bluuebunny/crossref_metadata_2025 huggingface dataset:
On the encapsulation of nickel clusters by molecular nitrogen
Authors: Nigra Pablo , Freeman David L. , Sabo Dubravko , Doll J. D.
Published: June 2004

The structures and energetic effects of molecular nitrogen adsorbates on nickel clusters are investigated using an extended Hückel model coupled with two models of the adsorbate–nickel interaction. The potential parameters for the adsorbates are chosen to mimic experimental information about the binding strength of nitrogen on both cluster and bulk surface phases of nickel. The first model potential is a simple Lennard-Jones interaction that leads to binding sites in holes defined by sets of near-neighbor nickel atoms. The second model potential has a simple three-body form that forces the model nitrogen adsorbates to bind directly to single nickel atoms. Significant rearrangement of the core nickel structures are found in both models. A disconnectivity graph analysis of the potential energy surfaces implies that the rearrangements arise from low transition state barriers and the small differences between available isomers in the nickel core.
Transmission coefficient calculation for proton transfer in triosephosphate isomerase based on the reaction path potential method
Authors: Wang Mingliang , Lu Zhenyu , Yang Weitao
Published: June 2004

A global potential energy surface has been constructed through interpolation of our recently developed reaction path potential for chemical reactions in enzymes which is derived from combined ab initio quantum mechanical and molecular mechanical calculations. It has been implemented for the activated molecular dynamics simulations of the initial proton transfer reaction catalyzed by triosephosphate isomerase. To examine the dynamical effects on the rate constants of the enzymatic reaction, the classical transmission coefficient κ(t) is evaluated to be 0.47 with the reactive flux approach, demonstrating considerable deviations from transition state theory. In addition, the fluctuations of protein environments have small effects on the barrier recrossing, and the transmission coefficient κ(t) strongly depends on the fluctuations of atoms near the active site of the enzyme.
Effect of adsorbates on field-electron emission from ZnO nanoneedle arrays
Authors: Zhang H. Z. , Wang R. M. , Zhu Y. W.
Published: June 2004

We studied the influence of adsorbates on field emission (FE) properties of well-aligned ZnO nanoneedle arrays with varying initial electric field, vacuum gap, and ambient pressure. The FE current exhibits hysteresis upon a loop of applied voltage. On applying an initial electric field of 3.85×106 V/m, the turn-on voltage increases ∼50%, Fowler-Nordheim plots show better linearity, as well as the hysteretic behavior can be annihilated. It is found that the FE current depends on the vacuum gap and the ambient pressure. The FE current increased sensitively with increasing the ambient pressure P when P<∼7×10−5 Pa, and it saturates in the pressure range of 7×10−5–3×10−4 Pa above which the FE current drops. The phenomena can be explained by the adsorbate effects. The adsorbate states modify the effective work function of the samples, and two emission regimes, adsorption-controlled and desorption-controlled processes, were proposed. Our results are useful for practical applications as the I–V characteristics can be affected by environmental parameters, especially the ambient pressure.
Microwave attenuation properties of W-type barium ferrite BaZn2−xCoxFe16O27 composites
Authors: Li Z. W. , Chen Linfeng , Wu Yuping , Ong C. K.
Published: June 2004

The complex permeability and permittivity, the relationship between dynamic and static properties, and attenuation properties have been studied for BaZn2−xCoxFe16O27 composites with x=0.7–2.0. The results show that the resonance frequency fR is controlled by the out-of-plane anisotropy field Hθ, and the static permeability μ0′ is related to the in-plane anisotropy field Hφ. For appropriate resonance frequency and high complex permeability, the percentage bandwidths of ΔW=Δf/f0>90% for attenuation of 10 dB or more can be achieved by composites with x=0.7 and 1.0. Therefore, W-type barium ferrites with easy c-plane anisotropy are good candidates for electromagnetic materials with low reflectivity over broad frequency range at microwaves.
Extra electron in (H2O)24− cluster isomers: A theoretical study
Authors: Khan Arshad
Published: June 2004

The isomers of (H2O)24− tetrakaidecahedral cluster are studied by applying the Becke-3-parameter density functional theory and Lee–Yang–Parr correlation functional (B3LYP) and 6-311++G** basis set. Three isomers are selected on the basis of stabilization energy values. The vertical electron dissociation energies (VDE) of these isomers are 1.353, 0.404, and 0.258 eV, respectively. The experimental VDE value of 1.31 eV [J. Chem. Phys. 92, 3980 (1990)] for this cluster size is in excellent agreement with that calculated for isomer 1, suggesting the dominance of this isomer in the experiment. Four water molecules in this isomer share most of the −1 charge. These four water molecules have non-H-bonding H (NHB H) atoms turned toward the cavity, and the inward turned H atoms exhibit a significant lowering of O–H stretch frequency compared to that of a monomer. Isomers 2 and 3 have all 12 NHB H atoms projected outward and have the −1 charge distributed among 7–8 water molecules on the cluster surface.
High resolution infrared spectra of a carbon dioxide molecule solvated with helium atoms
Authors: Tang Jian , McKellar A. R. W.
Published: June 2004

