bluuebunny/crossref_metadata_2025 huggingface dataset:
Zur Nullstellenverifikation bei Besselfunktionen erster Gattung
Authors: Hofschuster Werner
Published: December 2005

Gesucht werden verifizierte Einschließungen aller Nullstellen von Besselfunktionen erster Gattung in einem vorgegebenen Definitionsbereich. Durch Einsatz von bekannten Näherungsverfahren werden zunächst hochgenaue Intervalleinschließungen von “Verdachtsstellen” berechnet. Für jede dieser Verdachtsstellen wird die Existenz einer Nullstelle durch den Nachweis eines Vorzeichenwechsels gezeigt. Die Vollständigkeit aller berechneten Nullstellen kann mit Hilfe des Sturmschen Vergleichssatzes oder über den topologischen Abbildungsgrad gezeigt werden. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
On the Quasivector Space of Zonotopes in the Plane
Authors: Markov Svetoslav
Published: December 2005

In this work we consider centred zonogons represented implicitly as Minkowski sums of centred segments. Using this representation the order relation inclusion (containment) of zonogons has been studied. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Computer algebraic methods for the structural analysis of linear controlsystems
Authors: Zerz Eva , Levandovskyy Viktor
Published: December 2005

We give an overview of the mathematical background of the Singular control library. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Dynamic utility maximization with bounded shortfall risks
Authors: Gabih Abdelali , Wunderlich Ralf
Published: December 2005

We address the dynamic portfolio optimization problem where the expected utility from terminal wealth has to be maximized. The special feature of this paper is an additional constraint on the portfolio strategy modeling bounded shortfall risks. We consider the risk, that the terminal wealth of the portfolio falls short of a certain benchmark. This benchmark is chosen to be proportional to the stock price. The risk is measured by the Expected Utility Loss.

Using a continuous‐time model of a complete financial market and applying martingale methods, analytic expressions for the optimal terminal wealth and the optimal portfolio strategies are given. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Stochastic optimisation: sensitivity and Delta Theorem
Authors: Lachout Petr
Published: December 2005

The contribution investigates stability of a stochastic optimisation problem to a random perturbation. We work with bounded real functions under general setting. Stability is investigated by means of Delta Theorem. That is possible and convenient since the infimum mapping is Hadamard directionally differentiable. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Numerical Implementation of Optimal Feedback Control for Nonlinear Systems
Authors: Balashevich Natalia
Published: December 2005

A method of on‐line constructing an optimal feedback control for nonlinear systems with bang‐bang optimal control is suggested. The realization of the algorithm of constructing a closed‐loop solution is oriented on fast corrections of optimal open‐loop control subject to small variations of initial state. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
On the convergence of the MG/OPT method
Authors: Borzì Alfio
Published: December 2005

Global convergence of the MG/OPT method for optimization is discussed. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Efficient Aerodynamic Shape Optimization in MDO Context
Authors: Fazzolari Antonio , Gauger Nicolas R. , Brezillon Jöel
Published: December 2005

The aerospace industry is increasingly relying on advanced numerical flow simulation tools in the early aircraft design phase. Today's flow solvers, which are based on the solution of the compressible Euler and Navier‐Stokes equations, are able to predict aerodynamic behaviour of aircraft components under different flow conditions quite well [1]. Within the next few years numerical shape optimization will play a strategic role for future aircraft design. It offers the possibility of designing or improving aircraft components with respect to a pre‐specified figure of merit, subject to geometrical and physical constraints. Here, aero‐structural analysis is necessary to reach physically meaningful optimum wing designs. The use of single disciplinary optimizations applied in sequence is not only inefficient but in some cases is known to lead to wrong, non‐optimal designs [2]. Although multidisciplinary optimizations (MDO) are possible with classical approaches for sensitivity evaluations by means of finite differences, these methods are extremely expensive in terms of calculation time, requiring the reiterated solution of the coupled problem for every design variable.

However, adjoint approaches allow the evaluation of these sensitivities in an efficient way and lead to high accuracy. Firstly, we present the development and application of a continuous adjoint approach for single disciplinary aerodynamic shape design. This approach was previously developed at the German Aerospace Center (DLR) [3] and was the starting point for the extension to aero‐structural wing designs. Secondly, we describe the adjoint approach and its implementation for the evaluation of the sensitivities for coupled aero‐structure optimization problems [4] and its application to the drag reduction of the AMP wing by constant lift while taking into account the static deformation of this wing caused by the aerodynamic forces (see figures). Finally, we show the application of the coupled aero‐structural adjoint approach for the Breguet formula of aircraft range, where in addition to the lift to drag ratio the weight of the AMP wing is taken into account (see figures). (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Preconditioning of One‐Shot Pseudo‐Timestepping Methods for Shape Optimization
Authors: Gherman Ilia , Schulz Volker
Published: December 2005

