@article{RamosKuehn2022, author = {Ramos, Alejandro and K{\"u}hn, Oliver}, title = {Manipulating the dynamics of a Fermi resonance with light. A direct optimal control theory approach}, journal = {Chemical Physics}, year = {2022}, language = {en} } @article{XuChenZhangetal.2022, author = {Xu, Xiaofei and Chen, Ying and Zhang, Ge and Koch, Thorsten}, title = {Modeling Functional Time Series and Mixed-Type Predictors With Partially Functional Autoregressions}, volume = {42}, journal = {Journal of Business \& Economic Statistics}, number = {2}, publisher = {Informa UK Limited}, issn = {0735-0015}, doi = {https://doi.org/10.1080/07350015.2021.2011299}, pages = {349 -- 366}, year = {2022}, language = {en} } @article{HartzerRoehrigWolffetal.2022, author = {Hartzer, Jacob and R{\"o}hrig, Olivia and Wolff, Timo and Y{\"u}r{\"u}k, Oğuzhan}, title = {Initial steps in the classification of maximal mediated sets}, journal = {Journal of Symbolic Computation}, year = {2022}, language = {en} } @article{Kerdreuxd'AspremontPokutta2022, author = {Kerdreux, Thomas and d'Aspremont, Alexandre and Pokutta, Sebastian}, title = {Restarting Frank-Wolfe: Faster Rates under H{\"o}lderian Error Bounds}, journal = {Journal of Optimization Theory and Applications}, year = {2022}, language = {en} } @article{BarrosCavalarMotaetal.2022, author = {Barros, Gabriel F. and Cavalar, Bruno P. and Mota, Guilherme O. and Parczyk, Olaf}, title = {Anti-Ramsey threshold of cycles for sparse graphs}, journal = {Discrete Applied Mathematics}, year = {2022}, language = {en} } @article{GebhardHahnKlimrothPenschucketal.2022, author = {Gebhard, Oliver and Hahn-Klimroth, Max and Penschuck, Manuel and Rolvien, Maurice and Scarlett, Jonathan and Tan, Nelvin and Parczyk, Olaf}, title = {Near optimal sparsity-constrained group testing: improved bounds}, journal = {IEEE Transactions on Information Theory}, year = {2022}, language = {en} } @article{BoettcherSguegliaSkokanetal.2022, author = {B{\"o}ttcher, Julia and Sgueglia, Amedeo and Skokan, Jozef and Parczyk, Olaf}, title = {Triangles in randomly perturbed graphs}, journal = {Combinatorics, Probability and Computing}, year = {2022}, language = {en} } @article{HunkenschroederPokuttaWeismantel2022, author = {Hunkenschr{\"o}der, Christoph and Pokutta, Sebastian and Weismantel, Robert}, title = {Optimizing a low-dimensional convex function over a high-dimensional cube}, journal = {SIAM Journal on Optimization}, year = {2022}, language = {en} } @article{CombettesWoodstock2022, author = {Combettes, P. L. and Woodstock, Zev}, title = {a variational inequality model for the construction of signals from inconsistent nonlinear equations}, journal = {SIAM Journal on Imaging Sciences}, year = {2022}, language = {en} } @article{WilkenBesanconKratochviletal.2022, author = {Wilken, St. Elmo and Besan{\c{c}}on, Mathieu and Kratochv{\´i}l, Miroslav and Kuate, Chilperic Armel Foko and Trefois, Christophe and Gu, Wei and Ebenh{\"o}h, Oliver}, title = {Interrogating the effect of enzyme kinetics on metabolism using differentiable constraint-based models}, journal = {Metabolic Engineering}, year = {2022}, language = {en} } @article{BolusaniRalphs2022, author = {Bolusani, Suresh and Ralphs, Ted K.}, title = {a framework for generalized Benders' decomposition and its applications to multilevel optimization}, journal = {Mathematical Programming}, year = {2022}, language = {en} } @article{YokoyamaShinanoWakui2022, author = {Yokoyama, Ryohei and Shinano, Yuji and Wakui, Tetsuya}, title = {時間集約によるエネルギー供給システムの 近似最適設計解の導出および評価 (階層的最適化を援用した設計解の評価)}, journal = {エネルギー・資源学会第38回エネルギーシステム・経済・環境コンファレンス講演論文集}, pages = {468 -- 473}, year = {2022}, abstract = {For the purpose of attaining the highest performance of energy supply systems, it is important to design the systems optimally in consideration of their operational strategies for seasonal and hourly variations in energy demands. An ap- proach to solve such an optimal design problem with a large number of periods efficiently is to derive an approximate optimal design solution by aggregating periods with a clustering method. However, such an approach does not provide any information on the accuracy for the optimal value of the objective function. The purpose of this paper is to provide a time aggregation method for deriving aprroximate optimal design solutions and evaluting their values of the objective function. Especially, a method of evaluating design solutions is presented here using both methods of evaluating the robustness under uncertain energy demands and solving optimal design problems by a hierarchical approach. A case study is conducted for a cogeneration system with a practical configuration, and it turns out that the proposed approach enables one to evaluate effective lower bounds for the optimal value of the objective function as compared with those obtained by a conventional approach.}, language = {ja} } @article{YokoyamaShinanoWakui2022, author = {Yokoyama, Ryohei and Shinano, Yuji and Wakui, Tetsuya}, title = {時間集約によるエネルギー供給システムの 近似最適設計解の導出および評価 (階層的最適化を援用した近似最適設計)}, journal = {第41回エネルギー・資源学会研究発表会講演論文集}, pages = {144 -- 148}, year = {2022}, abstract = {For the purpose of attaining the highest performance of energy supply systems, it is important to design the systems optimally in consideration of their operational strategies for seasonal and hourly variations in energy demands. An ap- proach to efficiently solve such an optimal design problem with a large number of periods for variations in energy de- mands is to derive an approximate optimal design solution by aggregating periods with a clustering method. However, such an approach does not provide any information on the accuracy for the optimal value of the objective function. The purpose of this paper is to propose a time aggregation approach for deriving suitable aprroximate optimal design solutions and evaluting their values of the objective function accurately. This time aggregation approach is realized by combining a robust optimal design method under uncertain energy demands and a hierarchical approach for solving large scale optimal design problems. A case study is conducted for a cogeneration system with a practical configuration, and it turns out that the proposed approach enables one to evaluate effective upper and lower bounds for the optimal value of the objective function as compared with those obtained by a conventional approach.