Infrared spectra of HeN–CO2 clusters with N up to about 20 have been studied in the region of the CO2 ν3 fundamental band (∼2350 cm−1) using a tunable diode laser spectrometer and pulsed supersonic jet source with cooled (>−150 °C) pinhole or slit nozzles and high backing pressures (<40 atm). Compared to previous studies of HeN–OCS and –N2O clusters, the higher symmetry of CO2 results in simpler spectra but less information content. Discrete rotation–vibration transitions have been assigned for N=3–17, and their analysis yields the variation of the vibrational band origin and B rotational constant over this size range. The band origin variation is similar to HeN–OCS, with an initial blueshift up to N=5, followed by a monotonic redshift, consistent with a model where the first five He atoms fill a ring around the equator of the molecule, forcing subsequent He atom density to locate closer to the ends. The B value initially drops as expected for a normal molecule, reaching a minimum for N=5. Its subsequent rise for N=6 to 11 can be interpreted as the transition from a normal (though floppy) molecule to a quantum solvation regime, where the CO2 molecule starts to rotate separately from the He atoms. For N>13, the B value becomes approximately constant with a value about 17% larger than that measured in much larger helium nanodroplets.
Metal-to-nonmetal transition in copper nanoshells grown on copper oxide nanoparticles
Authors: Chatterjee K. , Satpati B. , Satyam P. V. , Chakravorty D.
Published: June 2004

Copper oxide nanoparticles of median diameter 17 nm were synthesized by a chemical method. By subjecting these to a reduction treatment at 373 K for a duration extending to 1 h copper shells of thicknesses in the range 2–6.5 nm were grown. Optical absorption measurements were carried out on these core-shell structured nanosystems in the temperature range 274–343 K. Analyses of the data show that below a shell thickness of 3 nm the copper shell conductivity has a value below the Mott’s minimum metallic conductivity and shows a semiconducting behavior. Electrical conductivity measurements on pellets of the nanostructured powders show a resistivity variation at low temperatures with activation energies in satisfactory agreement with those obtained from the optical studies.
Low-temperature growth of ZnO nanostructure networks
Authors: Zhang B. P. , Wakatsuki K. , Binh N. T. , Segawa Y. , Usami N.
Published: June 2004

Networks consisting of one-dimensional ZnO nanowires and two-dimensional ZnO nanowalls were synthesized using a catalyst-free low-temperature approach. The size of the nanostructure was much smaller than that obtained by the previous catalyst-assisted method. The nanostructures exhibited stable excitonic states at room temperature, and emission due to exciton-exciton scattering was observed.
Explicit expressions for the dynamic polarization behavior in ferroelectrics with symmetric/asymmetric electrical conductivity
Authors: Wong C. K. , Tsang C. H. , Shin F. G.
Published: June 2004

We model the dynamic polarization behavior of ferroelectric films by an analytical approach. Using a parallelogramlike P-E hysteresis model, explicit expressions were obtained for describing the D-E loops of ferroelectric films as would be measured from a Sawyer-Tower circuit. By introducing the consideration of electrical conduction, resistive losses inflate the ferroelectric loop to some extent. In addition, an asymmetric conduction will result in polarization offsets with the magnitude and direction depending on the asymmetric conductivities of the materials. The inflated loop, as well as the offset phenomena, which have been observed experimentally [e.g., L. Zheng, C. Lin, W.-P. Xu, and M. Okuyama, J. Appl. Phys. 79, 8634 (1996)], will be discussed by means of our modeled results. Some simple exact formulas have been derived and the effects of electric, dielectric, and ferroelectric parameters, as well as the applied field on the “apparent” polarization were also examined.
Tunable normal incidence Ge quantum dot midinfrared detectors
Authors: Tong Song , Liu Fei , Khitun A. , Wang K. L. , Liu J. L.
Published: June 2004

Midinfrared photodetectors in the 3–5 μm region were demonstrated by using molecular beam epitaxy grown self-assembled Ge quantum dots at normal incidence. The structure was a p-i-p with p-type doped Ge dots embedded in the intrinsic layer sandwiched in the two heavily p-doped regions. The dark current density at 77 K is 6.4 mA/cm2 at 1 V. The as-grown sample has a response at normal incidence in the wavelength range of 2.2 to 3.2 μm and peaked at 2.7 μm. Thermal annealing at 900 °C for 10 min shifted the peak response to 3.6 μm. Annealing effect was simulated with the interdiffusion behavior of Ge and Si atoms to explain the shift of the response wavelength.
Micropipes and the closure of axial screw dislocation cores in silicon carbide crystals
Authors: Vetter William M. , Dudley Michael
Published: June 2004

Micropipes in 6H, 4H, and 15R-SiC semiconductor wafers were studied by scanning electron microscopy (SEM) and atomic force microscopy (AFM). The screw dislocations intersecting wafers surface were located by etch pitting, and their Burgers vectors determined by x-ray topography. The etch pits were eroded into smooth craters by ion milling to expose levels of dislocation line from inside the samples bulk, so that the micropipes diameters were removed from the influence of prior surface treatments and surface relaxation effects. The bases of these craters were examined by SEM and AFM to determine whether hollow dislocation cores (micropipes) were present. In the case of 6H-SiC, hollow cores were never observed at the base of the craters whose screw dislocations had Burgers vectors of magnitude two multiples of the c-lattice parameter or less. In the 4H polytype, most 3c screw dislocations displayed hollow cores, but one was observed that did not. All axial screw dislocations in 15R-SiC crystals, because of this polytypes larger c-lattice parameter, had hollow cores.
Thickness independence of true phase transition temperatures in barium strontium titanate films
Authors: Lookman A. , Bowman R. M. , Gregg J. M. , Kut J. , Rios S. , Dawber M. , Ruediger A. , Scott J. F.
Published: June 2004