One‐shot pseudo‐timestepping [1, 2] has proven to be a powerful approach for the solution of optimal design problems in engineering applications. It blends well in within pre‐existing pseudo‐timestepping simulation solvers. The goal of this approach is to transform the equations for the necessary optimality conditions of the optimal design problem into an ordinary differential equation (ODE) and then solve the pseudo‐time embedded state, co‐state and design equations all at once. Similar approaches have been considered in [4, 5]. An application of this method to a real‐world example within the MEGADESIGN‐Project has been presented in [3]. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Simultaneous pseudo‐time stepping for aerodynamic shape optimization
Authors: Hazra Subhendu Bikash , Gauger Nicolas R.
Published: December 2005

In this paper we discuss about numerical methods for aerodynamic shape optimization problems. These problems require efficient CFD techniques to solve the state (as well as costate) equations and fast algorithms for solving the optimization problems. Both of these are independent active areas of research since long time. Wide range of applications in science and engineering involve solution of optimization problems where the governing PDEs appear as constraints. Therefore, merging the two for the purpose of practical applicability is relatively new. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Real‐Time Solution of Bi‐Level Optimal Control Problems
Authors: Knauer Matthias , Büskens Christof , Lasch Peter
Published: December 2005

Bi‐level optimal control problems are presented as an extension to classical optimal control problems. Hereby, additional constraints for the primary problem are considered, which depend on the optimal solution of a secondary optimal control problem. A demanding problem is the numerical complexity, since at any point in time the solution of the optimal control problem as well as a complete solution of the secondary problem have to be determined. Hence we deal with two dependent variables in time. The numerical solution of the bi‐level problem is illustrated by an application of a container crane. Jerk and energy optimal trajectories with free final time are calculated under the terminal condition that the crane system comes to be at rest at a predefined location. In enlargement additional constraints are investigated to ensure that the crane system can be brought to a rest position by a safety stop at a free but admissible location in minimal time from any state of the trajectory. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Static Output Feedback ℋ︁∞–Synthesis by solving the ℋ︁∞–NSDP
Authors: Leibfritz Friedemann
Published: December 2005

We consider the solution of the static output feedback (SOF) ℋ︁∞ control design problem. In particular, we solve the corresponding non–convex and nonlinear semidefinite program (NSDP), the so–called ℋ︁∞–NSDP, by a suitable optimization solver. Finally, we demonstrate the behavior of the solver on the COMPleibbenchmark collection. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Optimization of open cross sections of thin‐walled beams with plate‐shell‐flanges
Authors: Maćkiewicz Mikołaj , Magnucki Krzysztof
Published: December 2005

The paper is devoted to a monosymetrical cold‐formed thin‐walled beam with open cross section. Its flange consists of plates and circular shells. The beam is under pure bending. The cross section is characterized by dimensionless parameters. The authors are searching for an optimal cross section shape of considered beam. This optimal shape is determined by means of parametric optimization. The dimensionless objective function is so defined as to comprise both cross section area and a maximal allowable bending moment. The constraints follow from the local buckling conditions and geometric restrictions. Moreover, there are optimized cross sections of beams, for which the shear center is located either in the web or in the centroid of the cross section. Results are compared and analyzed. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Different Optimization Models for Crack‐Free Laser Welding
Authors: Petzet Verena , Pesch Hans Josef , Prikhodovsky Andrey , Ploshikhin Vasily
Published: December 2005

Conventional laser beam welding of aluminum alloys often leads to hot cracking. This is caused by a complex process where thermo‐mechanical and metallurgical aspects are involved; cf. [3], [2]. A possibility to prevent hot crack initiation yields the multi‐beam welding technique (cf. [2]), where additional laser beams are led parallelly besides the main laser beam. There by optimal positions, sizes, and powers of the additional laser beams play an important role otherwise hot cracking can even be enhanced.

In [1], [4], resp., a mechanical 1D and thermal 2D model of hot cracking was derived. It provides the basis for different formulations of constrained nonlinear programming problems to identify the optimal parameters of the additional laser beams. In the present paper a comparison between these formulations and between two different optimizers for the so far best formulation are presented. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
On Low Mach Number Preconditioning of Finite Volume Schemes
Authors: Birken Philipp , Meister Andreas
Published: December 2005

A finite volume method for inviscid unsteady flows at low Mach numbers is studied. The method uses a preconditioning of the dissipation term within the numerical flux function only. It can be observed by numerical experiments, as well as by analysis, that the preconditioned scheme yields a physically corrected pressure distribution and combined with an explicit time integrator it is stable if the time step Δt satisfies the requirement to be 𝒪(M 2) as the Mach number M tends to zero, whereas the corresponding standard method remains stable up to Δt = 𝒪(M ),M → 0, though producing unphysical results. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Oscillatory instabilities of high‐resolution TVD central schemes for hyperbolic conservation laws
Authors: Breuß Michael
Published: December 2005

Even if a numerical scheme for hyperbolic conservation laws is total variation diminishing, it can create oscillations at data extrema. We show that such oscillations can reduce the overall accuracy of a method considerably, effectively reducing a high‐resolution scheme to first order accuracy. The phenomenon is investigated and we derive accurate non‐staggered accurate central schemes not featuring this weakness. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Adaptive Frame Algorithms for Elliptic Operator Equations
Authors: Dahlke Stephan , Fornasier Massimo , Raasch Thorsten
Published: December 2005

