@article{OzelKulkarniHasanetal.2019, author = {Ozel, Mehmet Neset and Kulkarni, Abhishek and Hasan, Amr and Brummer, Josephine and Moldenhauer, Marian and Daumann, Ilsa-Maria and Wolfenberg, Heike and Dercksen, Vincent J. and Kiral, Ferdi Ridvan and Weiser, Martin and Prohaska, Steffen and von Kleist, Max and Hiesinger, Peter Robin}, title = {Serial synapse formation through filopodial competition for synaptic seeding factors}, volume = {50}, journal = {Developmental Cell}, number = {4}, doi = {10.1016/j.devcel.2019.06.014}, pages = {447 -- 461}, year = {2019}, abstract = {Following axon pathfinding, growth cones transition from stochastic filopodial exploration to the formation of a limited number of synapses. How the interplay of filopodia and synapse assembly ensures robust connectivity in the brain has remained a challenging problem. Here, we developed a new 4D analysis method for filopodial dynamics and a data-driven computational model of synapse formation for R7 photoreceptor axons in developing Drosophila brains. Our live data support a 'serial synapse formation' model, where at any time point only a single 'synaptogenic' filopodium suppresses the synaptic competence of other filopodia through competition for synaptic seeding factors. Loss of the synaptic seeding factors Syd-1 and Liprin-α leads to a loss of this suppression, filopodial destabilization and reduced synapse formation, which is sufficient to cause the destabilization of entire axon terminals. Our model provides a filopodial 'winner-takes-all' mechanism that ensures the formation of an appropriate number of synapses.}, language = {en} } @misc{SchneckWeiserWende2019, author = {Schneck, Jakob and Weiser, Martin and Wende, Florian}, title = {Impact of mixed precision and storage layout on additive Schwarz smoothers}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-71305}, year = {2019}, abstract = {The growing discrepancy between CPU computing power and memory bandwidth drives more and more numerical algorithms into a bandwidth- bound regime. One example is the overlapping Schwarz smoother, a highly effective building block for iterative multigrid solution of elliptic equations with higher order finite elements. Two options of reducing the required memory bandwidth are sparsity exploiting storage layouts and representing matrix entries with reduced precision in floating point or fixed point format. We investigate the impact of several options on storage demand and contraction rate, both analytically in the context of subspace correction methods and numerically at an example of solid mechanics. Both perspectives agree on the favourite scheme: fixed point representation of Cholesky factors in nested dissection storage.}, language = {en} } @article{WilsonGutscheHerrmannetal.2019, author = {Wilson, Jon and Gutsche, Philipp and Herrmann, Sven and Burger, Sven and McPeak, Kevin}, title = {Correlation of circular differential optical absorption with geometric chirality in plasmonic meta-atoms}, volume = {27}, journal = {Opt. Express}, doi = {10.1364/OE.27.005097}, pages = {5097}, year = {2019}, language = {en} } @article{ReidelbachWeberImhof2018, author = {Reidelbach, Marco and Weber, Marcus and Imhof, Petra}, title = {Prediction of perturbed proton transfer networks}, volume = {13}, journal = {PLoS ONE}, number = {12}, doi = {https://doi.org/10.1371/journal.pone.0207718}, pages = {e0207718 -- e0207718}, year = {2018}, abstract = {The transfer of protons through proton translocating channels is a complex process, for which direct samplings of different protonation states and side chain conformations in a transition network calculation provide an efficient, bias-free description. In principle, a new transition network calculation is required for every unsampled change in the system of interest, e.g. an unsampled protonation state change, which is associated with significant computational costs. Transition networks void of or including an unsampled change are termed unperturbed or perturbed, respectively. Here, we present a prediction method, which is based on an extensive coarse-graining of the underlying transition networks to speed up the calculations. It uses the minimum spanning tree and a corresponding sensitivity analysis of an unperturbed transition network as initial guess and refinement parameter for the determination of an unknown, perturbed transition network. Thereby, the minimum spanning tree defines a sub-network connecting all nodes without cycles and minimal edge weight sum, while the sensitivity analysis analyzes the stability of the minimum spanning tree towards individual edge weight reductions. Using the prediction method, we are able to reduce the calculation costs in a model system by up to 80\%, while important network properties are maintained in most predictions.