TY - JOUR A1 - Ranneberg, Maximilian A1 - Weiser, Martin A1 - Weihrauch, Mirko A1 - Budach, Volker A1 - Gellermann, Johanna A1 - Wust, Peter T1 - Regularized Antenna Profile Adaptation in Online Hyperthermia Treatment JF - Medical Physics Y1 - 2010 U6 - https://doi.org/10.1118/1.3488896 VL - 37 SP - 5382 EP - 5394 ER - TY - JOUR A1 - Jäger, Klaus A1 - Barth, Carlo A1 - Hammerschmidt, Martin A1 - Herrmann, Sven A1 - Burger, Sven A1 - Schmidt, Frank A1 - Becker, Christiane T1 - Simulations of sinusoidal nanotextures for coupling light into c-Si thin-film solar cells JF - Opt. Express Y1 - 2016 U6 - https://doi.org/10.1364/OE.24.00A569 VL - 24 SP - A569 ER - TY - JOUR A1 - Ledentsov, Jr., Nikolay A1 - Shchukin, Vitaly A1 - Kropp, Jörg-R. A1 - Burger, Sven A1 - Schmidt, Frank A1 - Ledentsov, Jr., Nikolay T1 - Direct visualization of the in-plane leakage of high-order transverse modes in vertical-cavity surface-emitting lasers mediated by oxide-aperture engineering JF - Proc. SPIE Y1 - 2016 U6 - https://doi.org/10.1117/12.2208909 VL - 9766 SP - 976608 ER - TY - GEN A1 - Fackeldey, Konstantin T1 - Challenges in Atomistic-to-Continuum Coupling T2 - ZIB Report N2 - This paper is concerned with the design, analysis, and implementation of concurrent coupling approaches where different (atomic and continuous) models are used simultaneously within a single simulation process. Thereby, several problems or pitfalls can happen, for example, the reflection of molecular movements at the “boundary” between the atomic and continuum regions which leads to an unphysical increase in energy in the atomic model. We investigate the problems with the aim of giving an introduction into this field and preventing errors for scientists starting their research towards multiscale methods. Y1 - 2010 U6 - https://doi.org/10.1155/2015/834517 VL - 2010 ET - 10-12 ER - TY - JOUR A1 - Durmaz, Vedat T1 - Markov model-based polymer assembly from force field-parameterized building blocks JF - Journal of Computer-Aided Molecular Design N2 - A conventional by hand construction and parameterization of a polymer model for the purpose of molecular simulations can quickly become very workintensive and time-consuming. Using the example of polyglycerol, I present a polymer decompostion strategy yielding a set of five monomeric residues that are convenient for an instantaneous assembly and subsequent force field simulation of a polyglycerol polymer model. Force field parameters have been developed in accordance with the classical Amber force field. Partial charges of each unit were fitted to the electrostatic potential using quantumchemical methods and slightly modified in order to guarantee a neutral total polymer charge. In contrast to similarly constructed models of amino acid and nucleotide sequences, the glycerol building blocks may yield an arbitrary degree of bifurcations depending on the underlying probabilistic model. The iterative development of the overall structure as well as the relation of linear to branching units is controlled by a simple Markov model which is presented with few algorithmic details. The resulting polymer is highly suitable for classical explicit water molecular dynamics simulations on the atomistic level after a structural relaxation step. Moreover, the decomposition strategy presented here can easily be adopted to many other (co)polymers. Y1 - 2015 U6 - https://doi.org/10.1007/s10822-014-9817-0 VL - 29 SP - 225 EP - 232 ER - TY - JOUR A1 - Heye, Katharina A1 - Becker, Dennis A1 - Lütke-Eversloh, Christian A1 - Durmaz, Vedat A1 - Ternes, Thomas A1 - Oetken, Matthias A1 - Oehlmann, Jörg T1 - Effects of carbamazepine and two of its metabolites on the non-biting midge Chironomus riparius in a sediment full life cycle toxicity test JF - Water Research N2 - The antiepileptic drug carbamazepine (CBZ) and its main metabolites carbamazepine-10,11-epoxide (EP-CBZ) and 10,11-dihydro-10,11-dihydroxy-carbamazepine (DiOH-CBZ) were chosen as test substances to assess chronic toxicity on the non-biting midge Chironomus riparius. All three substances were tested in a 40-day sediment full life cycle test (according to OECD 233) in which