@inproceedings{TillmannJaegerKatzetal.2021, author = {Tillmann, Peter and J{\"a}ger, Klaus and Katz, Eugene and Becker, Christiane}, title = {Relaxed current-matching constraints by bifacial operation and luminescent coupling in perovskite/silicon tandem solar cells}, booktitle = {2021 IEEE 48th Photovoltaic Specialists Conference (PVSC)}, doi = {10.1109/PVSC43889.2021.9518891}, pages = {1086}, year = {2021}, language = {en} } @misc{BetzBinkowskiBurger2021, author = {Betz, Fridtjof and Binkowski, Felix and Burger, Sven}, title = {RPExpand: Software for Riesz projection expansion of resonance phenomena [Source Code]}, doi = {10.24433/CO.2372084.v1}, year = {2021}, language = {de} } @article{WuArrivaultDurufleetal.2021, author = {Wu, Tong and Arrivault, Denis and Durufl{\´e}, Marc and Gras, Alexandre and Binkowski, Felix and Burger, Sven and Yan, Wei and Lalanne, Philippe}, title = {Efficient hybrid method for the modal analysis of optical microcavities and nanoresonators}, volume = {38}, journal = {J. Opt. Soc. Am. A}, doi = {10.1364/JOSAA.428224}, pages = {1224}, year = {2021}, language = {en} } @article{BetzBinkowskiBurger2021, author = {Betz, Fridtjof and Binkowski, Felix and Burger, Sven}, title = {RPExpand: Software for Riesz projection expansion of resonance phenomena}, volume = {15}, journal = {SoftwareX}, doi = {10.1016/j.softx.2021.100763}, pages = {100763}, year = {2021}, language = {en} } @article{NegrinMonteceloMovsesyanGaoetal.2022, author = {Negrin-Montecelo, Yoel and Movsesyan, Artur and Gao, Jie and Burger, Sven and Wang, Zhiming and Nlate, Sylvain and Pouget, Emilie and Oda, Reiko and Comesana-Hermo, Miguel and Govorov, Alexander O. and Correa-Duarte, Miguel}, title = {Chiral Generation of Hot Carriers for Polarization-Sensitive Plasmonic Photocatalysis with Hybrid Nanostructures}, volume = {144}, journal = {J. Am. Chem. Soc.}, doi = {10.1021/jacs.1c10526}, pages = {1663}, year = {2022}, language = {en} } @inproceedings{SchnauberSchallBounouaretal.2021, author = {Schnauber, Peter and Schall, Johannes and Bounouar, Samir and Srinivasan, Kartik and Davanco, Marcelo and Song, Jin-Dong and Burger, Sven and Rodt, Sven and Reitzenstein, Stephan}, title = {Deterministically fabricated quantum dot - waveguide systems for on-chip quantum optics}, volume = {11806}, booktitle = {Proc. SPIE}, doi = {10.1117/12.2596042}, pages = {118060G}, year = {2021}, language = {en} } @inproceedings{PerevoznikBoseBurgeretal.2021, author = {Perevoznik, Dmitrii and Bose, Surajit and Burger, Sven and Demircan, Ayhan and Morgner, Uwe}, title = {Writing Photonic Components in Polymers Using Femtosecond Pulses}, booktitle = {Conference on Lasers and Electro-Optics (CLEO)}, doi = {10.1364/CLEO_AT.2021.ATh4P.4}, pages = {ATh4P.4}, year = {2021}, language = {en} } @article{delRazoFroembergStraubeetal.2022, author = {del Razo, Mauricio and Fr{\"o}mberg, Daniela and Straube, Arthur and Sch{\"u}tte, Christof and H{\"o}fling, Felix and Winkelmann, Stefanie}, title = {A probabilistic framework for particle-based reaction-diffusion dynamics using classical Fock space representations}, volume = {112}, journal = {Letters in Mathematical Physics}, number = {49}, arxiv = {http://arxiv.org/abs/arXiv:2109.13616}, doi = {10.1007/s11005-022-01539-w}, year = {2022}, language = {en} } @article{StraubeWinkelmannSchuetteetal.2021, author = {Straube, Arthur and Winkelmann, Stefanie and Sch{\"u}tte, Christof and H{\"o}fling, Felix}, title = {Stochastic pH oscillations in a model of the urea-urease reaction confined to lipid vesicles}, volume = {12}, journal = {J. Phys. Chem. Lett.}, doi = {10.1021/acs.jpclett.1c03016}, pages = {9888 -- 9893}, year = {2021}, abstract = {The urea-urease clock reaction is a pH switch from acid to basic that can turn into a pH oscillator if it occurs inside a suitable open reactor. We numerically study the confinement of the reaction to lipid vesicles, which permit the exchange with an external reservoir by differential transport, enabling the recovery of the pH level and yielding a constant supply of urea molecules. For microscopically small vesicles, the discreteness of the number of molecules requires a stochastic treatment of the reaction dynamics. Our analysis shows that intrinsic noise induces a significant statistical variation of the oscillation period, which increases as the vesicles become smaller. The mean period, however, is found to be remarkably robust for vesicle sizes down to approximately 200 nm, but the periodicity of the rhythm is gradually destroyed for smaller vesicles. The observed oscillations are explained as a canard-like limit cycle that differs from the wide class of conventional feedback oscillators.}, language = {en} } @article{BetzBinkowskiHammerschmidtetal.2023, author = {Betz, Fridtjof and Binkowski, Felix and Hammerschmidt, Martin and Zschiedrich, Lin and Burger, Sven}, title = {Resonance expansion of quadratic quantities with regularized quasinormal modes}, volume = {220}, journal = {Phys. Status Solidi A}, arxiv = {http://arxiv.org/abs/2212.11117}, doi = {10.1002/pssa.202200892}, pages = {2200892}, year = {2023}, language = {en} } @article{BenSoltaneColomStoutetal.2023, author = {Ben Soltane, Isam and Colom, R{\´e}mi and Stout, Brian and Bonod, Nicolas}, title = {Derivation of the Transient and Steady Optical States from the Poles of the S-Matrix}, volume = {17}, journal = {Laser Photon. Rev.