We discuss the use of Gelfand frames for the adaptive numerical solution of linear elliptic operator equations. After a transformation into an equivalent infinite–dimensional system Lu = f in frame coordinates, the operator equation can be solved within a prescribed target accuracy by approximate Richardson or gradient iteration schemes. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Fast Wavelet BEM on Complex Geometries
Authors: Harbrecht H. , Kähler U. , Schneider R.
Published: December 2005

This paper is devoted to the fast solution of boundary integral equations on unstructured meshes by the Galerkin scheme. Since traditional discretizations yield densely populated system matrices it is necessary to use fast techniques like ACA, the multipole method or wavelet matrix compression, which will be the topic of the present paper. On the given, possibly unstructered, mesh we construct a wavelet basis providing vanishing moments with respect to the traces of polynomials in the space. With this basis at hand, the system matrix in wavelet coordinates can be compressed to 𝒪(N logN ) relevant matrix coefficients, where N denotes the number of unknowns. The compressed system matrix can be computed within suboptimal complexity by using fast multipole or ℋ︁‐matrix techniques. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Multiscale Flow Simulation by Adaptive Finite Volume Particle Methods
Authors: Iske Armin
Published: December 2005

We report on recent developments concerning adaptive finite particle methods, which are used for the numerical simulation of multiscale phenomena in time‐dependent evolution processes. The proposed concept relies on a finite volume approach, which we combine with WENO reconstruction from particle average values. In this method, polyharmonic splines are key tools for both the optimal recovery from scattered particle averages and the construction of customized adaption rules. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
On the Turbulence Modelling of 3D‐Atmospheric Boundary Layer Flow
Authors: Sládek I. , Kozel K. , Jaňour Z.
Published: December 2005

The paper presents a mathematical and numerical investigation of the 3D–flow in the atmospheric boundary layer (ABL) over complex relief. The two–equation k ‐ ε model is applied to account for the turbulence. The flow is also supposed to be viscous, incompressible and stationary. The boundary conditions are realized through the wall‐functions. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Numerical simulation of a three dimensional quantum dot
Authors: Voss Heinrich
Published: December 2005

We consider the problem to compute relevant energy states and corresponding wave functions of a three dimensional semiconductor quantum dot. Let Ωq ⊂ ℝ3 be a domain occupied by the quantum dot, which is embedded in a matrix Ωm of different material. A typical example is an InAs pyramidal quantum dot embedded in a cuboid GaAs matrix. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Approximating Jacobians by the TR2 formula
Authors: Griewank Andreas , Korzec Maciek
Published: December 2005

In the context of KKT systems for nonlinear optimization one wishes to approximate rectangular Jacobian matrices of active constraints. A possible approximation is the Two‐Sided‐Rank‐One update (TR1) motivated in [1]. Since its denominator can easily become small we tried to prevent a possible blow up and achieve better approximations with the newly introduced Two‐Sided‐Rank‐Two update (TR2), which otherwise preserves the good qualities of the TR1. We motivate, introduce and discuss the two low‐rank‐updates. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Efficient similarity factorization of rank‐1 modifications
Authors: Schlenkrich Sebastian , Griewank Andreas , Walther Andrea
Published: December 2005

For the solution of stiff ODEs by implicit methods one has to solve sequences of algebraic systems, whose Jacobian is the identity minus a multiple of the 'system' Jacobian of the right hand side. The latter can be successively approximated by a new 'two‐sided rank‐1' formula yielding only a moderate increase in the number of iterations compared to Newton's method. However, so far we have only been able to achieve the reduction in the linear algebra effort per integration step from O (n 3) to O (n 2) as long as the size is kept constant. To obtain an effort of O (n 2) seems to require an update of a similarity reduction of the system Jacobian to Hessenberg form or even a band matrix. As we have found no O (n 2) algorithms for updating such factorizations in literature, we discuss an idea to approximate the update with enough accuracy to ensure rapid convergence of the underlying implicit equation solver. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
An Iterative Technique for Construction of Invariant Subspaces
Authors: Zítko Jan , Ulrychová Iveta
Published: December 2005

The restarted GMRES(m ) method for solving linear systems Ax = b is attractive when a good preconditioner is available. The determining of efficient preconditioners is often connected to a construction of an A –invariant subspace corresponding to eigenvalues closest to zero. One class of methods for determination of invariant subspaces is based on the construction of polynomial filters. We study the usage of Tchebychev polynomials for constructing suitable filters. Applying filters on the initial restart vectors amplifies the components of eigenvectors belonging to the small (wanted) eigenvalues and damp the remaining (unwanted) components. The presented convergence theorem describes the repeated application of filters for the construction of the wanted eigenspace of the matrix A . (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Verringerung der thermischen Belastung eines Hyperschall‐Flugsystems durch Trajektorienoptimierung
Authors: Chudej Kurt , Wächter Markus , LeBras Florent
Published: December 2005