}, language = {ja} } @article{YokoyamaHiramatsuShinanoetal.2022, author = {Yokoyama, Ryohei and Hiramatsu, Yuto and Shinano, Yuji and Wakui, Tetsuya}, title = {Evaluation of robustness in multiple performance criteria for designing energy supply systems based on a mixed-integer linear model}, journal = {The 35th International Conference on Efficiency, Cost, Optimization, Simulation and Environmental Impact of Energy Systems (ECOS 2022)}, pages = {1937 -- 1948}, year = {2022}, abstract = {In designing energy supply systems, it is important to consider the uncertainty in energy demands, evaluate the robustness in some performance criteria, and heighten the robustness. A robust optimal design method has been previously proposed to maximize the robustness in a single performance criterion against the uncertainty in energy demands based on a mixed-integer linear model. In this paper, as a preliminary step toward multiobjective robust optimal design, a method of evaluating robustness in multiple performance criteria against the uncertainty in energy demands is proposed based on a mixed-integer linear model. The problems of evaluating the robustness in the performance criteria are formulated as bilevel mixed-integer linear programming (MILP) ones. They are solved by evaluating lower and upper bounds for the maximum regrets in the performance criteria alternately and repeatedly with the aid of a solution method based on reformulation and decomposition. In addition, for the purpose of applying the proposed method to practical problems, a hierarchical MILP method is used to efficiently solve some MILP problems in the solution process. Through a case study on a cogeneration system, the robustness in the annual total cost and primary energy consumption is evaluated and its trade-off relationship is clarified. As a result, it turns out how the values of these performance criteria are close to the optimal ones in relation to the uncertainty in energy demands. This work will be an important step toward developing a multiobjective robust optimal design method.}, language = {en} } @article{YokoyamaShinanoWakui2022, author = {Yokoyama, Ryohei and Shinano, Yuji and Wakui, Tetsuya}, title = {Day and time aggregations for optimal design of energy supply systems with storage units by a hierarchical MILP method}, journal = {The 35th International Conference on Efficiency, Cost, Optimization, Simulation and Environmental Impact of Energy Systems (ECOS 2022)}, pages = {1891 -- 1902}, year = {2022}, abstract = {Mixed-integer linear programming (MILP) methods have been applied widely to optimal design of energy supply systems. A hierarchical MILP method has been proposed to solve such optimal design problems efficiently. In addition, some strategies have been proposed to enhance the computation efficiency furthermore. As one of the strategies, a method of reducing model by time aggregation has been proposed to search design candidates efficiently in the relaxed optimal design problem at the upper level. In this paper, the hierarchical MILP method with the strategies is extendedly applied to the optimal design of energy supply systems with storage units. Especially, the method of reducing model is extended by aggregating both representative days and sampling times separately in consideration of the characteristics of energy storage units. A case study is conducted on the optimal design of a cogeneration system with a thermal storage tank. Through the study, it turns out the hierarchical MILP method is effective to derive the optimal solutions in short computation times. It also turns out that the model reduction with day and time aggregations is effec- tive to shorten the computation times furthermore when the number of candidates for equipment capacities is relatively small.}, language = {en} } @article{YokoyamaHiramatsuShinanoetal.2022, author = {Yokoyama, Ryohei and Hiramatsu, Yuto and Shinano, Yuji and Wakui, Tetsuya}, title = {Evaluation of robustness in multiple performance criteria for designing energy supply systems based on a mixed-integer linear model}, journal = {Proceedings of the 35th International Conference on Efficiency, Cost, Optimization, Simulation and Environmental Impact of Energy Systems (ECOS 2022)}, pages = {1937 -- 1948}, year = {2022}, abstract = {In designing energy supply systems, it is important to consider the uncertainty in energy demands, evaluate the robustness in some performance criteria, and heighten the robustness. A robust optimal design method has been previously proposed to maximize the robustness in a single performance criterion against the uncertainty in energy demands based on a mixed-integer linear model. In this paper, as a preliminary step toward multiobjective robust optimal design, a method of evaluating robustness in multiple performance criteria against the uncertainty in energy demands is proposed based on a mixed-integer linear model. The problems of evaluating the robustness in the performance criteria are formulated as bilevel mixed-integer linear programming (MILP) ones. They are solved by evaluating lower and upper bounds for the maximum regrets in the performance criteria alternately and repeatedly with the aid of a solution method based on reformulation and decomposition. In addition, for the purpose of applying the proposed method to practical problems, a hierarchical MILP method is used to efficiently solve some MILP problems in the solution process. Through a case study on a cogeneration system, the robustness in the annual total cost and primary energy consumption is evaluated and its trade-off relationship is clarified.