The functional properties of two types of barium strontium titanate (BST) thin film capacitor structures were studied: one set of structures was made using pulsed-laser deposition (PLD) and the other using chemical solution deposition. While initial observations on PLD films looking at the behavior of Tm (the temperature at which the maximum dielectric constant was observed) and Tc* (from Curie-Weiss analysis) suggested that the paraelectric-ferroelectric phase transition was progressively depressed in temperature as BST film thickness was reduced, further work suggested that this was not the case. Rather, it appears that the temperatures at which phase transitions occur in the thin films are independent of film thickness. Further, the fact that in many cases three transitions are observable, suggests that the sequence of symmetry transitions that occur in the thin films are the same as in bulk single crystals. This new observation could have implications for the validity of the theoretically produced thin film phase diagrams derived by Pertsev et al. [Phys. Rev. Lett. 80, 1988 (1998)] and extended by Ban and Alpay [J. Appl. Phys. 91, 9288 (2002)]. In addition, the fact that Tm measured for virgin films does not correlate well with the inherent phase transition behavior, suggests that the use of Tm alone to infer information about the thermodynamics of thin film capacitor behavior, may not be sufficient.
High quality heteroepitaxial AlN films on diamond
Authors: Vogg G. , Miskys C. R. , Garrido J. A. , Hermann M. , Eickhoff M. , Stutzmann M.
Published: June 2004

Heteroepitaxial AlN films grown on (100)- and (111)-oriented diamond (Cα) substrates by plasma-induced molecular beam epitaxy have been investigated by x-ray diffraction (XRD) and atomic force microscopy (AFM). High quality epitaxial growth of almost strain-free wurtzite AlN is observed for both orientations. For the AlN/Cα(111) heterostructures, the epitaxial orientation relationship (0001)[101̄0] AlN∥(111)[011̄] Cα is obtained. However, a significant fraction of up to 20% of the epitaxial layer is oriented differently with (101̄1) AlN∥(111) Cα. In case of AlN on Cα(100), a double-domain structure with either (0001)[101̄0] AlNI∥(100)[011] Cα or (0001)[1̄21̄0] AlNII∥(100)[011] Cα is found. The linewidths of the XRD ω and 2θ/ω scans of the symmetric AlN 002 reflection have been determined as 1.4 and 0.17° for AlN/Cα(100), 0.55° and 0.11° for AlN/Cα(111), as well as 0.51 and 0.05° for an AlN/sapphire (0001) reference sample grown under similar conditions. Thus, the crystal quality of AlN on Cα(111) is close to that of AlN on sapphire. The corresponding AlN rms roughness values found by AFM are 1.9 nm on Cα(100), 1.7 nm on Cα(111), and 3.2 nm on sapphire (0001), respectively.
Alignment of liquid crystal on a polyimide surface exposed to an Ar ion beam
Authors: Gwag Jin Seog , Jhun Chul Gyu , Kim Jae Chang , Yoon Tae-Hoon , Lee Gi-Dong , Cho Seong Jin
Published: June 2004

In this paper properties of nematic liquid crystals aligned on polyimide surfaces exposed to a low-energy Ar ion beam are investigated. We studied how the pretilt angle of a liquid crystal cell is affected by ion-beam conditions, such as the energy of the incident ions, the angle of incidence, and the exposure time. X-ray photoelectron spectroscopy data indicate that ion-beam exposure changes the chemical bonding states of the polyimide surface, which may be one of the main causes of anisotropic liquid crystal alignment. We also found that twisted-nematic cells fabricated by the ion-beam alignment method have the voltage holding time enough for application to thin-film-transistor liquid crystal displays.
Epitaxial growth of the Heusler alloy Co2Cr1−xFexAl
Authors: Kelekar R. , Clemens B. M.
Published: June 2004

We report a method for the growth of single-phase epitaxial thin films of compounds from the family of Heusler alloys Co2Cr1−xFexAl. Elemental targets were dc magnetron sputtered in 1.5 mtorr Ar gas onto MgO substrates held at 500 °C at a total growth rate of ≈0.8 Å/s. As the Fe content increases, the structural quality improves, the level of chemical ordering increases, and the slope of the resistivity versus temperature, dρ/dt, above 50 K changes from negative to positive. An extraordinary Hall resistivity exceeding 1×10−8 Ω m is observed in the Cr-containing alloys at low temperature and room temperature. Preliminary work on the incorporation of a single quaternary alloy into spin valves shows maximum giant magnetoresistances ranging from 4% at 15 K to 2% at room temperature.
Growth and physical properties of epitaxial HfN layers on MgO(001)
Authors: Seo H.-S. , Lee T.-Y. , Wen J. G. , Petrov I. , Greene J. E. , Gall D.
Published: June 2004

