@article{SherrattSrivastavaAinslieetal.2024, author = {Sherratt, Katharine and Srivastava, Ajitesh and Ainslie, Kylie and Singh, David E. and Cublier, Aymar and Marinescu, Maria Cristina and Carretero, Jesus and Garcia, Alberto Cascajo and Franco, Nicolas and Willem, Lander and Abrams, Steven and Faes, Christel and Beutels, Philippe and Hens, Niel and M{\"u}ller, Sebastian and Charlton, Billy and Ewert, Ricardo and Paltra, Sydney and Rakow, Christian and Rehmann, Jakob and Conrad, Tim and Sch{\"u}tte, Christof and Nagel, Kai and Abbott, Sam and Grah, Rok and Niehus, Rene and Prasse, Bastian and Sandmann, Frank and Funk, Sebastian}, title = {Characterising information gains and losses when collecting multiple epidemic model outputs}, volume = {47}, journal = {Epidemics}, publisher = {Elsevier BV}, issn = {1755-4365}, doi = {10.1016/j.epidem.2024.100765}, year = {2024}, abstract = {Collaborative comparisons and combinations of epidemic models are used as policy-relevant evidence during epidemic outbreaks. In the process of collecting multiple model projections, such collaborations may gain or lose relevant information. Typically, modellers contribute a probabilistic summary at each time-step. We compared this to directly collecting simulated trajectories. We aimed to explore information on key epidemic quantities; ensemble uncertainty; and performance against data, investigating potential to continuously gain information from a single cross-sectional collection of model results. Methods We compared July 2022 projections from the European COVID-19 Scenario Modelling Hub. Five modelling teams projected incidence in Belgium, the Netherlands, and Spain. We compared projections by incidence, peaks, and cumulative totals. We created a probabilistic ensemble drawn from all trajectories, and compared to ensembles from a median across each model's quantiles, or a linear opinion pool. We measured the predictive accuracy of individual trajectories against observations, using this in a weighted ensemble. We repeated this sequentially against increasing weeks of observed data. We evaluated these ensembles to reflect performance with varying observed data. Results. By collecting modelled trajectories, we showed policy-relevant epidemic characteristics. Trajectories contained a right-skewed distribution well represented by an ensemble of trajectories or a linear opinion pool, but not models' quantile intervals. Ensembles weighted by performance typically retained the range of plausible incidence over time, and in some cases narrowed this by excluding some epidemic shapes. Conclusions. We observed several information gains from collecting modelled trajectories rather than quantile distributions, including potential for continuously updated information from a single model collection. The value of information gains and losses may vary with each collaborative effort's aims, depending on the needs of projection users. Understanding the differing information potential of methods to collect model projections can support the accuracy, sustainability, and communication of collaborative infectious disease modelling efforts. Data availability All code and data available on Github: https://github.com/covid19-forecast-hub-europe/aggregation-info-loss}, language = {en} } @article{MartinMuellerPapeetal.2017, author = {Martin, Alex and M{\"u}ller, J. and Pape, S. and Peter, A. and Pokutta, Sebastian and Winter, T.