Wir stellen eine Flugbahnoptimierung eines Hyperschall‐Flugsystems vor, die Beschränkungen der thermischen Belastung beinhaltet. Hierzu wird ein neu entwickeltes zweidimensionales Modell für das Thermalschutzsystem benutzt. Die Nebenbedingung in Form einer partiellen Differentialgleichung wird durch die Linienmethode in eine gewöhnliche Differentialgleichung transformiert. Außerdem wurde die aktive Kühlung des Triebwerks mitberücksichtigt. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Stability Analysis of a Reduced Heat Exchanger Model
Authors: Hanke Michael , Olsson K. Henrik A. , Strömgren Magnus
Published: December 2005

We consider the mathematical model of a heat exchanger in a heat pumping system using carbon dioxide as refridgerant. From the Euler equations of compressible fluid flow we derive a reduced model, called the zero Mach‐number limit, by eliminating time scales associated with soundwaves. The reduced model is a highly nonlinear partial differential‐algebraic equation (PDAE). We analyse the stability of this model and show that it is possible to use simple spatial discretisations within the method of lines (MOL), a standard practice in many system simulation software, to simulate the system. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Warped MPDAE Models including Minimisation Criteria for the Simulation of RF Signals
Authors: Pulch Roland
Published: December 2005

In radio frequency (RF) applications, electric circuits produce signals including widely separated time scales. A multidimensional representation yields an efficient model by decoupling the time scales. Consequently, a warped multirate partial differential algebraic equation (MPDAE) describes the circuit's behaviour. The appropriate determination of an arising local frequency function is crucial for the efficiency of this approach. Variational calculus implies a necessary condition to a specific solution, which exhibits a minimal amount of oscillations in the whole domain of dependence. We apply a similar strategy to minimise oscillatory performance in some boundary values only. Now variational calculus yields a boundary condition, which can easily be used in numerical methods. We compare the results of both minimisation criteria in a simulation of a warped MPDAE model. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Explicit Order 1.5 Schemes for the Strong Approximation of Itô Stochastic Differential Equations
Authors: Rößler Andreas
Published: December 2005

A new class of stochastic Runge‐Kutta (SRK) methods for the strong approximation of It ô stochastic differential equation systems w.r.t. an one‐dimensionalWiener process is introduced. Some coefficients for a SRK method converging at least with order 1.5 in the strong sense are presented. Further, a special SRK scheme having deterministic order 4.0 is proposed for stochastic differential equations with small noise. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Multirate hierarchical time integration for electronic circuits
Authors: ter Maten J. , Verhoeven A. , El Guennouni A. , Beelen Th.
Published: December 2005

Electrical circuits are hierarchically defined, in which electrical components are combined with submodels. These last ones may contain submodels themselves. This construction gives options for dedicated time integration procedures. We describe an extension that allows for a dynamically partitioned multirate time integration that retains a number of hierarchical efficiencies. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
State of the Art on the Error Reduction in AFEM
Authors: Carstensen Carsten
Published: December 2005

The a priori convergence of finite element methods (FEMs) is justified by some density property of the sequence of finite element spaces which essentially assumes some global mesh‐refining. Adaptive finite element methods (AFEMs) avoid an overall refinement in each refinement step to save degrees of freedom and hopefully lead to an improved efficiency. Hence, the a priori convergence of AFEMs isnotguaranteed automatically and, in fact, crucially depends on algorithmic details. This presentation aims at a survey on error reduction and convergence properties. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Convergence of adaptive finite element methods in elastoplasticity
Authors: Carstensen Carsten , Orlando Antonio
Published: December 2005

We show that an adaptive conforming finite element method for the solution of a variational inequality of the second kind, as model of one implicit time step of the primal problem of plasticity with positive hardening, yields the energy reduction property and the R ‐linear convergence of the stresses. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Performance Optimization for the Parallel Gauss–Seidel Smoother
Authors: Gräbel Jens , Lang Bruno , Ueberholz Peer
Published: December 2005

Simulation, e.g., in the field of computational fluid dynamics, accounts for a major part of the computing time on highperformance systems. Many simulation packages still rely on Gauss–Seidel iteration, either as the main linear solver or as a smoother for multigrid schemes. Straight‐forward implementations of this solver have efficiency problems on today's most common high‐performance computers, i.e., multiprocessor clusters with pronounced memory hierarchies. In this work we present two simple techniques for improving the performance of the parallel Gauss–Seidel method for the 3D Poisson equation by optimizing cache usage as well as reducing the number of communication steps. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
On the strong stability of differential equations and difference schemes
Authors: Jovanović Boško S.
Published: December 2005

Paper deals with the construction of a priori estimates for the solution of Cauchy problem for an abstract linear differential equation in Hilbert space under perturbations of the initial condition, right‐hand side, and operators of the problem. It is shown that a priori estimates of strong stability can be obtained directly on the basis of various a priori estimates for the solution of the Cauchy problem. The perturbations of the operators of the problem are estimated in the corresponding operator norms. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
First Order LSFEM for Second Order Hyperbolic Problems
Authors: Kayser‐Herold O. , Matthies H. G.
Published: December 2005

