bluuebunny/crossref_metadata_2025 huggingface dataset:
A fast multipole method combined with a reaction field for long-range electrostatics in molecular dynamics simulations: The effects of truncation on the properties of water
Authors: Mathias Gerald , Egwolf Bernhard , Nonella Marco , Tavan Paul
Published: June 2003

We present a combination of the structure adapted multipole method with a reaction field (RF) correction for the efficient evaluation of electrostatic interactions in molecular dynamics simulations under periodic boundary conditions. The algorithm switches from an explicit electrostatics evaluation to a continuum description at the maximal distance that is consistent with the minimum image convention, and, thus, avoids the use of a periodic electrostatic potential. A physically motivated switching function enables charge clusters interacting with a given charge to smoothly move into the solvent continuum by passing through the spherical dielectric boundary surrounding this charge. This transition is complete as soon as the cluster has reached the so-called truncation radius Rc. The algorithm is used to examine the dependence of thermodynamic properties and correlation functions on Rc in the three point transferable intermolecular potential water model. Our test simulations on pure liquid water used either the RF correction or a straight cutoff and values of Rc ranging from 14 Å to 40 Å. In the RF setting, the thermodynamic properties and the correlation functions show convergence for Rc increasing towards 40 Å. In the straight cutoff case no such convergence is found. Here, in particular, the dipole–dipole correlation functions become completely artificial. The RF description of the long-range electrostatics is verified by comparison with the results of a particle-mesh Ewald simulation at identical conditions.
Steady-state thermodynamics of shearing linear viscoelastic fluids
Authors: Daivis P. J. , Matin M. L.
Published: June 2003

A detailed theory of the thermodynamics of linear viscoelastic fluids in steady shear is presented. This theory is exact and gives simple and easily computed expressions for the change in the internal energy and free energy due to the imposition of steady shear for a general linear viscoelastic fluid. It has strong similarities to the extended irreversible thermodynamics approach, but differs from it in a few crucial ways. An important element of our theory is the division of the viscoelastic work into elastic and viscous parts, and the identification of these components as the reversible and irreversible parts of the work. This leads to a natural definition of reversible heat transfer that can be used in the definition of the steady-state entropy. We present the results of nonequilibrium molecular-dynamics computer simulations and evaluate the thermodynamic properties of a simple model fluid as a function of strain rate, showing how the entropy difference of the fluid between the equilibrium and shearing steady states can be computed. We find that, at low strain rates, the entropy change of a simple atomic fluid at constant temperature is positive and proportional to the square of the strain rate. A helpful geometrical interpretation of the decomposition of viscoelastic work into elastic and viscous components using a hysteresis loop construction is also discussed.
Six-dimensional ab initio potential energy surfaces for H3O+ and NH3: Approaching the subwave number accuracy for the inversion splittings
Authors: Rajamäki Timo , Miani Andrea , Halonen Lauri
Published: June 2003

New potential energy surfaces are calculated for the hydronium ion using high-order coupled cluster ab initio methods. Large basis sets are used especially for the inversion part of the full surface. Electronic energies obtained with different correlation consistent basis sets are extrapolated to the infinite basis set limit. Core-valence and first order relativistic effects are also included. The influence of these two contributions and basis set sizes on both the inversion barrier height and equilibrium geometry are investigated thoroughly. The same methods are also adopted for ammonia in order to further improve a recently published surface [J. Chem. Phys. 118, 6358 (2003)]. The vibrational eigenvalues are calculated variationally both for the symmetric and asymmetric isotopomers using exact six-dimensional kinetic energy operators and successive basis set contractions. With the new surfaces, the mean absolute deviations obtained for all experimentally observed inversion splittings for different isotopomers of H3O+ (8 states) and NH314 (17 states) are 0.78 and 0.25 cm−1, respectively. Inversion levels are calculated with almost similar accuracy. These results indicate that the calculated inversion barrier heights for H3O+ and NH3, 650 and 1792 cm−1, respectively, are close to the real values. The value for ammonia is also close to the height determined from published experimental data in our previous work. The lowest energies for the high-frequency modes are computed with the mean absolute deviation being less than 2 cm−1 for isotopomers of H3O+ and less than 4.5 cm−1 for NH314 with respect to experimental energies.
Two interacting electrons confined within a sphere: An accurate solution
Authors: Jung J. , Alvarellos J. E.
Published: June 2003

We present highly accurate configuration interaction results for two nonrelativistic electrons confined within a sphere and interacting via a Coulomb force. In such a system, the radius of the sphere R can be considered as a measure of the strenght of the electronic repulsion. So, distinct correlation regimes, from the noninteracting limit to a high correlated regime, can be achieved by varying R. The results clearly show how very high correlation effects might appear in the system. Energies, density distributions, conditional probabilities and the exchange–correlation hole have been evaluated for different values of R. The essentially exact results here presented can be used as benchmarks for new exchange–correlation functionals and/or other approximate methods.
N-representability and variational stability in natural orbital functional theory
Authors: Herbert John M. , Harriman John E.
Published: June 2003