}, title = {Pricing and clearing combinatorial markets with singleton and swap orders}, volume = {85}, journal = {Mathematical Methods of Operations Research}, number = {2}, arxiv = {http://arxiv.org/abs/1404.6546}, pages = {155 -- 177}, year = {2017}, language = {en} } @article{MartinMuellerPokutta2014, author = {Martin, Alexander and M{\"u}ller, J. and Pokutta, Sebastian}, title = {Strict linear prices in non-convex European day-ahead electricity markets}, volume = {29}, journal = {Optimization Methods and Software}, number = {1}, pages = {189 -- 221}, year = {2014}, language = {en} } @inproceedings{GesingGrunzkeBalaskoetal.2011, author = {Gesing, Sandra and Grunzke, Richard and Balasko, Akos and Birkenheuer, Georg and Blunk, Dirk and Breuers, Sebastian and Brinkmann, Andr{\´e} and Fels, Gregor and Herres-Pawlis, Sonja and Kacsuk, Peter and Kozlovszky, Miklos and Kr{\"u}ger, Jens and Packschies, Lars and Sch{\"a}fer, Patrick and Schuller, Bernd and Schuster, Johannes and Steinke, Thomas and Szikszay Fabri, Anna and Wewior, Martin and M{\"u}ller-Pfefferkorn, Ralph and Kohlbacher, Oliver}, title = {Granular Security for a Science Gateway in Structural Bioinformatics}, booktitle = {Proc. IWSG-Life 2011}, year = {2011}, language = {en} } @inproceedings{BirkenheuerBlunkBreuersetal.2011, author = {Birkenheuer, Georg and Blunk, Dirk and Breuers, Sebastian and Brinkmann, Andre and Fels, Gregor and Gesing, Sandra and Grunzke, Richard and Herres-Pawlis, Sonja and Kohlbacher, Oliver and Kr{\"u}ger, Jens and Lang, Ulrich and Packschies, Lars and M{\"u}ller-Pfefferkorn, Ralph and Sch{\"a}fer, Patrick and Schuster, Johannes and Steinke, Thomas and Warzecha, Klaus Dieter and Wewior, Martin}, title = {MoSGrid: Progress of Workflow driven Chemical Simulations}, volume = {826}, booktitle = {Proc. of Grid Workflow Workshop 2011, Cologne, Germany}, publisher = {CEUR Workshop Proceedings}, year = {2011}, language = {en} } @article{BirkenheuerBlunkBreuersetal.2011, author = {Birkenheuer, Georg and Blunk, Dirk and Breuers, Sebastian and Brinkmann, Andre and dos Santos Vieira, Ines and Fels, Gregor and Gesing, Sandra and Grunzke, Richard and Herres-Pawlis, Sonja and Kohlbacher, Oliver and Kr{\"u}ger, Jens and Lang, Ulrich and Packschies, Lars and M{\"u}ller-Pfefferkorn, Ralph and Sch{\"a}fer, Patrick and Schmalz, Hans-G{\"u}nther and Steinke, Thomas and Warzecha, Klaus Dieter and Wewior, Martin}, title = {A Molecular Simulation Grid as new tool for Computational Chemistry, Biology and Material Science}, volume = {3}, journal = {Journal of Cheminformatics 2011}, number = {Suppl 1}, doi = {10.1186/1758-2946-3-S1-P14}, year = {2011}, language = {en} } @inproceedings{GesingKacsukKozlovszkyetal.2011, author = {Gesing, Sandra and Kacsuk, Peter and Kozlovszky, Miklos and Birkenheuer, Georg and Blunk, Dirk and Breuers, Sebastian and Brinkmann, Andre and Fels, Gregor and Grunzke, Richard and Herres-Pawlis, Sonja and Kr{\"u}ger, Jens and Packschies, Lars and M{\"u}ller-Pfefferkorn, Ralph and Sch{\"a}fer, Patrick and Steinke, Thomas and Szikszay Fabri, Anna and Warzecha, Klaus Dieter and Wewior, Martin and Kohlbacher, Oliver}, title = {A Science Gateway for Molecular Simulations}, booktitle = {EGI (European Grid Infrastructure) User Forum 2011, Book of Abstracts}, pages = {94 -- 95}, year = {2011}, language = {en} } @article{BirkenheuerBlunkBreuersetal.2012, author = {Birkenheuer, Georg and Blunk, Dirk and Breuers, Sebastian and Brinkmann, Andr{\´e} and dos Santos Vieira, Ines and Fels, Gregor and Gesing, Sandra and Grunzke, Richard and Herres-Pawlis, Sonja and Kohlbacher, Oliver and Kr{\"u}ger, Jens and Lang, Ulrich and Packschies, Lars and M{\"u}ller-Pfefferkorn, Ralph and Sch{\"a}fer, Patrick and Steinke, Thomas and Warzecha, Klaus Dieter