}, language = {en} } @inproceedings{ManciniMariMassinietal.2018, author = {Mancini, Toni and Mari, Federico and Massini, Annalisa and Melatti, Igor and Salvo, Ivano and Sinisi, Stefano and Tronci, Enrico and Ehrig, Rainald and R{\"o}blitz, Susanna and Leeners, Brigitte}, title = {Computing Personalised Treatments through In Silico Clinical Trials. A Case Study on Downregulation in Assisted Reproduction}, booktitle = {Experimental Evaluation of Algorithms for Solving Problems with Combinatorial Explosion, Workshop of the Federated Logic Conference 2018 (FLoC 2018), Oxford}, doi = {10.29007/g864}, pages = {1 -- 16}, year = {2018}, abstract = {In Silico Clinical Trials (ISCT), i.e., clinical experimental campaigns carried out by means of computer simulations, hold the promise to decrease time and cost for the safety and efficacy assessment of pharmacological treatments, reduce the need for animal and human testing, and enable precision medicine. In this paper we present a case study aiming at quantifying, by means of a multi-arm ISCT supervised by intelligent search, the potential impact of precision medicine approaches on a real pharmacological treatment, namely the downregulation phase of a complex clinical protocol for assisted reproduction.}, language = {en} } @article{KoltaiSchuette2018, author = {Koltai, P{\´e}ter and Sch{\"u}tte, Christof}, title = {A multiscale perturbation expansion approach for Markov state modeling of non-stationary molecular dynamics}, volume = {16}, journal = {SIAM J. Multiscale Model. Simul.}, number = {4}, publisher = {SIAM}, doi = {10.1137/17M1146403}, pages = {1455 -- 1485}, year = {2018}, abstract = {We investigate metastable dynamical systems subject to non-stationary forcing as they appear in molecular dynamics for systems driven by external fields. We show, that if the strength of the forcing is inversely proportional to the length of the slow metastable time scales of the unforced system, then the effective behavior of the forced system on slow time scales can be described by a low-dimensional reduced master equation. Our construction is explicit and uses the multiscale perturbation expansion method called two-timing, or method of multiple scales. The reduced master equation—a Markov state model—can be assembled by constructing two equilibrium Markov state models; one for the unforced system, and one for a slightly perturbed one.}, language = {en} } @misc{FackeldeySikorskiWeber2018, author = {Fackeldey, Konstantin and Sikorski, Alexander and Weber, Marcus}, title = {Spectral Clustering for Non-reversible Markov Chains}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-70218}, year = {2018}, abstract = {Spectral clustering methods are based on solving eigenvalue problems for the identification of clusters, e.g. the identification of metastable subsets of a Markov chain. Usually, real-valued eigenvectors are mandatory for this type of algorithms. The Perron Cluster Analysis (PCCA+) is a well-known spectral clustering method of Markov chains. It is applicable for reversible Markov chains, because reversibility implies a real-valued spectrum. We also extend this spectral clustering method to non-reversible Markov chains and give some illustrative examples. The main idea is to replace the eigenvalue problem by a real-valued Schur decomposition. By this extension non-reversible Markov chains can be analyzed. Furthermore, the chains do not need to have a positive stationary distribution. In addition to metastabilities, dominant cycles and sinks can also be identified. This novel method is called GenPCCA (i.e. Generalized PCCA), since it includes the case of non reversible processes. We also apply the method to real world eye tracking data.