}, language = {en} } @article{YokoyamaShinanoWakui2022, author = {Yokoyama, Ryohei and Shinano, Yuji and Wakui, Tetsuya}, title = {Day and time aggregations for optimal design of energy supply systems with storage units by a hierarchical MILP method}, journal = {PROCEEDINGS OF ECOS 2022 - THE 35 TH INTERNATIONAL CONFERENCE ON EFFICIENCY, COST, OPTIMIZATION, SIMULATION AND ENVIRONMENTAL IMPACT OF ENERGY SYSTEMS}, pages = {1891 -- 1902}, year = {2022}, abstract = {Mixed-integer linear programming (MILP) methods have been applied widely to optimal design of energy supply systems. A hierarchical MILP method has been proposed to solve such optimal design problems efficiently. In addition, some strategies have been proposed to enhance the computation efficiency furthermore. As one of the strategies, a method of reducing model by time aggregation has been proposed to search design candidates efficiently in the relaxed optimal design problem at the upper level. In this paper, the hierarchical MILP method with the strategies is extendedly applied to the optimal design of energy supply systems with storage units. Especially, the method of reducing model is extended by aggregating both representative days and sampling times separately in consideration of the characteristics of energy storage units. A case study is conducted on the optimal design of a cogeneration system with a thermal storage tank. Through the study, it turns out the hierarchical MILP method is effective to derive the optimal solutions in short computation times. It also turns out that the model reduction with day and time aggregations is effective to shorten the computation times furthermore when the number of candidates for equipment capacities is relatively small.}, language = {en} } @article{FernandesChaowdharySalehetal.2022, author = {Fernandes, Rita and Chaowdhary, Suvrat and Saleh, Noureldin and Mikula, Natalia and Kanevche, Katerina and Berlepsch, Hans and Hosogi, Naoki and Heberle, Joachim and Weber, Marcus and B{\"o}ttcher, Christoph and Koksch, Beate}, title = {Cyanine Dye Coupling Mediates Self-assembly of a pH Sensitive Peptide into Novel 3D Architectures}, volume = {61}, journal = {Angewandte Chemie}, number = {48}, pages = {e202208647}, year = {2022}, abstract = {A conjugated Cy5 dye-peptide system reveals the formation of two novel and structurally distinct supramolecular assemblies with photo-physical characteristics of H-type dimers or tetramers, respectively. The molecular ultrastructures are triggered by the complementary interplay of mutual chromophore coupling and pH induced changes in the peptide charge pattern.}, language = {en} } @article{GelssKlusKnebeletal.2022, author = {Gelß, Patrick and Klus, Stefan and Knebel, Sebastian and Shakibaei, Zarin and Pokutta, Sebastian}, title = {Low-Rank Tensor Decompositions of Quantum Circuits}, journal = {Journal of Computational Physics}, arxiv = {http://arxiv.org/abs/2205.09882}, year = {2022}, abstract = {Quantum computing is arguably one of the most revolutionary and disruptive technologies of this century. Due to the ever-increasing number of potential applications as well as the continuing rise in complexity, the development, simulation, optimization, and physical realization of quantum circuits is of utmost importance for designing novel algorithms. We show how matrix product states (MPSs) and matrix product operators (MPOs) can be used to express certain quantum states, quantum gates, and entire quantum circuits as low-rank tensors. This enables the analysis and simulation of complex quantum circuits on classical computers and to gain insight into the underlying structure of the system. We present different examples to demonstrate the advantages of MPO formulations and show that they are more efficient than conventional techniques if the bond dimensions of the wave function representation can be kept small throughout the simulation.}, language = {en} } @article{GelssKleinMateraetal.2022, author = {Gelß, Patrick and Klein, Rupert and Matera, Sebastian and Schmidt, Burkhard}, title = {Solving the time-independent Schr{\"o}dinger equation for chains of coupled excitons and phonons using tensor trains}, volume = {156}, journal = {The Journal of Chemical Physics}, number = {2}, arxiv = {http://arxiv.org/abs/2109.15104}, doi = {10.1063/5.0074948}, pages = {024109}, year = {2022}, abstract = {We demonstrate how to apply the tensor-train format to solve the time-independent Schr{\"o}dinger equation for quasi-one-dimensional excitonic chain systems with and without periodic boundary conditions. The coupled excitons and phonons are modeled by Fr{\"o}hlich-Holstein type Hamiltonians with on-site and nearest-neighbor interactions only. We reduce the memory consumption as well as the computational costs significantly by employing efficient decompositions to construct low-rank tensor-train representations, thus mitigating the curse of dimensionality. In order to compute also higher quantum states, we introduce an approach that directly incorporates the Wielandt deflation technique into the alternating linear scheme for the solution of eigenproblems. Besides systems with coupled excitons and phonons, we also investigate uncoupled problems for which (semi-)analytical results exist. There, we find that in the case of homogeneous systems, the tensor-train ranks of state vectors only marginally depend on the chain length, which results in a linear growth of the storage consumption. However, the central processing unit time increases slightly faster with the chain length than the storage consumption because the alternating linear scheme adopted in our work requires more iterations to achieve convergence for longer chains and a given rank. Finally, we demonstrate that the tensor-train approach to the quantum treatment of coupled excitons and phonons makes it possible to directly tackle the phenomenon of mutual self-trapping. We are able to confirm the main results of the Davydov theory, i.e., the dependence of the wave packet width and the corresponding stabilization energy on the exciton-phonon coupling strength, although only for a certain range of that parameter. In future work, our approach will allow calculations also beyond the validity regime of that theory and/or beyond the restrictions of the Fr{\"o}hlich-Holstein type Hamiltonians.}, language = {en} } @article{NohadaniSharma2022, author = {Nohadani, Omid and Sharma, Kartikey}, title = {Optimization under Connected Uncertainty}, volume = {4}, journal = {INFORMS Journal on Optimization}, number = {3}, doi = {10.1287/ijoo.2021.0067}, pages = {326 -- 346}, year = {2022}, abstract = {Robust optimization methods have shown practical advantages in a wide range of decision-making applications under uncertainty. Recently, their efficacy has been extended to multiperiod settings. Current approaches model uncertainty either independent of the past or in an implicit fashion by budgeting the aggregate uncertainty. In many applications, however, past realizations directly influence future uncertainties. For this class of problems, we develop a modeling framework that explicitly incorporates this dependence via connected uncertainty sets, whose parameters at each period depend on previous uncertainty realizations. To find optimal here-and-now solutions, we reformulate robust and distributionally robust constraints for popular set structures and demonstrate this modeling framework numerically on broadly applicable knapsack and portfolio-optimization problems.