Stoichiometric HfN layers, with N/Hf=1.0±0.03, were grown on MgO(001) substrates at 650 °C by ultrahigh-vacuum magnetically unbalanced magnetron sputter deposition in mixed N2/Ar discharges at 20 mTorr (2.67 Pa). High-resolution x-ray diffraction ω-2θ and azimuthal φ scans combined with cross-sectional transmission electron microscopy establish that HfN grows epitaxially with a cube-on-cube orientational relationship to the substrate: (001)HfN∥(001)MgO and [100]HfN∥[100]MgO. The layers are fully relaxed at the growth temperature and have a room-temperature bulk lattice constant of 0.4524 nm. Electronic transport measurements show that HfN is metallic with a room-temperature resistivity of 14.2 μΩ cm, an n-type carrier concentration of 4.8×1021 cm−3, and an electron mobility of 86 cm2 V−1 s−1. The resistivity ρ remains constant at 3.5 μΩ cm, limited by defect scattering, between 10 and 50 K, while at higher temperatures ρ increases linearly and is limited primarily by phonon scattering. HfN(001) is also superconducting with a critical temperature of 9.18 K. The hardness and elastic modulus of HfN(001) were determined from nanoindentation measurements to be 25.2±0.7 and 450±9 GPa, respectively.
Low-temperature photoluminescence of hydrogen Ion and plasma implanted silicon and porous silicon
Authors: An Zhenghua , Fu Ricky K. Y. , Li Weili , Chen Peng , Chu Paul K. , Li K. F. , Luo L. , Tam H. L. , Cheah K. W. , Lin Chenglu
Published: June 2004

Low-temperature photoluminescence in the infrared region of hydrogen implanted single crystalline silicon is investigated. Both beam-line ion implantation and plasma immersion ion implantation (PIII) are used. The beam-line implanted samples show a broad photoluminescence band below the band gap, whereas the PIII implanted samples show at least one more peak at 1.17 eV and a much wider photoluminescence band. The origins are investigated and the peak at 1.17 eV appears to originate from nonphonon emission enhanced by lattice disorder. Our results suggest that PIII may be a better technique than beam-line ion implantation in introducing a certain disorder into the silicon lattice to circumvent the conservation of quasimomentum and consequently enhance the light emission efficiency from the modified Si samples. Our conclusion is further supported by results from plasma implanted porous Si.
Experimental and numerical research on shock initiation of pentaerythritol tetranitrate by laser driven flyer plates
Authors: Zhuowei Gu , Chengwei Sun , Jianheng Zhao , Ning Zhang
Published: June 2004

The unconfined fine grain pentaerythritol tetranitrate explosive columns whose size of φ5×5 mm2 and density of 1.2 g/cm3 were impacted and initiated by laser driven flyers launched from substrate backed aluminum films. The flyers were driven by single pulse from a Q-switched Nd:YAG (yttrium aluminum garnet) laser. The aluminum flyer plates were 5.5 and 10 μm in thickness, and had diameters of ∼1 mm. The induced stress in samples was intense but of only nanosecond duration. The initiation threshold of the explosive under such short pressure pulse (3.8 ns) was obtained in experiments as 7.1±0.2 GPa. The whole process of initiation had been simulated successfully using one-dimensional Lagrange hydrodynamic code SSS and a forest fire burn technique had been used in the simulation. The pressure and reaction fraction of explosive during the initiation process have been obtained and the theoretical results may be 20% higher than that of experiments.
Embedding and self-organization of nanoparticles in phospholipid multilayers
Authors: Terheiden Annegret , Rellinghaus Bernd , Stappert Sonja , Acet Mehmet , Mayer Christian
Published: June 2004

Multilayers of various phospholipids on silicon substrates are used to induce spontaneous embedding of nanoparticles deposited from the gas phase. The resulting nanoparticle arrangement on the substrate surface is characterized using atomic force and scanning electron microscopy. In the intermediate phase and the liquid crystalline phase of the lipid, a monolayer is formed around individual nanoparticles which leads to an increase in interparticle distances. At the same time, the molecular mobility of the multilayers allows for self-assembly of the particles in regular two-dimensional arrangements.
Quantum-size resonance tunneling in the field emission phenomenon
Authors: Litovchenko V. , Evtukh A. , Kryuchenko Yu. , Goncharuk N. , Yilmazoglu O. , Mutamba K. , Hartnagel H. L. , Pavlidis D.
Published: June 2004

Theoretical analyses have been performed of the quantum-size (QS) resonance tunneling in the field-emission (FE) phenomenon for different models of the emitting structures. Such experimentally observed peculiarities have been considered as the enhancement of the FE current, the deviation from the Fowler-Nordheim law, the appearance of sharp current peaks, and a negative resistance. Different types of FE cathodes with QS structures (quantized layers, wires, or dots) have been studied experimentally. Resonance current peaks have been observed, from which the values of the energy-level splitting can be estimated.
Dynamic formation of columnar lattices in magnetic fluid thin films subjected to oscillating perpendicular magnetic fields
Authors: Jiang I. M. , Shih C. C. , Lu C. K. , Jang D. J. , Chiang J. C. , Tsai M. S. , Horng H. E.
Published: June 2004

The application of a low-frequency oscillating magnetic field perpendicular to a magnetic fluid thin film leads to the separation of a phase that is concentrated in particles from a dilute phase. The concentrated phase forms cylindrical columns that construct two-dimensional lattices. The ordered structure of magnetic fluid thin films is the basis for potential optical applications. We investigate the dynamical ordering formation of columnar lattices in magnetic fluid thin films subjected to oscillating perpendicular magnetic fields.
Component-Based Approach in the Development of a Knowledge-Based Planning Support System (KBPSS). Part 1: The Architecture of KBPSS
Authors: Yeh Anthony G O , Qiao Jimmy J
Published: June 2004