}, language = {en} } @article{FackeldeySikorskiWeber2018, author = {Fackeldey, Konstantin and Sikorski, Alexander and Weber, Marcus}, title = {Spectral Clustering for Non-Reversible Markov Chains}, volume = {37}, journal = {Computational and Applied Mathematics}, number = {5}, doi = {https://doi.org/10.1007/s40314-018-0697-0}, pages = {6376 -- 6391}, year = {2018}, abstract = {Spectral clustering methods are based on solving eigenvalue problems for the identification of clusters, e.g., the identification of metastable subsets of a Markov chain. Usually, real-valued eigenvectors are mandatory for this type of algorithms. The Perron Cluster Analysis (PCCA+) is a well-known spectral clustering method of Markov chains. It is applicable for reversible Markov chains, because reversibility implies a real-valued spectrum. We also extend this spectral clustering method to non-reversible Markov chains and give some illustrative examples. The main idea is to replace the eigenvalue problem by a real-valued Schur decomposition. By this extension non-reversible Markov chains can be analyzed. Furthermore, the chains do not need to have a positive stationary distribution. In addition to metastabilities, dominant cycles and sinks can also be identified. This novel method is called GenPCCA (i.e., generalized PCCA), since it includes the case of non-reversible processes. We also apply the method to real-world eye-tracking data.}, language = {en} } @article{KewesBinkowskiBurgeretal.2018, author = {Kewes, G{\"u}nter and Binkowski, Felix and Burger, Sven and Zschiedrich, Lin and Benson, Oliver}, title = {Heuristic Modeling of Strong Coupling in Plasmonic Resonators}, volume = {5}, journal = {ACS Photonics}, arxiv = {http://arxiv.org/abs/1904.04584}, doi = {10.1021/acsphotonics.8b00766}, pages = {4089}, year = {2018}, language = {en} } @article{SchneiderSantiagoSoltwischetal.2019, author = {Schneider, Philipp-Immanuel and Santiago, Xavier Garcia and Soltwisch, Victor and Hammerschmidt, Martin and Burger, Sven and Rockstuhl, Carsten}, title = {Benchmarking five global optimization approaches for nano-optical shape optimization and parameter reconstruction}, volume = {6}, journal = {ACS Photonics}, arxiv = {http://arxiv.org/abs/1809.06674}, doi = {10.1021/acsphotonics.9b00706}, pages = {2726}, year = {2019}, language = {en} } @inproceedings{WerdehausenStaudeBurgeretal.2018, author = {Werdehausen, Daniel and Staude, Isabelle and Burger, Sven and Petschulat, J{\"o}rg and Scharf, Toralf and Pertsch, Thomas and Decker, Manuel}, title = {Using effective medium theories to design tailored nanocomposite materials for optical systems}, volume = {10745}, booktitle = {Proc. SPIE}, arxiv = {http://arxiv.org/abs/1810.10265}, doi = {10.1117/12.2320525}, pages = {107450H}, year = {2018}, language = {en} } @article{BinkowskiZschiedrichBurger2020, author = {Binkowski, Felix and Zschiedrich, Lin and Burger, Sven}, title = {A Riesz-projection-based method for nonlinear eigenvalue problems}, volume = {419}, journal = {J. Comput. Phys.}, arxiv = {http://arxiv.org/abs/1811.11624}, doi = {10.1016/j.jcp.2020.109678}, pages = {109678}, year = {2020}, language = {en} } @article{LalanneYanGrasetal.2019, author = {Lalanne, P. and Yan, W. and Gras, A. and Sauvan, C. and Hugonin, J.-P. and Besbes, M. and Dem{\´e}sy, G. and Truong, M. D. and Gralak, B. and Zolla, F. and Nicolet, A. and Binkowski, Felix and Zschiedrich, Lin and Burger, Sven and Zimmerling, J. and Remis, R. and Urbach, H. Paul and Liu, H. T. and Weiss, T.}, title = {Quasinormal mode solvers for resonators with dispersive materials}, volume = {36}, journal = {J. Opt. Soc. Am. A}, arxiv = {http://arxiv.org/abs/1811.11751}, doi = {10.1364/JOSAA.36.000686}, pages = {686}, year = {2019}, language = {en} } @article{LieSullivan2018, author = {Lie, Han Cheng and Sullivan, T. J.}, title = {Erratum: Equivalence of weak and strong modes of measures on topological vector spaces (2018 Inverse Problems 34 115013)}, volume = {34}, journal = {Inverse Problems}, number = {12}, doi = {10.1088/1361-6420/aae55b}, pages = {129601}, year = {2018}, language = {en} } @article{KlusBittracherSchusteretal.2018, author = {Klus, Stefan and Bittracher, Andreas and Schuster, Ingmar and Sch{\"u}tte, Christof}, title = {A kernel-based approach to molecular conformation analysis}, volume = {149}, journal = {Journal of Chemical Physics}, number = {24}, doi = {10.1063/1.5063533}, year = {2018}, abstract = {We present a novel machine learning approach to understanding conformation dynamics of biomolecules. The approach combines kernel-based techniques that are popular in the machine learning community with transfer operator theory for analyzing dynamical systems in order to identify conformation dynamics based on molecular dynamics simulation data. We show that many of the prominent methods like Markov State Models, EDMD, and TICA can be regarded as special cases of this approach and that new efficient algorithms can be constructed based on this derivation. The results of these new powerful methods will be illustrated with several examples, in particular the alanine dipeptide and the protein NTL9.