layer. When the recording layer was deposited on such an intermediate layer, the grain size of the recording layer was also observed to be smaller (about 6.4nm center-to-center distances). The results indicate that the introduction of RuCr-oxide-based intermediate layers is a possible approach to reduce the grain size in perpendicular recording media.
Electric-field control of ferromagnetism in (Ga,Mn)As
Authors: Chiba D. , Matsukura F. , Ohno H.
Published: October 2006

The authors show modulation of Curie temperature TC and coercivity μ0Hc by applying external electric fields E in a ferromagnetic semiconductor (Ga,Mn)As, where a field-effect transistor structure with an Al2O3 gate insulator is utilized. Application of E=+5(–5)MV∕cm decreases (increases) TC of the channel layer. μ0Hc also decreases (increases) with increasing (decreasing) E below TC. The mechanism of the modulation of μ0Hc by E is discussed.
Direct strain measurement in a 65nm node strained silicon transistor by convergent-beam electron diffraction
Authors: Zhang Peng , Istratov Andrei A. , Weber Eicke R. , Kisielowski Christian , He Haifeng , Nelson Chris , Spence John C. H.
Published: October 2006

Using the energy-filtered convergent-beam electron diffraction (CBED) technique in a transmission electron microscope, the authors report here a direct measurement of the lattice parameters of uniaxially strained silicon as close as 25nm below the gate in a 65nm node p-type metal-oxide-semiconductor field-effect transistor with SiGe source and drain. It is found that the dominant strain component (0.58%) is compressive along the source-drain direction. The compressive stress is 1.1GPa along this direction. These findings demonstrate that CBED can serve as a strain metrology technique for the development of strained silicon device technology.
Fiber Bragg grating microphone system
Authors: Mohanty Lipi , Koh Liang Mong , Tjin Swee Chuan
Published: October 2006

A fiber Bragg grating microphone has been developed and tested in the audible frequency range. The fiber Bragg grating is longitudinally attached to a membrane that vibrates in response to acoustic vibrations and is prestrained. The frequency and amplitude of the sound are encoded in the wavelength shift. The microphone can also pick up voices dynamically from a distance of a few meters. The simplicity of principle and structure of this fiber grating sensor provides scope for commercialization as an optical microphone.
Spatial and energetic distribution of border traps in the dual-layer HfO2∕SiO2 high-k gate stack by low-frequency capacitance-voltage measurement
Authors: Wu Wei-Hao , Tsui Bing-Yue , Chen Mao-Chieh , Hou Yong-Tian , Jin Yin , Tao Hun-Jan , Chen Shih-Chang , Liang Mong-Song
Published: October 2006

Threshold voltage instability measured by the pulse current-voltage technique has been recognized as the transient charging and discharging of the preexisting bulk traps in Hf-based high-k gate dielectrics, and these high-k traps or called border traps can instantly exchange charge carriers with the underlying Si substrate by tunneling through the thin interfacial oxide. Based on an elastic tunneling model through trapezoidal potential barriers, the spatial and energetic distribution of border traps in the HfO2∕SiO2 high-k gate stack can be profiled as a smoothed, three-dimensional mesh by measuring the low-frequency capacitance-voltage characteristics of high-k metal-oxide-semiconductor capacitors with n-type Si substrate.
Label-free DNA sequence detection using oligonucleotide functionalized optical fiber
Authors: Wang Xingwei , Cooper Kristie L. , Wang Anbo , Xu Juncheng , Wang Zhuang , Zhang Yan , Tu Zhijian
Published: October 2006

The authors present a label-free method for direct detection of deoxyribonucleic acid (DNA) sequences. The capture DNA is immobilized onto the surface of a silica optical fiber tip by means of the layer-by-layer electrostatic self-assembly technique. Hybridization of target DNA with complementary capture DNA increases the optical thickness of the fiber tip. This phenomenon can be detected by demodulation of the spectrum of a Fabry-Pérot cavity fabricated in the optical fiber. Experimental results demonstrate sequence specificity and sensitivity to nanogram quantities of target DNA sequences with short (∼5min) hybridization time.
Diffraction-aided laser-induced microstructuring of thin TiO2 films on glass
Authors: Van Overschelde O. , Wautelet M.
Published: October 2006