}, language = {en} } @article{MontefuscoSharmaTse2022, author = {Montefusco, Alberto and Sharma, Upanshu and Tse, Oliver}, title = {Fourier-Cattaneo equation: stochastic origin, variational formulation, and asymptotic limits}, year = {2022}, abstract = {We introduce a variational structure for the Fourier-Cattaneo (FC) system which is a second-order hyperbolic system. This variational structure is inspired by the large-deviation rate functional for the Kac process which is closely linked to the FC system. Using this variational formulation we introduce appropriate solution concepts for the FC equation and prove an a priori estimate which connects this variational structure to an appropriate Lyapunov function and Fisher information, the so-called FIR inequality. Finally, we use this formulation and estimate to study the diffusive and hyperbolic limits for the FC system.}, language = {en} } @article{Rehfeldt2022, author = {Rehfeldt, Daniel}, title = {Faster Algorithms for Steiner Tree and related Problems: From Theory to Practice}, journal = {OR News: Das Magazin der GOR}, year = {2022}, language = {en} } @article{KruegerLeenersTroncietal.2022, author = {Kr{\"u}ger, Tillmann and Leeners, Brigitte and Tronci, Enrico and Mancini, Toni and Ille, Fabian and Egli, Marcel and Engler, Harald and R{\"o}blitz, Susanna and Frieling, Helge and Sinke, Christopher and Jahn, Kirsten}, title = {The androgen system across the menstrual cycle: Hormonal, (epi-)genetic and psychometric alterations}, journal = {Physiology and Behavior}, doi = {https://doi.org/10.1016/j.physbeh.2022.114034}, year = {2022}, language = {en} } @article{FischerHolzhausenRoeblitz2022, author = {Fischer-Holzhausen, Sophie and R{\"o}blitz, Susanna}, title = {Mathematical modelling of follicular growth and ovarian stimulation}, journal = {Current Opinion in Endocrine and Metabolic Research}, doi = {https://doi.org/10.1016/j.coemr.2022.100385}, year = {2022}, language = {en} } @article{FischerHolzhausenRoeblitz2022, author = {Fischer-Holzhausen, Sophie and R{\"o}blitz, Susanna}, title = {Hormonal regulation of ovarian follicle growth in humans: Model-based exploration of cycle variability and parameter sensitivities}, journal = {Journal of Theoretical Biology}, doi = {https://doi.org/10.1016/j.jtbi.2022.111150}, year = {2022}, abstract = {We present a modelling and simulation framework for the dynamics of ovarian follicles and key hormones along the hypothalamic-pituitary-gonadal axis throughout consecutive human menstrual cycles. All simulation results (hormone concentrations and ovarian follicle sizes) are in biological units and can easily be compared to clinical data. The model takes into account variability in follicles' response to stimulating hormones, which introduces variability between cycles. The growth of ovarian follicles in waves is an emergent property in our model simulations and further supports the hypothesis that follicular waves are also present in humans. We use Approximate Bayesian Computation and cluster analysis to construct a population of virtual subjects and to study parameter distributions and sensitivities. The model can be used to compare and optimize treatment protocols for ovarian hyperstimulation, thus potentially forming the integral part of a clinical decision support system in reproductive endocrinology.}, language = {en} } @article{ŠofranacGleixnerPokutta2022, author = {Šofranac, Boro and Gleixner, Ambros and Pokutta, Sebastian}, title = {An Algorithm-independent Measure of Progress for Linear Constraint Propagation}, volume = {27}, journal = {Constraints}, doi = {10.1007/s10601-022-09338-9}, pages = {432 -- 455}, year = {2022}, language = {en} } @article{LangVesterFerreiraGomesetal.2022, author = {Lang, Annemarie and Vester, Antja and Ferreira-Gomes, M. and Guerra, G.M. and Heinrich, Fredrich R. and G{\"o}tzke, C.C. and Kurmies, Sebastian and Sunkara, Vikram and Durek, Pawel and Boerckel, Joel D. and Mashreghi, Mir-Farzin}, title = {PIPELINE FOR SINGLE CELL SEQUENCING OF HUMAN CHONDROCYTE PELLET CULTURES TO DELINEATE IL-1β MODULATED CHANGES IN CELL HETEROGENEITY}, volume = {30}, journal = {Osteoarthritis and Cartilage}, number = {Supplement 1}, doi = {10.1016/j.joca.2022.02.112}, pages = {S90}, year = {2022}, language = {en} } @article{SunkaraLewisNguyenetal.2022, author = {Sunkara, Vikram and Lewis, Angus and Nguyen, Giang T. and O'Reilly, Malgorzata M. and Bean, Nigel}, title = {A discontinuous Galerkin method for approximating the stationary distribution of stochastic fluid-fluid processes}, journal = {Methodology and Computing in Applied Probability}, doi = {10.1007/s11009-022-09945-2}, year = {2022}, language = {en} } @article{KochBertholdPedersenetal.2022, author = {Koch, Thorsten and Berthold, Timo and Pedersen, Jaap and Vanaret, Charlie}, title = {Progress in mathematical programming solvers from 2001 to 2020}, volume = {10}, journal = {EURO Journal on Computational Optimization}, doi = {10.1016/j.ejco.2022.100031}, pages = {100031}, year = {2022}, abstract = {This study investigates the progress made in lp and milp solver performance during the last two decades by comparing the solver software from the beginning of the millennium with the codes available today. On average, we found out that for solving lp/milp, computer hardware got about 20 times faster, and the algorithms improved by a factor of about nine for lp and around 50 for milp, which gives a total speed-up of about 180 and 1,000 times, respectively. However, these numbers have a very high variance and they considerably underestimate the progress made on the algorithmic side: many problem instances can nowadays be solved within seconds, which the old codes are not able to solve within any reasonable time.