}, doi = {10.1002/lpor.202200141}, pages = {2200141}, year = {2023}, language = {en} } @article{HelfmannConradLorenzSpreenetal.2023, author = {Helfmann, Luzie and Conrad, Natasa Djurdjevac and Lorenz-Spreen, Philipp and Sch{\"u}tte, Christof}, title = {Modelling opinion dynamics under the impact of influencer and media strategies}, volume = {13}, journal = {Scientific Reports}, arxiv = {http://arxiv.org/abs/2301.13661}, doi = {10.1038/s41598-023-46187-9}, pages = {19375}, year = {2023}, abstract = {Digital communication has made the public discourse considerably more complex, and new actors and strategies have emerged as a result of this seismic shift. Aside from the often-studied interactions among individuals during opinion formation, which have been facilitated on a large scale by social media platforms, the changing role of traditional media and the emerging role of "influencers" are not well understood, and the implications of their engagement strategies arising from the incentive structure of the attention economy even less so. Here we propose a novel opinion dynamics model that accounts for these different roles, namely that media and influencers change their own positions on slower time scales than individuals, while influencers dynamically gain and lose followers. Numerical simulations show the importance of their relative influence in creating qualitatively different opinion formation dynamics: with influencers, fragmented but short-lived clusters emerge, which are then counteracted by more stable media positions. Mean-field approximations by partial differential equations reproduce this dynamic. Based on the mean-field model, we study how strategies of influencers to gain more followers can influence the overall opinion distribution. We show that moving towards extreme positions can be a beneficial strategy for influencers to gain followers. Finally, we demonstrate that optimal control strategies allow other influencers or media to counteract such attempts and prevent further fragmentation of the opinion landscape. Our modelling framework contributes to better understanding the different roles and strategies in the increasingly complex information ecosystem and their impact on public opinion formation.}, language = {en} } @article{WolfFuerstGeigesetal.2023, author = {Wolf, Sarah and F{\"u}rst, Steffen and Geiges, Andreas and Laublichler, Manfred and Mielke, Jahel and Steudle, Gesine and Winter, Konstantin and Jaeger, Carlo}, title = {The Decision Theatre Triangle for societal challenges - an example case and research needs}, volume = {394}, journal = {Journal of Cleaner Production}, doi = {10.1016/j.jclepro.2023.136299}, pages = {136299}, year = {2023}, abstract = {Tackling societal challenges relating to sustainability requires both an understanding of the underlying complex socio-ecological systems and participation of scientists as well as relevant stakeholders, such as practice experts, decision makers, and citizens. This paper introduces the Decision Theatre Triangle, a method which combines empirical information, mathematical modelling and simulation, and a format for dialogue between scientists and stakeholders. While it builds on previous Decision Theatre work, the new structuring into these three elements emphasizes what is needed for setting up a Decision Theatre for a given challenge. Based on experience with a specific example - sustainable mobility in Germany - it is argued that agent-based models are particularly suitable for Decision Theatres and that the method is useful not only for decision support but also for science communication and co-creation of a deeper knowledge of the system under discussion. As a step towards facilitating a broader use of the Decision Theatre Triangle method, the paper then sketches research needs for each of its three elements, with a focus on mathematical modelling and simulation.}, 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{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{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} } @inproceedings{BinkowskiBetzHammerschmidtetal.2022, author = {Binkowski, Felix and Betz, Fridtjof and Hammerschmidt, Martin and Schneider, Philipp-Immanuel and Zschiedrich, Lin and Burger, Sven}, title = {Numerical methods for the investigation of resonances in nanophotonics}, booktitle = {The 12th International Conference on Metamaterials, Photonic Crystals and Plasmonics (META 2022)}, editor = {Zouhdi, S.}, issn = {2429-1390}, pages = {247}, year = {2022}, language = {en} } @inproceedings{MovsesyanSantiagoBurgeretal.2022, author = {Movsesyan, Artur and Santiago, Eva Yazmin and Burger, Sven and Correa-Duarte, Miguel and Besteiro, Lucas V. and Wang, Zhiming and Govorov, Alexander O.}, title = {The anisotropy of hot carriers' spatial distribution contrasts the isotropy of photothermal effects in complex and small plasmonic nanocrystals with complex shapes}, booktitle = {The 12th International Conference on Metamaterials, Photonic Crystals and Plasmonics (META 2022)}, editor = {Zouhdi, S.}, issn = {2429-1390}, pages = {285}, year = {2022}, language = {en} } @inproceedings{BinkowskiBetzColometal.2021, author = {Binkowski, Felix and Betz, Fridtjof and Colom, Remi and Hammerschmidt, Martin and Schneider, Philipp-Immanuel and Zschiedrich, Lin and Burger, Sven}, title = {Contour integral methods for resonance phenomena in nano-optics}, booktitle = {The 11th International Conference on Metamaterials, Photonic Crystals and Plasmonics (META 2021)}, editor = {Zouhdi, S. and Pawlak, D. and Kudelski, A.