Several “reconstructive” proposals for density matrix functional theory are investigated, each of which expresses the two-electron density matrix, and therefore the electronic energy, as a functional of the natural orbitals and their occupation numbers. It is shown that for each of these functionals, half of the parallel-spin eigenvalues of the reconstructed two-electron density matrix are necessarily negative. Illustrative all-electron calculations for Be and LiH, in a variety of Gaussian basis sets, demonstrate that these spurious negative eigenvalues lower the electronic energy substantially. In spite of this, there is no indication that the variationally optimized energy diverges as the basis set approaches completeness, as has been suggested based on calculations with a small number of active orbitals. The apparent variational instability reported previously is attributed to qualitative differences between the minimal-basis and extended-basis potential curves, for certain functionals. However, we identify one functional that yields accurate LiH potential curves—comparable to full configuration interaction results—in both minimal and extended basis sets. Explicitly antisymmetric reconstructions are recommended as a remedy for the positivity problem.
Correlation between density variation and electrical conductivity in supercritical selenium probed by small angle x-ray scattering
Authors: Coulet Marie-Vanessa , Simonet Virginie , Calzavara Yoann , Testemale Denis , Hazemann Jean-Louis , Raoux Denis , Bley Françoise , Simon Jean-Paul
Published: June 2003

Small angle x-ray scattering experiments were performed in order to investigate the semiconductor–metal and metal–nonmetal transitions that take place in supercritical fluid selenium. At the semiconductor to metal transition, we do not observe any density fluctuations indicating the homogeneity of the fluid at this scale. On the other hand, we observe the onset of density fluctuations and a sharp density variation in the pressure-temperature range of the metal–nonmetal transition. We show that the supercritical domain can be separated into two regions: a crossover takes place between a liquidlike density region and a gaslike one. The onset of density fluctuations, i.e., the development of rare and dense domains, forbids any percolation and induces the loss of the metallic character.
Suppression of multiple scattering for the critical mixture polystyrene/cyclohexane: Application of the one-beam cross correlation technique
Authors: Schröder Jörg-Michael , Becker Alfons , Wiegand Simone
Published: June 2003

Multiple scattering becomes a problem close to the critical point, especially in systems with a large difference in the refractive index and large correlation length amplitudes as for the case of polystyrene/cyclohexane. In this work we demonstrate the application of the one-beam cross correlation technique and show that in the reduced temperature range of tred=1.66×10−5–0.03 the multiple scattering is successfully suppressed. Furthermore, we measured the angular dependent static scattering intensity. By using the amplitude of the cross correlation function we obtained the correct singly scattered intensities. Those corrected intensities can be analyzed in the framework of the Ornstein–Zernike plot to obtain the correlation length ξ. The analysis of the obtained static data is in good agreement with the dynamic data. Limitations for temperature and angular dependent measurements in the Ornstein–Zernike plot close to Tc are discussed in detail.
Glycine-Zn+/Zn2+ and their hydrates: On the number of water molecules necessary to stabilize the switterionic glycine-Zn+/Zn2+ over the nonzwitterionic ones
Authors: Ai Hongqi , Bu Yuxiang , Han Keli
Published: June 2003

Several interaction modes of glycine with one Zn+ or Zn2+ and further with one and even two H2O molecules in the gas phase are studied at the hybrid three-parameter B3LYP and Hartree–Fock level, respectively. On the basis of these optimized geometries, single point calculations are performed using different theoretical methods and larger basis sets. The calculated results imply that the most stable glycine-Zn+ isomer is a five-membered ring with Zn+ bound to both amino nitrogen and carbonyl oxygen (NO) of glycine, and the next most stable glycine-Zn+ species is a four-membered ring with Zn+ coordinated at both oxygen ends (OO) of the zwitterionic glycine. The binding energy of the most stable glycine-Zn+ is 68.5 kcal/mol calibrated at the BHLYP/6-311+G*//6-311+G* level. On the contrary with glycine-Zn+ isomers, the most stable glycine-Zn2+ species holds the similar coordination mode to that of next most stable glycine-Zn2+ complex, while the next most stable glycine-Zn2+ exhibits the similar coordination mode to that of the most stable glycine-Zn+. The binding strength of these glycine-Zn2+ isomers are all far more than those of their corresponding counterparts of glycine-Zn+ isomers, such as the binding energy of the most stable glycine-Zn2+ being 234.4 kcal/mol, showing stronger electrostatic interaction. The reoptimization for the two most stable modes with the different valent states (+1,+2) to combine a H2O molecule at their each end of Zn ion show that the relative energy ordering does not change, and also resembles their no-H2O-combined counterparts. However, an interesting and important observation has been first obtained that single hydration effect can strikingly strengthen the stability of the monovalent OO form though it is still higher by 0.1 kcal/mol in energy than the NO counterpart. Hydration effect of double waters can reverse their relative stability due to the strong hydrogen bond effect in the OO form. Different from the case of the two monovalent hydrated complexes, calculated results for the divalent zinc ion chelated complexes show that with or without single hydration hardly change the value of their relative energy, and hydration strength and glycine deformation difference induced with or without hydration in the two different modes display surprising similarity. So we predict that the further hydration basically do not yield any effect on the relative stability. The prediction for the hydration effect on the glycine-Zn+/Zn2+ system would be also suitable for its analogs, such as glycine-Cu+/Cu2+ and glycine-Ni+/Ni2+ systems, and even suitable for other similar transition metal ion-chelated glycine systems.
A Monte Carlo study of shells of hydrophobically modified amphiphilic copolymer micelles in polar solvents
Authors: Uhlı́k Filip , Limpouchová Zuzana , Jelı́nek Karel , Procházka Karel
Published: June 2003