}, language = {en} } @article{LoesserWitzkeSchintkeetal.2022, author = {L{\"o}ßer, Angar and Witzke, Joel and Schintke, Florian and Scheuermann, Bj{\"o}rn}, title = {BottleMod: Modeling Data Flows and Tasks for Fast Bottleneck Analysis}, journal = {arXiv}, arxiv = {http://arxiv.org/abs/2209.05358}, doi = {10.48550/arXiv.2209.05358}, pages = {1 -- 20}, year = {2022}, language = {en} } @article{ReidelbachBaiZoellneretal.2022, author = {Reidelbach, Marco and Bai, Mei and Z{\"o}llner, Martin Sebastian and Schneeberger, Michaela and Kubicek, Katharina and Kirchberg, Henning and Bressler, Christian and Thorwart, Michael and Herrmann, Carmen}, title = {Solvent dynamics of aqueous halides before and after photoionization}, journal = {Journal of Physical Chemistry}, year = {2022}, language = {en} } @article{RaharinirinaFackeldeyWeber2022, author = {Raharinirina, N. Alexia and Fackeldey, Konstantin and Weber, Marcus}, title = {Qualitative Euclidean embedding of Disjoint Sets of Points}, year = {2022}, abstract = {We consider two disjoint sets of points with a distance metric, or a proximity function, associated with each set. If each set can be separately embedded into separate Euclidean spaces, then we provide sufficient conditions for the two sets to be jointly embedded in one Euclidean space. In this joint Euclidean embedding, the distances between the points are generated by a specific relation-preserving function. Consequently, the mutual distances between two points of the same set are specific qualitative transformations of their mutual distances in their original space; the pairwise distances between the points of different sets can be constructed from an arbitrary proximity function (might require scaling).}, language = {en} } @article{MasingLindnerBorndoerfer2022, author = {Masing, Berenike and Lindner, Niels and Bornd{\"o}rfer, Ralf}, title = {The price of symmetric line plans in the Parametric City}, volume = {166}, journal = {Transportation Research Part B: Methodological}, doi = {10.1016/j.trb.2022.10.009}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-88613}, pages = {419 -- 443}, year = {2022}, abstract = {We consider the line planning problem in public transport in the Parametric City, an idealized model that captures typical scenarios by a (small) number of parameters. The Parametric City is rotation symmetric, but optimal line plans are not always symmetric. This raises the question to quantify the symmetry gap between the best symmetric and the overall best solution. For our analysis, we formulate the line planning problem as a mixed integer linear program, that can be solved in polynomial time if the solutions are forced to be symmetric. We prove that the symmetry gap is small when a specific Parametric City parameter is fixed, and we give an approximation algorithm for line planning in the Parametric City in this case. While the symmetry gap can be arbitrarily large in general, we show that symmetric line plans are a good choice in most practical situations.}, language = {de} } @article{RaharinirinaAcevedoTrejosMerico2022, author = {Raharinirina, N. Alexia and Acevedo-Trejos, Esteban and Merico, Agostino}, title = {Modelling the acclimation capacity of coral reefs to a warming ocean}, journal = {PLOS COMPUTATIONAL BIOLOGY}, doi = {10.1371/journal.pcbi.1010099}, year = {2022}, abstract = {The symbiotic relationship between corals and photosynthetic algae is the foundation of coral reef ecosystems. This relationship breaks down, leading to coral death, when sea temperature exceeds the thermal tolerance of the coral-algae complex. While acclimation via phenotypic plasticity at the organismal level is an important mechanism for corals to cope with global warming, community-based shifts in response to acclimating capacities may give valuable indications about the future of corals at a regional scale. Reliable regional-scale predictions, however, are hampered by uncertainties on the speed with which coral communities will be able to acclimate. Here we present a trait-based, acclimation dynamics model, which we use in combination with observational data, to provide a first, crude estimate of the speed of coral acclimation at the community level and to investigate the effects of different global warming scenarios on three iconic reef ecosystems of the tropics: Great Barrier Reef, South East Asia, and Caribbean. The model predicts that coral acclimation may confer some level of protection by delaying the decline of some reefs such as the Great Barrier Reef. However, the current rates of acclimation will not be sufficient to rescue corals from global warming. Based on our estimates of coral acclimation capacities, the model results suggest substantial declines in coral abundances in all three regions, ranging from 12\% to 55\%, depending on the region and on the climate change scenario considered. Our results highlight the importance and urgency of precise assessments and quantitative estimates, for example through laboratory experiments, of the natural acclimation capacity of corals and of the speed with which corals may be able to acclimate to global warming.}, language = {en} } @article{LaguilloDiegoKiewiszMartiGomezetal.2022, author = {Laguillo-Diego, Alejandra and Kiewisz, Robert and Mart{\´i}-G{\´o}mez, Carlos and Baum, Daniel and M{\"u}ller-Reichert, Thomas and Vernos, Isabelle}, title = {MCRS1 modulates the heterogeneity of microtubule minus-end morphologies in mitotic spindles}, volume = {34}, journal = {Molecular Biology of the Cell}, number = {1}, doi = {10.1091/mbc.E22-08-0306-T}, year = {2022}, abstract = {Faithful chromosome segregation requires the assembly of a bipolar spindle, consisting of two antiparallel microtubule (MT) arrays having most of their minus ends focused at the spindle poles and their plus ends overlapping in the spindle midzone. Spindle assembly, chromosome alignment and segregation require highly dynamic MTs. The plus ends of MTs have been extensively investigated; instead, their minus end structure remains poorly characterized. Here, we used large-scale electron tomography to study the morphology of the MT minus ends in 3D-reconstructed metaphase spindles in HeLa cells. In contrast to the homogeneous open morphology of the MT plus ends at the kinetochores, we found that MT minus ends are heterogeneous showing either open or closed morphologies. Silencing the minus-end specific stabilizer, MCRS1 increased the proportion of open MT minus ends. Altogether, these data suggest a correlation between the morphology and the dynamic state of the MT ends. Taking this heterogeneity of the MT minus end morphologies into account, our work indicates an unsynchronized behavior of MTs at the spindle poles, thus laying the ground for further studies on the complexity of MT dynamics regulation.