bluuebunny/crossref_metadata_2025 huggingface dataset:
Eddy‐current braking of a translating solid bar by a magnetic dipole
Authors: Kirpo Maksims , Boeck Thomas , Thess Andrè
Published: November 2010

The paper addresses the problem of a conducting rectangular bar of square cross‐section which is moving with constant velocity in the field of an arbitrarily oriented magnetic dipole. The braking Lorentz force on the bar is obtained by FEM and compared with the analytical solution for a moving infinite plate in the field of a magnetic dipole [2]. The computation of the induced currents requires solution of a Laplace equation with mixed boundary conditions for the electric potential inside the moving bar. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
An inhomogeneous, anisotropic, elastically modified Gibbs­Thomson law as singular limit of a diffuse interface model
Authors: Kraus Christiane , Garcke Harald
Published: November 2010

We consider the sharp interface limit of a diffuse phase‐field model with prescribed total mass taking into account a spatially inhomogeneous, anisotropic interfacial energy and an elastic energy. The main aim is to establish a weak formulation of an inhomogeneous, anisotropic, elastically modified Gibbs‐Thomson law in the sharp interface limit. To this end we pass to the limit in the weak formulation of the Euler‐Lagrange equation of the diffuse phase‐field energy. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
1D wave propagation in a rod: analytic treatment for non‐trivial boundary conditions
Authors: Schwarz Cornelia , Werner Ewald , Dirschmid H.J.
Published: November 2010

An analytic solution method for the one‐dimensional wave propagation problem in a rod based on the Laplace transform is applied to a simple stamping model. While the rod is mounted at its lower end to a spring, it is hit at its upper end by an impacting mass, the separation of which can be correctly treated by the method. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Multiscale Simulation of the mechanical properties and the structural dynamics of a copper foam
Authors: Schwarzer Daniel , Proppe Carsten
Published: November 2010

In this contribution, a simulation chain for the prediction of the structural dynamics behavior of metal foam is proposed: Starting with investigations of the mesoscopic structure and topology, the linear elastic material properties and their scatter are computed with the help of mesoscopic non‐representative volume elements. Also their probability functions are estimated. In order to be able to describe the mechanical properties as random fields, the autocorrelation function and the power spectral density are determined.

The next step in the proposed simulation chain is to generate realisations of the random fields with the help of the Karhunen‐Loeve expansion or the Spectral Representation. Afterwards, these realisations are used in Monte‐Carlo‐Simulations on the macroscale in order to predict the eigenfrequencies of beams and their scatter.

With this multiscale approach, the mechanical properties of an open‐celled Copper foam are determined by simulations and the eigenfrequencies are compared to experimental results. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Evolutionary Iterative Optimum‐Optimorum Theory with Aerospace Applications
Authors: Nastase Adriana
Published: November 2010

In this paper, the author tries to improve the accuracy of the start solutions for the aerodynamical global optimization of the FC shapes by replacing the three‐dimensional, analytical hyperbolical potential solutions with new own developed hybrid numerical solutions for the Navier‐Stokes layer (NSL). These solutions have also analytical properties and are split. It follows a more rapid convergence and, consequently, a speed up of the computation time. The evolutionary iterative optimum‐optimorum theory uses these hybrid solutions after the first step of iteration and easy allows the weak interactions with the structure, via new and/or modified initial constraints, requested for the structure point of view. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Optimal Open‐Loop Feedback Control of Robots under uncertainty
Authors: Schacher Michael
Published: November 2010

The aim of this presentation is to construct an optimal open‐loop feedback controller for robots, which takes into account stochastic uncertainties. This way, optimal regulators being insensitive with respect to random parameter variations can be obtained.

Usually, a precomputed feedback control is based on exactly known or estimated model parameters. However, in practice, often exact informations about model parameters, e.g. the payload mass, are not given. Supposing now that the probability distribution of the random parameter variation is known, in the following, stochastic optimisation methods will be applied in order to obtain robust open‐loop feedback control.

Taking into account stochastic parameter variations, the method works with expected cost functions evaluating the primary control expenses and the tracking error. The expectation of the total costs has then to be minimized. Corresponding to Model Predictive Control (MPC), here a sliding horizon is considered. This means that, instead of minimizing an integral from a starting time point t0 to the final time tf, the future time range [t; t+T], with a small enough positive time unit T, will be taken into account. The resulting optimal regulator problem under stochastic uncertainty will be solved by using the Hamiltonian of the problem. After the computation of a H‐minimal control, the related stochastic two‐point boundary value problem is then solved in order to find a robust optimal open‐loop feedback control.