and Wewior, Martin}, title = {MoSGrid: efficient data management and a standardized data exchange format for molecular simulations in a grid environment}, volume = {4}, journal = {Journal of Cheminformatics}, number = {Suppl 1}, doi = {10.1186/1758-2946-4-S1-P21}, pages = {21}, year = {2012}, language = {en} } @article{GesingGrunzkeKruegeretal.2012, author = {Gesing, Sandra and Grunzke, Richard and Kr{\"u}ger, Jens and Birkenheuer, Georg and Wewior, Martin and Sch{\"a}fer, Patrick and Schuller, Bernd and Schuster, Johannes and Herres-Pawlis, Sonja and Breuers, Sebastian and Balasko, Akos and Kozlovszky, Miklos and Szikszay Fabri, Anna and Packschies, Lars and Kacsuk, Peter and Blunk, Dirk and Steinke, Thomas and Brinkmann, Andr{\´e} and Fels, Gregor and M{\"u}ller-Pfefferkorn, Ralph and J{\"a}kel, Ren{\´e} and Kohlbacher, Oliver}, title = {A Single Sign-On Infrastructure for Science Gateways on a Use Case for Structural Bioinformatics}, journal = {Journal of Grid Computing}, year = {2012}, language = {en} } @inproceedings{GrunzkeBirkenheuerBlunketal.2012, author = {Grunzke, Richard and Birkenheuer, Georg and Blunk, Dirk and Breuers, Sebastian and Brinkmann, Andr{\´e} and Gesing, Sandra and Herres-Pawlis, Sonja and Kohlbacher, Oliver and Kr{\"u}ger, Jens and Kruse, Martin and M{\"u}ller-Pfefferkorn, Ralph and Sch{\"a}fer, Patrick and Schuller, Bernd and Steinke, Thomas and Zink, Andreas}, title = {A Data Driven Science Gateway for Computational Workflows}, booktitle = {Proceedings of the UNICORE Summit}, address = {Dresden, Germany}, year = {2012}, language = {en} } @inproceedings{MartinMuellerPokutta2010, author = {Martin, Alexander and M{\"u}ller, J. and Pokutta, Sebastian}, title = {On clearing coupled day-ahead electricity markets}, booktitle = {Proceedings of 23rd Australasian Finance and Banking Conference}, year = {2010}, language = {en} } @inproceedings{MuellerGoetschelWeiseretal.2017, author = {M{\"u}ller, Jan and G{\"o}tschel, Sebastian and Weiser, Martin and Maierhofer, Christiane}, title = {Thermografie mit optimierter Anregung f{\"u}r die quantitative Untersuchung von Delaminationen in kohlenstofffaserverst{\"a}rkten Kunststoffen}, booktitle = {NDT.net Proc. DGZfP 2017}, year = {2017}, abstract = {Da kohlenstofffaserverst{\"a}rkte Kunststoffe (CFK) in anspruchsvollen sicherheitsrelevanten Einsatzgebieten wie im Automobilbau und in der Luftfahrt eingesetzt werden, besteht ein zunehmender Bedarf an zerst{\"o}rungsfreien Pr{\"u}fmethoden. Ziel ist die Gew{\"a}hrleistung der Sicherheit und Zuverl{\"a}ssigkeit der eingesetzten Bauteile. Aktive Thermografieverfahren erm{\"o}glichen die effiziente Pr{\"u}fung großer Fl{\"a}chen mit hoher Aufl{\"o}sung in wenigen Arbeitsschritten. Ein wichtiges Teilgebiet der Pr{\"u}fungen ist die Ortung und Charakterisierung von Delaminationen, die sowohl bereits in der Fertigung als auch w{\"a}hrend der Nutzung eines Bauteils auftreten k{\"o}nnen, und dessen strukturelle Integrit{\"a}t schw{\"a}chen. ;In diesem Beitrag werden CFK-Strukturen mit k{\"u}nstlichen und nat{\"u}rlichen Delaminationen mit Hilfe unterschiedlich zeitlich modulierter Strahlungsquellen experimentell untersucht. Verwendet werden dabei Anregungen mit Blitzlampen und mit frequenzmodulierten Halogenlampen. Mittels Filterfunktionen im Zeit- und Frequenzbereich wird das Kontrast-zu-Rausch-Verh{\"a}ltnis (CNR) der detektierten Fehlstellen optimiert. Verglichen werden anschließend die Nachweisempfindlichkeit, das CNR und die Ortsaufl{\"o}sung der zu charakterisierenden Delaminationen f{\"u}r die unterschiedlichen Anregungs- und Auswertungstechniken. Erg{\"a}nzt werden die Experimente durch numerische Simulationen des dreidimensionalen W{\"a}rmetransportes.