}, language = {en} } @article{HunkenschroederPokuttaWeismantel2022, author = {Hunkenschr{\"o}der, Christoph and Pokutta, Sebastian and Weismantel, Robert}, title = {Optimizing a low-dimensional convex function over a high-dimensional cub}, journal = {SIAM Journal on Optimization}, year = {2022}, language = {en} } @article{KossenHirzelMadaietal.2022, author = {Kossen, Tabea and Hirzel, Manuel A. and Madai, Vince I. and Boenisch, Franziska and Hennemuth, Anja and Hildebrand, Kristian and Pokutta, Sebastian and Sharma, Kartikey and Hilbert, Adam and Sobesky, Jan and Galinovic, Ivana and Khalil, Ahmed A. and Fiebach, Jochen B. and Frey, Dietmar}, title = {Towards Sharing Brain Images: Differentially Private TOF-MRA Images with Segmentation Labels Using Generative Adversarial Networks}, journal = {Frontiers in Artificial Intelligence}, doi = {https://doi.org/10.3389/frai.2022.813842}, year = {2022}, abstract = {Sharing labeled data is crucial to acquire large datasets for various Deep Learning applications. In medical imaging, this is often not feasible due to privacy regulations. Whereas anonymization would be a solution, standard techniques have been shown to be partially reversible. Here, synthetic data using a Generative Adversarial Network (GAN) with differential privacy guarantees could be a solution to ensure the patient's privacy while maintaining the predictive properties of the data. In this study, we implemented a Wasserstein GAN (WGAN) with and without differential privacy guarantees to generate privacy-preserving labeled Time-of-Flight Magnetic Resonance Angiography (TOF-MRA) image patches for brain vessel segmentation. The synthesized image-label pairs were used to train a U-net which was evaluated in terms of the segmentation performance on real patient images from two different datasets. Additionally, the Fr{\´e}chet Inception Distance (FID) was calculated between the generated images and the real images to assess their similarity. During the evaluation using the U-Net and the FID, we explored the effect of different levels of privacy which was represented by the parameter ϵ. With stricter privacy guarantees, the segmentation performance and the similarity to the real patient images in terms of FID decreased. Our best segmentation model, trained on synthetic and private data, achieved a Dice Similarity Coefficient (DSC) of 0.75 for ϵ = 7.4 compared to 0.84 for ϵ = ∞ in a brain vessel segmentation paradigm (DSC of 0.69 and 0.88 on the second test set, respectively). We identified a threshold of ϵ <5 for which the performance (DSC <0.61) became unstable and not usable. Our synthesized labeled TOF-MRA images with strict privacy guarantees retained predictive properties necessary for segmenting the brain vessels. Although further research is warranted regarding generalizability to other imaging modalities and performance improvement, our results mark an encouraging first step for privacy-preserving data sharing in medical imaging.}, language = {en} } @article{KamčevSpiegel2022, author = {Kamčev, Nina and Spiegel, Christoph}, title = {Another note on intervals in the Hales-Jewett theorem}, volume = {29}, journal = {Electronic Journal of Combinatorics}, number = {1}, doi = {10.37236/6730}, pages = {P1.62}, year = {2022}, abstract = {The Hales-Jewett Theorem states that any r-colouring of [m]ⁿ contains a monochromatic combinatorial line if n is large enough. Shelah's proof of the theorem implies that for m = 3 there always exists a monochromatic combinatorial line whose set of active coordinates is the union of at most r intervals. For odd r, Conlon and Kamčev constructed r-colourings for which it cannot be fewer than r intervals. However, we show that for even r and large n, any r-colouring of [3]ⁿ contains a monochromatic combinatorial line whose set of active coordinates is the union of at most r-1 intervals. This is optimal and extends a result of Leader and R{\"a}ty for r=2.}, language = {en} } @article{DonatiWeberKeller2022, author = {Donati, Luca and Weber, Marcus and Keller, Bettina G.}, title = {A review of Girsanov Reweighting and of Square Root Approximation for building molecular Markov State Models}, volume = {63}, journal = {Journal of Mathematical Physics}, number = {12}, publisher = {AIP Publishing}, doi = {10.1063/5.0127227}, pages = {123306-1 -- 123306-21}, year = {2022}, abstract = {Dynamical reweighting methods permit to estimate kinetic observables of a stochastic process governed by a target potential U(x) from trajectories that have been generated at a different potential V(x). In this article, we present Girsanov reweighting and Square Root Approximation (SqRA): the first method reweights path probabilities exploiting the Girsanov theorem and can be applied to Markov State Models (MSMs) to reweight transition probabilities; the second method was originally developed to discretize the Fokker-Planck operator into a transition rate matrix, but here we implement it into a reweighting scheme for transition rates. We begin by reviewing the theoretical background of the methods, then present two applications relevant to Molecular Dynamics (MD), highlighting their strengths and weaknesses.}, language = {en} } @article{DjurdjevacConradKoepplDjurdjevac2022, author = {Djurdjevac Conrad, Natasa and K{\"o}ppl, Jonas and Djurdjevac, Ana}, title = {Feedback Loops in Opinion Dynamics of Agent-Based Models with Multiplicative Noise}, volume = {24(10)}, journal = {Entropy}, arxiv = {http://arxiv.org/abs/2209.07151}, doi = {10.3390/e24101352}, year = {2022}, abstract = {We introduce an agent-based model for co-evolving opinions and social dynamics, under the influence of multiplicative noise. In this model, every agent is characterized by a position in a social space and a continuous opinion state variable. Agents' movements are governed by the positions and opinions of other agents and similarly, the opinion dynamics are influenced by agents' spatial proximity and their opinion similarity. Using numerical simulations and formal analyses, we study this feedback loop between opinion dynamics and the mobility of agents in a social space. We investigate the behaviour of this ABM in different regimes and explore the influence of various factors on the appearance of emerging phenomena such as group formation and opinion consensus. We study the empirical distribution, and, in the limit of infinite number of agents, we derive a corresponding reduced model given by a partial differential equation (PDE). Finally, using numerical examples, we show that a resulting PDE model is a good approximation of the original ABM.