In the last years the interest in least squares finite element methods has grown due to some interesting properties of these methods (cf. the monographs [1], [2]). While for many elliptic problems the theoretical background has been established, only a few articles analyse least squares methods for transient problems. In this article some new stability estimates for the least squares method for the wave equation in 1 and 2 dimensions are derived. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Finite element and matched asymptotic expansion methods for chemical reactor flow problems
Authors: Skrzypacz Piotr , Tobiska Lutz
Published: December 2005

The study of flow behaviour in packed beds is an important part of the development of powerful and economical reactors. The considered averaged flow in the reactor channel filled with pelletes is modelled by the Brinkman‐Forchheimer‐extended Darcy equation. For the nonlinear problem subjected to Dirichlet boundary conditions we show existence and uniqueness (for small data) of weak solutions. The velocity profiles exhibit boundary layers which have to be resolved numerically. We present error estimates for inf‐sup stable finite element pairs. In the case of fully developed flow and high Reynolds number the finite element solution can be compared to the flow profile obtained by using the method of matched asymptotic expansions. Finally, numerical simulations for flows in fixed bed and packed bed membrane reactors are discussed. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Error estimates for discretizations of coupled electromagnetic‐mechanical problems
Authors: Stiemer Marcus
Published: December 2005

In this note, a method is outlined to obtain a priori error estimates for the finite element discretization of coupled electromagnetic mechanical problems as arise, e.g., in electromagnetic metal forming. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
FLIM ‐ A Variant of FEM based on Line Integration
Authors: Synka Josef , Kraus Johannes
Published: December 2005

A variant of the finite element method (FEM) for modelling and solving partial differential equations based on triangular and tetrahedral meshes is proposed. While FEM is based on integration over finite elements, the new approach ‐ briefly denoted as FLIM hereafter ‐ uses integration along edges (finite lines). The stiffness matrix, which ‐ for linear triangles and tetrahedra ‐ is identical with the one obtained with FEM, as well as the load vector can solely be obtained by summing up the edge contributions. This new variant requires much lower storage than FEM, especially for three‐dimensional problems, but yields the same approximation error and convergence rate as the finite element method. It is shown that its performance, when applied to linear problems, is in close agreement with the performance of the finite element method. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The numerical methods in the field of operators
Authors: Takači Djurdjica , Štrboja Mirjana
Published: December 2005

The approximate solution of a class of nonlinear differential equations, in the field of Mikusiński operators is constructed by using the Euler method. The obtained results are applied to a class of partial integro–differential equations. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Proteomics profiling of epidermal mucus secretion of a cichlid (Symphysodon aequifasciata) demonstrating parental care behavior
Authors: Chong Kenny , Joshi Shashikant , Jin Lam Toong , Shu‐Chien Alexander Chong
Published: December 2005

The discus fish (Symphysodon aequifasciata) is a cichlid demonstrating advanced mode of parental care towards fry. Both male and female fish utilized epidermal mucus secreted from specialized epidermal cells to feed developing fry. We utilized proteomics to compare protein profile from parental and nonparental fish. Gel analysis revealed a total of 35 spots that were up‐regulated in parental mucus. In tandem, another 18 spots were uniquely expressed in parental mucus. MS analysis of these spots identified proteins such as fructose biphosphate aldolase, nucleoside diphosphate kinase, and heat shock proteins, which are essential to support energy provision, cell repair and proliferation, stress mediation, and defense mechanism in parental fish during parental‐care period. Concurrently, the detection of several antioxidant‐related proteins such as thioredoxin peroxidase and hemopexin suggests a need to overcome oxidative stress during hypermucosal production in parental‐care behavior. A C‐type lectin was also found to be uniquely expressed in parental mucus and could have important role in providing antimicrobial defense to both parental fish and fry. In summary, our study shows that discus mucus proteome undergoes changes in protein expression during parental‐care period.
Spectroscopic Diagnostics of Atmospheric Pressure Helium Dielectric Barrier Discharges in Divergent Fields
Authors: Poenariu Viorel , Wertheimer Michael R. , Bartnikas Raymond
Published: December 2005

Summary: We present optical emission spectroscopy studies of atmospheric pressure glow discharges in flowing pure helium (He), and He/nitrogen (N2) mixtures. Two different metallic high‐voltage electrode geometries have been examined, namely needle and cylindrical, the grounded dielectric‐covered electrode being planar. The axial and radial distributions of gas temperature have been evaluated from rotational spectra of molecular nitrogen ion emissions as a function of the electrode geometries, the gap spacings and the partial pressure of N2 in He. Also, the spatiotemporal distribution of discharge species in the needle‐plane geometry and the link between gas temperature and light emission intensity are presented. The physical interpretations of these results are discussed with reference to recent work reported by the present authors and by others.

Axial and time‐dependent intensity distribution of the total light emission during the positive voltage half‐cycle, across a needle‐ (dielectric) plane gap.