Multimolecular micelles in polar solvents formed by polystyrene-block-poly(methacrylic acid) (PS-PMA), hydrophobically modified by a naphthalene tag between blocks and an anthracene tag at the end of PMA block, are studied by a lattice Monte Carlo method. The model is parametrized according to available experimental data and several structural characteristics of the PMA shell together with the fluorometric decay functions are calculated and compared with results obtained for system without anthracene tags. The hydrophobic tags at the ends of shell-forming blocks try to avoid the polar medium and bury in the shell forcing the chains to loop back. The resulting distribution of traps is bimodal with a smaller peak in the vicinity of the core and a larger one farther from the core than the maximum on the distribution of segments.
Widnall instabilities in vortex pairs
Authors: Sipp Denis , Jacquin Laurent
Published: June 2003

In this article we analyze the cooperative three-dimensional short-wave instabilities developing on concentrated vortex dipoles that have been obtained by means of two-dimensional direct numerical simulations. These dipoles are characterized by their aspect ratio a/b where a is the radius of the vortices based on the polar moments of vorticity and b is the separation between the vortex centroids. In the inviscid case, we show that the selection of the antisymmetric eigenmode smoothly increases with a/b: for a/b=0.208, the amplification rate of the antisymmetric eigenmode is only 1.4% larger than the amplification rate of the symmetric eigenmode. When a/b=0.288, this difference increases up to 7%. The results of the normal mode analysis may be compared to those of an asymptotic stability analysis of a Lamb–Oseen vortex subjected to a weak straining field, following Moore and Saffman [Proc. R. Soc. London, Ser. A 346, 413 (1975)]. This theory shows that the instability may occur whenever two Kelvin waves exist with the same frequency ω, the same axial wavenumber k and with azimuthal wavenumbers m and m+2. Contrary to the case of a Rankine vortex [Tsai and Widnall, J. Fluid Mech. 73, 721 (1976)], the presence of critical layers in a Lamb–Oseen vortex prevents a large number of possible resonances. For example, resonances between m=−2 and m=0 modes lead to damped modes. The only resonances that occur are related to the stationary (ω=0) bending waves (m=±1) obtained for specific values of the axial wavenumber. All these predictions are found to be in good agreement with the results obtained by the stability analysis of the considered vortex pairs. At last, we present a nonautonomous amplitude equation which takes into account all effects of viscosity, i.e., the viscous damping of the amplification rate of the perturbation but also the increase of the dipole aspect ratio a/b due to the viscous diffusion of the basic flowfield. The low-Reynolds number experiment of Leweke and Williamson [J. Fluid Mech. 360, 85 (1998)] is revisited under the light of these theoretical results. We show that these theoretical results yield predictions for the amplification rate and for the wavenumber that agree with the experimental observations.
Ab initio 0 K isotherm for crystalline 1,1-diamino-2,2-dinitroethylene
Authors: Kuklja Maija M. , Zerilli Frank J. , Peiris Suhithi M.
Published: June 2003

The ab initio calculation of the 0 K isotherm of the organic molecular crystal 1,1-diamino-2,2-dinitroethylene (C2H4N4O4), also known as FOX-7, is accomplished by means of solutions of the many-body Schrödinger equation in a periodic crystal lattice. It was found that the Hartree–Fock method is adequate to represent the behavior of the material and that, in general, density functional methods give inferior results. Initially, calculations were done assuming rigid molecules under compression. In further calculations the internal molecular bond lengths were optimized for each value of compression. Finally, calculations were performed in which all the molecular coordinates were optimized. The results are compared with experimental x-ray diffraction data obtained by compressing samples in diamond anvil cells. Excellent agreement is obtained when the molecular coordinates are completely optimized. In addition, FOX-7 is highly anisotropic and this anisotropy must be taken into account to obtain good agreement with hydrostatic compression data.
Chaotic advection of finite-size bodies in a cavity flow
Authors: Vikhansky A.
Published: June 2003

We considered advection of neutrally buoyant discs in two-dimensional chaotic Stokes flow. The goal of the study is to explore a possibility to enhance laminar mixing in batch-flow mixers. Addition of freely moving bodies to periodically driven chaotic flow renders the flowfield nonperiodic [D. F. Zhang and D. A. Zumbrunnen, AIChE J. 42, 3301 (1996)], i.e., the Lagrangian chaos of the bodies motion induces Eulerian chaos of the flow that makes mixing more intensive. The presence of three bodies creates new topological features that do not exist in “pure” fluid. The trajectories of the discs in the augmented phase space tangle and form a braid that leads to so-called topological chaos [P. L. Boyland, H. Aref, and M. A. Stremler, J. Fluid Mech. 403, 277 (2000)]. Simulations were performed using a new variant of the immersed boundaries method that allows the direct numerical simulation of fluid–solid flows on a regular rectangular grid without explicit calculation of the forces that the particles exert on the fluid.
Spreading fronts and fluctuations in sedimentation
Authors: Bergougnoux Laurence , Ghicini Sébastien , Guazzelli Élisabeth , Hinch John
Published: June 2003