}, language = {en} } @article{DonatiWeber2022, author = {Donati, Luca and Weber, Marcus}, title = {Assessing transition rates as functions of environmental variables}, volume = {157}, journal = {The Journal of Chemical Physics}, number = {22}, publisher = {AIP Publishing}, doi = {10.1063/5.0109555}, pages = {224103-1 -- 224103-14}, year = {2022}, abstract = {We present a method to estimate the transition rates of molecular systems under different environmental conditions which cause the formation or the breaking of bonds and require the sampling of the Grand Canonical Ensemble. For this purpose, we model the molecular system in terms of probable "scenarios", governed by different potential energy functions, which are separately sampled by classical MD simulations. Reweighting the canonical distribution of each scenario according to specific environmental variables, we estimate the grand canonical distribution, then we use the Square Root Approximation (SqRA) method to discretize the Fokker-Planck operator into a rate matrix and the robust Perron Cluster Cluster Analysis (PCCA+) method to coarse-grain the kinetic model. This permits to efficiently estimate the transition rates of conformational states as functions of environmental variables, for example, the local pH at a cell membrane. In this work we formalize the theoretical framework of the procedure and we present a numerical experiment comparing the results with those provided by a constant-pH method based on non-equilibrium Molecular Dynamics Monte Carlo simulations. The method is relevant for the development of new drug design strategies which take into account how the cellular environment influences biochemical processes.}, language = {en} } @article{GorgullaJayarajFackeldeyetal.2022, author = {Gorgulla, Christoph and Jayaraj, Abhilash and Fackeldey, Konstantin and Arthanari, Haribabu}, title = {Emerging frontiers in virtual drug discovery: From quantum mechanical methods to deep learning approaches}, volume = {69}, journal = {Current Opinion in Chemical Biology}, doi = {10.1016/j.cbpa.2022.102156}, pages = {102156 -- 102156-12}, year = {2022}, abstract = {Virtual screening-based approaches to discover initial hit and lead compounds have the potential to reduce both the cost and time of early drug discovery stages, as well as to find inhibitors for even challenging target sites such as protein-protein interfaces. Here in this review, we provide an overview of the progress that has been made in virtual screening methodology and technology on multiple fronts in recent years. The advent of ultra-large virtual screens, in which hundreds of millions to billions of compounds are screened, has proven to be a powerful approach to discover highly potent hit compounds. However, these developments are just the tip of the iceberg, with new technologies and methods emerging to propel the field forward. Examples include novel machine-learning approaches, which can reduce the computational costs of virtual screening dramatically, while progress in quantum-mechanical approaches can increase the accuracy of predictions of various small molecule properties.}, language = {en} } @article{MohammadzadehHNascimentoCdeLamareetal.2022, author = {Mohammadzadeh, Saeed and H. Nascimento, V{\´i}tor and C. de Lamare, Rodrigo and Hajarolasvadi, Noushin}, title = {Robust Beamforming Based on Complex-Valued Convolutional Neural Networks for Sensor Arrays}, volume = {29}, journal = {IEEE Signal Processing Letters}, doi = {10.1109/LSP.2022.3212637}, pages = {2018 -- 2021}, year = {2022}, abstract = {Robust adaptive beamforming (RAB) plays a vital role in modern communications by ensuring the reception of high-quality signals. This article proposes a deep learning approach to robust adaptive beamforming. In particular, we propose a novel RAB approach where the sample covariance matrix (SCM) is used as the input of a deep 1D Complex-Valued Convolutional Neural Network (CVCNN). The network employs complex convolutional and pooling layers, as well as a Cartesian Scaled Exponential Linear Unit activation function to directly compute the nearly-optimum weight vector through the training process and without prior knowledge about the direction of arrival of the desired signal. This means that reconstruction of the interference plus noise (IPN) covariance matrix is not required. The trained CVCNN accurately computes the nearly-optimum weight vector for data not used during training. The computed weight vector is employed to estimate the signal-to-interference plus noise ratio. Simulations show that the proposed RAB can provide performance close to that of the optimal beamformer.}, language = {en} } @article{SechiFackeldeyChewleetal.2022, author = {Sechi, Renata and Fackeldey, Konstantin and Chewle, Surahit and Weber, Marcus}, title = {SepFree NMF: A Toolbox for Analyzing the Kinetics of Sequential Spectroscopic Data}, volume = {15}, journal = {Algorithms}, number = {9}, doi = {10.3390/a15090297}, pages = {297}, year = {2022}, abstract = {This work addresses the problem of determining the number of components from sequential spectroscopic data analyzed by non-negative matrix factorization without separability assumption (SepFree NMF). These data are stored in a matrix M of dimension "measured times" versus "measured wavenumbers" and can be decomposed to obtain the spectral fingerprints of the states and their evolution over time. SepFree NMF assumes a memoryless (Markovian) process to underline the dynamics and decomposes M so that M=WH, with W representing the components' fingerprints and H their kinetics. However, the rank of this decomposition (i.e., the number of physical states in the process) has to be guessed from pre-existing knowledge on the observed process. We propose a measure for determining the number of components with the computation of the minimal memory effect resulting from the decomposition; by quantifying how much the obtained factorization is deviating from the Markovian property, we are able to score factorizations of a different number of components. In this way, we estimate the number of different entities which contribute to the observed system, and we can extract kinetic information without knowing the characteristic spectra of the single components. This manuscript provides the mathematical background as well as an analysis of computer generated and experimental sequentially measured Raman spectra.