}, language = {de} } @article{WulkowConradDjurdjevacConradetal.2021, author = {Wulkow, Hanna and Conrad, Tim and Djurdjevac Conrad, Natasa and M{\"u}ller, Sebastian A. and Nagel, Kai and Sch{\"u}tte, Christof}, title = {Prediction of Covid-19 spreading and optimal coordination of counter-measures: From microscopic to macroscopic models to Pareto fronts}, volume = {16}, journal = {PLOS One}, number = {4}, publisher = {Public Library of Science}, doi = {10.1371/journal.pone.0249676}, year = {2021}, language = {en} } @misc{BirkenheuerBlunkBreuersetal.2010, author = {Birkenheuer, Georg and Blunk, Dirk and Breuers, Sebastian and Brinkmann, Andr{\´e} and d. Santos Vieira, I. and Fels, Gregor and Gesing, Sandra and Grunzke, Richard and Herres-Pawlis, Sonja and Kohlbacher, Oliver and Kruber, Nico and Kr{\"u}ger, Jens and Lang, U. and Packschies, Lars and M{\"u}ller-Pfefferkorn, Ralph and Sch{\"a}fer, Patrick and Schmalz, Hans-G{\"u}nther and Steinke, Thomas and Warzecha, Klaus Dieter and Wewior, Martin}, title = {MoSGrid - A Molecular Simulation Grid as a new tool in Computational Chemistry, Biology and Material Science}, journal = {6. German Conference on Chemoinformatics}, year = {2010}, language = {en} } @inproceedings{KruegerBirkenheuerBlunketal.2010, author = {Kr{\"u}ger, Jens and Birkenheuer, Georg and Blunk, Dirk and Breuers, Sebastian and Brinkmann, Andr{\´e} and Fels, Gregor and Gesing, Sandra and Grunzke, Richard and Herres-Pawlis, Sonja and Kohlbacher, Oliver and Kruber, Nico and Lang, U. and Packschies, Lars and M{\"u}ller-Pfefferkorn, Ralph and Sch{\"a}fer, Patrick and Schmalz, Hans-G{\"u}nther and Steinke, Thomas and Warzecha, Klaus Dieter and Wewior, Martin}, title = {Molecular Simulation Grid}, booktitle = {6. German Conference on Chemoinformatics}, publisher = {Gesellschaft Deutscher Chemiker (GDCh)}, year = {2010}, language = {en} } @inproceedings{GoetschelMaierhoferMuelleretal.2016, author = {G{\"o}tschel, Sebastian and Maierhofer, Christiane and M{\"u}ller, Jan and Rothbart, Nick and Weiser, Martin}, title = {Quantitative Defect Reconstruction in Active Thermography for Fiber-Reinforced Composites}, booktitle = {Proceedings 19th World Conference on Non-Destructive Testing (WCNDT 2016)}, year = {2016}, language = {en} } @inproceedings{MuellerGoetschelMaierhoferetal.2017, author = {M{\"u}ller, Jan and G{\"o}tschel, Sebastian and Maierhofer, Christiane and Weiser, Martin}, title = {Determining the material parameters for the reconstruction of defects in carbon fiber reinforced polymers from data measured by flash thermography}, volume = {1806}, booktitle = {AIP Conference Proceedings}, doi = {10.1063/1.4974671}, year = {2017}, language = {en} } @article{RedemannBaumgartLindowetal.2017, author = {Redemann, Stefanie and Baumgart, Johannes and Lindow, Norbert and Shelley, Michael and Nazockdast, Ehssan and Kratz, Andrea and Prohaska, Steffen and Brugu{\´e}s, Jan and F{\"u}rthauer, Sebastian and M{\"u}ller-Reichert, Thomas}, title = {C. elegans chromosomes connect to centrosomes by anchoring into the spindle network}, volume = {8}, journal = {Nature Communications}, number = {15288}, doi = {10.1038/ncomms15288}, year = {2017}, abstract = {The mitotic spindle ensures the faithful segregation of chromosomes. Here we combine the first large-scale serial electron tomography of whole mitotic spindles in early C. elegans embryos with live-cell imaging to reconstruct all microtubules in 3D and identify their plus- and minus-ends. We