A diffuse interface or “front” at the top of the suspension is investigated experimentally and numerically. The width of the front is found to grow linearly in time, mainly due to a polydispersity of particle size in the very dilute experiments, and due only to fluctuations in particle density in the simulations. Away from the front, the fluctuations in the particle velocities are found not to decay.
Role of extrinsic atoms on the morphology and field emission properties of carbon nanotubes
Authors: Chan L. H. , Hong K. H. , Xiao D. Q. , Hsieh W. J. , Lai S. H. , Shih H. C. , Lin T. C. , Shieu F. S. , Chen K. J. , Cheng H. C.
Published: June 2003

Extrinsic atoms were doped into multiwalled carbon nanotubes (MWCNTs) using microwave plasma-enhanced chemical vapor deposition. Doped nitrogen atoms alter the original parallel graphenes into highly curved ones including some fullerene-like structures. Doped nitrogen atoms could replace carbon atoms in MWCNTs and therefore increase the electronic density that enhances the electron field emission properties. On the other hand, the incorporation of boron into the carbon network apparently increases the concentration of electron holes that become electron traps and eventually impedes the electron field emission properties. Fowler–Nordheim plots show two different slopes in the curve, indicating that the mechanism of field emission is changed from low to high bias voltages. β values could be increased by an amount of 42% under low bias voltages and 60% under high bias voltages in the N-doped MWCNTs, but decreased by an amount of 8% under low bias region and 68% under high bias voltage in the B-doped MWCNTs.
A new matched asymptotic expansion for the intermediate and far flow behind a finite body
Authors: Tordella D. , Belan M.
Published: June 2003

An approximated Navier–Stokes steady solution is here presented for the two dimensional bluff body wake region that is intermediate between the field on the body scale LD, which includes the two symmetric counter-rotating eddies, and the ultimate far wake. The nonparallelism of the streamlines in the intermediate wake cannot yet be considered negligible. The R is of the order of the critical value for the onset of the first instability and the limiting behavior for large R is not considered. The solution is obtained by matching an inner solution—a Navier–Stokes expansion in powers of the inverse of the longitudinal coordinate—and an outer solution, which is a Navier–Stokes asymptotic expansion in powers of the inverse of the distance from the body. The matching is built on the criteria that, where the two solutions meet, the longitunal pressure gradients and the vorticities must be equal and the flow toward the inner layer must be equal to the outflow from the external stream. At high orders in the inner expansion solution, the lateral decay turns out to be algebraic. This approximate solution is here examined in relation to the class of asymptotic solutions that, in the past, were obtained by adopting the rapid decay principle, which implies an irrotational outer flow. The theme running through this paper is the necessity of the addition of this criterion to the equations of motion to build a solution that describes the intermediate wake. The present solution has been obtained by relaxing the imposition of the rapid decay principle. It can be concluded that, at Reynolds numbers as low as the first critical value and where the nonparallelism of the streamlines is not yet negligible, the division of the field into two basic parts—an inner vortical boundary layer flow and an outer potential flow—is spontaneously shown up to the second order of accuracy: at higher orders in the expansion solution the vorticity is first convected and then diffused in the outer field. If exploited to represent the basic flow of bluff body wakes, the analytical simplicity of this asymptotic expansion could be useful for the nonparallel analysis of the instability of two-dimensional wakes.
Bistable chiral-splay nematic liquid crystal device using horizontal switching
Authors: Lee Seo Hern , Park Kyoung-Ho , Yoon Tae-Hoon , Kim Jae Chang
Published: June 2003

The bistability in a chiral-splay nematic liquid crystal cell, which is obtained by adding a chiral additive to a splay cell, is proposed. In this letter, we describe a horizontal way of switching between the two states of the bistable chiral-splay cell, one state being characterized by a nontwisted director field with splay, the second state showing a director-field with 180° twist. The optimization of the various parameters of the device is described.
Quality assessment of CuInS2-based solar cells by Raman scattering
Authors: Rudigier E. , Luck I. , Scheer R.
Published: June 2003

In this work spectroscopic features of the Raman A1 mode of CuInS2 thin films are investigated. A broadening of the A1 mode in combination with an asymmetry towards larger wave numbers is observed. The comparison with parameters of the solar cells formed out of these thin films reveal a direct correlation between the linewidth of the A1 mode and the solar cell data. A significant decrease of open circuit voltage and fill factor of the cells is found for linewidths larger than 3.8 cm−1. For linewidths smaller than 3.8 cm−1, a saturated behavior of the solar cell parameters is observed. This saturation indicates other origins of performance limitation to be present in CuInS2 based devices.
Impact of Si doping on radio frequency dispersion in unpassivated GaN/AlGaN/GaN high-electron-mobility transistors grown by plasma-assisted molecular-beam epitaxy
Authors: Mitrofanov Oleg , Manfra Michael , Weimann Nils
Published: June 2003