The performance of the method will be demonstrated by a numerical example, which will be the control of robot under random variations of the payload mass. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Optimal design and sensitivity of large scale plane frames for the case of uncertainty
Authors: Zier Simone
Published: November 2010

This paper deals with the optimal design and the robustness of large scale plane frames in dependence of their height. Using the first collapse theorem, the necessary and sufficient survival conditions of an elasto‐plastic structure consist of the yield condition and the equilibrium condition. The basis for our consideration is provided by a plane n‐storey frame which will be increased successively, and which is affected by applied random forces and moments. Taking into account these random applied loads, we get a stochastic structural optimization problem which cannot be solved using the traditional methods. Instead of that, an appropriate (deterministic) substitute problem is formulated. First, the recourse problem will be formulated in general and in the standard form of stochastic linear programming (SLP), and after the formulation of the stochastic optimization problem, the Recourse Problem based on Discretization (RPD) is introduced as a representative of substitute problems. The resulting (large scale) linear program (LP) can be solved efficiently by means of usual LP‐solvers. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Error bounds for non‐selfadjoint PDE eigenvalue problems
Authors: Mehrmann Volker , Międlar Agnieszka
Published: November 2010

We introduce a posteriori bounds for the eigenfunctions (eigenvalues) of non‐selfadjoint diagonalizable PDE‐eigenvalue problems which incorporates an inexact solution of the corresponding generalized matrix eigenvalue problem. The estimates combine the standard perturbation results with the saturation assumption for the eigenfunctions. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
On the Convergence Theory of Preconditioned Subspace Iterations for Eigenvalue Problems
Authors: Zhou Ming
Published: November 2010

We consider preconditioned subspace iterations for the numerical solution of discretized elliptic eigenvalue problems. For these iterative solvers, the convergence theory is still an incomplete puzzle. We generalize some results from the classical convergence theory of inverse subspace iterations, as given by Parlett, and some recent results on the convergence of preconditioned vector iterations. To this end, we use a geometric cone representation and prove some new trigonometric inequalities for subspace angles and canonical angles. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Choosing norms in adaptive FSI calculations
Authors: Birken Philipp , Quint Karsten , Hartmann Stefan , Meister Andreas
Published: November 2010

The thermal coupling of a fluid and a structure is of great significance for many industrial processes. As a model for cooling processes in heat treatment of steel we consider the coupling of the compressible Navier‐Stokes equations along a surface with the heat equation. A partitioned approach is considered, where different codes for the sub‐problems are employed. We use a finite volume method (FVM) for the fluid and a finite element method (FEM) for the heat equation.

The semi‐discrete coupled system is solved using stiffly stable SDIRK methods, where on each stage an FSI problem is solved. This has a black box character, since a stage calculation corresponds to a specific Backward‐Euler integration step. For the resulting method it was shown by numerical experiments in [1] that second order convergence rate is obtained. This property is used for a simple time‐step control, which saves considerable computational time and guarantees a specified maximum error of time integration. Here, we will consider different norms for measuring the error. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A Weakly Singular Collocation Boundary Element Formulation for Linear Poroelasticity
Authors: Messner M. , Schanz M.
Published: November 2010

One major problem when discretizing boundary integral equations are the spatial singularities of the appearing integral kernels. For some classical problems, e.g. elastodynamics, this problem has been solved through partial integration yielding at most weakly singular integrals. The aim is to adopt this procedure to the modelling of porous media with boundary elements. This idea is justified by the fact that in saturated linear poroelasticity, Biot's theory couples a linear elastic solid with an acoustic fluid. Therefore, the reduction of the singularities can be achieved by the same techniques as for those problems. Due to the use of the convolution quadrature method, which permits a time domain discretization of boundary integral equations based on the Laplace domain fundamental solution, this is done in Laplace domain. For domains with closed surfaces, a weakly singular representation of the first boundary integral equation is presented. This equation is used for a collocation boundary element formulation involving only the numerical evaluation of weakly singular integrals. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Numerical analysis for phase field simulations of moving interfaces with topological changes
Authors: Bartels Sören , Müller Rüdiger
Published: November 2010

Phase field methods are a widely accepted tool for the approximation of moving free interfaces in sharp interface problems. Topological changes in the solution, such as nucleation or vanishing of particles or merging or pinching of interfaces, lead to singularities in the free boundary. In the sharp interface model, these singularities cause both numerical and theoretical problems, whereas they are handled “automatically” in phase field simulations. Phase field models contain a length scale ε > 0 that vanishes in the sharp interface limit. Therefore, when ε → 0, practical numerical methods have to be robust in the sense that error estimates may only depend polynomially on ε‐1, not exponentially. We show that robust error control is possible past the occurrence of topological changes and without restrictive assumptions on the initial data. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Parallelization of the time integration for time‐periodic flow problems
Authors: Obrist Dominik , Henniger Rolf , Arbenz Peter
Published: November 2010

The solution of a time‐periodic flow problem is expanded into a discrete Fourier series. This yields a large nonlinear system of equations which can be solved in parallel. We show for a one‐dimensional model problem that this method for the parallelization of the time domain converges in a robust and efficient manner. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A Posteriori Estimates for Modelling Errors of the Stationary Diffusion Equation with Complicated Coefficients
Authors: Repin Sergej , Samrowski Tatiana , Sauter Stefan
Published: November 2010

