@article{OkaforntaFarhadifarFabigetal.2025, author = {Okafornta, Chukwuebuka William and Farhadifar, Reza and Fabig, Gunar and Wu, Hai-Yin and K{\"o}ckert, Maria and Vogel, Martin and Baum, Daniel and Haase, Robert and Shelley, Michael J. and Needleman, Daniel J. and M{\"u}ller-Reichert, Thomas}, title = {Cell size reduction scales spindle elongation but not chromosome segregation in C. elegans}, journal = {bioRxiv}, doi = {10.1101/2025.10.13.681585}, year = {2025}, abstract = {How embryos adapt their internal cellular machinery to reductions in cell size during development remains a fundamental question in cell biology. Here, we use high-resolution lattice light-sheet fluorescence microscopy and automated image analysis to quantify lineage-resolved mitotic spindle and chromosome segregation dynamics from the 2- to 64-cell stages in Caenorhabditis elegans embryos. While spindle length scales with cell size across both wild-type and size-perturbed embryos, chromosome segregation dynamics remain largely invariant, suggesting that distinct mechanisms govern these mitotic processes. Combining femtosecond laser ablation with large-scale electron tomography, we find that central spindle microtubules mediate chromosome segregation dynamics and remain uncoupled from cell size across all stages of early development. In contrast, spindle elongation is driven by cortically anchored motor proteins and astral microtubules, rendering it sensitive to cell size. Incorporating these experimental results into an extended stoichiometric model for both the spindle and chromosomes, we find that allowing only cell size and microtubule catastrophe rates to vary reproduces elongation dynamics across development. The same model also accounts for centrosome separation and pronuclear positioning in the one-cell C. elegans embryo, spindle-length scaling across nematode species spanning ~100 million years of divergence, and spindle rotation in human cells. Thus, a unified stoichiometric framework provides a predictive, mechanistic account of spindle and nuclear dynamics across scales and species.}, 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{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} } @article{FabigKiewiszLindowetal.2020, author = {Fabig, Gunar and Kiewisz, Robert and Lindow, Norbert and Powers, James A. and Cota, Vanessa and Quintanilla, Luis J. and Brugu{\´e}s, Jan and Prohaska, Steffen and Chu, Diana S. and M{\"u}ller-Reichert, Thomas}, title = {Sperm-specific meiotic chromosome segregation in C. elegans}, volume = {9}, journal = {eLife}, doi = {10.7554/eLife.50988}, pages = {e50988}, year = {2020}, language = {en} } @article{LindowBruenigDercksenetal.2020, author = {Lindow, Norbert and Br{\"u}nig, Florian and Dercksen, Vincent J. and Fabig, Gunar and Kiewisz, Robert and Redemann, Stefanie and M{\"u}ller-Reichert, Thomas and Prohaska, Steffen and Baum, Daniel}, title = {Semi-automatic stitching of filamentous structures in image stacks from serial-section electron tomography}, journal = {bioRxiv}, doi = {10.1101/2020.05.28.120899}, year = {2020}, abstract = {We present a software-assisted workflow for the alignment and matching of filamentous structures across a 3D stack of serial images. This is achieved by combining automatic methods, visual validation, and interactive correction. After an initial alignment, the user can continuously improve the result by interactively correcting landmarks or matches of filaments. Supported by a visual quality assessment of regions that have been already inspected, this allows a trade-off between quality and manual labor. The software tool was developed to investigate cell division by quantitative 3D analysis of microtubules (MTs) in both mitotic and meiotic spindles. For this, each spindle is cut into a series of semi-thick physical sections, of which electron tomograms are acquired. The serial tomograms are then stitched and non-rigidly aligned to allow tracing and connecting of MTs across tomogram boundaries. In practice, automatic stitching alone provides only an incomplete solution, because large physical distortions and a low signal-to-noise ratio often cause experimental difficulties. To derive 3D models of spindles despite the problems related to sample preparation and subsequent data collection, semi-automatic validation and correction is required to remove stitching mistakes. However, due to the large number of MTs in spindles (up to 30k) and their resulting dense spatial arrangement, a naive inspection of each MT is too time consuming. Furthermore, an interactive visualization of the full image stack is hampered by the size of the data (up to 100 GB). Here, we present a specialized, interactive, semi-automatic solution that considers all requirements for large-scale stitching of filamentous structures in serial-section image stacks. The key to our solution is a careful design of the visualization and interaction tools for each processing step to guarantee real-time response, and an optimized workflow that efficiently guides the user through datasets.