}, language = {en} } @article{PetkovicZakiyeva2022, author = {Petkovic, Milena and Zakiyeva, Nazgul}, title = {Mathematical Optimization for Analyzing and Forecasting Nonlinear Network Time Series}, journal = {Operations Research Proceedings 2022}, year = {2022}, abstract = {This work presents an innovative short to mid-term forecasting model that analyzes nonlinear complex spatial and temporal dynamics in energy networks under demand and supply balance constraints using Network Nonlinear Time Series (TS) and Mathematical Programming (MP) approach. We address three challenges simultaneously, namely, the adjacency matrix is unknown; the total amount in the network has to be balanced; dependence is unnecessarily linear. We use a nonparametric approach to handle the nonlinearity and estimate the adjacency matrix under the sparsity assumption. The estimation is conducted with the Mathematical Optimisation method. We illustrate the accuracy and effectiveness of the model on the example of the natural gas transmission network of one of the largest transmission system operators (TSOs) in Germany, Open Grid Europe. The obtained results show that, especially for shorter forecasting horizons, proposed method outperforms all considered benchmark models, improving the avarage nMAPE for 5.1\% and average RMSE for 79.6\% compared to the second-best model. The model is capable to capture the nonlinear dependencies in the complex spatial-temporal network dynamics and benefits from both sparsity assumption and the demand and supply balance constraint.}, language = {en} } @article{BeckerTeepleCharlesetal.2022, author = {Becker, Kaitlyn P and Teeple, Clark and Charles, Nicholas and Jung, Yeonsu and Baum, Daniel and Weaver, James C and Mahadevan, L. and Wood, Robert J}, title = {Active entanglement enables stochastic, topological grasping}, volume = {119}, journal = {PNAS}, number = {42}, doi = {10.1073/pnas.2209819119}, pages = {e2209819119}, year = {2022}, abstract = {Grasping, in both biological and engineered mechanisms, can be highly sensitive to the gripper and object morphology, as well as perception and motion planning. Here we circumvent the need for feedback or precise planning by using an array of fluidically-actuated slender hollow elastomeric filaments to actively entangle with objects that vary in geometric and topological complexity. The resulting stochastic interactions enable a unique soft and conformable grasping strategy across a range of target objects that vary in size, weight, and shape. We experimentally evaluate the grasping performance of our strategy, and use a computational framework for the collective mechanics of flexible filaments in contact with complex objects to explain our findings. Overall, our study highlights how active collective entanglement of a filament array via an uncontrolled, spatially distributed scheme provides new options for soft, adaptable grasping.}, language = {en} } @article{GlatzederKomnikAmbellanetal.2022, author = {Glatzeder, Korbinian and Komnik, Igor and Ambellan, Felix and Zachow, Stefan and Potthast, Wolfgang}, title = {Dynamic pressure analysis of novel interpositional knee spacer implants in 3D-printed human knee models}, volume = {12}, journal = {Scientific Reports}, doi = {10.1038/s41598-022-20463-6}, year = {2022}, abstract = {Alternative treatment methods for knee osteoarthritis (OA) are in demand, to delay the young (< 50 Years) patient's need for osteotomy or knee replacement. Novel interpositional knee spacers shape based on statistical shape model (SSM) approach and made of polyurethane (PU) were developed to present a minimally invasive method to treat medial OA in the knee. The implant should be supposed to reduce peak strains and pain, restore the stability of the knee, correct the malalignment of a varus knee and improve joint function and gait. Firstly, the spacers were tested in artificial knee models. It is assumed that by application of a spacer, a significant reduction in stress values and a significant increase in the contact area in the medial compartment of the knee will be registered. Biomechanical analysis of the effect of novel interpositional knee spacer implants on pressure distribution in 3D-printed knee model replicas: the primary purpose was the medial joint contact stress-related biomechanics. A secondary purpose was a better understanding of medial/lateral redistribution of joint loading. Six 3D printed knee models were reproduced from cadaveric leg computed tomography. Each of four spacer implants was tested in each knee geometry under realistic arthrokinematic dynamic loading conditions, to examine the pressure distribution in the knee joint. All spacers showed reduced mean stress values by 84-88\% and peak stress values by 524-704\% in the medial knee joint compartment compared to the non-spacer test condition. The contact area was enlarged by 462-627\% as a result of the inserted spacers. Concerning the appreciable contact stress reduction and enlargement of the contact area in the medial knee joint compartment, the premises are in place for testing the implants directly on human knee cadavers to gain further insights into a possible tool for treating medial knee osteoarthritis.}, language = {en} } @article{RejSantiagoBaturinaetal.2022, author = {Rej, Sourav and Santiago, Eva Yazmin and Baturina, Olga and Zhang, Yu and Burger, Sven and Kment, Stepan and Govorov, Alexander O. and Naldoni, Alberto}, title = {Colloidal Titanium Nitride Nanobars for Broadband Inexpensive Plasmonics and Photochemistry from Visible to Mid-IR Wavelengths}, volume = {104}, journal = {Nano Energy}, arxiv = {http://arxiv.org/abs/2209.04678}, doi = {10.1016/j.nanoen.2022.107989}, pages = {107989}, year = {2022}, language = {en} } @article{RamosLeiteZschiedrichKizilkayaetal.2022, author = {Ramos Leite, Tiago and Zschiedrich, Lin and Kizilkaya, Orhan and McPeak, Kevin M.}, title = {Resonant Plasmonic-Biomolecular Chiral Interactions in the Far-Ultraviolet: Enantiomeric Discrimination of sub-10 nm Amino Acid Films}, volume = {22}, journal = {Nano Lett.}, doi = {10.1021/acs.nanolett.2c01724}, pages = {7343}, year = {2022}, language = {en} }