}, language = {en} } @article{OatesSullivan2019, author = {Oates, Chris and Sullivan, T. J.}, title = {A modern retrospective on probabilistic numerics}, volume = {29}, journal = {Statistics and Computing}, number = {6}, arxiv = {http://arxiv.org/abs/1901.04457}, doi = {10.1007/s11222-019-09902-z}, pages = {1335 -- 1351}, year = {2019}, abstract = {This article attempts to place the emergence of probabilistic numerics as a mathematical-statistical research field within its historical context and to explore how its gradual development can be related to modern formal treatments and applications. We highlight in particular the parallel contributions of Sul'din and Larkin in the 1960s and how their pioneering early ideas have reached a degree of maturity in the intervening period, mediated by paradigms such as average-case analysis and information-based complexity. We provide a subjective assessment of the state of research in probabilistic numerics and highlight some difficulties to be addressed by future works.}, language = {en} } @misc{OatesCockaynePrangleetal.2020, author = {Oates, Chris and Cockayne, Jon and Prangle, Dennis and Sullivan, T. J. and Girolami, Mark}, title = {Optimality criteria for probabilistic numerical methods}, volume = {27}, journal = {Multivariate Algorithms and Information-Based Complexity}, editor = {Hickernell, F. J. and Kritzer, P.}, publisher = {De Gruyter}, arxiv = {http://arxiv.org/abs/1901.04326}, doi = {10.1515/9783110635461-005}, pages = {65 -- 88}, year = {2020}, abstract = {It is well understood that Bayesian decision theory and average case analysis are essentially identical. However, if one is interested in performing uncertainty quantification for a numerical task, it can be argued that the decision-theoretic framework is neither appropriate nor sufficient. To this end, we consider an alternative optimality criterion from Bayesian experimental design and study its implied optimal information in the numerical context. This information is demonstrated to differ, in general, from the information that would be used in an average-case-optimal numerical method. The explicit connection to Bayesian experimental design suggests several distinct regimes in which optimal probabilistic numerical methods can be developed.}, language = {en} } @article{KerstingSullivanHennig2020, author = {Kersting, Hans and Sullivan, T. J. and Hennig, Philipp}, title = {Convergence rates of Gaussian ODE filters}, volume = {30}, journal = {Statistics and Computing}, publisher = {Springer}, address = {Statistics and Computing}, arxiv = {http://arxiv.org/abs/1807.09737}, doi = {10.1007/s11222-020-09972-4}, pages = {1791 -- 1816}, year = {2020}, language = {en} } @article{ShaoBjaanaesHellandetal.2019, author = {Shao, Borong and Bjaanaes, Maria and Helland, Aslaug and Sch{\"u}tte, Christof and Conrad, Tim}, title = {EMT network-based feature selection improves prognosis prediction in lung adenocarcinoma}, volume = {14}, journal = {PLOS ONE}, number = {1}, doi = {10.1371/journal.pone.0204186}, year = {2019}, abstract = {Various feature selection algorithms have been proposed to identify cancer prognostic biomarkers. In recent years, however, their reproducibility is criticized. The performance of feature selection algorithms is shown to be affected by the datasets, underlying networks and evaluation metrics. One of the causes is the curse of dimensionality, which makes it hard to select the features that generalize well on independent data. Even the integration of biological networks does not mitigate this issue because the networks are large and many of their components are not relevant for the phenotype of interest. With the availability of multi-omics data, integrative approaches are being developed to build more robust predictive models. In this scenario, the higher data dimensions create greater challenges. We proposed a phenotype relevant network-based feature selection (PRNFS) framework and demonstrated its advantages in lung cancer prognosis prediction. We constructed cancer prognosis relevant networks based on epithelial mesenchymal transition (EMT) and integrated them with different types of omics data for feature selection. With less than 2.5\% of the total dimensionality, we obtained EMT prognostic signatures that achieved remarkable prediction performance (average AUC values above 0.8), very significant sample stratifications, and meaningful biological interpretations. In addition to finding EMT signatures from different omics data levels, we combined these single-omics signatures into multi-omics signatures, which improved sample stratifications significantly. Both single- and multi-omics EMT signatures were tested on independent multi-omics lung cancer datasets and significant sample stratifications were obtained.