Urban planners need to have a flexible, interactive, and intelligent computer-based tool to support their use of analytical models and to structure their planning process. Existing spatial information systems have not developed appropriate procedures and mechanisms to enable easy construction and manipulation of models within their system environment, and to allow various information resources to be shared by different application systems and platforms. Recent research and development of planning support systems (PSS) provide a range of interesting concepts and frameworks that can be adopted by system developers to design a multifunctional and planning-specific decision support system to meet the multifaceted needs of the planning process. In this paper we aim to go beyond the current approaches of PSS and spatial decision support systems (SDSS) in designing a knowledge-based PSS (KBPSS) that uses the component-based software development (CBSD) approach. We introduce the features of CBSD and its technical advantages in the design of a multifunctional PSS. An architecture of a component-based KBPSS is subsequently proposed which incorporates four essential component systems: MapObjects GIS, Database Manager database management system, ModelObjects model-management system, and KBSAgents knowledge-based system. The first two components are based on proprietary components systems and can be easily adapted into the KBPSS environment. The ModelObjects and KBSAgents components were developed by the authors. Based on these components and their associated information layers, two application subsystems are constructed: a Model and Knowledge Development System and an Intelligent Model Selection System. These application systems can be used to assist users and model developers to build new models or to select predefined models from an existing model library for their problems. In order to implement these functions, we propose and define a number of procedures and techniques for component communication and model and knowledge development.
The Automatic Definition and Generation of Axial Lines and Axial Maps
Authors: Batty Michael , Rana Sanjay
Published: June 2004

Space syntax is a technique for measuring the relative accessibility of different locations in a spatial system which has been loosely partitioned into convex spaces. These spaces are approximated by straight lines, called axial lines, and the topological graph associated with their intersection is used to generate indices of distance, called integration, which are then used as proxies for accessibility. The most controversial problem in applying the technique involves the definition of these lines. There is no unique method for their generation; hence different users generate different sets of lines for the same application. In this paper we explore this problem, arguing that to make progress, there need to be unambiguous, agreed procedures for generating such maps. The methods we suggest for generating such lines depend on defining viewsheds, called isovists, which can be approximated by their maximum diameters, these lengths being used to form axial maps similar to those used in space syntax. We propose a generic algorithm for sorting isovists according to various measures, approximating them by their diameters and using the axial map as a summary of the extent to which isovists overlap (intersect) and are accessible to one another. We demonstrate our techniques for the small French town of Gassin used originally by Hillier and Hanson in a 1984 book to illustrate the theory, exploring different criteria for sorting isovists, and generating different axial maps by changing the level of resolution.
Functional Scalability through Generative Representations: The Evolution of Table Designs
Authors: Hornby Gregory S
Published: June 2004

One of the main limitations for the functional scalability of automated design systems is the representation used for encoding designs. I argue that generative representations, those which are capable of reusing elements of the encoded design in the translation to the actual artifact, are better suited for automated design because reuse of building blocks captures some design dependencies and improves the ability to make large changes in design space. To support this argument I compare a generative and a nongenerative representation on a table-design problem and find that designs evolved with the generative representation have higher fitness and a more regular structure. Additionally the generative representation was found to capture better the height dependency between table legs and also produced a wider range of table designs.
Space Syntax: Some Inconsistencies
Authors: Ratti Carlo
Published: June 2004

This paper reports on a number of inconsistencies that appear in space syntax—a well-known technique of urban analysis—when dealing with certain geometrical configurations. At a simple level, the analysis of regularly gridded urban textures (such as Manhattan's) reveals the difficulty of accepting the claim that space syntax allows the modelling of pedestrian choice making. In more complex cases, the distortion of two ideal textures produces a topological discontinuity, leading to the unacceptable situation where one single urban configuration produces two conflicting outcomes when analysed with space syntax tools. Several other points are also discussed, such as the difficulty of space syntax to take into account building height and land use, and its sensitivity to boundary conditions. Conclusions seem to suggest that the topological representation of cities, on which space syntax is based, discards precious metric information and is rather limiting. It is envisaged that with current increases in computational power new algorithms might allow a deeper understanding of urban texture, based on the full exploration of its metric and topological properties. This would contribute to answer the fascinating question which space syntax has helped to frame: what is the influence of urban configuration on social life?
Rejoinder to Carlo Ratti
Authors: Hillier Bill , Penn Alan
Published: June 2004

In this rejoinder, we answer questions about space syntax raised in Carlo Ratti's paper “Urban texture and space syntax: some inconsistencies”, and discuss theoretical assumptions underlying some of his criticisms.
Rejoinder to Hillier and Penn
Authors: Ratti Carlo
Published: June 2004

Some questions about space syntax—a well-known technique of urban analysis developed over the past decades by Bill Hillier et al—were raised by Ratti in this journal. Hillier and Penn produced a detailed rejoinder, rebutting most of the criticisms and restating the assumptions made by the technique. However, their arguments, if accepted, lead to paradoxical consequences.
The Impact of Surrounding Land Use and Vegetation on Single-Family House Prices
Authors: Kestens Yan , Thériault Marius , Des Rosiers François
Published: June 2004

The aim of this paper is to assess the marginal effect of land-use locational externalities on the sale price of single-family houses, considering various spatial scales—in accordance with perception theories—and trade-off with accessibility to the city centre. From land-use and vegetation data derived from aerial photographs and Landsat TM satellite images, two sets of hedonic models, using OLS regression, are built from two samples of single-family properties sold in Quebec City. A standard model integrates property-specific factors, census factors, accessibility, and location attributes. In a second model, land-use and vegetation variables are considered on various spatial scales; a third step introduces the interaction effect of the surrounding land use with location, with car-time distance to the main activity centres being used as the main indicator. This allows for an analysis of the spatial variation of the environmental impact throughout the city considering relative proximity to the centre. The successful integration of environmental variables concerning location enhances our understanding of the local land-use and vegetation effects. It also improves the overall performance of the model while virtually removing spatial autocorrelation among residuals. Such models could be used in order to assess the fiscal impacts of various land zoning by law policies, thereby providing planning administrations with a useful decisionmaking tool.
Toward a Cognitive Approach to Urban Dynamics
Authors: Portugali Juval
Published: June 2004