}, issn = {2429-1390}, pages = {523}, year = {2021}, language = {en} } @article{ErnstUngerSchuetteetal.2023, author = {Ernst, Ariane and Unger, Nathalie and Sch{\"u}tte, Christof and Walter, Alexander and Winkelmann, Stefanie}, title = {Rate-limiting recovery processes in neurotransmission under sustained stimulation}, volume = {362}, journal = {Mathematical Biosciences}, arxiv = {http://arxiv.org/abs/2302.01635}, doi = {10.1016/j.mbs.2023.109023}, year = {2023}, abstract = {At chemical synapses, an arriving electric signal induces the fusion of vesicles with the presynaptic membrane, thereby releasing neurotransmitters into the synaptic cleft. After a fusion event, both the release site and the vesicle undergo a recovery process before becoming available for reuse again. Of central interest is the question which of the two restoration steps acts as the limiting factor during neurotrans-mission under high-frequency sustained stimulation. In order to investigate this question, we introduce a novel non-linear reaction network which involves explicit recovery steps for both the vesicles and the release sites, and includes the induced time-dependent output current. The associated reaction dynamics are formulated by means of ordinary differential equations (ODEs), as well as via the associated stochastic jump process. While the stochastic jump model describes a single release site, the average over many release sites is close to the ODE solution and shares its periodic structure. The reason for this can be traced back to the insight that recovery dynamics of vesicles and release sites are statistically almost independent. A sensitivity analysis on the recovery rates based on the ODE formulation reveals that neither the vesicle nor the release site recovery step can be identified as the essential rate-limiting step but that the rate- limiting feature changes over the course of stimulation. Under sustained stimulation the dynamics given by the ODEs exhibit transient dynamics leading from an initial depression of the postsynaptic response to an asymptotic periodic orbit, while the individual trajectories of the stochastic jump model lack the oscillatory behavior an asymptotic periodicity of the ODE-solution.}, language = {de} } @article{SeckerFackeldeyWeberetal.2023, author = {Secker, Christopher and Fackeldey, Konstantin and Weber, Marcus and Ray, Sourav and Gorgulla, Christoph and Sch{\"u}tte, Christof}, title = {Novel multi-objective affinity approach allows to identify pH-specific μ-opioid receptor agonists}, volume = {15}, journal = {Journal of Cheminformatics}, doi = {10.1186/s13321-023-00746-4}, year = {2023}, abstract = {Opioids are essential pharmaceuticals due to their analgesic properties, however, lethal side effects, addiction, and opioid tolerance are extremely challenging. The development of novel molecules targeting the μ-opioid receptor (MOR) in inflamed, but not in healthy tissue, could significantly reduce these unwanted effects. Finding such novel molecules can be achieved by maximizing the binding affinity to the MOR at acidic pH while minimizing it at neutral pH, thus combining two conflicting objectives. Here, this multi-objective optimal affinity approach is presented, together with a virtual drug discovery pipeline for its practical implementation. When applied to finding pH-specific drug candidates, it combines protonation state-dependent structure and ligand preparation with high-throughput virtual screening. We employ this pipeline to characterize a set of MOR agonists identifying a morphine-like opioid derivative with higher predicted binding affinities to the MOR at low pH compared to neutral pH. Our results also confirm existing experimental evidence that NFEPP, a previously described fentanyl derivative with reduced side effects, and recently reported β-fluorofentanyls and -morphines show an increased specificity for the MOR at acidic pH when compared to fentanyl and morphine. We further applied our approach to screen a >50K ligand library identifying novel molecules with pH-specific predicted binding affinities to the MOR. The presented differential docking pipeline can be applied to perform multi-objective affinity optimization to identify safer and more specific drug candidates at large scale.}, language = {en} } @article{NiemannUramWolfetal.2024, author = {Niemann, Jan-Hendrik and Uram, Samuel and Wolf, Sarah and Conrad, Natasa Djurdjevac and Weiser, Martin}, title = {Multilevel Optimization for Policy Design with Agent-Based Epidemic Models}, volume = {77}, journal = {Computational Science}, arxiv = {http://arxiv.org/abs/2304.02281}, doi = {10.1016/j.jocs.2024.102242}, pages = {102242}, year = {2024}, abstract = {Epidemiological models can not only be used to forecast the course of a pandemic like COVID-19, but also to propose and design non-pharmaceutical interventions such as school and work closing. In general, the design of optimal policies leads to nonlinear optimization problems that can be solved by numerical algorithms. Epidemiological models come in different complexities, ranging from systems of simple ordinary differential equations (ODEs) to complex agent-based models (ABMs). The former allow a fast and straightforward optimization, but are limited in accuracy, detail, and parameterization, while the latter can resolve spreading processes in detail, but are extremely expensive to optimize. We consider policy optimization in a prototypical situation modeled as both ODE and ABM, review numerical optimization approaches, and propose a heterogeneous multilevel approach based on combining a fine-resolution ABM and a coarse ODE model. Numerical experiments, in particular with respect to convergence speed, are given for illustrative examples.