}, language = {en} } @article{GuptaPeterJungetal.2019, author = {Gupta, Pooja and Peter, Sarah and Jung, Markus and Lewin, Astrid and Hemmrich-Stanisak, Georg and Franke, Andre and von Kleist, Max and Sch{\"u}tte, Christof and Einspanier, Ralf and Sharbati, Soroush and zur Bruegge, Jennifer}, title = {Analysis of long non-coding RNA and mRNA expression in bovine macrophages brings up novel 2 aspects of Mycobacterium avium subspecies paratuberculosis infections}, volume = {9}, journal = {Scientific Reports in Nature}, doi = {10.1038/s41598-018-38141-x}, year = {2019}, abstract = {Paratuberculosis is a major disease in cattle that severely affects animal welfare and causes huge economic losses worldwide. Development of alternative diagnostic methods is of urgent need to control the disease. Recent studies suggest that long non-coding RNAs (lncRNAs) play a crucial role in regulating immune function and may confer valuable information about the disease. However, their role has not yet been investigated in cattle with respect to infection towards Paratuberculosis. Therefore, we investigated the alteration in genomic expression profiles of mRNA and lncRNA in bovine macrophages in response to Paratuberculosis infection using RNA-Seq. We identified 397 potentially novel lncRNA candidates in macrophages of which 38 were differentially regulated by the infection. A total of 820 coding genes were also significantly altered by the infection. Co-expression analysis of lncRNAs and their neighbouring coding genes suggest regulatory functions of lncRNAs in pathways related to immune response. For example, this included protein coding genes such as TNIP3, TNFAIP3 and NF-κB2 that play a role in NF-κB2 signalling, a pathway associated with immune response. This study advances our understanding of lncRNA roles during Paratuberculosis infection.}, language = {en} } @misc{GoetschelMinion2019, author = {G{\"o}tschel, Sebastian and Minion, Michael L.}, title = {An Efficient Parallel-in-Time Method for Optimization with Parabolic PDEs}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-71490}, year = {2019}, abstract = {To solve optimization problems with parabolic PDE constraints, often methods working on the reduced objective functional are used. They are computationally expensive due to the necessity of solving both the state equation and a backward-in-time adjoint equation to evaluate the reduced gradient in each iteration of the optimization method. In this study, we investigate the use of the parallel-in-time method PFASST in the setting of PDE constrained optimization. In order to develop an efficient fully time-parallel algorithm we discuss different options for applying PFASST to adjoint gradient computation, including the possibility of doing PFASST iterations on both the state and adjoint equations simultaneously. We also explore the additional gains in efficiency from reusing information from previous optimization iterations when solving each equation. Numerical results for both a linear and a non-linear reaction-diffusion optimal control problem demonstrate the parallel speedup and efficiency of different approaches.}, language = {en} } @inproceedings{JaegerManleyEisenhaueretal.2018, author = {J{\"a}ger, Klaus and Manley, Phillip and Eisenhauer, David and Tockhorn, Philipp and Sutter, Johannes and Hammerschmidt, Martin and Burger, Sven and Albrecht, Steve and Becker, Christiane}, title = {Light management with sinusoidal nanotextures}, booktitle = {Light, Energy and the Environment 2018}, doi = {10.1364/OSE.2018.OT5C.5}, pages = {OT5C.5}, year = {2018}, language = {en} } @misc{NaegelDeuflhardWittum2018, author = {N{\"a}gel, Arne and Deuflhard, Peter and Wittum, Gabriel}, title = {Efficient Stiff Integration of Density Driven Flow Problems}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-70891}, year = {2018}, abstract = {The paper investigates the efficient use of a linearly implicit stiff integrator for the numerical solution of density driven flow problems. Upon choosing a one-step method of extrapolation type (code LIMEX), the use of full Jacobians and reduced approximations are discussed. Numerical experiments include nonlinear density flow problems such as diffusion from a salt dome (2D), a (modified) Elder problem (3D), the saltpool benchmark (3D) and a real life salt dome problem (2D). The arising linear equations are solved using either a multigrid preconditioner from the software package UG4 or the sparse matrix solver SuperLU.