In this paper, we suggest a new computational strategy for diffusion type problems with coefficients that may sharply change values and have a complicated distribution over the domain. We solve models, which approximate the coefficients, numerically and estimate the corresponding approximation errors by the a posteriori estimates of functional type. We show that the modelling error can be also explicitly calculated. This allows to obtain numerical solutions of complicated diffusion problems by solving much simpler problems that do not require full detailization of the structure of coefficients. Balancing modelling and discretization errors provides an economical way of getting an approximate solution with an a priori given accuracy. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Numerical treatment of a free surface problem in ferrohydrodynamics
Authors: Knobloch Petr , Schütze Stephan , Tobiska Lutz
Published: November 2010

The interactions between a ferrofluid with a free surface and an immersed permanent magnet are studied. We consider a strategy for the computation of equilibrium positions of the free surface for various geometric positions of the magnet. It will be used for the numerical simulation of devices that are used in spacecraft technology to damp oscillations of satellites. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Solving optimal control problems by using inherent dynamical properties
Authors: Flaßkamp Kathrin , Ober‐Blöbaum Sina , Kobilarov Marin
Published: November 2010

We present a technique for computing optimal control trajectories by exploiting the inherent structure of the dynamics arising from symmetries and invariant (un)stable manifolds of fixed points. Our approach is based on sequencing motions along relative equilibria and invariant manifolds joined by simple optimized maneuvers. Our main goal is to compute an approximate globally optimal solution which can serve as a good initial guess for iterative nonlinear control optimization. The described approach is exemplified by the optimal control of the spherical pendulum. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Shape Optimization for Stokes Flows using Conformal Metrics
Authors: Leithäuser Christian , Feßler Robert , Pinnau René
Published: November 2010

We derive a shape optimization approach for a two‐dimensional Stokes flow problem. Our goal is to compute a geometry whose wall shear stress is L2‐close to a desired target stress. Computations are carried out on a fixed domain, while shape variations are described through conformal metric changes. Tools from differential geometry are used to handle metric dependent operators. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Error analysis and improvement of first‐order design sensitivity relations
Authors: Materna Daniel , Barthold Franz‐Joseph
Published: November 2010

This contribution is concerned with novel approaches for error estimation and the improvement of first‐order design sensitivities for the state. These approaches are based on an exact representation of the design sensitivity of the state, which is obtained by performing different Taylor expansions with integral remainders. We consider a general variational framework and present the application of the proposed approach to shape sensitivity for the model problem of nonlinear elasticity. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Reconstruction of Geophysical Layers with Shape Optimization and Level Set Methods
Authors: Papadopoulos Dimitrios , Herty Michael , Behr Marek , Rath Volker
Published: November 2010

A shape optimization method is used to reconstruct the unknown shape of geophysical layers from boundary heat flux measurements by the use of adjoint fields and level sets. The identification of the shape of the geophysical layers by boundary heat flux measurements is necessary for the efficient use of geothermal energy. The method of speed is used to calculate the shape sensitivities, and the continuous adjoint approach is followed for the computation of the shape derivatives. The unknown shape is described with the help of the level set function; the advantage of the shape function is that no mesh movement or remeshing is necessary, but an additional Hamilton‐Jacobi equation has to be solved. This equation is solved in an artificial time, where the velocity represents the movement in the direction of the normal vector of the interface. For large optimization steps, re‐initialization of the level set function is also necessary, in order to keep the magnitude of the level set function near unity and also to smooth the level set function. Numerical results are given for measured heat fluxes on the boundary of the domain for different time steps and conductivity ratios. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Adjoint Based Optimization of a Free Surface Flow for Film Casting
Authors: Repke Sabine , Marheineke Nicole
Published: November 2010

Motivated by the industrial process of film casting, we discuss an optimal control approach for a viscous free surface flow that is asymptotically described by 2d Stokes equations. The aim is to optimize the shape of the free boundaries by adjusting the ambient pressure. A PDE‐constrained optimization problem is set up, where the free surfaces are described as graphs. The first‐order optimality system is derived via the Lagrangian formalism. The resulting minimization problem is solved by a steepest descent method, where the gradient is expressed in terms of the adjoint variables. Numerical results are presented. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Suboptimality Estimates for the Semi‐Discretized LQR Problem for Parabolic PDEs
Authors: Benner Peter , Saak Jens
Published: November 2010