}, language = {en} } @inproceedings{GanderKrauseWeiseretal.2023, author = {Gander, Lia and Krause, Rolf and Weiser, Martin and Costabal, Francisco and Pezzuto, Simone}, title = {On the Accuracy of Eikonal Approximations in Cardiac Electrophysiology in the Presence of Fibrosis}, volume = {13958}, booktitle = {Functional Imaging and Modeling of the Heart. FIMH 2023.}, publisher = {Springer, Cham}, doi = {10.1007/978-3-031-35302-4_14}, year = {2023}, abstract = {Fibrotic tissue is one of the main risk factors for cardiac arrhythmias. It is therefore a key component in computational studies. In this work, we compare the monodomain equation to two eikonal models for cardiac electrophysiology in the presence of fibrosis. We show that discontinuities in the conductivity field, due to the presence of fibrosis, introduce a delay in the activation times. The monodomain equation and eikonal-diffusion model correctly capture these delays, contrarily to the classical eikonal equation. Importantly, a coarse space discretization of the monodomain equation amplifies these delays, even after accounting for numerical error in conduction velocity. The numerical discretization may also introduce artificial conduction blocks and hence increase propagation complexity. Therefore, some care is required when comparing eikonal models to the discretized monodomain equation.}, language = {en} } @inproceedings{TockhornSutterCruzetal.2022, author = {Tockhorn, Philipp and Sutter, Johannes and Cruz, Alexandros and Wagner, Philipp and J{\"a}ger, Klaus and Yoo, Danbi and Lang, Felix and Grischek, Max and Li, Bor and Al-Ashouri, Amran and K{\"o}hnen, Eike and Stolterfoht, Martin and Neher, Dieter and Schlatmann, Rutger and Rech, Bernd and Stannowski, Bernd and Albrecht, Steve and Becker, Christiane}, title = {Nanooptically Enhanced Perovskite/Silicon Tandem Solar Cells with 29.80\% Power Conversion Efficiency}, booktitle = {OSA Adv. Photonics}, doi = {10.1364/NOMA.2022.JTu4H.2}, pages = {JTu4H.2}, year = {2022}, language = {en} } @article{SemlerWeiser2023, author = {Semler, Phillip and Weiser, Martin}, title = {Adaptive Gaussian Process Regression for Efficient Building of Surrogate Models in Inverse Problems}, volume = {39}, journal = {Inverse Problems}, number = {12}, arxiv = {http://arxiv.org/abs/2303.05824}, doi = {10.1088/1361-6420/ad0028}, pages = {125003}, year = {2023}, abstract = {In a task where many similar inverse problems must be solved, evaluating costly simulations is impractical. Therefore, replacing the model y with a surrogate model y(s) that can be evaluated quickly leads to a significant speedup. The approximation quality of the surrogate model depends strongly on the number, position, and accuracy of the sample points. With an additional finite computational budget, this leads to a problem of (computer) experimental design. In contrast to the selection of sample points, the trade-off between accuracy and effort has hardly been studied systematically. We therefore propose an adaptive algorithm to find an optimal design in terms of position and accuracy. Pursuing a sequential design by incrementally appending the computational budget leads to a convex and constrained optimization problem. As a surrogate, we construct a Gaussian process regression model. We measure the global approximation error in terms of its impact on the accuracy of the identified parameter and aim for a uniform absolute tolerance, assuming that y(s) is computed by finite element calculations. A priori error estimates and a coarse estimate of computational effort relate the expected improvement of the surrogate model error to computational effort, resulting in the most efficient combination of sample point and evaluation tolerance. We also allow for improving the accuracy of already existing sample points by continuing previously truncated finite element solution procedures.}, language = {en} } @phdthesis{Tillmann2023, author = {Tillmann, Peter}, title = {Optimizing bifacial tandem solar cells for realistic operation conditions}, doi = {10.17169/refubium-39571}, year = {2023}, language = {en} } @inproceedings{MukherjeeKalasBurgeretal.2023, author = {Mukherjee, Deshabrato and Kalas, Benj{\´a}min and Burger, Sven and S{\´a}fr{\´a}n, Gy{\"o}rgy and Ser{\´e}nyi, Mikl{\´o}s and Fried, Mikl{\´o}s and Petrik, P{\´e}ter}, title = {Nanostructures for in-situ surface-enhanced Kretschmann-Raether ellipsometry}, volume = {12428}, booktitle = {Proc. SPIE}, arxiv = {http://arxiv.org/abs/2303.14636}, doi = {10.1117/12.2649080}, pages = {124280S}, year = {2023}, language = {en} } @misc{BetzBinkowskiHammerschmidtetal.2022, author = {Betz, Fridtjof and Binkowski, Felix and Hammerschmidt, Martin and Zschiedrich, Lin and Burger, Sven}, title = {Source code and simulation results for computing resonance expansions of quadratic quantities with regularized quasinormal modes}, journal = {Zenodo}, doi = {10.5281/zenodo.7376556}, year = {2022}, language = {en} } @inproceedings{CheginiSteinkeWeiser2022, author = {Chegini, Fatemeh and Steinke, Thomas and Weiser, Martin}, title = {Efficient adaptivity for simulating cardiac electrophysiology with spectral deferred correction methods}, arxiv = {http://arxiv.org/abs/2311.07206}, year = {2022}, abstract = {The locality of solution features in cardiac electrophysiology simulations calls for adaptive methods. Due to the overhead incurred by established mesh refinement and coarsening, however, such approaches failed in accelerating the computations. Here we investigate a different route to spatial adaptivity that is based on nested subset selection for algebraic degrees of freedom in spectral deferred correction methods. This combination of algebraic adaptivity and iterative solvers for higher order collocation time stepping realizes a multirate integration with minimal overhead. This leads to moderate but significant speedups in both monodomain and cell-by-cell models of cardiac excitation, as demonstrated at four numerical examples.