Thin films of TiO2 are deposited by magnetron sputtering on glass substrate and are irradiated by ultraviolet radiation using a KrF excimer laser. These thin films are patterned with a razor blade placed in the way of the radiation. When the fluence is in the 1250–1550mJ∕cm2 range, a regular structure appears, with controlled ablation of the films. It is shown that above a critical local fluence, the ablated depth varies linearly with the local fluence. The proportionality factor is shown to be equal to two photons per evaporated molecule.
Grounded Visualization: Integrating the Analysis of Qualitative and Quantitative Data through Grounded Theory and Visualization
Authors: Knigge LaDona , Cope Meghan
Published: October 2006

Our purpose in this paper is to conceptualize and demonstrate an integrated analytical method for using both qualitative and quantitative data through geographic information systems (GIS) and ethnography. We acknowledge that the use of both types of data has been possible in GIS for some time, particularly for representation purposes. However, a recursive integration of different forms of data at the analysis level has been less explored and minimally theorized. Drawing on recent work in critical GIS and feminist perspectives, we suggest that visualization offers a strong technique for this effort but we approach it from the analytical base of grounded theory. Thus, we present an example of how grounded theory and visualization might be used together to construct an integrated analysis strategy that is both iterative and reflexive, both contextual and conceptual. We use Knigge's work on community gardens in Buffalo, New York, to provide a substantive example of the proposed methods.
Property Readjustment and a Tenants' Cooperative in Mumbai: Some Lessons and Questions
Authors: Mukhija Vinit
Published: October 2006

A key virtue of urbanization is the possibility of using the market value of land to pay for its development costs. Many urban-redevelopment strategies, such as urban renewal, land readjustment, and land sharing, are based on this principle. Mumbai's tenement, or chawl, redevelopment programme is also a variation on the theme. The key promise of the programme is the resettlement of tenement residents in new, cross-subsidized housing on the original sites. The city's property readjustment strategy is ambitious, but deals with difficult contexts—contested claims by tenants and owners, potential for disagreements and conflicts, underdeveloped housing-finance institutions, reliance on real-estate values, and the risk of failure, overburdened infrastructure, and so on—and is hard to implement. Nonetheless, an advantage of the approach, and a partial explanation for the difficulties in implementation, is the ability to redistribute wealth to tenants. My normative position in this paper is that the pace of implementation should not be increased at the cost of the welfare of tenants. Although the strategy is far from being a panacea, I focus on public-policy recommendations to support redevelopment led by tenants' cooperatives, including technical assistance, conflict resolution, access to information, and housing-development finance. I illustrate and elaborate these arguments through a single redevelopment case.
Using undisturbed columns to predict long term behaviour of effluent irrigated soils under field conditions
Authors: Dawes L. , Goonetilleke A.
Published: October 2006

Soils have only a finite capacity for the removal of wastewater pollutants, and with time this capacity could decline. Not all soil types have the capacity to provide adequate treatment and dispersal of sewage effluent. For continued long-term application to be successful, it is essential that infiltration and drainage characteristics of soils do not decline. Also critical is how long-term application of nutrients and cations affects the soils and whether any leaching occurs. The research project described compares the outcomes of detailed field studies with results from an undisturbed soil column study where typical soils in the south-east region of Queensland, Australia, have been subjected to sewage effluent application over a period of 12 months. Multivariate analysis helped to classify the influential soil characteristics and to identify relative changes in each soil after the application of effluent. Identification and correlation of influential soil characteristics in field and accelerated column studies confirmed that undisturbed soil column studies can be useful in predicting long-term behaviour of effluent-irrigated soils.
A B lymphocyte mitogen is aBrucella abortusvirulence factor required for persistent infection
Authors: Spera Juan Manuel , Ugalde Juan Esteban , Mucci Juan , Comerci Diego J. , Ugalde Rodolfo Augusto
Published: October 2006