The linear quadratic regulator problem (LQR) for parabolic partial differential equations (PDEs) has been understood to be an infinite‐dimensional Hilbert space equivalent of the finite‐dimensional LQR problem known from mathematical systems theory. The matrix equations from the finite‐dimensional case become operator equations in the infinite‐dimensional Hilbert space setting. A rigorous convergence theory for the approximation of the infinite‐dimensional problem by Galerkin schemes in the space variable has been developed over the past decades. Numerical methods based on this approximation have been proven capable of solving the case of linear parabolic PDEs. Embedding these solvers in a model predictive control (MPC) scheme, also nonlinear systems can be handled. Convergence rates for the approximation in the linear case are well understood in terms of the PDE's solution trajectories, as well as the solution operators of the underlying matrix/operator equations. However, in practice engineers are often interested in suboptimality results in terms of the optimal cost, i.e., evaluation of the quadratic cost functional. In this contribution, we are closing this gap in the theory. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Identification of Temperature Dependent Parameters in Radiative Heat Transfer
Authors: Tse Oliver , Pinnau René , Siedow Norbert
Published: November 2010

Laser‐induced thermotherapy (LITT) is an established minimally invasive percutaneous technique of tumor ablation. Nevertheless, there is a need to predict the effect of laser applications and optimizing irradiation planning in LITT. Optical attributes (absorption, scattering) change due to thermal denaturation. The work presents the possibility to identify these temperature dependent parameters from given temperature measurements via an optimal control problem. The solvability of the optimal control problem is analyzed and results of successful implementations are shown. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Optimal Control of the Euler Equations via Relaxation Approaches
Authors: Veelken Sonja , Herty Michael , Ngnotchouye Jean‐Medard T. , Banda Mapundi K.
Published: November 2010

We discuss two linear relaxation approaches to the optimal control of nonlinear hyperbolic systems, in particular the control of Euler flows in gas dynamics. The first method is a relaxation system that is due to Jin and Xin [2], the second one is a Lattice‐Boltzman approach [3], where we use one spatial dimension and five velocities (D1Q5 model). Both methods are incorporated in an adjoint based steepest‐descent algorithm for the optimisation. Convincing numerical results are presented for both methods for an example with discontinuous solutions. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Positivity inheritance for linear problems
Authors: Baum A.K. , Mehrmann Volker
Published: November 2010

We discuss the numerical solution of positive Differential‐Algebraic‐Equations (DAEs). For Ordinary Differential Equations (ODEs) where the system matrix is a ‐M‐Matrix, Runge‐Kutta‐ or Multistep‐Method are positive if the stepsize is chosen within the absolutely monotonicity radius of the considered method. We extend this concept to matrix pairs and present conditions for positivity preserving discretizations of linear, time‐invariant DAEs. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Worst case vs. average performance estimates for unconstrained NMPC schemes
Authors: Grüne Lars
Published: November 2010

We consider performance estimates for unconstrained NMPC schemes under a controllability assumption. By means of worst case and average estimates, we investigate the effect of varying control horizons on the performance and compare the results with numerical simulations. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A Multi‐Layered Potential Field Method for Multi‐Agent Navigation, Searching and Tracking
Authors: Hackbarth Axel , Hedrick Karl , Kreuzer Edwin
Published: November 2010

Collaborating multi‐agent systems can handle complex tasks with several or changing mission objectives. We developed a potential field method that allows various information layers to influence the control over a group of vehicles. The gradient of the potential field is the driving force for local action, whereas the global waypoint is determined by the minimum of the agent's potential field. The driving force to the global waypoint is a virtual spring‐mass‐damper system that pulls the agent towards its waypoint, restricted by the local gradient of the agent's potential field. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Flatness based trajectory planning for the shallow water equations
Authors: Knüppel Torsten , Woittennek Frank , Rudolph Joachim
Published: November 2010

A flatness based feed‐forward control design approach for an open channel flow modelled by the shallow water equations is discussed. The control input consists of the adjustable height of opening of a delimiting sluice gate. In order to compute the trajectory of the control input, the problem is reduced to an initial value problem w.r.t. the spatial coordinate. The solution to this problem can be obtained with the method of characteristics. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Certification with optimal control strategies
Authors: Leyendecker Sigrid , Lucas Leonard J. , Owhadi Houman , Ortiz Michael
Published: November 2010

The optimal control methodology called concentration‐of‐measure optimal control (COMOC), seeks to minimise a concen‐ tration‐of‐measure upper bound on the probability of failure of an uncertain system. This bound is computed for a system characterised by a single performance measure depending on random inputs.

This work considers controlled multibody dynamics taking place in an uncertain environment. The goal is to quantify uncertainty in a controlled robot manoeuvre and to minimise the probability of failure with regard to a performance measure. First, a deterministic optimal control problem is solved, yielding state and control trajectories that minimise an objective function. Boundary conditions for the optimal control problem are chosen such that the system performs ideally in the sense of the performance measure. Secondly, the obtained manoeuvre is reconsidered in the presence of uncertainty. Using a concentration‐of‐measure inequality, a rigorous upper bound for the probability of failure is derived. Finally, an optimisation is performed that searches for a control sequence (in the neighbourhood of the given one), that minimises the probability of failure. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
On Passivity‐Based Control of Non‐Classical Electromechanical Systems
Authors: Müller Andreas , Jungnickel Uwe , Kielau Gerald , Maiser Peter
Published: November 2010