}, language = {en} } @article{StraubeWinkelmannHoefling2023, author = {Straube, Arthur and Winkelmann, Stefanie and H{\"o}fling, Felix}, title = {Accurate reduced models for the pH oscillations in the urea-urease reaction confined to giant lipid vesicles}, volume = {127}, journal = {The Journal of Physical Chemistry B}, number = {13}, arxiv = {http://arxiv.org/abs/arXiv:2212.14503}, doi = {10.1021/acs.jpcb.2c09092}, pages = {2955 -- 2967}, year = {2023}, abstract = {This theoretical study concerns a pH oscillator based on the urea-urease reaction confined to giant lipid vesicles. Under suitable conditions, differential transport of urea and hydrogen ion across the unilamellar vesicle membrane periodically resets the pH clock that switches the system from acid to basic, resulting in self-sustained oscillations. We analyse the structure of the phase flow and of the limit cycle, which controls the dynamics for giant vesicles and dominates the pronouncedly stochastic oscillations in small vesicles of submicrometer size. To this end, we derive reduced models, which are amenable to analytic treatments that are complemented by numerical solutions, and obtain the period and amplitude of the oscillations as well as the parameter domain, where oscillatory behavior persists. We show that the accuracy of these predictions is highly sensitive to the employed reduction scheme. In particular, we suggest an accurate two-variable model and show its equivalence to a three-variable model that admits an interpretation in terms of a chemical reaction network. The faithful modeling of a single pH oscillator appears crucial for rationalizing experiments and understanding communication of vesicles and synchronization of rhythms.}, language = {en} } @article{BoltzKurchanLiu2021, author = {Boltz, Horst-Holger and Kurchan, Jorge and Liu, Andrea J.}, title = {Fluctuation distributions of energy minima in complex landscapes}, volume = {3}, journal = {Physical Review Research}, number = {1}, doi = {10.1103/PhysRevResearch.3.013061}, pages = {013061}, year = {2021}, abstract = {We discuss the properties of the distributions of energies of minima obtained by gradient descent in complex energy landscapes. We find strikingly similar phenomenology across several prototypical models. We particularly focus on the distribution of energies of minima in the analytically well-understood p-spin-interaction spin-glass model. We numerically find non-Gaussian distributions that resemble the Tracy-Widom distributions often found in problems of random correlated variables, and nontrivial finite-size scaling. Based on this, we propose a picture of gradient-descent dynamics that highlights the importance of a first-passage process in the eigenvalues of the Hessian. This picture provides a concrete link to problems in which the Tracy-Widom distribution is established. Aspects of this first-passage view of gradient-descent dynamics are generic for nonconvex complex landscapes, rationalizing the commonality that we find across models.}, language = {en} } @article{CardereraPokuttaSchuetteetal.2021, author = {Carderera, Alejandro and Pokutta, Sebastian and Sch{\"u}tte, Christof and Weiser, Martin}, title = {An efficient first-order conditional gradient algorithm in data-driven sparse identification of nonlinear dynamics to solve sparse recovery problems under noise}, journal = {Journal of Computational and Applied Mathematics}, arxiv = {http://arxiv.org/abs/2101.02630}, year = {2021}, abstract = {Governing equations are essential to the study of nonlinear dynamics, often enabling the prediction of previously unseen behaviors as well as the inclusion into control strategies. The discovery of governing equations from data thus has the potential to transform data-rich fields where well-established dynamical models remain unknown. This work contributes to the recent trend in data-driven sparse identification of nonlinear dynamics of finding the best sparse fit to observational data in a large library of potential nonlinear models. We propose an efficient first-order Conditional Gradient algorithm for solving the underlying optimization problem. In comparison to the most prominent alternative algorithms, the new algorithm shows significantly improved performance on several essential issues like sparsity-induction, structure-preservation, noise robustness, and sample efficiency. We demonstrate these advantages on several dynamics from the field of synchronization, particle dynamics, and enzyme chemistry.}, language = {en} } @article{JaegerSutterHammerschmidtetal.2021, author = {J{\"a}ger, Klaus and Sutter, Johannes and Hammerschmidt, Martin and Schneider, Philipp-Immanuel and Becker, Christiane}, title = {Prospects of light management in perovskite/silicon tandem solar cells}, volume = {10}, journal = {Nanophotonics}, doi = {10.1515/nanoph-2020-0674}, pages = {1991}, year = {2021}, language = {en} } @article{LiuZhouWangetal.2021, author = {Liu, Yongtao and Zhou, Zhiguang and Wang, Fan and Kewes, G{\"u}nter and Wen, Shihui and Burger, Sven and Wakiani, Majid Ebrahimi and Xi, Peng and Yang, Jiong and Yang, Xusan and Benson, Oliver and Jin, Dayong}, title = {Axial localization and tracking of self-interference nanoparticles by lateral point spread functions}, volume = {12}, journal = {Nat. Commun.