We report on the effect of Si doping on the transient behavior of unpassivated high-power GaN/AlGaN/GaN high-electron-mobility transistors grown by plasma-assisted molecular-beam epitaxy on 6H–SiC. The incorporation of Si into the heterostructure barrier is found to reduce the level of radio frequency dispersion as compared to undoped structures. In some devices which incorporate Si doping of the barrier, the pulsed and steady-state current–voltage characteristics coincide, and gate lag is found to be insignificant. More typically, ∼90% of the dc value of drain current is restored at 1 μs after pulsing the gate from pinch off to VGS=0 V. Significant gate lag is observed in devices that are not doped with Si. In the undoped structure, the drain current reaches only ∼70% of the dc value within 1 μs. The transient behavior in the two designs is attributed to the same defect state with activation energy of 0.22 eV. Dispersion reduction is correlated with an increase of gate leakage current in Si-doped devices.
Nonvolatile two-color holographic recording in nondoped near-stoichiometric lithium tantalate crystals with continuous-wave lasers
Authors: Liu Youwen , Kitamura Kenji , Takekawa Shunji , Nakamura Masaru , Furukawa Yasunori , Hatano Hideki
Published: June 2003

Nonvolatile holograms have been recorded in nondoped near-stoichiometric LiTaO3 crystals by use of a near infrared (IR) laser for writing and a ultraviolet beam as a gating source. This material exhibits good overall two-color holographic recording characteristics including a high sensitivity of 0.086 cm/J with a gating intensity of 1 W/cm2 at 350 nm, a large refractive index change of as much as 1×10−4, a high resistance to IR erasure, and a long hologram lifetime of five years. The sensitivity can be further enhanced using writing and gating beams of a shorter wavelength without sacrificing readout nonvolatility.
Formation of free-standing micropyramidal colloidal crystals grown on silicon substrate
Authors: Matsuo Shigeki , Fujine Takatomi , Fukuda Koichi , Juodkazis Saulius , Misawa Hiroaki
Published: June 2003

The self-organization of microspheres is one of the simplest methods for fabricating three-dimensional (3D) photonic crystals (PhCs), but the 3D structure of such organized microspheres, colloidal crystals, is difficult to control. In this letter, we report a method for forming face-centered-cubic colloidal crystals into a pyramidal shape on an anisotropically etched silicon (100) and (110) substrate. The colloidal crystals were lifted from the substrate for observation after thermal bonding. Free-standing colloidal crystals with a well-defined “micropyramid” shape were obtained. This type of PhC formation is suitable for batch production as well as for handling a single pyramid.
Preparation of clean reconstructed InAs(001) surfaces using HCl/isopropanol wet treatments
Authors: Tereshchenko O. E. , Paget D. , Chiaradia P. , Bonnet J. E. , Wiame F. , Taleb-Ibrahimi A.
Published: June 2003

A simple treatment method using HCl/isopropanol solutions is given for preparation of high-quality InAs(001) surfaces. The surface structure and chemistry were characterized using low-energy electron diffraction and photoemission spectroscopy as a function of UHV temperature. The treatment removes the natural oxide and leaves on the surface a physisorbed overlayer containing arsenic and small amounts of InClx. Annealing at 330 °C induces desorption of this overlayer and reveals a clean arsenic-rich (2×4)/c(2×8) surface. The indium-rich (4×2)/c(8×2) reconstruction is obtained upon further annealing to 410 °C.
Temperature dependence on current–voltage characteristics of nickel/diamond Schottky diodes on high quality boron-doped homoepitaxial diamond film
Authors: Chen Y. G. , Ogura M. , Okushi H.
Published: June 2003

Ni/diamond Schottky diodes were fabricated on boron-doped homoepitaxial diamond films. Temperature dependence on electrical characteristics of the Schottky diodes was investigated in a temperature range 148 to ∼448 K. The current–voltage characteristics of the diodes show excellent rectification behavior. Temperature dependence on the ideality factor and apparent barrier height was determined, including the effect of series resistance. The evaluated ideality factor was observed to decrease from 1.78 to 1.05, while the apparent barrier height increased from 0.95 to 1.55 eV in this temperature range. The temperature dependence of the forward characteristics can be well explained by thermionic-field-emission theory at low temperature and thermionic emission theory at high temperature, respectively. A possible mechanism of the correlation of the ideality factor and barrier height has been proposed.
First-principles study of n-type dopants and their clustering in SiC
Authors: Rurali R. , Godignon P. , Rebollo J. , Hernández E. , Ordejón P.
Published: June 2003

We report the results of an ab initio study of N and P dopants in SiC. We find that while N substitutes most favorably at a C lattice site, P does so preferably at a Si site, except in n-doping and Si-rich 3C-SiC. Furthermore, we consider a series of dopant complexes that could form in high-dose implantation, in order to investigate the dopant activation behavior in this limit. We find that all N complexes considered lead to passivation through the formation of a deep level. For P, the most stable aggregate is still an active dopant, while passivation is only observed for complexes with a higher formation energy. We discuss how these results could help in the understanding of the observed experimental high-dose doping and codoping behavior of these species.
Barrier heights of Schottky contacts on strained AlGaN/GaN heterostructures: Determination and effect of metal work functions
Authors: Lin Zhaojun , Lu Wu , Lee Jaesun , Liu Dongmin , Flynn Jeffrey S. , Brandes George R.
Published: June 2003

