@article{Weber2013, author = {Weber, Marcus}, title = {Adaptive Spectral Clustering in Molecular Simulation. In: Studies in Classification, Data Analysis, and Knowledge Organization}, journal = {XIV: Classification and Data Mining, A. Giusti, G. Ritter, M. Vichi (Eds.), Springer Series}, pages = {147 -- 157}, year = {2013}, language = {de} } @article{FackeldeyRoeblitzScharkoietal.2011, author = {Fackeldey, Konstantin and R{\"o}blitz, Susanna and Scharkoi, O. and Weber, Marcus}, title = {Soft Versus Hard Metastable Conformations in Molecular Simulations}, journal = {Particle Methods II, Fundamentals and Applications, Barcelona, Spain 26-28 Oct. 2011, E. Onate and D.R.J. Owen (eds.)}, pages = {899 -- 909}, year = {2011}, language = {de} } @article{ShanBujotzekAbendrothetal.2011, author = {Shan, Min and Bujotzek, Alexander and Abendroth, Frank and Seitz, Oliver and Weber, Marcus and Haag, Rainer}, title = {Conformational Analysis of Bivalent Estrogen Receptor-Ligands: From Intramolecular to Intermolecular Binding}, journal = {ChemBioChem, 12(17)}, doi = {10.1002/cbic.201100529}, pages = {2587 -- 2598}, year = {2011}, language = {en} } @article{GuentherLameckerWeiser2013, author = {G{\"u}nther, Andreas and Lamecker, Hans and Weiser, Martin}, title = {Flexible Shape Matching with Finite Element Based LDDMM}, volume = {105}, journal = {International Journal of Computer Vision}, number = {2}, doi = {10.1007/s11263-012-0599-3}, pages = {128 -- 143}, year = {2013}, abstract = {We consider Large Deformation Diffeomorphic Metric Mapping of general \$m\$-currents. After stating an optimization algorithm in the function space of admissable morph generating velocity fields, two innovative aspects in this framework are presented and numerically investigated: First, we spatially discretize the velocity field with conforming adaptive finite elements and discuss advantages of this new approach. Second, we directly compute the temporal evolution of discrete \$m\$-current attributes.}, language = {en} } @misc{GuentherLameckerWeiser2011, author = {G{\"u}nther, Andreas and Lamecker, Hans and Weiser, Martin}, title = {Direct LDDMM of Discrete Currents with Adaptive Finite Elements}, journal = {Proceedings of the Third International Workshop on Mathematical Foundations of Computational Anatomy - Geometrical and Statistical Methods for Modelling Biological Shape Variability}, editor = {Pennec, X. and Joshi, S. and Nielsen, M.}, pages = {1 -- 14}, year = {2011}, abstract = {We consider Large Deformation Diffeomorphic Metric Mapping of general \$m\$-currents. After stating an optimization algorithm in the function space of admissable morph generating velocity fields, two innovative aspects in this framework are presented and numerically investigated: First, we spatially discretize the velocity field with conforming adaptive finite elements and discuss advantages of this new approach. Second, we directly compute the temporal evolution of discrete \$m\$-current attributes.}, language = {en} } @misc{SchielaWeiser2010, author = {Schiela, Anton and Weiser, Martin}, title = {Barrier methods for a control problem from hyperthermia treatment planning}, journal = {Recent Advances in Optimization and its Applications in Engineering (Proceedings of 14th Belgian-French-German Conference on Optimization 2009)}, editor = {Diehl, M. and Glineur, F. and Jarlebring, E. and Michiels, W.}, publisher = {Springer}, pages = {419 -- 428}, year = {2010}, abstract = {We consider an optimal control problem from hyperthermia treatment planning and its barrier regularization. We derive basic results, which lay the groundwork for the computation of optimal solutions via an interior point path-following method. Further, we report on a numerical implementation of such a method and its performance at an example problem.}, language = {en} } @article{WeiserRoelligArndtetal.2010, author = {Weiser, Martin and R{\"o}llig, Mathias and Arndt, Ralf and Erdmann, Bodo}, title = {Development and test of a numerical model for pulse thermography in civil engineering}, volume = {46}, journal = {Heat and Mass Transfer}, number = {11-12}, pages = {1419 -- 1428}, year = {2010}, abstract = {Pulse thermography of concrete structures is used in civil engineering for detecting voids, honeycombing and delamination. The physical situation is readily modeled by Fourier's law. Despite the simplicity of the PDE structure, quantitatively realistic numerical 3D simulation faces two major obstacles. First, the short heating pulse induces a thin boundary layer at the heated surface which encapsulates all information and therefore has to be resolved faithfully. Even with adaptive mesh refinement techniques, obtaining useful accuracies requires an unsatisfactorily fine discretization. Second, bulk material parameters and boundary conditions are barely known exactly. We address both issues by a semi-analytic reformulation of the heat transport problem and by parameter identification. Numerical results are compared with measurements of test specimens.}, language = {en} } @article{BlomeMaurerGreenhalgh2011, author = {Blome, Mark and Maurer, HR and Greenhalgh, S.