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Axial and time‐dependent intensity distribution of the total light emission during the positive voltage half‐cycle, across a needle‐ (dielectric) plane gap.
Parametric Study of Zirconium Oxide Films Using Plasma‐Based Ion Implantation and Deposition
Authors: Yukimura Ken , Ono Hiroyuki , Akashi Shuhei , Ma Xinxin
Published: December 2005

Summary: Zirconium oxide films were prepared using a zirconium arc discharge in a gas mixture of argon‐diluted with oxygen, where the gas flow rate was varied from 100 sccm to 600 sccm, which corresponded to a gas pressure of 1.9 to 4.6 Pa. The voltage applied to the target was, unless otherwise specified, set to a value of −5 kV, with a pulse width of 20 µs at a repetition rate of 400 Hz. It was observed from XPS measurements that the oxygen and zirconium were mostly present in the deposited film in a stoichiometric state. The prepared films changed from amorphous state to orthorhombic structure by increasing the pressure of the gas mixture. At an applied voltage as high as −9 kV, the crystal size becomes small due to high energy ion bombardment. Thus, the structure of the prepared film is changed into a micro‐structural state. By applying a pulse voltage of −5 kV to the substrate, the deposited film shows a smooth surface, with roughness which is smaller by a factor of 1/7 compared to that in the absence of the applied voltage.

Films surface morphology as measured by AFM.

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Films surface morphology as measured by AFM.
Graft Polymerisation of Functional Acrylic Monomers onto Cotton Fibres Activated by Continuous Ar Plasma
Authors: Castelvetro Valter , Fatarella Enrico , Corsi Leopoldo , Giaiacopi Simone , Ciardelli Gianluca
Published: December 2005

Summary: Continuous cold Ar plasmas were used to activate the mercerised cotton fabric towards surface‐initiated graft polymerisation of glycidyl methacrylate, 2‐hydroxyethyl methacrylate (HEMA) and 1,1,2,2‐tetrahydroperfluorodecyl methacrylate (XFDMA). Single and multi‐step processes, carried out either in the plasma chamber (one‐step and two‐step processes) or ex situ after plasma treatment, were explored to optimise the grafting efficiency. The mechanical properties of the grafted cotton were substantially unaffected. Grafting with XFDMA gave good results only when the plasma activation was performed on monomer‐impregnated fabrics, as shown by gravimetry, ATR FT‐IR spectroscopy, and water and oil repellence tests. On the contrary, with HEMA better results were obtained by in situ grafting from monomer vapours.

Mercerized cotton fabric before (left) and after (right) graft polymerisation of the fluorinated methacrylate XFDMA from the plasma‐activated surface.

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Mercerized cotton fabric before (left) and after (right) graft polymerisation of the fluorinated methacrylate XFDMA from the plasma‐activated surface.
Structure/function of KRAB repression domains: Structural properties of KRAB modules inferred from hydrodynamic, circular dichroism, and FTIR spectroscopic analyses
Authors: Mannini Riccardo , Rivieccio Vincenzo , D'Auria Sabato , Tanfani Fabio , Ausili Alessio , Facchiano Aangelo , Pedone Carlo , Grimaldi Giovanna
Published: December 2005

The abundant zinc finger proteins (ZFPs) sharing the KRAB motif, a potent transcription repression domain, direct the assembly on templates of multiprotein repression complexes. A pivotal step in this pathway is the assembly of a KRAB domain‐directed complex with a primary corepressor, KAP1/KRIP‐1/TIF1β. The structure/function dependence of KRAB/TIF1β protein–protein interaction and properties of the complex, therefore, play pivotal roles in diverse cellular processes depending on KRAB‐ZFPs regulation. KRAB domains are functionally bipartite. The 42 amino acid‐long KRAB‐A module, indeed, is necessary and sufficient for transcriptional repression and for the interaction with the tripartite RBCC region of TIF1β, while the KRAB‐B motif seems to potentiate the assembly of the complex. The structural properties of KRAB‐A and KRAB‐AB domains from the human ZNF2 protein have been investigated by characterizing highly purified lone (A) and composite (AB) modules. Hydrodynamic and spectroscopic features, investigated by means of gel filtration, circular dichroism, and infrared spectroscopy, provide evidence that both KRAB‐A and KRAB‐AB domains present low compactness, structural disorder, residual secondary structure content, flexibility, and tendency to molecular aggregation. Comparative analysis among KRAB‐A and KRAB‐AB modules suggests that the presence of the ‐B module may influence the properties of lone KRAB‐A by affecting the structural flexibility and stability of the conformers. The combined experimental data and the intrinsic features of KRAB‐A and KRAB‐AB primary structures indicate a potential role of specific subregions within the modules in driving structural flexibility, which is proposed to be of importance for their function. Proteins 2006. © 2005 Wiley‐Liss, Inc.
A folding inhibitor of the HIV‐1 protease
Authors: Broglia R. A. , Provasi D. , Vasile F. , Ottolina G. , Longhi R. , Tiana G.
Published: December 2005