Ir, Ni, and Re Schottky contacts on strained Al0.25Ga0.75N/GaN heterostructures are characterized using capacitance–voltage (C–V) and I–V techniques. Based on the measured C–V characteristics, two dimensional electron gas sheet carrier concentrations at the AlGaN/GaN interface and barrier heights of Ir, Ni, and Re Schottky contacts are calculated. The barrier heights of 1.12, 1.27, and 1.68 eV are obtained for Ir, Ni, and Re Schottky contacts, respectively. The results show that the barrier heights of Schottky contacts on strained AlGaN/GaN heterostructures are strongly dependent on the metal work functions. However, contrary to Schottky contacts on bulk AlGaN or GaN, the barrier height on strained AlGaN/GaN heterostructures is lower for a Schottky contact with a higher metal work function. This is attributed to the stronger wave function coupling between electrons in the Schottky metal and surface donor electrons. The I–V characteristics for Ir, Ni, and Re Schottky contacts confirm the results obtained by C–V characteristics.
The prevalences of overweight and obesity in children aged 4 to 12 years in Gibraltar
Authors: Kirk Sara FL , McLeod Melanie
Published: June 2003

Objective:

To determine the prevalences of overweight and obesity in children aged 4 to 12 years, using the standard definitions proposed by the International Obesity Taskforce.

Design:

Population prevalence cross-sectional survey involving measurement of height and weight. Data collection took place in 1998.

Setting:

Schools in Gibraltar.

Subjects:

In total 2994 children, aged 4–12 years, attending these schools (1540 boys, 1454 girls).

Results:

Prevalence of overweight in boys was 19.7%, while obesity prevalence was 10.8%. For the girls, overweight prevalence was 21.4%, while obesity prevalence was 10.6%. There were no significant differences in the proportions of overweight or obesity between boys and girls.

Conclusions:

This was the first time that the prevalences of overweight and obesity have been estimated in children from Gibraltar. These data provide further information on prevalence rates of overweight and obesity, using defined cut-offs for comparison with data from other countries.
Impact of ready-to-eat breakfast cereal (RTEBC) consumption on adequacy of micronutrient intakes and compliance with dietary recommendations in Irish adults
Authors: Galvin MA , Kiely M , Flynn A
Published: June 2003

Objective:

To describe the consumption of ready-to-eat-breakfast cereals (RTEBCs) in Irish adults and its impact on adequacy and safety of micronutrient intakes and compliance with dietary recommendations.

Design:

Analysis for this paper used data from the North/South Ireland Food Consumption Survey that estimated habitual food intake using a 7-day food diary in a representative sample of adults aged 18–64 years (n=1379; 662 men, 717 women).

Results:

Despite the small quantity consumed (mean 28.6gday-1or 4.7% of total energy intake), RTEBCs made an important contribution to the mean daily intake of carbohydrate (8.1%), starch (10.8%), dietary fibre (9.8%) and non-starch polysaccharides (NSP) (10.8%) in consumers. Increased consumption was associated with a more fibre-dense diet and with greater compliance with dietary recommendations for fat, carbohydrate and NSP. Fortified RTEBCs contributed significantly to mean daily intakes of iron (18%), thiamin (14%), riboflavin (17%), niacin (15%), vitamin B6(13%), total folate (18%) and vitamin D (10%) and most of the contribution was from micronutrients added to RTEBCs. Increased consumption of fortified RTEBCs was associated with an increased nutrient density for a number of micronutrients and with a lower prevalence of dietary inadequacy of calcium, iron, riboflavin and folate, particularly in women. However, it was not associated with intakes in excess of the Tolerable Upper Intake Level for any micronutrient.

Conclusions:

The consumption of RTEBCs is associated with improved compliance with dietary recommendations for fat, carbohydrate and fibre, with a more micronutrient-dense diet and a reduced risk of dietary inadequacy for calcium, iron, riboflavin and folate, without increasing the risk of excessive intakes of micronutrients.
Statistical adjustment of signal censoring in gene expression experiments
Authors: Wit Ernst , McClure John
Published: June 2003

Motivation: Numerical output of spotted microarrays displays censoring of pixel intensities at some software dependent threshold. This reduces the quality of gene expression data, because it seriously violates the linearity of expression with respect to signal intensity. Statistical methods based on typically available spot summaries together with some parametric assumptions can suggest ways to correct for this defect

Results: A maximum likelihood approach is suggested together with a sensible approximation to the joint density of the mean, median and variance—which are typically available to the biological end-user. The method ‘corrects’ the gene expression values for pixel censoring. A by-product of our approach is a comparison between several two-parameter models for pixel intensity values. It suggests that pixels separated by one or two other pixels can be considered independent draws from a Lognormal or a Gamma distribution

Availability: The R/S-Plus code is available at http://www.stats.gla.ac.uk/~microarray/software