}, language = {en} } @article{GoetschelWeiser2019, author = {G{\"o}tschel, Sebastian and Weiser, Martin}, title = {Compression Challenges in Large Scale Partial Differential Equation Solvers}, volume = {12}, journal = {Algorithms}, number = {9}, doi = {10.3390/a12090197}, pages = {197}, year = {2019}, abstract = {Solvers for partial differential equations (PDEs) are one of the cornerstones of computational science. For large problems, they involve huge amounts of data that need to be stored and transmitted on all levels of the memory hierarchy. Often, bandwidth is the limiting factor due to the relatively small arithmetic intensity, and increasingly due to the growing disparity between computing power and bandwidth. Consequently, data compression techniques have been investigated and tailored towards the specific requirements of PDE solvers over the recent decades. This paper surveys data compression challenges and discusses examples of corresponding solution approaches for PDE problems, covering all levels of the memory hierarchy from mass storage up to the main memory. We illustrate concepts for particular methods, with examples, and give references to alternatives.}, language = {en} } @article{StoopStraubeJohansenetal.2020, author = {Stoop, Ralph L. and Straube, Arthur and Johansen, Tom H. and Tierno, Pietro}, title = {Collective directional locking of colloidal monolayers on a periodic substrate}, volume = {124}, journal = {Phys. Rev. Lett.}, doi = {10.1103/PhysRevLett.124.058002}, pages = {058002}, year = {2020}, abstract = {We investigate the directional locking effects that arise when a monolayer of paramagnetic colloidal particles is driven across a triangular lattice of magnetic bubbles. We use an external rotating magnetic field to generate a two-dimensional traveling wave ratchet forcing the transport of particles along a direction that intersects two crystallographic axes of the lattice. We find that, while single particles show no preferred direction, collective effects induce transversal current and directional locking at high density via a spontaneous symmetry breaking. The colloidal current may be polarized via an additional bias field that makes one transport direction energetically preferred.}, language = {en} } @article{LieSullivanTeckentrup2021, author = {Lie, Han Cheng and Sullivan, T. J. and Teckentrup, Aretha}, title = {Error bounds for some approximate posterior measures in Bayesian inference}, journal = {Numerical Mathematics and Advanced Applications ENUMATH 2019}, publisher = {Springer}, arxiv = {http://arxiv.org/abs/1911.05669}, doi = {10.1007/978-3-030-55874-1_26}, pages = {275 -- 283}, year = {2021}, language = {en} } @article{KhorashadBesteiroCorreaDuarteetal.2020, author = {Khorashad, Larousse Khosravi and Besteiro, Lucas V. and Correa-Duarte, Miguel and Burger, Sven and Wang, Zhiming M. and Govorov, Alexander O.}, title = {Hot electrons generated in chiral plasmonic nanocrystals as a mechanism for surface photochemistry and chiral growth}, volume = {142}, journal = {J. Am. Chem. Soc.}, doi = {10.1021/jacs.9b11124}, pages = {4193}, year = {2020}, language = {en} } @article{WerdehausenBurgerStaudeetal.2020, author = {Werdehausen, Daniel and Burger, Sven and Staude, Isabelle and Pertsch, Thomas and Decker, Manuel}, title = {General design formalism for highly efficient flat optics for broadband applications}, volume = {28}, journal = {Opt. Express}, doi = {10.1364/OE.386573}, pages = {6452}, year = {2020}, language = {en} } @article{PfluegerKlineFernandezHerreroetal.2020, author = {Pfl{\"u}ger, Mika and Kline, R. Joseph and Fern{\´a}ndez Herrero, Analia and Hammerschmidt, Martin and Soltwisch, Victor and Krumrey, Michael}, title = {Extracting dimensional parameters of gratings produced with self-aligned multiple patterning using grazing-incidence small-angle x-ray scattering}, volume = {19}, journal = {J. Micro Nanolithogr. MEMS MOEMS}, arxiv = {http://arxiv.org/abs/1910.08532}, doi = {10.1117/1.JMM.19.1.014001}, pages = {014001}, year = {2020}, language = {en} } @article{EndresBurgerWurmetal.2013, author = {Endres, Johannes and Burger, Sven and Wurm, Matthias and Bodermann, Bernd}, title = {Numerical investigations of the influence of different commonly applied approximations in scatterometry}, volume = {8789}, journal = {Proc. SPIE}, doi = {10.1117/12.2022108}, pages = {878904}, year = {2013}, language = {en} } @article{SoltwischBurgerScholze2013, author = {Soltwisch, Victor and Burger, Sven and Scholze, Frank}, title = {Scatterometry sensitivity analysis for conical diffraction versus in-plane diffraction geometry with respect to the side wall angle}, volume = {8789}, journal = {Proc. SPIE}, doi = {10.1117/12.2020487}, pages = {878905}, year = {2013}, language = {en} } @article{HansenBurger2013, author = {Hansen, Poul-Erik and Burger, Sven}, title = {Investigation of microstructured fiber geometries by scatterometry}, volume = {8789}, journal = {Proc. SPIE}, doi = {10.1117/12.2020526}, pages = {87890R}, year = {2013}, language = {en} } @article{LieFackeldeyWeber2013, author = {Lie, Han Cheng and Fackeldey, Konstantin and Weber, Marcus}, title = {A Square Root Approximation of Transition Rates for a Markov State Model}, volume = {34}, journal = {SIAM. J. Matrix Anal. Appl.}, number = {2}, doi = {10.1137/120899959}, pages = {738 -- 756}, year = {2013}, language = {en} } @article{ScharkoiFackeldeyMerkulowetal.2013, author = {Scharkoi, Olga and Fackeldey, Konstantin and Merkulow, Igor and Andrae, Karsten and Weber, Marcus and Nehls, Irene}, title = {Conformational Analysis of Alternariol on the Quantum Level}, volume = {19}, journal = {J. Mol. Model.}, number = {6}, doi = {10.1007/s00894-013-1803-2}, pages = {2567 -- 2572}, year = {2013}, language = {en} } @article{HornWulkow2005, author = {Horn, H. and Wulkow, Michael}, title = {Simulation von Wachstum und Abtrag der Biomasse - Eine exemplarische Betrachtung f{\"u}r eine 2D-Modellierung}, volume = {77}, journal = {Chem. Ing. Technik}, number = {4}, pages = {418 -- 424}, year = {2005}, language = {en} } @article{HornWulkow1996, author = {Horn, H. and Wulkow, Michael}, title = {Modellierung von Einleitungen in kleine Fließgew{\"a}sser}, volume = {137}, journal = {gwf Wasser Abwasser}, year = {1996}, language = {en} } @article{HuisingaTelgmannWulkow2006, author = {Huisinga, Wilhelm and Telgmann, R. and Wulkow, Michael}, title = {The virtual lab approach to pharmacokinetic}, volume = {11}, journal = {Drug Discov Today}, pages = {800 -- 805}, year = {2006}, language = {en} } @article{HungenbergChenZhangetal.2001, author = {Hungenberg, K.-D. and Chen, C.-C. and Zhang, F. and Wulkow, Michael and Stubbe, G. and Nieken, U.}, title = {Design of Polymer Processes Using the Coupling of Commercial Simulation Packages Polymers Plus and PREDICI}, volume = {137}, journal = {DECHEMA Monographs}, pages = {237 -- 245}, year = {2001}, language = {en} } @article{HungenbergKnollWulkow1997, author = {Hungenberg, K.-D. and Knoll, K. and Wulkow, Michael}, title = {Absolute Propagation Rate Coefficients in Radical Polymerization from Gel Permeation Chromatography of Polymers Produced by Intermittent Initiation}, volume = {6}, journal = {Macromol. Theory Simul.}, year = {1997}, language = {en} } @article{IedemaWulkowHoefsloot2007, author = {Iedema, P. and Wulkow, Michael and Hoefsloot, H.}, title = {Conditional Monte Carlo sampling to find branching architectures of polymers from radical polymerizations with transfer to polymer and recombination termination}, volume = {48}, journal = {Polymer}, number = {6}, pages = {1770 -- 1784}, year = {2007}, language = {en} } @article{IedemaWulkowHoefsloot:2000, author = {Iedema, P. and Wulkow, Michael and Hoefsloot:, H.}, title = {Modeling Molecular Weight and Degree of Branching Distribution of low density Polyethylene}, volume = {33}, journal = {Macromolecules}, pages = {7173 -- 7184}, year = {2000}, language = {en} } @article{KatzerPauerMoritzetal.2012, author = {Katzer, J. and Pauer, W. and Moritz, H.-U. and Wulkow, Michael}, title = {Thermal polymerization of styrene Part B}, volume = {6}, journal = {Macromol. React. Eng}, pages = {225 -- 238}, year = {2012}, language = {en} } @article{LinGrimmWulkowetal.2008, author = {Lin, P.-J. and Grimm, L. and Wulkow, Michael and Hempel, D. and Krull, R.