Because the human immunodeficiency virus type 1 protease (HIV‐1‐PR) is an essential enzyme in the viral life cycle, its inhibition can control AIDS. The folding of single‐domain proteins, like each of the monomers forming the HIV‐1‐PR homodimer, is controlled by local elementary structures (LES, folding units stabilized by strongly interacting, highly conserved, as a rule hydrophobic, amino acids). These LES have evolved over myriad generations to recognize and strongly attract each other, so as to make the protein fold fast and be stable in its native conformation. Consequently, peptides displaying a sequence identical to those segments of the monomers associated with LES are expected to act as competitive inhibitors and thus destabilize the native structure of the enzyme. These inhibitors are unlikely to lead to escape mutants as they bind to the protease monomers through highly conserved amino acids, which play an essential role in the folding process. The properties of one of the most promising inhibitors of the folding of the HIV‐1‐PR monomers found among these peptides are demonstrated with the help of spectrophotometric assays and circular dichroism spectroscopy. Proteins 2006. © 2005 Wiley‐Liss, Inc.
SSALN: An alignment algorithm using structure‐dependent substitution matrices and gap penalties learned from structurally aligned protein pairs
Authors: Qiu Jian , Elber Ron
Published: December 2005

In template‐based modeling of protein structures, the generation of the alignment between the target and the template is a critical step that significantly affects the accuracy of the final model. This paper proposes an alignment algorithm SSALN that learns substitution matrices and position‐specific gap penalties from a database of structurally aligned protein pairs. In addition to the amino acid sequence information, secondary structure and solvent accessibility information of a position are used to derive substitution scores and position‐specific gap penalties. In a test set of CASP5 targets, SSALN outperforms sequence alignment methods such as a Smith‐Waterman algorithm with BLOSUM50 and PSI_BLAST. SSALN also generates better alignments than PSI_BLAST in the CASP6 test set. LOOPP server prediction based on an SSALN alignment is ranked the best for target T0280_1 in CASP6. SSALN is also compared with several threading methods and sequence alignment methods on the ProSup benchmark. SSALN has the highest alignment accuracy among the methods compared. On the Fischer's benchmark, SSALN performs better than CLUSTALW and GenTHREADER, and generates more alignments with accuracy >50%, >60% or >70% than FUGUE, but fewer alignments with accuracy >80% than FUGUE. All the supplemental materials can be found at http://www.cs.cornell.edu/∼jianq/research.htm. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Optimal design of protein docking potentials: Efficiency and limitations
Authors: Tobi Dror , Bahar Ivet
Published: December 2005

Protein–protein docking is a challenging computational problem in functional genomics, particularly when one or both proteins undergo conformational change(s) upon binding. The major challenge is to define scoring function soft enough to tolerate these changes and specific enough to distinguish between near‐native and “misdocked” conformations. Using a linear programming technique, we derived protein docking potentials (PDPs) that comply with this requirement. We considered a set of 63 nonredundant complexes to this aim, and generated 400,000 putative docked complexes (decoys) based on shape complementarity criterion for each complex. The PDPs were required to yield for the native (correctly docked) structure a potential energy lower than those of all the nonnative (misdocked) structures. The energy constraints applied to all complexes led to ca. 25 million inequalities, the simultaneous solution of which yielded an optimal set of PDPs that discriminated the correctly docked (up to 4.0 Å root‐mean‐square deviation from known complex structure) structure among the 85 top‐ranking (0.02%) decoys in 59/63 examined bound–bound cases. The high performance of the potentials was further verified in jackknife tests and by ranking putative docked conformation submitted to CAPRI. In addition to their utility in identifying correctly folded complexes, the PDPs reveal biologically meaningful features that distinguish docking potentials from folding potentials. Proteins 2006. © 2005 Wiley‐Liss, Inc.
The astroglial cell that guides nerve fibers from growth cone to synapse in organotypic cultures of the fetal mouse spinal cord
Authors: Sobkowicz Hanna M. , Waclawik Andrew J. , August Benjamin K.
Published: December 2005

We present electron microscopic and autoradiographic studies done using organotypic cultures of spinal cord explants excised from 15 days of gestation mouse embryos. Nerve fibers growing from the spinal cord explant carry at their tips immature mitotic astrocytic cells that lead their growth cones. These glial cells divide only during the active phase of neuronal growth, and correspond ultrastructurally to radial glia. They provide a specific cellular substrate for neuronal growth. Some growth cones form axoglial synapses with smooth membranes of immature glial cells. In contrast, maturing glial cells sprout cytoplasmic processes that tightly wrap individual growth cones and effectively arrest their growth. Next, the processes gather nerve endings into islets and nerve fibers into bundles. After internalizing nerve endings, the glial processes withdraw, bringing the endings into contact with each other. The direct neuronal appositions lead to the transformation of growth cones into presynaptic endings, signaled by their collection of presynaptic vesicles. Clustering of the vesicles at presynaptic axoglial or axodendritic membranes indicates the onset of synaptogenesis—completed by differentiation of spinous and compound synapses. Concomitant with the progress of synaptogenesis, astrocytic investment within the neuropil progressively diminishes. The differentiating astrocytic processes show secretory and tethering activity toward nerve fibers and their endings. Our observations demonstrate that astroglial cells—depending on their developmental stage—first promote and then arrest neuronal growth, and induce synaptogenesis. Thus, at any time, the growing nerve fibers are not only supported but also controlled by the astroglial cells. Synapse 59:183–200, 2006. © 2005 Wiley‐Liss, Inc.
Autoradiography of 2‐[18F]F‐A‐85380 on nicotinic acetylcholine receptors in the porcine brain in vitro
Authors: Deuther‐Conrad Winnie , Wevers Andrea , Becker Georg , Schildan Andreas , Patt Marianne , Sabri Osama , Steinbach Jörg , Brust Peter
Published: December 2005