mortality, emergence, fertility, and clutch size were evaluated. In addition, these parameters were integrated into the population growth rate to reveal population relevant effects. With an LC50 of 0.203 mg/kg (time-weighted mean), the metabolite EP-CBZ was significantly more toxic than the parent substance CBZ (LC50: 1.11 mg/kg). Especially mortality, emergence, and fertility showed to be sensitive parameters under the exposure to CBZ and EP-CBZ. By using classical molecular dynamics (MD) simulations, the binding of CBZ to the ecdysone receptor was investigated as one possible mode of action but showed to be unlikely. The second metabolite DiOH-CBZ did not show any effects within the tested concentration rage (0.171 – 1.22 mg/kg). Even though CBZ was less toxic compared to EP-CBZ, CBZ is found in the environment at much higher concentrations and causes therefore a higher potential risk for sediment dwelling organisms compared to its metabolites. Nevertheless, the current study illustrates the importance of including commonly found metabolites into the risk assessment of parent substances. Y1 - 2016 VL - 98 SP - 19 EP - 27 ER - TY - JOUR A1 - Lubkoll, Lars A1 - Schiela, Anton A1 - Weiser, Martin T1 - An affine covariant composite step method for optimization with PDEs as equality constraints JF - Optimization Methods and Software N2 - We propose a composite step method, designed for equality constrained optimization with partial differential equations. Focus is laid on the construction of a globalization scheme, which is based on cubic regularization of the objective and an affine covariant damped Newton method for feasibility. We show finite termination of the inner loop and fast local convergence of the algorithm. We discuss preconditioning strategies for the iterative solution of the arising linear systems with projected conjugate gradient. Numerical results are shown for optimal control problems subject to a nonlinear heat equation and subject to nonlinear elastic equations arising from an implant design problem in craniofacial surgery. Y1 - 2017 U6 - https://doi.org/10.1080/10556788.2016.1241783 VL - 32 IS - 5 SP - 1132 EP - 1161 ER - TY - JOUR A1 - Bienefeld, Kaspar A1 - Zautke, Fred A1 - Gupta, Pooja T1 - A novel method for undisturbed long-term observation of the honey bee (Apis mellifera) behaviour – illustrated by the hygienic behaviour towards Varroa infestation JF - Journal of Apicultural Research Y1 - 2016 VL - 54(5) SP - 541 EP - 547 ER - TY - JOUR A1 - Spötter, Andreas A1 - Gupta, Pooja A1 - Mayer, Manfred A1 - Reinsch, Norbert A1 - Bienefeld, Kaspar T1 - Genome-wide association study of a Varroa-specific defense behavior in honeybees (Apis mellifera) JF - Journal of Heredity Y1 - 2016 VL - 107 IS - 3 SP - 220 EP - 227 ER - TY - GEN A1 - Götschel, Sebastian A1 - Maierhofer, Christiane A1 - Müller, Jan P. A1 - Rothbart, Nick A1 - Weiser, Martin T1 - Quantitative Defect Reconstruction in Active Thermography for Fiber-Reinforced Composites N2 - Carbon-fiber reinforced composites are becoming more and more important in the production of light-weight structures, e.g., in the automotive and aerospace industry. Thermography is often used for non-destructive testing of these products, especially to detect delaminations between different layers of the composite. In this presentation, we aim at methods for defect reconstruction from thermographic measurements of such carbon-fiber reinforced composites. The reconstruction results shall not only allow to locate defects, but also give a quantitative characterization of the defect properties. We discuss the simulation of the measurement process using finite element methods, as well as the experimental validation on flat bottom holes. Especially in pulse thermography, thin boundary layers with steep temperature gradients occurring at the heated surface need to be resolved. Here we use the combination of a 1D analytical solution combined with numerical solution of the remaining defect equation. We use the simulations to identify material parameters from the measurements. Finally, fast heuristics for reconstructing defect geometries are applied to the acquired data, and compared