}, language = {en} } @misc{LindowBruenigDercksenetal.2019, author = {Lindow, Norbert and Br{\"u}nig, Florian and Dercksen, Vincent J. and Fabig, Gunar and Kiewisz, Robert and Redemann, Stefanie and M{\"u}ller-Reichert, Thomas and Prohaska, Steffen}, title = {Semi-automatic Stitching of Serial Section Image Stacks with Filamentous Structures}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-73739}, year = {2019}, abstract = {In this paper, we present a software-assisted workflow for the alignment and matching of filamentous structures across a stack of 3D serial image sections. This is achieved by a combination of automatic methods, visual validation, and interactive correction. After an initial alignment, the user can continuously improve the result by interactively correcting landmarks or matches of filaments. This is supported by a quality assessment that visualizes regions that have been already inspected and, thus, allows a trade-off between quality and manual labor. The software tool was developed in collaboration with biologists who investigate microtubule-based spindles during cell division. To quantitatively understand the structural organization of such spindles, a 3D reconstruction of the numerous microtubules is essential. Each spindle is cut into a series of semi-thick physical sections, of which electron tomograms are acquired. The sections then need to be stitched, i.e. non-rigidly aligned; and the microtubules need to be traced in each section and connected across section boundaries. Experiments led to the conclusion that automatic methods for stitching alone provide only an incomplete solution to practical analysis needs. Automatic methods may fail due to large physical distortions, a low signal-to-noise ratio of the images, or other unexpected experimental difficulties. In such situations, semi-automatic validation and correction is required to rescue as much information as possible to derive biologically meaningful results despite of some errors related to data collection. Since the correct stitching is visually not obvious due to the number of microtubules (up to 30k) and their dense spatial arrangement, these are difficult tasks. Furthermore, a naive inspection of each microtubule is too time consuming. In addition, interactive visualization is hampered by the size of the image data (up to 100 GB). Based on the requirements of our collaborators, we present a practical solution for the semi-automatic stitching of serial section image stacks with filamentous structures.}, language = {en} } @misc{GamrathAndersonBestuzhevaetal.2020, author = {Gamrath, Gerald and Anderson, Daniel and Bestuzheva, Ksenia and Chen, Wei-Kun and Eifler, Leon and Gasse, Maxime and Gemander, Patrick and Gleixner, Ambros and Gottwald, Leona and Halbig, Katrin and Hendel, Gregor and Hojny, Christopher and Koch, Thorsten and Le Bodic, Pierre and Maher, Stephen J. and Matter, Frederic and Miltenberger, Matthias and M{\"u}hmer, Erik and M{\"u}ller, Benjamin and Pfetsch, Marc and Schl{\"o}sser, Franziska and Serrano, Felipe and Shinano, Yuji and Tawfik, Christine and Vigerske, Stefan and Wegscheider, Fabian and Weninger, Dieter and Witzig, Jakob}, title = {The SCIP Optimization Suite 7.0}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-78023}, year = {2020}, abstract = {The SCIP Optimization Suite provides a collection of software packages for mathematical optimization centered around the constraint integer programming frame- work SCIP. This paper discusses enhancements and extensions contained in version 7.0 of the SCIP Optimization Suite. The new version features the parallel presolving library PaPILO as a new addition to the suite. PaPILO 1.0 simplifies mixed-integer linear op- timization problems and can be used stand-alone or integrated into SCIP via a presolver plugin. SCIP 7.0 provides additional support for decomposition algorithms. Besides im- provements in the Benders' decomposition solver of SCIP, user-defined decomposition structures can be read, which are used by the automated Benders' decomposition solver and two primal heuristics. Additionally, SCIP 7.0 comes with a tree size estimation that is used to predict the completion of the overall solving process and potentially trigger restarts. Moreover, substantial performance improvements of the MIP core were achieved by new developments in presolving, primal heuristics, branching rules, conflict analysis, and symmetry handling. Last, not least, the report presents updates to other components and extensions of the SCIP Optimization Suite, in particular, the LP solver SoPlex and the mixed-integer semidefinite programming solver SCIP-SDP.