Contact: ernst@stats.gla.ac.uk

* To whom correspondence should be addressed.
K-ary clustering with optimal leaf ordering
for gene expression data
Authors: Bar-Joseph Ziv , Demaine Erik D. , Gifford David K. , Srebro Nathan , Hamel Angèle M. , Jaakkola Tommi S.
Published: June 2003

Motivation: A major challenge in gene expression analysis is effective data organization and visualization. One of the most popular tools for this task is hierarchical clustering. Hierarchical clustering allows a user to view relationships in scales ranging from single genes to large sets of genes, while at the same time providing a global view of the expression data. However, hierarchical clustering is very sensitive to noise, it usually lacks of a method to actually identify distinct clusters, and produces a large number of possible leaf orderings of the hierarchical clustering tree. In this paper we propose a new hierarchical clustering algorithm which reduces susceptibility to noise, permits up to k siblings to be directly related, and provides a single optimal order for the resulting tree

Results: We present an algorithm that efficiently constructs a k-ary tree, where each node can have up to k children, and then optimally orders the leaves of that tree. By combining k clusters at each step our algorithm becomes more robust against noise and missing values. By optimally ordering the leaves of the resulting tree we maintain the pairwise relationships that appear in the original method, without sacrificing the robustness.

Our k-ary construction algorithm runs in O(n3) regardless of k and our ordering algorithm runs in O(4kn3). We present several examples that show that our k-ary clustering algorithm achieves results that are superior to the binary tree results in both global presentation and cluster identification

Availability: We have implemented the above algorithms in C++ on the Linux operating system. Source code is available upon request from zivbj@mit.edu

Contact: zivbj@mit.edu

* To whom correspondence should be addressed.
Learning rule-based models of biological process from
gene expression time profiles using Gene Ontology
Authors: Hvidsten Torgeir R. , Lægreid Astrid , Komorowski Jan
Published: June 2003

Motivation: Microarray technology enables large-scale inference of the participation of genes in biological process from similar expression profiles. Our aim is to induce classificatory models from expression data and biological knowledge that can automatically associate genes with novel hypotheses of biological process

Results: We report a systematic supervised learning approach to predicting biological process from time series of gene expression data and biological knowledge. Biological knowledge is expressed using gene ontology and this knowledge is associated with discriminatory expression-based features to form minimal decision rules. The resulting rule model is first evaluated on genes coding for proteins with known biological process roles using cross validation. Then it is used to generate hypotheses for genes for which no knowledge of participation in biological process could be found. The theoretical foundation for the methodology based on rough sets is outlined in the paper, and its practical application demonstrated on a data set previously published by Cho et al. (Nat. Genet., 27, 48–54, 2001)

Availability: The Rosetta system is available at http://www.idi.ntnu.no/~aleks/rosetta

Contact: Jan.Komorowski@lcb.uu.se

Supplementary Information: http://www.lcb.uu.se/~hvidsten/bioinf_cho/

* To whom correspondence should be addressed.
Novel clustering algorithm for microarray expression data in a truncated SVD space
Authors: Horn David , Axel Inon
Published: June 2003

Motivation: This paper introduces the application of a novel clustering method to microarray expression data. Its first stage involves compression of dimensions that can be achieved by applying SVD to the gene–sample matrix in microarray problems. Thus the data (samples or genes) can be represented by vectors in a truncated space of low dimensionality, 4 and 5 in the examples studied here. We find it preferable to project all vectors onto the unit sphere before applying a clustering algorithm. The clustering algorithm used here is the quantum clustering method that has one free scale parameter. Although the method is not hierarchical, it can be modified to allow hierarchy in terms of this scale parameter

Results: We apply our method to three data sets. The results are very promising. On cancer cell data we obtain a dendrogram that reflects correct groupings of cells. In an AML/ALL data set we obtain very good clustering of samples into four classes of the data. Finally, in clustering of genes in yeast cell cycle data we obtain four groups in a problem that is estimated to contain five families

Availability: Software is available as Matlab programs at http://neuron.tau.ac.il/~horn/QC.htm

Contact: horn@post.tau.ac.il

* To whom correspondence should be addressed.
Gene interaction in DNA microarray data is
decomposed by information geometric measure
Authors: Nakahara Hiroyuki , Nishimura Shin-ichi , Inoue Masato , Hori Gen , Amari Shun-ichi
Published: June 2003

Motivation: Given the vast amount of gene expression data, it is essential to develop a simple and reliable method of investigating the fine structure of gene interaction. We show how an information geometric measure achieves this

Results: We introduce an information geometric measure of binary random vectors and show how this measure reveals the fine structure of gene interaction. In particular, we propose an iterative procedure by using this measure (called IPIG). The procedure finds higher-order dependencies which may underlie the interaction between two genes of interest. To demonstrate the method, we investigate the interaction between the two genes of interest in the data from human acute lymphoblastic leukemia cells. The method successfully discovered biologically known findings and also selected other genes as hidden causes that constitute the interaction

Availability: Softwares are currently not available but are possibly made available in future at http://www.mns.brain.riken.go.jp/~nakahara/DNA_pub.html where all the related information is also linked.