}, doi = {10.1038/s41467-021-22283-0}, pages = {2019}, year = {2021}, language = {en} } @article{LueckeLuQuevedo2022, author = {L{\"u}cke, Marvin and Lu, Jingyi and Quevedo, Daniel E.}, title = {Coding for secrecy in remote state estimation with an adversary}, volume = {67}, journal = {IEEE Transactions on Automatic Control}, number = {9}, doi = {10.1109/TAC.2022.3169839}, pages = {4955 -- 4962}, year = {2022}, abstract = {We study the problem of remote state estimation in the presence of an eavesdropper. A sensor transmits state information over a packet-dropping link to a legitimate user. This information is randomly overheard by an eavesdropper. To reduce information leakage to the eavesdropper, previous studies have shown that by encoding the estimate with the acknowledgments (Acks), perfect secrecy can be achieved. However, this strategy greatly relies on the accuracy of the Acks and may easily fail if the Acks are compromised by cyberattacks. In this article, we tackle this issue by proposing to switch between sending an encoded state and sending the plain state to stay resilient against fake Acks. Specifically, we assume the Acks to be randomly attacked and derive recursive expressions for the minimum-mean-squared error estimates and error covariance matrices at the legitimate user and at the eavesdropper. Based upon this, we propose a transmission policy that depends on the probability of synchronization. We formulate a partially observable Markov decision process to model the evolution of the synchronization status and derive associated optimal transmission policies. Numerical examples are provided to verify the theoretical results.}, language = {en} } @article{CheginiKopanicakovaKrauseetal.2021, author = {Chegini, Fatemeh and Kopanicakova, Alena and Krause, Rolf and Weiser, Martin}, title = {Efficient Identification of Scars using Heterogeneous Model Hierarchies}, volume = {23}, journal = {EP Europace}, doi = {10.1093/europace/euaa402}, pages = {i113 -- i122}, year = {2021}, abstract = {Aims. Detection and quantification of myocardial scars are helpful both for diagnosis of heart diseases and for building personalized simulation models. Scar tissue is generally charac­terized by a different conduction of electrical excitation. We aim at estimating conductivity-related parameters from endocardial mapping data, in particular the conductivity tensor. Solving this inverse problem requires computationally expensive monodomain simulations on fine discretizations. Therefore, we aim at accelerating the estimation using a multilevel method combining electrophysiology models of different complexity, namely the mono­domain and the eikonal model. Methods. Distributed parameter estimation is performed by minimizing the misfit between simulated and measured electrical activity on the endocardial surface, subject to the mono­domain model and regularization, leading to a constrained optimization problem. We formulate this optimization problem, including the modeling of scar tissue and different regularizations, and design an efficient iterative solver. We consider monodomain grid hierarchies and monodomain-eikonal model hierarchies in a recursive multilevel trust-region method. Results. From several numerical examples, both the efficiency of the method and the estimation quality, depending on the data, are investigated. The multilevel solver is significantly faster than a comparable single level solver. Endocardial mapping data of realistic density appears to be just sufficient to provide quantitatively reasonable estimates of location, size, and shape of scars close to the endocardial surface. Conclusion. In several situations, scar reconstruction based on eikonal and monodomain models differ significantly, suggesting the use of the more accurate but more expensive monodomain model for this purpose. Still, eikonal models can be utilized to accelerate the computations considerably, enabling the use of complex electrophysiology models for estimating myocardial scars from endocardial mapping data.}, language = {en} } @inproceedings{JaegerTillmannKatzetal.2020, author = {J{\"a}ger, Klaus and Tillmann, Peter and Katz, Eugene A. and Becker, Christiane}, title = {Simulating bifacial perovskite/silicon tandem solar cells in large PV fields}, booktitle = {OSA Advanced Photonics Congress}, doi = {10.1364/PVLED.2020.PvTh1G.3}, pages = {PvTh1G.3}, year = {2020}, language = {en} } @article{JaegerTillmannKatzetal.2021, author = {J{\"a}ger, Klaus and Tillmann, Peter and Katz, Eugene A. and Becker, Christiane}, title = {Perovskite/silicon tandem solar cells: Effect of luminescent coupling and bifaciality}, volume = {5}, journal = {Sol. RRL}, arxiv = {http://arxiv.org/abs/2008.13696}, doi = {10.1002/solr.202000628}, pages = {2000628}, year = {2021}, language = {en} } @article{ManleySegantiniAhibozetal.2021, author = {Manley, Phillip and Segantini, Michele and Ahiboz, Doguscan and Hammerschmidt, Martin and Arnaoutakis, Georgios and MacQueen, Rowan W. and Burger, Sven and Becker, Christiane}, title = {Double-layer metasurface for enhanced photon up-conversion}, volume = {6}, journal = {APL Photon.}, arxiv = {http://arxiv.org/abs/2012.03587}, doi = {10.1063/5.0040839}, pages = {036103}, year = {2021}, language = {en} } @article{PakhomovHammerschmidtBurgeretal.2021, author = {Pakhomov, Anton V. and Hammerschmidt, Martin and Burger, Sven and Pertsch, Thomas and Setzpfand, Frank}, title = {Modeling of surface-induced second-harmonic generation from multilayer structures by the transfer matrix method}, volume = {29}, journal = {Opt. Express}, doi = {10.1364/OE.417066}, pages = {9098}, year = {2021}, language = {en} } @article{BinkowskiWuLalanneetal.2021, author = {Binkowski, Felix and Wu, Tong and Lalanne, Philippe and Burger, Sven and Govorov, Alexander O.