}, language = {en} } @misc{GleixnerMaherMuelleretal.2017, author = {Gleixner, Ambros and Maher, Stephen J. and M{\"u}ller, Benjamin and Pedroso, Jo{\~a}o Pedro}, title = {Exact Methods for Recursive Circle Packing}, doi = {10.1007/s10479-018-3115-5}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-62039}, year = {2017}, abstract = {Packing rings into a minimum number of rectangles is an optimization problem which appears naturally in the logistics operations of the tube industry. It encompasses two major difficulties, namely the positioning of rings in rectangles and the recursive packing of rings into other rings. This problem is known as the Recursive Circle Packing Problem (RCPP). We present the first dedicated method for solving RCPP that provides strong dual bounds based on an exact Dantzig-Wolfe reformulation of a nonconvex mixed-integer nonlinear programming formulation. The key idea of this reformulation is to break symmetry on each recursion level by enumerating one-level packings, i.e., packings of circles into other circles, and by dynamically generating packings of circles into rectangles. We use column generation techniques to design a "price-and-verify" algorithm that solves this reformulation to global optimality. Extensive computational experiments on a large test set show that our method not only computes tight dual bounds, but often produces primal solutions better than those computed by heuristics from the literature.}, language = {en} } @misc{GleixnerBastubbeEifleretal.2018, author = {Gleixner, Ambros and Bastubbe, Michael and Eifler, Leon and Gally, Tristan and Gamrath, Gerald and Gottwald, Robert Lion and Hendel, Gregor and Hojny, Christopher and Koch, Thorsten and L{\"u}bbecke, Marco and Maher, Stephen J. and Miltenberger, Matthias and M{\"u}ller, Benjamin and Pfetsch, Marc and Puchert, Christian and Rehfeldt, Daniel and Schl{\"o}sser, Franziska and Schubert, Christoph and Serrano, Felipe and Shinano, Yuji and Viernickel, Jan Merlin and Walter, Matthias and Wegscheider, Fabian and Witt, Jonas T. and Witzig, Jakob}, title = {The SCIP Optimization Suite 6.0}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-69361}, year = {2018}, abstract = {The SCIP Optimization Suite provides a collection of software packages for mathematical optimization centered around the constraint integer programming framework SCIP. This paper discusses enhancements and extensions contained in version 6.0 of the SCIP Optimization Suite. Besides performance improvements of the MIP and MINLP core achieved by new primal heuristics and a new selection criterion for cutting planes, one focus of this release are decomposition algorithms. Both SCIP and the automatic decomposition solver GCG now include advanced functionality for performing Benders' decomposition in a generic framework. GCG's detection loop for structured matrices and the coordination of pricing routines for Dantzig-Wolfe decomposition has been significantly revised for greater flexibility. Two SCIP extensions have been added to solve the recursive circle packing problem by a problem-specific column generation scheme and to demonstrate the use of the new Benders' framework for stochastic capacitated facility location. Last, not least, the report presents updates and additions to the other components and extensions of the SCIP Optimization Suite: the LP solver SoPlex, the modeling language Zimpl, the parallelization framework UG, the Steiner tree solver SCIP-Jack, and the mixed-integer semidefinite programming solver SCIP-SDP.}, language = {en} } @article{LindowBruenigDercksenetal.2021, author = {Lindow, Norbert and Br{\"u}nig, Florian and Dercksen, Vincent J. and Fabig, Gunar and Kiewisz, Robert and Redemann, Stefanie and M{\"u}ller-Reichert, Thomas and Prohaska, Steffen and Baum, Daniel}, title = {Semi-automatic stitching of filamentous structures in image stacks from serial-section electron tomography}, volume = {284}, journal = {Journal of Microscopy}, number = {1}, doi = {10.1111/jmi.13039}, pages = {25 -- 44}, year = {2021}, abstract = {We present a software-assisted workflow for the alignment and matching of filamentous structures across a three-dimensional (3D) stack of serial images. This is achieved by combining automatic methods, visual validation, and interactive correction. After the computation of an initial automatic matching, the user can continuously improve the result by interactively correcting landmarks or matches of filaments. Supported by a visual quality assessment of regions that have been already inspected, this allows a trade-off between quality and manual labor. The software tool was developed in an interdisciplinary collaboration between computer scientists and cell biologists to investigate cell division by quantitative 3D analysis of microtubules (MTs) in both mitotic and meiotic