‘A cognitive approach to urban dynamics’ is proposed in this paper as a theorization of the dynamics of cities from the first principles of humans' cognitive capabilities. The aim is to initiate a discussion concerning the potential of such an approach. This is done by examining some of the cognitive processes that are relevant to cities and their dynamics, by considering some conceptual and methodological obstacles for such a project, and by suggesting SIRN (Synergetic Inter-Representation Networks) as an approach that can overcome these obstacles. I then discuss and exemplify the implications to urban simulation models and conclude by suggesting further research directions.
Comparative impacts of two major hurricane seasons on the Neuse River and western Pamlico Sound ecosystems
Authors: Burkholder JoAnn , Eggleston David , Glasgow Howard , Brownie Cavell , Reed Robert , Janowitz Gerald , Posey Martin , Melia Greg , Kinder Carol , Corbett Reide , Toms David , Alphin Troy , Deamer Nora , Springer Jeffrey
Published: June 2004

Ecosystem-level impacts of two hurricane seasons were compared several years after the storms in the largest lagoonal estuary in the U.S., the Albemarle–Pamlico Estuarine System. A segmented linear regression flow model was developed to compare mass-water transport and nutrient loadings to a major artery, the Neuse River Estuary (NRE), and to estimate mean annual versus storm-related volume delivery to the NRE and Pamlico Sound. Significantly less water volume was delivered by Hurricane Fran (1996), but massive fish kills occurred in association with severe dissolved oxygen deficits and high contaminant loadings (total nitrogen, total phosphorus, suspended solids, and fecal bacteria). The high water volume of the second hurricane season (Hurricanes Dennis, Floyd, and Irene in 1999) delivered generally comparable but more dilute contaminant loads, and no major fish kills were reported. There were no discernable long-term adverse impacts on water quality. Populations of undesirable organisms, such as toxic dinoflagellates, were displaced down-estuary to habitats less conducive for growth. The response of fisheries was species-dependent: there was no apparent impact of the hurricanes on commercial landings of bivalve molluscs or shrimp. In contrast, interacting effects of hurricane floodwaters in 1999 and intensive fishing pressure led to striking reductions in blue crabs. Overall, the data support the premise that, in shallow estuaries frequently disturbed by hurricanes, there can be relatively rapid recovery in water quality and biota, and benefit from the scouring activity of these storms.
Simulation method for calculating the entropy and free energy of peptides and proteins
Authors: Cheluvaraja Srinath , Meirovitch Hagai
Published: June 2004

A method called complete hypothetical scanning Monte Carlo has been introduced for calculating the absolute entropy,S, and free energy,F, of fluids. Here, the method is extended to peptide chains in vacuum. Thus,Sis calculated from a given sample by reconstructing each conformation step-by-step by using transition probabilities (TPs); at each step, part of the chain coordinates have already been determined (the “frozen past”), and the TP is obtained from a Monte Carlo simulation of the (future) part of the chain whose TPs as yet have not been calculated. Very accurate results forSandFare obtained for the helix, extended, and hairpin microstates of a simplified model of decaglycine (Gly)10and (Gly)16. These results agree well with results obtained by the quasiharmonic approximation and the local states method. The complete HSMC method can be applied to a macromolecule with any degree of flexibility, ranging from local fluctuations to a random coil. Also, the difference in stability, ΔFmn=Fm-Fnbetween significantly different microstatesmandncan be obtained from two simulations only without the need to resort to thermodynamic integration. Our long-term goal is to extend this method to any peptide and apply it to a peptide immersed in a box with explicit water.
Essential auditory contrast-sharpening is preneuronal
Authors: Stoop R. , Kern A.
Published: June 2004

Contrast-sharpening is a fundamental feature of mammalian sensory perception. Whereas visual contrast-sharpening has been fully understood in terms of the retinal neuronal wiring [DeVries, S. H. & Baylor, D. A. (1993)Cell72, Suppl., 139–149], a corresponding explanation of auditory contrast-sharpening is still lacking. Here, we show that the essentials of auditory contrast-sharpening can be explained by using cochlear biophysics. This finding indicates that the phenomenon is basically of preneuronal origin.
IL-7 regulates basal homeostatic proliferation of antiviral CD4
+
T cell memory
Authors: Lenz Derek C. , Kurz Sabine K. , Lemmens Edward , Schoenberger Stephen P. , Sprent Jonathan , Oldstone Michael B. A. , Homann Dirk
Published: June 2004