Passivity‐based control has exclusively been pursued for dynamical systems possessing energetic state functions that are quadratic in the generalized velocities. This assumption does not apply to many dynamical systems, for instance in electromechanics, thus passivity‐based control has not been established for these classes of systems. This contribution presents an augmented PD control scheme for such systems. To this end the system dynamics is represented in the event space considered as a Finsler space. It is shown that in this setting the skew symmetry property is retained. A passivity‐based augmented PD controller is designed in the event space, and restricted to the configuration space giving rise to a passivity‐base control law. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Modal Coupling for Active Damping of Load Swing of Container Cranes
Authors: Kreuzer Edwin , Rapp Christian
Published: November 2010

Oscillation control of container handling is dominated by open‐loop or closed‐loop control of the crane trolley, which highly effects the crane operator's well‐being. An alternative actuating approach is presented using the hoists of the crane system. Simulation and test stand results prove the effect of modal coupling control of container handling and its capability to assure improved work environment conditions for the operator of container cranes. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Flatness‐based control without prediction: example of a vibrating string
Authors: Rudolph Joachim , Woittennek Frank
Published: November 2010

Stable trajectory tracking by boundary control is discussed for a string with a mass at its free end. Based on the known fact that the ring of operators used to describe the system is a Bézout ring it is shown that predictions are not required for stabilization if distributed delays are admitted. The method is rather general for systems of boundary coupled wave equations with boundary control that can be modeled as delay systems with commensurate delays. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The inverse syzygy problem in algebraic systems theory
Authors: Seiler Werner M. , Zerz Eva
Published: November 2010

We present a constructive solution of the inverse syzygy problem over arbitrary coherent rings and show how it can be used to compute certain extension groups. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Proper Orthogonal Decomposition for steady aerodynamic applications
Authors: Vendl Alexander , Faßbender Heike
Published: November 2010

An approach combining proper orthogonal decomposition (POD) with linear regression, which is called gappy POD, is used to obtain complete flow solutions in steady aerodynamic applications from knowledge of a (suitable) POD basis and the solution at very few points. In aerodynamics the partial or gappy data can be gathered by wind tunnel experiments. The effectiveness of the Gappy POD will be demonstrated on an industrial testcase of the wing‐body configuration MEGAFLUG. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Displacement Regularization with Application to Image Zooming
Authors: Lenzen Frank
Published: November 2010

We study the problem of displacement errors, i.e. errors induced by a sampling process with distorted locations of the sampling points. Starting with a non‐convex regularization method, we apply a semi‐group concept and derive a partial differential equation, which allows for correcting displacement errors.

As main application for correction of displacement errors we consider image interpolation, in particular zooming, of digital color images. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Some contributions to the model order reduction of large scale non‐linear electric circuits
Authors: Amorocho D. Juan Pablo , Faßbender Heike
Published: November 2010

Model order Reduction (MOR) has become an ubiquitous technique in the simulation of large‐scale dynamical systems (i.e. 104 and more equations). One technique for non‐linear MOR is the trajectory piecewise‐linear approach (TPWL) [1]. TPWL approximates a non‐linear differential system by a weighted sum of linear systems which have a significantly reduced number of equations. One open question is which weight representations provide physical meaning of the weighted sum [2]. In this article we propose two representations. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Highly scalable multigrid algorithm for particle simulation
Authors: Bolten Matthias
Published: November 2010

We present a highly scalable method for the calculation of effects due to the Coulomb potential in atomistic systems. The method is based on a mathematical consistent formulation of the Coulomb problem in terms of the solution of a special Poisson equation. For the solution of these PDE a multigrid method is used. The whole method is parallelized using domain splitting and shows a very good strong scaling behavior. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Aspects of the Facet‐Edge Data Structure for the Construction of Voronoi Cells
Authors: Weber Christoph , Loehnert Stefan , Wriggers Peter
Published: November 2010

The construction of Voronoi diagrams has two main aspects: The construction algorithm and the data structure. For the construction of planar Voronoi diagrams e.g. the well known plane sweep algorithm can be applied. Another efficient method is the incremental construction of the Delaunay triangulation by using the quad‐edge data structure. Within this data structure the Delaunay triangulation is treated as a planar graph. Incremental construction implies that manipulations of the triangulation are allowed. Its Voronoi diagram is obtained simply by accessing the triangulation's dual graph. We extend this method to tree dimensions, by implementing a 3D Delaunay triangulation on the facet‐edge data structure. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Heterogeneous Coupling: A Comparison of two Approaches for the Modeling of thin Structures
Authors: Groß Christian , Krause Rolf , Steiner Johannes
Published: November 2010

Two different approaches for the modeling of a heterogeneous model consisting of, e.g., bone and ligaments, are presented and compared along a simple model problem. We describe both methods and briefly discuss their advantages and disadvantages. Furthermore, we present first numerical results in 3D. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Verified Distance Computation Between Convex Hulls of Octrees Using Interval Optimization Techniques
Authors: Dyllong Eva , Kiel Stefan
Published: November 2010