spindles. For this, each spindle is cut into a series of semi-thick physical sections, of which electron tomograms are acquired. The serial tomograms are then stitched and non-rigidly aligned to allow tracing and connecting of MTs across tomogram boundaries. In practice, automatic stitching alone provides only an incomplete solution, because large physical distortions and a low signal-to-noise ratio often cause experimental difficulties. To derive 3D models of spindles despite dealing with imperfect data related to sample preparation and subsequent data collection, semi-automatic validation and correction is required to remove stitching mistakes. However, due to the large number of MTs in spindles (up to 30k) and their resulting dense spatial arrangement, a naive inspection of each MT is too time-consuming. Furthermore, an interactive visualization of the full image stack is hampered by the size of the data (up to 100 GB). Here, we present a specialized, interactive, semi-automatic solution that considers all requirements for large-scale stitching of filamentous structures in serial-section image stacks. To the best of our knowledge, it is the only currently available tool which is able to process data of the type and size presented here. The key to our solution is a careful design of the visualization and interaction tools for each processing step to guarantee real-time response, and an optimized workflow that efficiently guides the user through datasets. The final solution presented here is the result of an iterative process with tight feedback loops between the involved computer scientists and cell biologists.}, language = {en} } @misc{SekulicSchaibleMuelleretal.2025, author = {Sekulic, Ivan and Schaible, Jonas and M{\"u}ller, Gabriel and Plock, Matthias and Burger, Sven and Martinez-Lahuerta, Victor J. and Gaaloul, Naceur and Schneider, Philipp-Immanuel}, title = {Data publication for Physics-informed Bayesian optimization of expensive-to-evaluate black-box functions}, journal = {Zenodo}, doi = {10.5281/zenodo.16751507}, year = {2025}, language = {en} } @article{MuellerMartinezLahuertaSekulicetal.2025, author = {M{\"u}ller, Gabriel and Mart{\´i}nez-Lahuerta, Victor J. and Sekulic, Ivan and Burger, Sven and Schneider, Philipp-Immanuel and Gaaloul, Naceur}, title = {Bayesian optimization for state engineering of quantum gases}, volume = {10}, journal = {Quantum Sci. Technol.}, arxiv = {http://arxiv.org/abs/2404.18234}, doi = {10.1088/2058-9565/ad9050}, pages = {015033}, year = {2025}, language = {en} } @misc{MaherFischerGallyetal.2017, author = {Maher, Stephen J. and Fischer, Tobias and Gally, Tristan and Gamrath, Gerald and Gleixner, Ambros and Gottwald, Robert Lion and Hendel, Gregor and Koch, Thorsten and L{\"u}bbecke, Marco and Miltenberger, Matthias and M{\"u}ller, Benjamin and Pfetsch, Marc and Puchert, Christian and Rehfeldt, Daniel and Schenker, Sebastian and Schwarz, Robert and Serrano, Felipe and Shinano, Yuji and Weninger, Dieter and Witt, Jonas T. and Witzig, Jakob}, title = {The SCIP Optimization Suite 4.0}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-62170}, year = {2017}, abstract = {The SCIP Optimization Suite is a powerful collection of optimization software that consists of the branch-cut-and-price framework and mixed-integer programming solver SCIP, the linear programming solver SoPlex, the modeling language Zimpl, the parallelization framework UG, and the generic branch-cut-and-price solver GCG. Additionally, it features the extensions SCIP-Jack for solving Steiner tree problems, PolySCIP for solving multi-objective problems, and SCIP-SDP for solving mixed-integer semidefinite programs. The SCIP Optimization Suite has been continuously developed and has now reached version 4.0. The goal of this report is to present the recent changes to the collection. We not only describe the theoretical basis, but focus on implementation aspects and their computational consequences.}, language = {en} } @misc{GamrathFischerGallyetal.2016, author = {Gamrath, Gerald and Fischer, Tobias and Gally, Tristan and Gleixner, Ambros and Hendel, Gregor and Koch, Thorsten and Maher, Stephen J. and Miltenberger, Matthias and M{\"u}ller, Benjamin and Pfetsch, Marc and Puchert, Christian and Rehfeldt, Daniel and Schenker, Sebastian and Schwarz, Robert and Serrano, Felipe and Shinano, Yuji and Vigerske, Stefan and Weninger, Dieter and Winkler, Michael and Witt, Jonas T. and Witzig, Jakob}, title = {The SCIP Optimization Suite 3.2}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-57675}, year = {2016}, abstract = {The SCIP Optimization Suite is a software toolbox for generating and solving various classes of mathematical optimization problems. Its major components are the modeling language ZIMPL, the linear programming solver SoPlex, the constraint integer programming framework and mixed-integer