}, title = {Hot Electron Generation through Near-Field Excitation of Plasmonic Nanoresonators}, volume = {8}, journal = {ACS Photonics}, arxiv = {http://arxiv.org/abs/2103.06652}, doi = {10.1021/acsphotonics.1c00231}, pages = {1243}, year = {2021}, language = {en} } @article{CvetkovicConradLie2021, author = {Cvetkovic, Nada and Conrad, Tim and Lie, Han Cheng}, title = {A Convergent Discretisation Method for Transition Path Theory for Diffusion Processes}, volume = {19}, journal = {Multiscale Modeling \& Simulation}, number = {1}, publisher = {Society for Industrial and Applied Mathematics}, doi = {10.1137/20M1329354}, pages = {242 -- 266}, year = {2021}, language = {en} } @book{DeuflhardWeiser2020, author = {Deuflhard, Peter and Weiser, Martin}, title = {Numerische Mathematik 3. Adaptive L{\"o}sung partieller Differentialgleichungen}, edition = {2}, publisher = {de Gruyter}, isbn = {978-3-11-069168-9}, doi = {10.1515/9783110689655}, pages = {456}, year = {2020}, language = {de} } @article{SikorskiWeberSchuette2021, author = {Sikorski, Alexander and Weber, Marcus and Sch{\"u}tte, Christof}, title = {The Augmented Jump Chain}, volume = {4}, journal = {Advanced Theory and Simulations}, number = {4}, publisher = {Wiley-VCH}, arxiv = {http://arxiv.org/abs/2008.04624}, doi = {10.1002/adts.202000274}, year = {2021}, abstract = {Modern methods of simulating molecular systems are based on the mathematical theory of Markov operators with a focus on autonomous equilibrated systems. However, non-autonomous physical systems or non-autonomous simulation processes are becoming more and more important. A representation of non-autonomous Markov jump processes is presented as autonomous Markov chains on space-time. Augmenting the spatial information of the embedded Markov chain by the temporal information of the associated jump times, the so-called augmented jump chain is derived. The augmented jump chain inherits the sparseness of the infinitesimal generator of the original process and therefore provides a useful tool for studying time-dependent dynamics even in high dimensions. Furthermore, possible generalizations and applications to the computation of committor functions and coherent sets in the non-autonomous setting are discussed. After deriving the theoretical foundations, the concepts with a proof-of-concept Galerkin discretization of the transfer operator of the augmented jump chain applied to simple examples are illustrated.}, language = {en} } @article{SechiSikorskiWeber2021, author = {Sechi, Renata and Sikorski, Alexander and Weber, Marcus}, title = {Estimation of the Koopman Generator by Newton's Extrapolation}, volume = {19}, journal = {Multiscale Modeling and Simulation}, number = {2}, publisher = {SIAM}, doi = {10.1137/20M1333006}, pages = {758 -- 774}, year = {2021}, abstract = {This article addresses the problem of estimating the Koopman generator of a Markov process. The direct computation of the infinitesimal generator is not easy because of the discretization of the state space, in particular because of the trade-off inherent in the choice of the best lag time to study the process. Short lag times implies a strong discretization of the state space and a consequent loss of Markovianity. Large lag times bypass events on fast timescales. We propose a method to approximate the generator with the computation of the Newton polynomial extrapolation. This technique is a multistep approach which uses as its input Koopman transfer operators evaluated for a series of lag times. Thus, the estimated infinitesimal generator combines information from different time resolutions and does not bias only fast- or slow-decaying dynamics. We show that the multi-scale Newton method can improve the estimation of the generator in comparison to the computation using finite difference or matrix logarithm methods.}, language = {en} } @phdthesis{Venkatareddy2020, author = {Venkatareddy, Narendra Lagumaddepalli}, title = {Revealing secrets of mussel-glue mimetic peptides - From advanced NMR to computational process modelling}, year = {2020}, language = {en} } @phdthesis{Eshtewy2020, author = {Eshtewy, Neveen Ali Salem}, title = {Mathematical Modeling of Metabolic-Genetic Networks}, year = {2020}, language = {en} } @article{OettingerMontefuscoPeletier2021, author = {{\"O}ttinger, Hans Christian and Montefusco, Alberto and Peletier, Mark A.}, title = {A Framework of Nonequilibrium Statistical Mechanics. I. Role and Types of Fluctuations}, volume = {46}, journal = {Journal of Non-Equilibrium Thermodynamics}, number = {1}, publisher = {De Gruyter}, doi = {10.1515/jnet-2020-0068}, pages = {1 -- 13}, year = {2021}, abstract = {Understanding the fluctuations by which phenomenological evolution equations with thermodynamic structure can be enhanced is the key to a general framework of nonequilibrium statistical mechanics. These fluctuations provide an idealized representation of microscopic details. We consider fluctuation-enhanced equations associated with Markov processes and elaborate the general recipes for evaluating dynamic material properties, which characterize force-flux constitutive laws, by statistical mechanics. Markov processes with continuous trajectories are conveniently characterized by stochastic differential equations and lead to Green-Kubo-type formulas for dynamic material properties. Markov processes with discontinuous jumps include transitions over energy barriers with the rates calculated by Kramers. We describe a unified approach to Markovian fluctuations and demonstrate how the appropriate type of fluctuations (continuous versus discontinuous) is reflected in the mathematical structure of the phenomenological equations.