Distance computation is an important task in many application areas, including biomechanics, robot systems and computer games. Depending on the intended use, requirements differ. For example, in a medical context, a verified result may be of interest. In this paper we will demonstrate the use of an interval optimization algorithm for computing a verified enclosure of the minimum distance between the convex hulls of two octrees. We will also discuss runtime improvements. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Numerical modelling of surface water waves generated by moving underwater landslide on irregular bottom
Authors: Shokina Nina
Published: November 2010

The numerical modelling of surface water waves generated by a moving underwater landslide on irregular bottom is considered. The non‐linear shallow water model is used with taking into account bottom mobility. The equations are obtained for an underwater landslide movement under the action of gravity force, buoyancy force, friction force and water resistance force. The predictor‐corrector scheme [5], preserving the monotonicity of the numerical solution profiles in a linear case, is used on adaptive grids. The scheme is validated on the problem with a known analytical solution. The analysis is done for the dependencies of wave regimes on bottom slope, initial landslide depth, its length and width. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Model reduction via quasistatic approximations
Authors: Weber Steffen , Arnold Martin
Published: November 2010

Stiff terms in second‐order differential equations may cause long computation time due to high frequencies. Quasi‐static approximations eliminate these high frequency solution components by neglecting inertia forces. In this interpretation, the equations of motion of systems with small masses correspond to a singularly perturbed problem. Results from singular perturbation theory will be extended to problems with perturbations of more than two different orders of magnitude. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The Machine of Bohnenberger: Bicentennial of the Gyro with Cardanic Suspension
Authors: F. Wagner Jörg , Trierenberg Andor
Published: November 2010

In 2004, a gyro with cardanic suspension was recovered in the physical collection of a school in Tübingen, Germany. Up to now, this instrument seems to be the only original corresponding explicitly with the first systematic explanation of such an apparatus. This description dates back to 1817 and was written by the inventor J.G.F. Bohnenberger (1765‐1831), who called the device simply Machine. At that time, Bohnenberger was professor for mathematics, physics, and astronomy at the University of Tübingen as well as the scientific head of the historic Württemberg land surveying. The discovery made aware that the historical background of the Machine of Bohnenberger was mainly unexplained. This is remarkable as the instrument was the basis for Foucault's famous work on gyros and as it paved the way to important mechanical navigation instruments like the directional gyro, the artificial horizon, and finally inertial platforms. Therefore, the finding in Tübingen prompted the authors to search for additional historical documents sheding light on Bohnenberger's invention. Meanwhile, several original specimen manufactured by Bohnenberger's instrument maker J.W.G. Buzengeiger (1778‐1836) could be identified, and it was possible to narrow the invention down to the year 1810. The paper outlines the historical background of the Machine of Bohnenberger currently known and sketches the biography of its inventor. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
L1‐regularisation for ill‐posed problems in variational data assimilation
Authors: Freitag Melina A. , Nichols Nancy K. , Budd Chris J.
Published: November 2010

We consider four‐dimensional variational data assimilation (4DVar) and show that it can be interpreted as Tikhonov or L2‐regularisation, a widely used method for solving ill‐posed inverse problems. It is known from image restoration and geophysical problems that an alternative regularisation, namely L1‐norm regularisation, recovers sharp edges better than L2‐norm regularisation. We apply this idea to 4DVar for problems where shocks and model error are present and give two examples which show that L1‐norm regularisation performs much better than the standard L2‐norm regularisation in 4DVar. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Goal‐Oriented Adaptivity for Optimization of Elliptic Systems subject to Pointwise Inequality Constraints: Application to Free Material Optimization
Authors: Wollner Winnifried
Published: November 2010

We are concerned with the derivation of goal‐oriented error estimates in the context of free material optimization. We will discuss the derivation of an error representation with respect to the cost functional of the optimization problem. Then we will use this representation in order to obtain a computable error estimator. The efficiency of the estimator is shown on a model problem in free material optimization. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A Regularized Sharp Interface Model for Phase Transformation Accounting for Prescribed Sharp Interface Kinetics
Authors: Hildebrand Felix , Miehe Christian
Published: November 2010

The macroscopic mechanical behavior of multi‐phasic materials depends on the formation and evolution of their microstructure by means of phase transformation. In case of martensitic transformations, the resulting phase boundaries are sharp interfaces. We carry out a geometrically motivated discussion of the regularization of such sharp interfaces by use of an order parameter/phase‐field and exploit the results for a regularized sharp interface model for two‐phase elastic materials with evolving phase boundaries. To account for the dissipative effects during phase transition, we model the material as a generalized standard medium with energy storage and a dissipation function that determines the evolution of the regularized interface. Making use of the level‐set equation, we are thereby able to directly translate prescribed sharp interface kinetic relations to the constitutive model in the regularized setting. We develop a suitable incremental variational three‐field framework for the dissipative phase transformation problem. Finally, the modeling capability and the associated numerical solution techniques are demonstrated by means of a representative numerical example. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Structures of the first and second double‐stranded RNA‐binding domains of human TAR RNA‐binding protein
Authors: Yamashita Seisuke , Nagata Takashi , Kawazoe Masahito , Takemoto Chie , Kigawa Takanori , Güntert Peter , Kobayashi Naohiro , Terada Takaho , Shirouzu Mikako , Wakiyama Motoaki , Muto Yutaka , Yokoyama Shigeyuki
Published: November 2010