linear and nonlinear programming solver SCIP, the UG framework for parallelization of branch-and-bound-based solvers, and the generic branch-cut-and-price solver GCG. It has been used in many applications from both academia and industry and is one of the leading non-commercial solvers. This paper highlights the new features of version 3.2 of the SCIP Optimization Suite. Version 3.2 was released in July 2015. This release comes with new presolving steps, primal heuristics, and branching rules within SCIP. In addition, version 3.2 includes a reoptimization feature and improved handling of quadratic constraints and special ordered sets. SoPlex can now solve LPs exactly over the rational number and performance improvements have been achieved by exploiting sparsity in more situations. UG has been tested successfully on 80,000 cores. A major new feature of UG is the functionality to parallelize a customized SCIP solver. GCG has been enhanced with a new separator, new primal heuristics, and improved column management. Finally, new and improved extensions of SCIP are presented, namely solvers for multi-criteria optimization, Steiner tree problems, and mixed-integer semidefinite programs.}, language = {en} } @misc{BestuzhevaBesanconChenetal.2021, author = {Bestuzheva, Ksenia and Besan{\c{c}}on, Mathieu and Chen, Wei-Kun and Chmiela, Antonia and Donkiewicz, Tim and van Doornmalen, Jasper and Eifler, Leon and Gaul, Oliver and Gamrath, Gerald and Gleixner, Ambros and Gottwald, Leona and Graczyk, Christoph and Halbig, Katrin and Hoen, Alexander and Hojny, Christopher and van der Hulst, Rolf and Koch, Thorsten and L{\"u}bbecke, Marco and Maher, Stephen J. and Matter, Frederic and M{\"u}hmer, Erik and M{\"u}ller, Benjamin and Pfetsch, Marc E. and Rehfeldt, Daniel and Schlein, Steffan and Schl{\"o}sser, Franziska and Serrano, Felipe and Shinano, Yuji and Sofranac, Boro and Turner, Mark and Vigerske, Stefan and Wegscheider, Fabian and Wellner, Philipp and Weninger, Dieter and Witzig, Jakob}, title = {The SCIP Optimization Suite 8.0}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-85309}, year = {2021}, abstract = {The SCIP Optimization Suite provides a collection of software packages for mathematical optimization centered around the constraint integer programming framework SCIP. This paper discusses enhancements and extensions contained in version 8.0 of the SCIP Optimization Suite. Major updates in SCIP include improvements in symmetry handling and decomposition algorithms, new cutting planes, a new plugin type for cut selection, and a complete rework of the way nonlinear constraints are handled. Additionally, SCIP 8.0 now supports interfaces for Julia as well as Matlab. Further, UG now includes a unified framework to parallelize all solvers, a utility to analyze computational experiments has been added to GCG, dual solutions can be postsolved by PaPILO, new heuristics and presolving methods were added to SCIP-SDP, and additional problem classes and major performance improvements are available in SCIP-Jack.}, language = {en} } @article{BestuzhevaBesanconChenetal.2023, author = {Bestuzheva, Ksenia and Besan{\c{c}}on, Mathieu and Chen, Wei-Kun and Chmiela, Antonia and Donkiewicz, Tim and Doornmalen, Jasper and Eifler, Leon and Gaul, Oliver and Gamrath, Gerald and Gleixner, Ambros and Gottwald, Leona and Graczyk, Christoph and Halbig, Katrin and Hoen, Alexander and Hojny, Christopher and Hulst, Rolf and Koch, Thorsten and L{\"u}bbecke, Marco and Maher, Stephen J. and Matter, Frederic and M{\"u}hmer, Erik and M{\"u}ller, Benjamin and Pfetsch, Marc and Rehfeldt, Daniel and Schlein, Steffan and Schl{\"o}sser, Franziska and Serrano, Felipe and Shinano, Yuji and Sofranac, Boro and Turner, Mark and Vigerske, Stefan and Wegscheider, Fabian and Wellner, Philipp and Weninger, Dieter and Witzig, Jakob}, title = {Enabling research through the SCIP optimization suite 8.0}, volume = {49}, journal = {ACM Transactions on Mathematical Software}, number = {2}, doi = {10.1145/3585516}, pages = {1 -- 21}, year = {2023}, abstract = {The SCIP Optimization Suite provides a collection of software packages for mathematical optimization centered around the constraint integer programming framework SCIP. The focus of this article is on the role of the SCIP Optimization Suite in supporting research. SCIP's main design principles are discussed, followed by a presentation of the latest performance improvements and developments in version 8.0, which serve both as examples of SCIP's application as a research tool and as a platform for further developments. Furthermore, this article gives an overview of interfaces to other programming and modeling languages, new features that expand the possibilities for user interaction with the framework, and the latest developments in several extensions built upon SCIP.}, language = {en} }