for their accuracy and utility in detecting different defects like back surface defects or delaminations. T3 - ZIB-Report - 16-13 KW - thermography KW - inverse problems KW - parameter identification KW - geometry identification KW - nondestructive testing Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-58374 UR - https://www.wcndt2016.com/portals/wcndt/bb/Th4C4.pdf SN - 1438-0064 ER - TY - GEN A1 - Götschel, Sebastian A1 - Höhne, Christian A1 - Kolkoori, Sanjeevareddy A1 - Mitzscherling, Steffen A1 - Prager, Jens A1 - Weiser, Martin T1 - Ray Tracing Boundary Value Problems: Simulation and SAFT Reconstruction for Ultrasonic Testing N2 - The application of advanced imaging techniques for the ultrasonic inspection of inhomogeneous anisotropic materials like austenitic and dissimilar welds requires information about acoustic wave propagation through the material, in particular travel times between two points in the material. Forward ray tracing is a popular approach to determine traveling paths and arrival times but is ill suited for inverse problems since a large number of rays have to be computed in order to arrive at prescribed end points. In this contribution we discuss boundary value problems for acoustic rays, where the ray path between two given points is determined by solving the eikonal equation. The implementation of such a two point boundary value ray tracer for sound field simulations through an austenitic weld is described and its efficiency as well as the obtained results are compared to those of a forward ray tracer. The results are validated by comparison with experimental results and commercially available UT simulation tools. As an application, we discuss an implementation of the method for SAFT (Synthetic Aperture Focusing Technique) reconstruction. The ray tracer calculates the required travel time through the anisotropic columnar grain structure of the austenitic weld. There, the formulation of ray tracing as a boundary value problem allows a straightforward derivation of the ray path from a given transducer position to any pixel in the reconstruction area and reduces the computational cost considerably. T3 - ZIB-Report - 16-14 KW - ray tracing KW - ODE boundary value problems KW - ultrasonics KW - nondestructive testing Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-58386 UR - https://www.wcndt2016.com/portals/wcndt/bb/Fr1H4.pdf SN - 1438-0064 ER - TY - JOUR A1 - Pomplun, Jan A1 - Burger, Sven A1 - Zschiedrich, Lin A1 - Gutsche, Philipp A1 - Schmidt, Frank T1 - Method for fast computation of angular light scattering spectra from 2D periodic arrays JF - Proc. SPIE Y1 - 2016 U6 - https://doi.org/10.1117/12.2219666 VL - 9778 SP - 977839 ER - TY - GEN A1 - Koltai, Peter A1 - Ciccotti, Giovanni A1 - Schütte, Christof T1 - On metastability and Markov state models for non-stationary molecular dynamics BT - 2016 Editor's Choice of The Journal of Chemical Physics T2 - The Journal of Chemical Physics N2 - We utilize the theory of coherent sets to build Markov state models for non- equilibrium molecular dynamical systems. Unlike for systems in equilibrium, “meta- stable” sets in the non-equilibrium case may move as time evolves. We formalize this concept by relying on the theory of coherent sets, based on this we derive finite-time non-stationary Markov state models, and illustrate the concept and its main differences to equilibrium Markov state modeling on simple, one-dimensional examples. T3 - ZIB-Report - 16-11 KW - coherent set, KW - Markov state model KW - non-equilibrium molecular dynamics KW - metastability Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-57869 SN - 1438-0064 VL - 174103 ET - 145 ER - TY - JOUR A1 - Gutsche, Philipp A1 - Poulikakos, Lisa A1 - Hammerschmidt, Martin A1 - Burger, Sven A1 - Schmidt, Frank T1 - Time-harmonic optical chirality in inhomogeneous space JF - Proc. SPIE Y1 - 2016 U6 - https://doi.org/10.1117/12.2209551 VL - 9756 SP - 97560X ER - TY - JOUR A1 - Djurdjevac Conrad, Natasa A1 - Weber, Marcus A1 - Schütte, Christof T1 - Finding dominant structures of nonreversible Markov processes JF - Multiscale Modeling and Simulation Y1 - 2016 U6 - https://doi.org/10.1137/15M1032272 VL - 14 IS - 4 SP - 1319 EP - 1340 ER - TY - JOUR A1 - Hammerschmidt, Martin A1 - Barth, Carlo A1 - Pomplun, Jan A1 - Burger, Sven A1 - Becker, Christiane A1 - Schmidt, Frank T1 - Reconstruction of photonic crystal geometries using a reduced basis method for nonlinear outputs JF - Proc. SPIE N2 - Maxwell solvers based on the hp-adaptive finite element method allow for accurate geometrical modeling and high numerical accuracy. These features are indispensable for the optimization of optical properties or reconstruction of parameters through inverse processes. High computational complexity prohibits the evaluation of the solution for many parameters. We present a reduced basis method (RBM) for the time-harmonic electromagnetic scattering problem allowing to compute solutions for a parameter configuration orders of magnitude faster. The RBM allows to evaluate linear and nonlinear outputs of interest like Fourier transform or the enhancement of the electromagnetic field in milliseconds. We apply the RBM to compute light-scattering off two dimensional photonic crystal structures made of silicon and reconstruct geometrical parameters. Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-58187 VL - 9756 SP - 97561R ER - TY - JOUR A1 - Hammerschmidt, Martin A1 - Herrmann, Sven A1 - Pomplun, Jan A1 - Burger, Sven A1 - Schmidt, Frank T1 - Model order reduction for the time-harmonic Maxwell equation applied to complex nanostructures JF - Proc. SPIE N2 - Fields such as optical metrology and computational lithography require fast and efficient methods for solving the time-harmonic Maxwell's equation. Highly accurate geometrical modelling and numerical accuracy at low computational costs are a prerequisite for any simulation study of complex nano-structured photonic devices. We present a reduced basis method (RBM) for the time-harmonic electromagnetic scattering problem based on the hp-adaptive finite element solver JCMsuite capable of handling geometric and non-geometric parameter dependencies allowing for online evaluations in milliseconds. We apply the RBM to compute light-scattering at optical wavelengths of periodic arrays of fin field-effect transistors (FinFETs) where geometrical properties such as the width and height of the fin and gate can vary in a large range. Y1 - 2016 U6 - https://doi.org/10.1117/12.2212367 VL - 9742 SP - 97420M ER - TY - GEN A1 - Gutsche, Philipp A1 - Läuter, Matthias A1 - Schmidt, Frank T1 - Parameter-dependent Parallel Block Sparse Arnoldi and Döhler Algorithms on Distributed Systems N2 - We summarize the basics and first results of the analyses within our ZIB Bridge Project and give an outlook on further studies broadening the usage of hardware acceleration within the Finite Element Method (FEM) based solution of Maxwell’s equations. T3 - ZIB-Report - 16-15 KW - Generalized Eigenvalue Problem KW - Many Integrated Core Coprocessor (MIC) KW - Finite Element Method Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-58202 SN - 1438-0064 ER - TY - JOUR A1 - Hammerschmidt, Martin A1 - Herrmann, Sven A1 - Pomplun, Jan A1 - Burger, Sven A1 - Schmidt, Frank T1 - Reduced basis method for electromagnetic scattering problem: a case study for FinFETs JF - Optical and Quantum Electronics N2 - Optical 3D simulations in many-query and real-time contexts require new solution strategies. We study an adaptive, error controlled reduced basis method for solving parametrized time-harmonic optical scattering problems. Application fields are, among others, design and optimization problems of nano-optical devices as well as inverse problems for parameter reconstructions occurring e. g. in optical metrology. The reduced basis method pre- sented here relies on a finite element modeling of the scattering problem with parametrization of materials, geometries and sources. Y1 - 2016 U6 - https://doi.org/10.1007/s11082-016-0530-1 VL - 48 SP - 250 ER - TY - THES A1 - Nielsen, Adam T1 - Computation Schemes for Transfer Operators Y1 - 2016 ER - TY - THES A1 - Sikorski, Alexander T1 - PCCA+ and Its Application to Spatial Time Series Clustering Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-58769 ER -