Microbial pathogens with the ability to establish chronic infections have evolved strategies to actively modulate the host immune response. Brucellosis is a disease caused by a Gram-negative intracellular pathogen that if not treated during the initial phase of the infection becomes chronic as the bacteria persist for the lifespan of the host. How this pathogen and others achieve this action is a largely unanswered question. We report here the identification of aBrucella abortusgene (prpA) directly involved in the immune modulation of the host. PrpA belongs to the proline-racemase family and elicits a B lymphocyte polyclonal activation that depends on the integrity of its proline-racemase catalytic site. Stimulation of splenocytes with PrpA also results in IL-10 secretion. Construction of aB. abortus-prpAmutant allowed us to assess the contribution of PrpA to the infection process. Mice infected withB. abortusinduced an early and transient nonresponsive status of splenocytes to bothEscherichia coliLPS and ConA. This phenomenon was not observed when mice were infected with aB. abortus-prpAmutant. Moreover, theB. abortus-prpAmutant had a reduced capacity to establish a chronic infection in mice. We propose that an early and transient nonresponsive immune condition of the host mediated by this B cell polyclonal activator is required for establishing a successful chronic infection byBrucella.
A genetic variant that disrupts
MET
transcription is associated with autism
Authors: Campbell Daniel B. , Sutcliffe James S. , Ebert Philip J. , Militerni Roberto , Bravaccio Carmela , Trillo Simona , Elia Maurizio , Schneider Cindy , Melmed Raun , Sacco Roberto , Persico Antonio M. , Levitt Pat
Published: October 2006

There is strong evidence for a genetic predisposition to autism and an intense interest in discovering heritable risk factors that disrupt gene function. Based on neurobiological findings and location within a chromosome 7q31 autism candidate gene region, we analyzed the gene encoding the pleiotropic MET receptor tyrosine kinase in a family based study of autism including 1,231 cases. MET signaling participates in neocortical and cerebellar growth and maturation, immune function, and gastrointestinal repair, consistent with reported medical complications in some children with autism. Here, we show genetic association (
P
= 0.0005) of a common C allele in the promoter region of the
MET
gene in 204 autism families. The allelic association at this
MET
variant was confirmed in a replication sample of 539 autism families (
P
= 0.001) and in the combined sample (
P
= 0.000005). Multiplex families, in which more than one child has autism, exhibited the strongest allelic association (
P
= 0.000007). In case-control analyses, the autism diagnosis relative risk was 2.27 (95% confidence interval: 1.41–3.65;
P
= 0.0006) for the CC genotype and 1.67 (95% confidence interval: 1.11–2.49;
P
= 0.012) for the CG genotype compared with the GG genotype. Functional assays showed that the C allele results in a 2-fold decrease in
MET
promoter activity and altered binding of specific transcription factor complexes. These data implicate reduced
MET
gene expression in autism susceptibility, providing evidence of a previously undescribed pathophysiological basis for this behaviorally and medically complex disorder.
Stability of inbred mouse strain differences in behavior and brain size between laboratories and across decades
Authors: Wahlsten Douglas , Bachmanov Alexander , Finn Deborah A. , Crabbe John C.
Published: October 2006

If we conduct the same experiment in two laboratories or repeat a classical study many years later, will we obtain the same results? Recent research with mice in neural and behavioral genetics yielded different results in different laboratories for certain phenotypes, and these findings suggested to some researchers that behavior may be too unstable for fine-scale genetic analysis. Here we expand the range of data on this question to additional laboratories and phenotypes, and, for the first time in this field, we formally compare recent data with experiments conducted 30–50 years ago. For ethanol preference and locomotor activity, strain differences have been highly stable over a period of 40–50 years, and most strain correlations are in the range of
r
= 0.85–0.98, as high as or higher than for brain weight. For anxiety-related behavior on the elevated plus maze, on the other hand, strain means often differ dramatically across laboratories or even when the same laboratory is moved to another site within a university. When a wide range of phenotypes is considered, no inbred strain appears to be exceptionally stable or labile across laboratories in any general sense, and there is no tendency to observe higher correlations among studies done more recently. Phenotypic drift over decades for most of the behaviors examined appears to be minimal.
Establishment of a Nipah virus rescue system
Authors: Yoneda Misako , Guillaume Vanessa , Ikeda Fusako , Sakuma Yuki , Sato Hiroki , Wild T. Fabian , Kai Chieko
Published: October 2006