The TAR RNA‐binding Protein (TRBP) is a double‐stranded RNA (dsRNA)‐binding protein, which binds to Dicer and is required for the RNA interference pathway. TRBP consists of three dsRNA‐binding domains (dsRBDs). The first and second dsRBDs (dsRBD1 and dsRBD2, respectively) have affinities for dsRNA, whereas the third dsRBD (dsRBD3) binds to Dicer. In this study, we prepared the single domain fragments of human TRBP corresponding to dsRBD1 and dsRBD2 and solved the crystal structure of dsRBD1 and the solution structure of dsRBD2. The two structures contain an α−β−β−β−α fold, which is common to the dsRBDs. The overall structures of dsRBD1 and dsRBD2 are similar to each other, except for a slight shift of the first α helix. The residues involved in dsRNA binding are conserved. We examined the small interfering RNA (siRNA)‐binding properties of these dsRBDs by isothermal titration colorimetry measurements. The dsRBD1 and dsRBD2 fragments both bound to siRNA, with dissociation constants of 220 and 113 nM, respectively. In contrast, the full‐length TRBP and its fragment with dsRBD1 and dsRBD2 exhibited much smaller dissociation constants (0.24 and 0.25 nM, respectively), indicating that the tandem dsRBDs bind simultaneously to one siRNA molecule. On the other hand, the loop between the first α helix and the first β strand of dsRBD2, but not dsRBD1, has a Trp residue, which forms hydrophobic and cation‐π interactions with the surrounding residues. A circular dichroism analysis revealed that the thermal stability of dsRBD2 is higher than that of dsRBD1 and depends on the Trp residue.
Structure of Sir2Tm bound to a propionylated peptide
Authors: Bheda Poonam , Wang Jennifer T. , Escalante‐Semerena Jorge C. , Wolberger Cynthia
Published: November 2010

Lysine propionylation is a recently identified post‐translational modification that has been observed in proteins such as p53 and histones and is thought to play a role similar to acetylation in modulating protein activity. Members of the sirtuin family of deacetylases have been shown to have depropionylation activity, although the way in which the sirtuin catalytic site accommodates the bulkier propionyl group is not clear. We have determined the 1.8 Å structure of a Thermotoga maritima sirtuin, Sir2Tm, bound to a propionylated peptide derived from p53. A comparison with the structure of Sir2Tm bound to an acetylated peptide shows that hydrophobic residues in the active site shift to accommodate the bulkier propionyl group. Isothermal titration calorimetry data show that Sir2Tm binds propionylated substrates more tightly than acetylated substrates, but kinetic assays reveal that the catalytic rate of Sir2Tm deacylation of propionyl‐lysine is slightly reduced to acetyl‐lysine. These results serve to broaden our understanding of the newly identified propionyl‐lysine modification and the ability of sirtuins to depropionylate, as well as deacetylate, substrates.
Site‐specific 19F NMR chemical shift and side chain relaxation analysis of a membrane protein labeled with an unnatural amino acid
Authors: Shi Pan , Wang Hu , Xi Zhaoyong , Shi Chaowei , Xiong Ying , Tian Changlin
Published: November 2010

Site‐specific 19F chemical shift and side chain relaxation analysis can be applied on large size proteins. Here, one‐dimensional 19F spectra and T1, T2 relaxation data were acquired on a SH3 domain in aqueous buffer containing 60% glycerol, and a nine‐transmembrane helices membrane protein diacyl‐glycerol kinase (DAGK) in dodecyl phosphochoine (DPC) micelles. The high quality of the data indicates that this method can be applied to site‐specifically analyze side chain internal mobility of membrane proteins or large size proteins.
Solution structure of the human HSPC280 protein
Authors: Lin Jinzhong , Zhou Tao , Wang Jinfeng
Published: November 2010