Heightened protection from infectious disease as conferred by vaccination or pathogen exposure relies on the effective generation and preservation of specific immunological memory. T cells are irreducibly required for the control of most viral infections, and maintenance of CD8
+
T cell memory is regulated by at least two cytokines, IL-7 and IL-15, which support survival (IL-7, IL-15) and basal homeostatic proliferation (IL-15) of specific CD8
+
memory T cells (T
M
). In contrast, the factors governing the homeostasis of pathogen-specific CD4
+
T
M
remain at present unknown. Here, we used a physiologic
in vivo
model system for viral infection to delineate homeostatic features and mechanisms of antiviral CD4
+
T
M
preservation in direct juxtaposition to CD8
+
T cell memory. Basal homeostatic proliferation is comparable between specific CD4
+
and CD8
+
T
M
and independent of immunodominant determinants and functional avidities but regulated in a tissue-specific fashion. IL-7, identified as the dominant cytokine, and IL-15, an accessory cytokine, regulate basal homeostatic proliferation and survival of antiviral CD4
+
T
M
. Interestingly, a role for these cytokines in regulation of CD4
+
T cell memory is not readily discernible in the generic “memory-phenotype” population, apparently a consequence of its heterogeneous composition. We also describe a prominent, nonredundant role for IL-7 in supporting basal homeostatic proliferation of CD8
+
T
M
. We propose that homeostatic control of antiviral CD4
+
and CD8
+
T cell memory is fundamentally similar and characterized by quantitative, rather than qualitative, differences.
Specific binding to intracellular proteins determines arterial transport properties for rapamycin and paclitaxel
Authors: Levin Andrew D. , Vukmirovic Neda , Hwang Chao-Wei , Edelman Elazer R.
Published: June 2004

Endovascular drug-eluting stents have changed the practice of medicine, and yet it is unclear how they so dramatically reduce restenosis and how to distinguish between the different formulations available. Biological drug potency is not the sole determinant of biological effect. Physicochemical drug properties also play important roles. Historically, two classes of therapeutic compounds emerged: hydrophobic drugs, which are retained within tissue and have dramatic effects, and hydrophilic drugs, which are rapidly cleared and ineffective. Researchers are now questioning whether individual properties of different drugs beyond lipid avidity can further distinguish arterial transport and distribution. In bovine internal carotid segments, tissue-loading profiles for hydrophobic paclitaxel and rapamycin are indistinguishable, reaching load steady state after 2 days. Hydrophilic dextran reaches equilibrium in several hours at levels no higher than surrounding solution concentrations. Both paclitaxel and rapamycin bind to the artery at 30–40 times bulk concentration. Competitive binding assays confirm binding to specific tissue elements. Most importantly, transmural drug distribution profiles are markedly different for the two compounds, reflecting, perhaps, different modes of binding. Rapamycin, which binds specifically to FKBP12 binding protein, distributes evenly through the artery, whereas paclitaxel, which binds specifically to microtubules, remains primarily in the subintimal space. The data demonstrate that binding of rapamycin and paclitaxel to specific intracellular proteins plays an essential role in determining arterial transport and distribution and in distinguishing one compound from another. These results offer further insight into the mechanism of local drug delivery and the specific use of existing drug-eluting stent formulations.
A plant plasma membrane Ca
2+
pump is required for normal pollen tube growth and fertilization
Authors: Schiøtt Morten , Romanowsky Shawn M. , Bækgaard Lone , Jakobsen Mia Kyed , Palmgren Michael G. , Harper Jeffrey F.
Published: June 2004

Ca
2+
signals are thought to play important roles in plant growth and development, including key aspects of pollen tube growth and fertilization. The dynamics of a Ca
2+
signal are largely controlled by influx (through channels) and efflux (through pumps and antiporters). The
Arabidopsis
genome encodes 14 Ca
2+
pumps, 10 of which belong to a family of autoinhibited Ca
2+
ATPases (ACA) that are predicted to be activated by Ca
2+
/calmodulin. Here, we show that isoform ACA9 is expressed primarily in pollen and localized to the plasma membrane. Three independent T-DNA [portion of the Ti (tumor-inducing) plasmid that is transferred to plant cells] gene disruptions of
ACA9
were found to result in partial male sterility. Complementation was observed by using a ACA9-yellow fluorescence protein (YFP) fusion that displayed plasma membrane localization. Mutant
aca9
pollen displayed a reduced growth potential and a high frequency of aborted fertilization, resulting in a >80% reduction in seed set. These findings identify a plasma membrane Ca
2+
transporter as a key regulator of pollen development and fertilization in flowering plants.
First- and second-generation total synthesis of ciguatoxin CTX3C
Authors: Inoue Masayuki , Miyazaki Keisuke , Uehara Hisatoshi , Maruyama Megumi , Hirama Masahiro
Published: June 2004

More than 20,000 people suffer annually from ciguatera seafood poisoning in subtropical and tropical regions. The extremely low content of the causative neurotoxins, designated as ciguatoxins, in fish has hampered isolation, detailed biological studies, and preparation of anti-ciguatoxin antibodies for detecting these toxins. Furthermore, the large (3 nm in length) and complex molecular structure of ciguatoxins has impeded chemists from completing their total synthesis. In this article, the full details of studies leading to the total synthesis of ciguatoxin CTX3C are provided. The key elements of the first-generation approach include
O
,
O
-acetal formation from the right and left wing fragments, conversion from
O
,
O
-acetal to
O
,
S
-acetal, a radical reaction to cyclize the G ring, a ring-closing metathesis reaction to close the F ring, and final removal of the 2-naphtylmethyl protective groups. Subsequent studies provided a second-generation total synthesis, which is more concise and results in a higher yield. Second-generation synthesis was accomplished by using a direct method of constructing the key intermediate
O
,
S
-acetal from α-chlorosulfide and a secondary alcohol. These syntheses ensure a practical supply of ciguatoxin for biological applications.
Exceptional record of mid-Pleistocene vertebrates helps differentiate climatic from anthropogenic ecosystem perturbations
Authors: Barnosky Anthony D. , Bell Christopher J. , Emslie Steven D. , Goodwin H. Thomas , Mead Jim I. , Repenning Charles A. , Scott Eric , Shabel Alan B.
Published: June 2004