Noninvasive molecular imaging of subtypes of neuronal nicotinic acetylcholine receptors (nAChRs) will provide information on the role of these receptors in neurodegenerative diseases. The binding of the positron emission tomography ligand 2‐[18F]F‐A‐85380 to nAChRs was investigated in the porcine brain by quantitative autoradiography in vitro. The high‐affinity binding of 2‐[18F]F‐A‐85380 to each of the investigated 12 brain areas was saturable and apparently monophasic (e.g., apparentKDvalue of 1.72 nM in the thalamus). The highest density of specific binding sites was observed in the thalamus (1,158 fmol/mg protein), and the lowest density was measured in the cerebellar gray matter (11 fmol/mg protein). An attempt to assess nAChR subtype specificity of 2‐[18F]F‐A‐85380 was made by competitive autoradiography. Binding of 2‐[18F]F‐A‐85380 coincubated with 2‐F‐A‐85380, epibatidine, cytisine, or methyllycaconitine, respectively, indicated a specificity of 2‐[18F]F‐A‐85380 to β2‐containing nAChRs in the porcine brain. The autoradiographic data confirmed the suitability of swine as a model for the evaluation of radioligands designed for imaging of nAChR subtypes in the living brain. Synapse 59:201–210, 2006. © 2005 Wiley‐Liss, Inc.
Quantitative autoradiography of ligands for dopamine receptors and transporters in brain of Göttingen minipig: Comparison with results in vivo
Authors: Minuzzi Luciano , Olsen Aage Kristian , Bender Dirk , Arnfred Sidse , Grant Rebecca , Danielsen Erik H. , Cumming Paul
Published: December 2005

The pig has been used as animal model for positron emission tomography (PET) studies of dopamine (DA) receptors and pharmacological perturbations of DA neurotransmission. However, the binding properties of DA receptors and transporters in pig brain have not been characterized in vitro. Therefore, the saturation binding parameters of [3H]SCH 23390 for DA D1 receptors and [3H]raclopride for DA D2/3 receptors were measured by quantitative autoradiography in cryostat sections from brain of groups of 8 week old and adult female Göttingen minipigs. The magnitudes of Bmax and Kd for these ligands were similar in young and old pigs, and were close to those reported for rat and human brain. Furthermore, gradients in the concentrations of D1 and D2/3 sites in striatum measured in vitro agreed with earlier findings in PET studies. However, the dopamine transporter (DAT) ligand [3H]GBR12935 did not bind in pig brain cryostat sections. Whereas the tropane derivative [125I]RTI‐55 labeled serotonin transporters (serotonin transporter (SERT)) in pig brain, use of the same ligand under conditions specific for DAT, revealed a pattern of binding similar to that observed for SERT conditions. Parallel studies revealed the presence of DAT in rat and ferret brain. The distribution volume (Vd) of the selective DAT ligand [11C]NS2214 ([11C]Brasofensine) was mapped in groups of normal and MPTP‐lesioned Göttingen miniature pigs. The in vivo pattern of Vd matched the distribution of SERT in vitro, and did not differ between the normal pigs and the lesioned animals with documented 60% DA depletions. However, the pattern of specific binding of the selective noradrenaline transporter ligand (S,S)‐[11C]MeNER in a single Landrace pig showed that, of the three monoamine transporters, only DAT could not be detected in pig brain. We conclude that the pig is a suitable model for PET studies of DA D1 and D2/3 binding sites, which are fully developed on the eighth postnatal week. However, well‐characterized piperazine and tropane radioligands failed to recognize DAT in pig brain; the two tropane radioligands lacked pharmacological specificity for DAT and SERT in pig brain in vitro and in vivo. Synapse 59:211–219, 2006. © 2005 Wiley‐Liss, Inc.
Variability of the MAX and MIN Statistic: A Theory of the Quantile Spread as a Function of Sample Size
Authors: Townsend James T. , Colonius Hans
Published: December 2005

The maximum and minimum of a sample from a probability distribution are extremely important random variables in many areas of psychological theory, methodology, and statistics. For instance, the behavior of the mean of the maximum or minimum processing time, as a function of the number of component random processing times (n), has been studied extensively in an effort to identify the underlying processing architecture (e.g., Townsend & Ashby, 1983; Colonius & Vorberg, 1994). Little is known concerning how measures of variability of the maximum or minimum change with n. Here, a new measure of random variability, the quantile spread, is introduced, which possesses sufficient strength to define distributional orderings and derive a number of results concerning variability of the maximum and the minimum statistics. The quantile spread ordering may be useful in many venues. Several interesting open problems are pointed out.