Nipah virus (NiV), a paramyxovirus, was first discovered in Malaysia in 1998 in an outbreak of infection in pigs and humans and incurred a high fatality rate in humans. Fruit bats, living in vast areas extending from India to the western Pacific, were identified as the natural reservoir of the virus. However, the mechanisms that resulted in severe pathogenicity in humans (up to 70% mortality) and that enabled crossing the species barrier were not known. In this study, we established a system that enabled the rescue of replicating NiVs from a cloned DNA by cotransfection of a constructed full-length cDNA clone and supporting plasmids coding virus nucleoprotein, phosphoprotein, and polymerase with the infection of the recombinant vaccinia virus, MVAGKT7, expressing T7 RNA polymerase. The rescued NiV (rNiV), by using the newly developed reverse genetics system, showed properties
in vitro
that were similar to the parent virus and retained the severe pathogenicity in a previously established animal model by experimental infection. A recombinant NiV was also developed, expressing enhanced green fluorescent protein (rNiV-EGFP). Using the virus, permissibility of NiV was compared with the presence of a known cellular receptor, ephrin B2, in a number of cell lines of different origins. Interestingly, two cell lines expressing ephrin B2 were not susceptible for rNiV-EGFP, indicating that additional factors are clearly required for full NiV replication. The reverse genetics for NiV will provide a powerful tool for the analysis of the molecular mechanisms of pathogenicity and cross-species infection.
Reaction mechanism of guanidinoacetate methyltransferase, concerted or step-wise
Authors: Zhang Xiaodong , Bruice Thomas C.
Published: October 2006

We describe a quantum mechanics/molecular mechanics investigation of the guanidinoacetate methyltransferase catalyzed reaction, which shows that proton transfer from guanidinoacetate (GAA) to Asp-134 and methyl transfer from
S
-adenosyl-
l
-methionine (AdoMet) to GAA are concerted. By self-consistent-charge density functional tight binding/molecular mechanics, the bond lengths in the concerted mechanism's transition state are 1.26 Å for both the OD1 (Asp-134)–H
E
(GAA) and H
E
(GAA)–N
E
(GAA) bonds, and 2.47 and 2.03 Å for the S8 (AdoMet)–C9 (AdoMet) and C9 (AdoMet)–N
E
(GAA) bonds, respectively. The potential-energy barrier (ΔE
‡
) determined by single-point B3LYP/6–31+G*//MM is 18.9 kcal/mol. The contributions of the entropy (−TΔS
‡
) and zero-point energy corrections Δ(ZPE)
‡
by normal mode analysis are 2.3 kcal/mol and −1.7 kcal/mol, respectively. Thus, the activation enthalpy of this concerted mechanism is predicted to be ΔH
‡
= ΔE
‡
+ Δ(ZPE)
‡
= 17.2 kcal/mol. The calculated free-energy barrier for the concerted mechanism is ΔG
‡
= 19.5 kcal/mol, which is in excellent agreement with the value of 19.0 kcal/mol calculated from the experimental rate constant (3.8 ± 0.2·min
−1
).
Structure of phosphorylated enzyme I, the phosphoenolpyruvate:sugar phosphotransferase system sugar translocation signal protein
Authors: Teplyakov Alexey , Lim Kap , Zhu Peng-Peng , Kapadia Geeta , Chen Celia C. H. , Schwartz Jennifer , Howard Andrew , Reddy Prasad T. , Peterkofsky Alan , Herzberg Osnat
Published: October 2006

Bacterial transport of many sugars, coupled to their phosphorylation, is carried out by the phosphoenolpyruvate (PEP):sugar phosphotransferase system and involves five phosphoryl group transfer reactions. Sugar translocation initiates with the Mg
2+
-dependent phosphorylation of enzyme I (EI) by PEP. Crystals of
Escherichia coli
EI were obtained by mixing the protein with Mg
2+
and PEP, followed by oxalate, an EI inhibitor. The crystal structure reveals a dimeric protein where each subunit comprises three domains: a domain that binds the partner PEP:sugar phosphotransferase system protein, HPr; a domain that carries the phosphorylated histidine residue, His-189; and a PEP-binding domain. The PEP-binding site is occupied by Mg
2+
and oxalate, and the phosphorylated His-189 is in-line for phosphotransfer to/from the ligand. Thus, the structure represents an enzyme intermediate just after phosphotransfer from PEP and before a conformational transition that brings His-189∼P in proximity to the phosphoryl group acceptor, His-15 of HPr. A model of this conformational transition is proposed whereby swiveling around an α-helical linker disengages the His domain from the PEP-binding domain. Assuming that HPr binds to the HPr-binding domain as observed by NMR spectroscopy of an EI fragment, a rotation around two linker segments orients the His domain relative to the HPr-binding domain so that His-189∼P and His-15 are appropriately stationed for an in-line phosphotransfer reaction.
Ancient polymorphism and functional variation in the primate MHC-DQA15′ cis-regulatory region
Authors: Loisel Dagan A. , Rockman Matthew V. , Wray Gregory A. , Altmann Jeanne , Alberts Susan C.
Published: October 2006