The human HSPC280 protein belongs to a new family of low molecular weight proteins, which is only present in eukaryotes, and is absent in fungi. The solution structure of HSPC280 was determined using multidimensional NMR spectroscopy. The overall structure consists of three α‐helices and four antiparallel β‐strands and has a winged helix‐like fold. However, HEPC280 is not a typical DNA‐binding winged helix protein in that it lacks DNA‐binding activity. Unlike most winged‐helix proteins, HSPC280 has an unusually long 13‐residue (P62–V74) wing 1 loop connecting the β3 and β4 strands of the protein. Molecules of HSPC280 have a positively charged surface on one side and a negatively charged surface on the other side of the protein structure. Comparisons with the C‐terminal 80‐residue domain of proteins in the Abra family reveal a conserved hydrophobic groove in the HSPC280 family, which may allow HSPC280 to interact with other proteins.
Idiosyncrasy and identity in the prokaryotic phe‐system: Crystal structure of E. coli phenylalanyl‐tRNA synthetase complexed with phenylalanine and AMP
Authors: Mermershtain Inbal , Finarov Igal , Klipcan Liron , Kessler Naama , Rozenberg Haim , Safro Mark G.
Published: November 2010

The crystal structure of Phenylalanyl‐tRNA synthetase from E. coli (EcPheRS), a class II aminoacyl‐tRNA synthetase, complexed with phenylalanine and AMP was determined at 3.05 Å resolution. EcPheRS is a (αβ)2 heterotetramer: the αβ heterodimer of EcPheRS consists of 11 structural domains. Three of them: the N‐terminus, A1 and A2 belong to the α‐subunit and B1‐B8 domains to the β subunit. The structure of EcPheRS revealed that architecture of four helix‐bundle interface, characteristic of class IIc heterotetrameric aaRSs, is changed: each of the two long helices belonging to CLM transformed into the coil‐short helix structural fragments. The N‐terminal domain of the α‐subunit in EcPheRS forms compact triple helix domain. This observation is contradictory to the structure of the apo form of TtPheRS, where N‐terminal domain was not detected in the electron density map. Comparison of EcPheRS structure with TtPheRS has uncovered significant rearrangements of the structural domains involved in tRNAPhe binding/translocation. As it follows from modeling experiments, to achieve a tighter fit with anticodon loop of tRNA, a shift of ∼5 Å is required for C‐terminal domain B8, and of ∼6 to 7 Å for the whole N terminus. EcPheRSs have emerged as an important target for the incorporation of novel amino acids into genetic code. Further progress in design of novel compounds is anticipated based on the structural data of EcPheRS.
Synthetic symmetrization in the crystallization and structure determination of CelA from Thermotoga maritima
Authors: Forse G. Jason , Ram Nina , Banatao D. Rey , Cascio Duilio , Sawaya Michael R. , Klock Heath E. , Lesley Scott A. , Yeates Todd O.
Published: November 2010

Protein crystallization continues to be a major bottleneck in X‐ray crystallography. Previous studies suggest that symmetric proteins, such as homodimers, might crystallize more readily than monomeric proteins or asymmetric complexes. Proteins that are naturally monomeric can be made homodimeric artificially. Our approach is to create homodimeric proteins by introducing single cysteines into the protein of interest, which are then oxidized to form a disulfide bond between the two monomers. By introducing the single cysteine at different sequence positions, one can produce a variety of synthetically dimerized versions of a protein, with each construct expected to exhibit its own crystallization behavior. In earlier work, we demonstrated the potential utility of the approach using T4 lysozyme as a model system. Here we report the successful application of the method to Thermotoga maritima CelA, a thermophilic endoglucanase enzyme with low sequence identity to proteins with structures previously reported in the Protein Data Bank. This protein had resisted crystallization in its natural monomeric form, despite a broad survey of crystallization conditions. The synthetic dimerization of the CelA mutant D188C yielded well‐diffracting crystals with molecules in a packing arrangement that would not have occurred with native, monomeric CelA. A 2.4 Å crystal structure was determined by single anomalous dispersion using a seleno‐methionine derivatized protein. The results support the notion that synthetic symmetrization can be a useful approach for enlarging the search space for crystallizing monomeric proteins or asymmetric complexes.
N‐glycosylation efficiency is determined by the distance to the C‐terminus and the amino acid preceding an Asn‐Ser‐Thr sequon
Authors: Bañó‐Polo Manuel , Baldin Francesca , Tamborero Silvia , Marti‐Renom Marc A. , Mingarro Ismael
Published: November 2010

N‐glycosylation is the most common and versatile protein modification. In eukaryotic cells, this modification is catalyzed cotranslationally by the enzyme oligosaccharyltransferase, which targets the β‐amide of the asparagine in an Asn‐Xaa‐Ser/Thr consensus sequon (where Xaa is any amino acid but proline) in nascent proteins as they enter the endoplasmic reticulum. Because modification of the glycosylation acceptor site on membrane proteins occurs in a compartment‐specific manner, the presence of glycosylation is used to indicate membrane protein topology. Moreover, glycosylation sites can be added to gain topological information. In this study, we explored the determinants of N‐glycosylation with the in vitro transcription/translation of a truncated model protein in the presence of microsomes and surveyed 25,488 glycoproteins, of which 2,533 glycosylation sites had been experimentally validated. We found that glycosylation efficiency was dependent on both the distance to the C‐terminus and the nature of the amino acid that preceded the consensus sequon. These findings establish a broadly applicable method for membrane protein tagging in topological studies.