}, title = {Population Balance Modeling of the Conidial Aggregation of Aspergillus niger}, volume = {99}, journal = {Biotechnology and Bioengineering}, number = {2}, pages = {341 -- 350}, year = {2008}, language = {en} } @article{MuellerYanWulkow1997, author = {M{\"u}ller, A. and Yan, D. and Wulkow, Michael}, title = {Molecular Parameters of Hyperbranched Polymers Made by Self-condensing Vinyl Polymerization, 1. Molecular weight distribution}, volume = {30}, journal = {Macromolecules}, pages = {7015}, year = {1997}, language = {en} } @article{OchoaWulkow2012, author = {Ochoa, J.G. and Wulkow, Michael}, title = {DNA damages as a Depolymerization Process}, volume = {23}, journal = {International Journal of Modern Physics C}, number = {03}, pages = {1250018 -- 1}, year = {2012}, language = {en} } @article{ReuterKrauseWulkowetal.2003, author = {Reuter, H. and Krause, G. and Wulkow, Michael and M{\"o}nig, A. and Horn, H.}, title = {A water quality management tool for river basins}, volume = {48}, journal = {Wat. Sci. Techn.}, number = {10}, pages = {47 -- 53}, year = {2003}, language = {en} } @article{ReynhoutMeuldijkDrinkenburgetal.2005, author = {Reynhout, X. and Meuldijk, J. and Drinkenburg, B. and Iedema, P. and Wulkow, Michael}, title = {A Novel Method to Model Emulsion Polymerization Kinetics}, volume = {44}, journal = {Polymer-Plastics Tech. Eng.}, number = {4}, pages = {707 -- 740}, year = {2005}, language = {en} } @article{SchmidtBuschLilgeetal.2005, author = {Schmidt, Christian-Ulrich and Busch, Markus and Lilge, Dieter and Wulkow, Michael}, title = {Detailed Molecular Structure Modeling - A Path Forward to Designing Application Properties of ldPE}, volume = {290}, journal = {Macromolecular Materials and Engineering}, pages = {404}, year = {2005}, language = {en} } @article{SchuetteWulkow2010, author = {Sch{\"u}tte, Christof and Wulkow, Michael}, title = {A hybrid Galerkin-Monte-Carlo approach to higher-dimensional population balances in polymerization kinetics}, volume = {4}, journal = {Macromol. React. Eng.}, pages = {562 -- 577}, year = {2010}, language = {en} } @article{TeichmannLiebeltReuschenbachetal.2001, author = {Teichmann, L. and Liebelt, U. and Reuschenbach, P. and Wulkow, Michael and Horn, H.}, title = {Two dimensional simulation of mass transport and nitrification in the river Rhine}, volume = {1}, journal = {Eng. Life Sci.}, number = {4}, pages = {145 -- 149}, year = {2001}, language = {en} } @article{Wulkow2008, author = {Wulkow, Michael}, title = {Feature article - Computer Aided Modeling of Polymer Reaction Engineering - The Status of Predici, 1 - Simulation}, volume = {2}, journal = {Macromol. React. Eng.}, pages = {461 -- 494}, year = {2008}, language = {en} } @article{Wulkow1996, author = {Wulkow, Michael}, title = {Feature article - The Simulation of Molecular Weight Distributions in Polyreaction Kinetics by Discrete Galerkin Methods}, volume = {5}, journal = {Macromol. Theory Simul.}, pages = {393 -- 416}, year = {1996}, language = {en} } @article{WulkowBuschDavisetal.2004, author = {Wulkow, Michael and Busch, Markus and Davis, Thomas P. and Barner-Kowollik, Christopher}, title = {Implementing the Reversible Addition Fragmentation Chain Transfer (RAFT) Process in Predici.}, volume = {42}, journal = {Journal of Polymer Science}, pages = {1441}, year = {2004}, language = {en} } @article{WulkowGerstlauerNieken2001, author = {Wulkow, Michael and Gerstlauer, A. and Nieken, U.}, title = {Modeling of Crystallization Processes using PARSIVAL}, volume = {56}, journal = {Chem. Eng. Sci.}, pages = {2575 -- 2588}, year = {2001}, language = {en} } @misc{BujotzekSchuettNielsenetal.2013, author = {Bujotzek, Alexander and Sch{\"u}tt, Ole and Nielsen, Adam and Fackeldey, Konstantin and Weber, Marcus}, title = {Efficient Conformational Analysis by Partition-of-Unity Coupling}, journal = {Math Chem}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42570}, year = {2013}, abstract = {Obtaining a sufficient sampling of conformational space is a common problem in molecular simulation. We present the implementation of an umbrella-like adaptive sampling approach based on function-based meshless discretization of conformational space that is compatible with state of the art molecular dynamics code and that integrates an eigenvector-based clustering approach for conformational analysis and the computation of inter-conformational transition rates. The approach is applied to three example systems, namely n-pentane, alanine dipeptide, and a small synthetic host-guest system, the latter two including explicitly modeled solvent.}, language = {en} }