Precise regulation of MHC gene expression is critical to vertebrate immune surveillance and response. Polymorphisms in the 5′ proximal promoter region of the human class II geneHLA-DQA1have been shown to influence its transcriptional regulation and may contribute to the pathogenesis of autoimmune diseases. We investigated the evolutionary history of this cis-regulatory region by sequencing theDQA15′ proximal promoter region in eight nonhuman primate species. We observed unexpectedly high levels of sequence variation and multiple strong signatures of balancing selection in this region. Specifically, the considerableDQA1promoter region diversity was characterized by abundant shared (or trans-species) polymorphism and a pronounced lack of fixed differences between species. The majority of transcription factor binding sites in theDQA1promoter region were polymorphic within species, and these binding site polymorphisms were commonly shared among multiple species despite evidence for negative selection eliminating a significant fraction of binding site mutations. We assessed the functional consequences of intraspecific promoter region diversity using a cell line-based reporter assay and detected significant differences among baboonDQA1promoter haplotypes in their ability to drive transcriptionin vitro. The functional differentiation of baboon promoter haplotypes, together with the significant deviations from neutral sequence evolution, suggests a role for balancing selection in the evolution ofDQA1transcriptional regulation in primates.
Innovation and Corporate Failure: Cyril Lord in U.K. Textiles, 1945–1968
Authors: Ollerenshaw Philip
Published: October 2006

This article is a response to Patrick Fridenson’s call for more research into the life cycle of enterprises and especially into business failure. Its subject is the textile group established in 1945 by Cyril Lord, which went on to encompass merchanting, manufacturing, retailing, and finance, operating in the United Kingdom, the United States, and South Africa. Using unpublished records as well as the financial and trade press, the article explains the nature of Lord’s financial, mercantile, and manufacturing networks, and his rapid growth, based on product innovation, novel sales techniques, and massive advertising. The article then examines his subsequent insolvency and receivership in 1968. It contributes to our understanding of corporate failure and the role of the receiver, financial institutions, and government in that process.
Jog my shape memory: dynamics as a challenge in mathematical materials science
Authors: Zimmer Johannes
Published: October 2006

Many complex phenomena in nature exhibit multiple scales. The challenge is to understand how the effects on one scale influence those on another. This review discusses some aspects of a multiscale analysis of martensitic materials as a prominent example of materials that exhibit nuanced structures and surprising implications on various scales. The emphasis is on dynamic issues. Some speculations are offered on future research directions.
ESPERR: Learning strong and weak signals in genomic sequence alignments to identify functional elements
Authors: Taylor James , Tyekucheva Svitlana , King David C. , Hardison Ross C. , Miller Webb , Chiaromonte Francesca
Published: October 2006

Genomic sequence signals—such as base composition, presence of particular motifs, or evolutionary constraint—have been used effectively to identify functional elements. However, approaches based only on specific signals known to correlate with function can be quite limiting. When training data are available, application of computational learning algorithms to multispecies alignments has the potential to capture broader and more informative sequence and evolutionary patterns that better characterize a class of elements. However, effective exploitation of patterns in multispecies alignments is impeded by the vast number of possible alignment columns and by a limited understanding of which particular strings of columns may characterize a given class. We have developed a computational method, called ESPERR (evolutionary and sequence pattern extraction through reduced representations), which uses training examples to learn encodings of multispecies alignments into reduced forms tailored for the prediction of chosen classes of functional elements. ESPERR produces a greatly improved Regulatory Potential score, which can discriminate regulatory regions from neutral sites with excellent accuracy (∼94%). This score captures strong signals (GC content and conservation), as well as subtler signals (with small contributions from many different alignment patterns) that characterize the regulatory elements in our training set. ESPERR is also effective for predicting other classes of functional elements, as we show for DNaseI hypersensitive sites and highly conserved regions with developmental enhancer activity. Our software, training data, and genome-wide predictions are available from our Web site (http://www.bx.psu.edu/projects/esperr).