classify them as kinetochore (KMTs), spindle (SMTs) or astral microtubules (AMTs) according to their positions, and quantify distinct properties of each class. While our light microscopy and mutant studies show that microtubules are nucleated from the centrosomes, we find only a few KMTs directly connected to the centrosomes. Indeed, by quantitatively analysing several models of microtubule growth, we conclude that minus-ends of KMTs have selectively detached and depolymerized from the centrosome. In toto, our results show that the connection between centrosomes and chromosomes is mediated by an anchoring into the entire spindle network and that any direct connections through KMTs are few and likely very transient.}, language = {en} } @article{KruegerGrunzkeGesingetal.2014, author = {Kr{\"u}ger, Jens and Grunzke, Richard and Gesing, Sandra and Breuers, Sebastian and Brinkmann, Andr{\´e} and de la Garza, Luis and Kohlbacher, Oliver and Kruse, Martin and Nagel, Wolfgang and Packschies, Lars and M{\"u}ller-Pfefferkorn, Ralph and Sch{\"a}fer, Patrick and Sch{\"a}rfe, Charlotta and Steinke, Thomas and Schlemmer, Tobias and Warzecha, Klaus Dieter and Zink, Andreas and Herres-Pawlis, Sonja}, title = {The MoSGrid Science Gateway - A Complete Solution for Molecular Simulations}, volume = {10}, journal = {Journal of Chemical Theory and Computation}, number = {6}, doi = {10.1021/ct500159h}, pages = {2232 -- 2245}, year = {2014}, language = {en} } @article{GrunzkeBreuersGesingetal.2013, author = {Grunzke, Richard and Breuers, Sebastian and Gesing, Sandra and Herres-Pawlis, Sonja and Kruse, Martin and Blunk, Dirk and de la Garza, Luis and Packschies, Lars and Sch{\"a}fer, Patrick and Sch{\"a}rfe, Charlotta and Schlemmer, Tobias and Steinke, Thomas and Schuller, Bernd and M{\"u}ller-Pfefferkorn, Ralph and J{\"a}kel, Ren{\´e} and Nagel, Wolfgang and Atkinson, Malcolm and Kr{\"u}ger, Jens}, title = {Standards-based metadata management for molecular simulations}, journal = {Concurrency and Computation: Practice and Experience}, doi = {10.1002/cpe.3116}, year = {2013}, 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} } @article{MuellerPaltraRehmannetal.2023, author = {M{\"u}ller, Sebastian and Paltra, Sydney and Rehmann, Jakob and Nagel, Kai and Conrad, Tim}, title = {Explicit modeling of antibody levels for infectious disease simulations in the context of SARS-CoV-2}, volume = {26}, journal = {iScience}, number = {9}, doi = {10.1016/j.isci.2023.107554}, year = {2023}, abstract = {Measurable levels of immunoglobulin G antibodies develop after infections with and vaccinations against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). These antibody levels are dynamic: due to waning, antibody levels will drop over time. During the COVID-19 pandemic, multiple models predicting infection dynamics were used by policymakers to support the planning of public health policies. Explicitly integrating antibody and waning effects into the models is crucial for reliable calculations of individual infection risk. However, only few approaches have been suggested that explicitly treat these effects. This paper presents a methodology that explicitly models antibody levels and the resulting protection against infection for individuals within an agent-based model. The model was developed in response to the complexity of different immunization sequences and types and is based on neutralization titer studies. This approach allows complex population studies with explicit antibody and waning effects. We demonstrate the usefulness of our model in two use cases.}, language = {en} }