}, language = {en} } @article{MontefuscoPeletierOettinger2021, author = {Montefusco, Alberto and Peletier, Mark A. and {\"O}ttinger, Hans Christian}, title = {A Framework of Nonequilibrium Statistical Mechanics. II. Coarse-Graining}, volume = {46}, journal = {Journal of Non-Equilibrium Thermodynamics}, number = {1}, publisher = {De Gruyter}, doi = {10.1515/jnet-2020-0069}, pages = {15 -- 33}, year = {2021}, abstract = {For a given thermodynamic system, and a given choice of coarse-grained state variables, the knowledge of a force-flux constitutive law is the basis for any nonequilibrium modeling. In the first paper of this series we established how, by a generalization of the classical fluctuation-dissipation theorem (FDT), the structure of a constitutive law is directly related to the distribution of the fluctuations of the state variables. When these fluctuations can be expressed in terms of diffusion processes, one may use Green-Kubo-type coarse-graining schemes to find the constitutive laws. In this paper we propose a coarse-graining method that is valid when the fluctuations are described by means of general Markov processes, which include diffusions as a special case. We prove the success of the method by numerically computing the constitutive law for a simple chemical reaction A⇄B. Furthermore, we show that, for such a system, one cannot find a consistent constitutive law by any Green-Kubo-like scheme.}, language = {en} } @article{SunkaraHeinzHeinrichetal.2020, author = {Sunkara, Vikram and Heinz, Gitta A. and Heinrich, Frederik F. and Durek, Pawel and Mobasheri, Ali and Mashreghi, Mir-Farzin and Lang, Annemarie}, title = {Combining segmental bulk- and single-cell RNA-sequencing to define the chondrocyte gene expression signature in the murine knee joint}, journal = {bioarxiv (Accepted in Osteoarthr. Cartil.)}, doi = {10.1101/2020.06.13.148056}, year = {2020}, language = {en} } @article{LangHelfmeierStefanowskietal.2020, author = {Lang, Annemarie and Helfmeier, Sarah and Stefanowski, Jonathan and Kuppe, Aditi and Sunkara, Vikram and Pfeiffenberger, Moritz and Wolter, Angelique and Damerau, Alexandra and Hemmati-Sadeghi, Shabnam and Ringe, Jochen and Haag, Rainer and Hauser, Anja E. and L{\"o}hning, Max and Perka, Carsten and Duda, Georg and Hoff, Paula and Schmidt-Bleek, Katharina and Gaber, Timo and Buttgereit, Frank}, title = {HIF-stabilization prevents delayed fracture healing}, journal = {bioarxiv}, doi = {10.1101/2020.07.02.182832}, year = {2020}, language = {en} } @article{LaydonSunkaraBoelenetal.2020, author = {Laydon, Daniel J. and Sunkara, Vikram and Boelen, Lies and Bangham, Charles R. M. and Asquith, Becca}, title = {The relative contributions of infectious and mitotic spread to HTLV-1 persistence}, journal = {PLOS Computational Biology}, doi = {10.1371/journal.pcbi.1007470}, year = {2020}, language = {en} } @article{SchielaStoeckleinWeiser2021, author = {Schiela, Anton and St{\"o}cklein, Matthias and Weiser, Martin}, title = {A primal dual projection algorithm for efficient constraint preconditioning}, volume = {43}, journal = {SIAM Journal on Scientific Computing}, number = {6}, doi = {10.1137/20M1380739}, pages = {A4095 -- A4120}, year = {2021}, abstract = {We consider a linear iterative solver for large scale linearly constrained quadratic minimization problems that arise, for example, in optimization with PDEs. By a primal-dual projection (PDP) iteration, which can be interpreted and analysed as a gradient method on a quotient space, the given problem can be solved by computing sulutions for a sequence of constrained surrogate problems, projections onto the feasible subspaces, and Lagrange multiplier updates. As a major application we consider a class of optimization problems with PDEs, where PDP can be applied together with a projected cg method using a block triangular constraint preconditioner. Numerical experiments show reliable and competitive performance for an optimal control problem in elasticity.}, language = {en} } @article{MielkeMontefuscoPeletier2021, author = {Mielke, Alexander and Montefusco, Alberto and Peletier, Mark A.}, title = {Exploring families of energy-dissipation landscapes via tilting: three types of EDP convergence}, volume = {33}, journal = {Continuum Mechanics and Thermodynamics}, publisher = {Springer}, doi = {10.1007/s00161-020-00932-x}, pages = {611 -- 637}, year = {2021}, abstract = {This paper revolves around a subtle distinction between two concepts: passing to the limit in a family of gradient systems, on one hand, and deriving effective kinetic relations on the other. The two concepts are strongly related, and in many examples they even appear to be the same. Our main contributions are to show that they are different, to show that well-known techniques developed for the former may give incorrect results for the latter, and to introduce new tools to remedy this. The approach is based on the Energy-Dissipation Principle that provides a variational formulation to gradient-flow equations that allows one to apply techniques from Γ-convergence of functional on states and functionals on trajectories.}, language = {en} } @phdthesis{Santiago2021, author = {Santiago, Xavier Garcia}, title = {Numerical methods for shape optimization of photonic nanostructures}, organization = {Karlsruher Institut f{\"u}r Technologie}, doi = {10.5445/IR/1000131006}, year = {2021}, language = {en} }