}, title = {Geoelectric experimental design — Efficient acquisition and exploitation of complete pole-bipole data sets}, volume = {76}, journal = {GEOPHYSICS}, number = {1}, doi = {10.1190/1.3511350}, pages = {F15 -- F26}, year = {2011}, language = {en} } @article{PlattnerMaurerVorloeperetal.2012, author = {Plattner, A. and Maurer, H. and Vorloeper, J. and Blome, Mark}, title = {3-D electrical resistivity tomography using adaptive wavelet parameter grids}, volume = {189}, journal = {Geophysical Journal International}, pages = {317 -- 330}, year = {2012}, language = {en} } @article{RannebergWeiserWeihrauchetal.2010, author = {Ranneberg, Maximilian and Weiser, Martin and Weihrauch, Mirko and Budach, Volker and Gellermann, Johanna and Wust, Peter}, title = {Regularized Antenna Profile Adaptation in Online Hyperthermia Treatment}, volume = {37}, journal = {Medical Physics}, doi = {10.1118/1.3488896}, pages = {5382 -- 5394}, year = {2010}, language = {en} } @article{JaegerBarthHammerschmidtetal.2016, author = {J{\"a}ger, Klaus and Barth, Carlo and Hammerschmidt, Martin and Herrmann, Sven and Burger, Sven and Schmidt, Frank and Becker, Christiane}, title = {Simulations of sinusoidal nanotextures for coupling light into c-Si thin-film solar cells}, volume = {24}, journal = {Opt. Express}, doi = {10.1364/OE.24.00A569}, pages = {A569}, year = {2016}, language = {en} } @article{LedentsovJrShchukinKroppetal.2016, author = {Ledentsov, Jr., Nikolay and Shchukin, Vitaly and Kropp, J{\"o}rg-R. and Burger, Sven and Schmidt, Frank and Ledentsov, Jr., Nikolay}, title = {Direct visualization of the in-plane leakage of high-order transverse modes in vertical-cavity surface-emitting lasers mediated by oxide-aperture engineering}, volume = {9766}, journal = {Proc. SPIE}, doi = {10.1117/12.2208909}, pages = {976608}, year = {2016}, language = {en} } @misc{Fackeldey2010, author = {Fackeldey, Konstantin}, title = {Challenges in Atomistic-to-Continuum Coupling}, volume = {2010}, journal = {ZIB Report}, edition = {10-12}, doi = {10.1155/2015/834517}, year = {2010}, abstract = {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.}, language = {en} } @article{Durmaz2015, author = {Durmaz, Vedat}, title = {Markov model-based polymer assembly from force field-parameterized building blocks}, volume = {29}, journal = {Journal of Computer-Aided Molecular Design}, doi = {10.1007/s10822-014-9817-0}, pages = {225 -- 232}, year = {2015}, abstract = {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.}, language = {en} } @article{HeyeBeckerLuetkeEverslohetal.2016, author = {Heye, Katharina and Becker, Dennis and L{\"u}tke-Eversloh, Christian and Durmaz, Vedat and Ternes, Thomas and Oetken, Matthias and Oehlmann, J{\"o}rg}, title = {Effects of carbamazepine and two of its metabolites on the non-biting midge Chironomus riparius in a sediment full life cycle toxicity test}, volume = {98}, journal = {Water Research}, pages = {19 -- 27}, year = {2016}, abstract = {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.}, language = {en} } @article{LubkollSchielaWeiser2017, author = {Lubkoll, Lars and Schiela, Anton and Weiser, Martin}, title = {An affine covariant composite step method for optimization with PDEs as equality constraints}, volume = {32}, journal = {Optimization Methods and Software}, number = {5}, doi = {10.1080/10556788.2016.1241783}, pages = {1132 -- 1161}, year = {2017}, abstract = {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.}, language = {en} } @article{BienefeldZautkeGupta2016, author = {Bienefeld, Kaspar and Zautke, Fred and Gupta, Pooja}, title = {A novel method for undisturbed long-term observation of the honey bee (Apis mellifera) behaviour - illustrated by the hygienic behaviour towards Varroa infestation}, volume = {54(5)}, journal = {Journal of Apicultural Research}, pages = {541 -- 547}, year = {2016}, language = {en} } @article{SpoetterGuptaMayeretal.2016, author = {Sp{\"o}tter, Andreas and Gupta, Pooja and Mayer, Manfred and Reinsch, Norbert and Bienefeld, Kaspar}, title = {Genome-wide association study of a Varroa-specific defense behavior in honeybees (Apis mellifera)}, volume = {107}, journal = {Journal of Heredity}, number = {3}, pages = {220 -- 227}, year = {2016}, language = {en} } @misc{GoetschelMaierhoferMuelleretal.2016, author = {G{\"o}tschel, Sebastian and Maierhofer, Christiane and M{\"u}ller, Jan P. and Rothbart, Nick and Weiser, Martin}, title = {Quantitative Defect Reconstruction in Active Thermography for Fiber-Reinforced Composites}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-58374}, year = {2016}, abstract = {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.}, language = {en} } @misc{GoetschelHoehneKolkoorietal.2016, author = {G{\"o}tschel, Sebastian and H{\"o}hne, Christian and Kolkoori, Sanjeevareddy and Mitzscherling, Steffen and Prager, Jens and Weiser, Martin}, title = {Ray Tracing Boundary Value Problems: Simulation and SAFT Reconstruction for Ultrasonic Testing}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-58386}, year = {2016}, abstract = {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.}, language = {en} } @article{PomplunBurgerZschiedrichetal.2016, author = {Pomplun, Jan and Burger, Sven and Zschiedrich, Lin and Gutsche, Philipp and Schmidt, Frank}, title = {Method for fast computation of angular light scattering spectra from 2D periodic arrays}, volume = {9778}, journal = {Proc. SPIE}, arxiv = {http://arxiv.org/abs/1603.04169}, doi = {10.1117/12.2219666}, pages = {977839}, year = {2016}, language = {en} }