Contact: hiro@brain.riken.go.jp

* To whom correspondence should be addressed.
Classification of multiple cancer types by multicategory
support vector machines using gene expression data
Authors: Lee Yoonkyung , Lee Cheol-Koo
Published: June 2003

Motivation: High-density DNA microarray measures the activities of several thousand genes simultaneously and the gene expression profiles have been used for the cancer classification recently. This new approach promises to give better therapeutic measurements to cancer patients by diagnosing cancer types with improved accuracy. The Support Vector Machine (SVM) is one of the classification methods successfully applied to the cancer diagnosis problems. However, its optimal extension to more than two classes was not obvious, which might impose limitations in its application to multiple tumor types. We briefly introduce the Multicategory SVM, which is a recently proposed extension of the binary SVM, and apply it to multiclass cancer diagnosis problems

Results: Its applicability is demonstrated on the leukemia data (Golub et al., 1999) and the small round blue cell tumors of childhood data (Khan et al., 2001). Comparable classification accuracy shown in the applications and its flexibility render the MSVM a viable alternative to other classification methods

Supplementary Information: http://www.stat.ohio-state.edu/~yklee/msvm.html

Contact: yklee@stat.ohio-state.edu

* To whom correspondence should be addressed.
The small-world dynamics of tree networks
and data mining in phyloinformatics
Authors: Piel William H. , Sanderson Michael J. , Donoghue Michael J.
Published: June 2003

Motivation: A noble and ultimate objective of phyloinformatic research is to assemble, synthesize, and explore the evolutionary history of life on earth. Data mining methods for performing these tasks are not yet well developed, but one avenue of research suggests that network connectivity dynamics will play an important role in future methods. Analysis of disordered networks, such as small-world networks, has applications as diverse as disease propagation, collaborative networks, and power grids. Here we apply similar analyses to networks of phylogenetic trees in order to understand how synthetic information can emerge from a database of phylogenies

Results: Analyses of tree network connectivity in TreeBASE show that a collection of phylogenetic trees behaves as a small-world network—while on the one hand the trees are clustered, like a non-random lattice, on the other hand they have short characteristic path lengths, like a random graph. Tree connectivities follow a dual-scale power-law distribution (first power-law exponent ≈1.87; second ≈4.82). This unusual pattern is due, in part, to the presence of alternative tree topologies that enter the database with each published study. As expected, small collections of trees decrease connectivity as new trees are added, while large collections of trees increase connectivity. However, the inflection point is surprisingly low: after about 600 trees the network suddenly jumps to a higher level of coherence. More stringent definitions of ‘neighbour’ greatly delay the threshold whence a database achieves sufficient maturity for a coherent network to emerge. However, more stringent definitions of ‘neighbour’ would also likely show improved focus in data mining

Availability: http://treebase.org

Contact: wpiel@buffalo.edu

* To whom correspondence should be addressed.

† Current address: Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
Genescript: DNA sequence annotation pipeline
Authors: Hudek Alexander K. , Cheung Joseph , Boright Andrew P. , Scherer Stephen W.
Published: June 2003

Summary: Genescript uses a number of publicly available analysis programs to annotate a DNA sequence. It provides an integrated display of results from each program, and includes an evidence-based scoring system that gives informative summaries of predicted gene models

Availability: Genescript is available for download from http:://tcag.bioinfo.sickkids.on.ca/genescript/

Contact: alex@genet.sickkids.on.ca

* To whom correspondence should be addressed.
Coupled two-way clustering server
Authors: Getz Gad , Domany Eytan
Published: June 2003

Summary: The CTWC server provides access to the software, CTWC1.00, that implements Coupled Two Way Clustering (Getz et al., 2000), a method designed to mine gene expression data

Availability: Free, at http://ctwc.weizmann.ac.il

Contact: ctwc_support@weizmann.ac.il

Supplementary information: The site has a link to an example which provides figures and detailed explanations

* To whom correspondence should be addressed.
The rapid tooling testbed: a distributed design‐for‐manufacturing system
Authors: Rosen David W. , Chen Yong , Sambu Shiva , Allen Janet K. , Mistree Farrokh
Published: June 2003

A new design‐for‐manufacturing method, called the geometric tailoring (GT), and the associated digital interface concept have been developed that enable the design activities to be separated from the manufacturing activities. Conditions for the successful application of this method are investigated. The GT method is demonstrated for rapid prototyping and rapid tooling technologies, where prototype parts are required to match the production properties as closely as possible. This method is embodied in a system called the rapid tooling testbed (RTTB). Research work is presented on GT and the distributed computing environment underlying the RTTB. Examples are summarized from the usage of this method and testbed.
Design for medical rapid prototyping of cranioplasty implants
Authors: Hieu L.C. , Bohez E. , Vander Sloten J. , Phien H.N. , Vatcharaporn E. , Binh P.H. , An P.V. , Oris P.
Published: June 2003

Design methods for medical rapid prototyping (RP) of personalized cranioplasty implants are presented in this paper. These methods are applicable to model cranioplasty implants for all types of the skull defects including beyond‐midline and multiple defects. The methods are based on two types of anatomical data, solid bone models (STereoLithography files – STL) and bone slice contours (Initial Graphics Exchange Specification – IGES and StrataSys Layer files – SSL). The bone solids and contours are constructed based on computed tomography scanning data, and these data are generated in medical image processing and STL slicing packages.