Mid-Pleistocene vertebrates in North America are scarce but important for recognizing the ecological effects of climatic change in the absence of humans. We report on a uniquely rich mid-Pleistocene vertebrate sequence from Porcupine Cave, Colorado, which records at least 127 species and the earliest appearances of 30 mammals and birds. By analyzing >20,000 mammal fossils in relation to modern species and independent climatic proxies, we determined how mammal communities reacted to presumed glacial–interglacial transitions between 1,000,000 and 600,000 years ago. We conclude that climatic warming primarily affected mammals of lower trophic and size categories, in contrast to documented human impacts on higher trophic and size categories historically. Despite changes in species composition and minor changes in small-mammal species richness evident at times of climatic change, overall structural stability of mammal communities persisted >600,000 years before human impacts.
Rabies virus nucleoprotein as a carrier for foreign antigens
Authors: Koser Martin L. , McGettigan James P. , Tan Gene S. , Smith Mary Ellen , Koprowski Hilary , Dietzschold Bernhard , Schnell Matthias J.
Published: June 2004

Rabies virus (RV) nucleoprotein (N) tightly encapsidates the genomic and antigenomic RNA of RV to form the viral ribonucleoprotein (RNP) complex. Antigens, such as N, presented in a highly organized structure are sufficient and even desirable to activate B cells to proliferate and produce antibodies. In addition to activating B cells to proliferate, it has been shown that RV N in the RNP complex induces potent T helper cell responses resulting in long-lasting and strong humoral immune responses against RV. The possibility to systematically incorporate foreign genes into the genome of RV and produce a recombinant virus allows us to examine whether the immunogenicity of foreign antigens can be enhanced by incorporation into the RV RNP structure. To test this hypothesis we constructed a recombinant RV expressing a RV N-GFP fusion protein. The chimeric N-GFP fusion protein was efficiently expressed and incorporated into RV RNP and virions. Moreover, the recombinant RNP induces a strong humoral immune response against GFP in mice. In contrast, mice inoculated with GFP alone or a combination of wild-type RV RNPs and GFP did not trigger any GFP-specific humoral responses using the same immunization schedule. These data indicate the usefulness of RV-based vectors as killed vaccines against other infectious diseases.
Protein tolerance to random amino acid change
Authors: Guo Haiwei H. , Choe Juno , Loeb Lawrence A.
Published: June 2004

Mutagenesis of protein-encoding sequences occurs ubiquitously; it enables evolution, accumulates during aging, and is associated with disease. Many biotechnological methods exploit random mutations to evolve novel proteins. To quantitate protein tolerance to random change, it is vital to understand the probability that a random amino acid replacement will lead to a protein's functional inactivation. We define this probability as the “
x
factor.” Here, we develop a broadly applicable approach to calculate
x
factors and demonstrate this method using the human DNA repair enzyme 3-methyladenine DNA glycosylase (AAG). Three gene-wide mutagenesis libraries were created, each with 10
5
diversity and averaging 2.2, 4.6, and 6.2 random amino acid changes per mutant. After determining the percentage of functional mutants in each library using high-stringency selection (>19,000-fold), the
x
factor was found to be 34% ± 6%. Remarkably, reanalysis of data from studies of diverse proteins reveals similar inactivation probabilities. To delineate the nature of tolerated amino acid substitutions, we sequenced 244 surviving AAG mutants. The 920 tolerated substitutions were characterized by substitutability index and mapped onto the AAG primary, secondary, and known tertiary structures. Evolutionarily conserved residues show low substitutability indices. In AAG, β strands are on average less substitutable than α helices; and surface loops that are not involved in DNA binding are the most substitutable. Our results are relevant to such diverse topics as applied molecular evolution, the rate of introduction of deleterious alleles into genomes in evolutionary history, and organisms' tolerance of mutational burden.
Antitumor activity of a homing peptide that targets tumor lymphatics and tumor cells
Authors: Laakkonen Pirjo , Åkerman Maria E. , Biliran Hector , Yang Meng , Ferrer Fernando , Karpanen Terhi , Hoffman Robert M. , Ruoslahti Erkki
Published: June 2004

LyP-1 is a peptide selected from a phage-displayed peptide library that specifically binds to tumor and endothelial cells of tumor lymphatics in certain tumors. Fluorescein-conjugated LyP-1 and a related peptide, LyP-1b, strongly accumulated in primary MDA-MB-435 breast cancer xenografts and their metastases from i.v. peptide injections, allowing visualization of orthotopic tumors in intact mice. The LyP peptide accumulation coincided with hypoxic areas in tumors. LyP-1 induced cell death in cultured human breast carcinoma cells that bind and internalize the peptide. Melanoma cells that do not bind LyP-1 were unaffected. Systemic LyP-1 peptide treatment of mice with xenografted tumors induced with the breast cancer cells inhibited tumor growth. The treated tumors contained foci of apoptotic cells and were essentially devoid of lymphatics. These results reveal an unexpected antitumor effect by the LyP-1 peptide that seems to be dependent on a proapoptotic/cytotoxic activity of the peptide. As LyP-1 affects the poorly vascularized tumor compartment, it may complement treatments directed at tumor blood vessels.