@misc{LieSullivanTeckentrup2018, author = {Lie, Han Cheng and Sullivan, T. J. and Teckentrup, Aretha}, title = {Random forward models and log-likelihoods in Bayesian inverse problems}, volume = {6}, journal = {SIAM/ASA Journal on Uncertainty Quantification}, number = {4}, issn = {1438-0064}, arxiv = {http://arxiv.org/abs/1712.05717}, doi = {10.1137/18M1166523}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-66324}, pages = {1600 -- 1629}, year = {2018}, abstract = {We consider the use of randomised forward models and log-likelihoods within the Bayesian approach to inverse problems. Such random approximations to the exact forward model or log-likelihood arise naturally when a computationally expensive model is approximated using a cheaper stochastic surrogate, as in Gaussian process emulation (kriging), or in the field of probabilistic numerical methods. We show that the Hellinger distance between the exact and approximate Bayesian posteriors is bounded by moments of the difference between the true and approximate log-likelihoods. Example applications of these stability results are given for randomised misfit models in large data applications and the probabilistic solution of ordinary differential equations.}, language = {en} } @inproceedings{AbebeGomardZschiedrichetal.2017, author = {Abebe, Muluneh G. and Gomard, Guillaume and Zschiedrich, Lin and Rockstuhl, Carsten and Paetzold, Ulrich W. and Abass, Aimi}, title = {Thermodynamics of Photon Recycling in Four Terminal Perovskite/si Tandem Solar Cells}, booktitle = {Optical Nanostructures and Advanced Materials for Photovoltaics}, doi = {10.1364/PV.2017.PM4A.2}, pages = {PM4A.2}, year = {2017}, language = {en} } @phdthesis{DjurdjevacConrad2012, author = {Djurdjevac Conrad, Natasa}, title = {Methods for analyzing complex networks using random walker}, year = {2012}, language = {en} } @article{BanischDjurdjevacConrad2014, author = {Banisch, Ralf and Djurdjevac Conrad, Natasa}, title = {Cycle-flow-based module detection in directed recurrence networks}, volume = {108}, journal = {EPL (Europhysics Letters)}, number = {6}, doi = {10.1209/0295-5075/108/68008}, year = {2014}, language = {en} } @article{LorenzWolfBraunetal.2017, author = {Lorenz, Philipp and Wolf, Frederik and Braun, Jonas and Djurdjevac Conrad, Natasa and H{\"o}vel, Philipp}, title = {Capturing the Dynamics of Hashtag-Communities}, journal = {International Workshop on Complex Networks and their Applications}, doi = {10.1007/978-3-319-72150-7_33}, pages = {401 -- 413}, year = {2017}, language = {en} } @article{VillatoroZuehlkeRiebeetal.2016, author = {Villatoro, Jose and Z{\"u}hlke, Martin and Riebe, Daniel and Riedel, Jens and Beitz, Toralf and L{\"o}hmannsr{\"o}ben, Hans-Gerd}, title = {IR-MALDI ion mobility spectrometry}, volume = {408}, journal = {Analytical and Bioanalytical Chemistry}, number = {23}, doi = {10.1007/s00216-016-9739-x}, pages = {6259 -- 6268}, year = {2016}, language = {en} } @article{IgdeRoeblitzMuelleretal.2017, author = {Igde, Sinaida and R{\"o}blitz, Susanna and M{\"u}ller, Anne and Kolbe, Katharina and Boden, Sophia and Fessele, Claudia and Lindhorst, Thisbe and Weber, Marcus and Hartmann, Laura}, title = {Linear Precision Glycomacromolecules with Varying Interligand Spacing and Linker Functionalities Binding to Concanavalin A and the Bacterial Lectin FimH}, volume = {17}, journal = {Marcomolecular Bioscience}, number = {12}, doi = {10.1002/mabi.201700198}, pages = {1700198}, year = {2017}, language = {en} } @misc{VolkweinWeiser2000, author = {Volkwein, Stefan and Weiser, Martin}, title = {Affine Invariant Convergence Analysis for Inexact Augmented Lagrangian-SQP Methods}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-6243}, number = {00-56}, year = {2000}, abstract = {An affine invariant convergence analysis for inexact augmented Lagrangian-SQP methods is presented. The theory is used for the construction of an accuracy matching between iteration errors and truncation errors, which arise from the inexact linear system solves. The theoretical investigations are illustrated numerically by an optimal control problem for the Burgers equation.}, language = {en} } @misc{ErdmannKoberLangetal.2001, author = {Erdmann, Bodo and Kober, Cornelia and Lang, Jens and Sader, Robert and Zeilhofer, Hans-Florian and Deuflhard, Peter}, title = {Efficient and Reliable Finite Element Methods for Simulation of the Human Mandible}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-6403}, number = {01-14}, year = {2001}, abstract = {By computed tomography data (CT), the individual geometry of the mandible is quite well reproduced, also the separation between cortical and trabecular bone. Using anatomical knowledge about the architecture and the functional potential of the masticatory muscles, realistic situations were approximated. The solution of the underlying partial differential equations describing linear elastic material behaviour is provided by an adaptive finite element method. Estimations of the discretization error, local grid refinement, and multilevel techniques guarantee the reliability and efficiency of the method.}, language = {en} } @misc{Weiser2002, author = {Weiser, Martin}, title = {Linear convergence of an interior point method for linear control constrained optimal control problems}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-6809}, number = {02-13}, year = {2002}, abstract = {The paper provides a detailed analysis of a short step interior point algorithm applied to linear control constrained optimal control problems. Using an affine invariant local norm and an inexact Newton corrector, the well-known convergence results from finite dimensional linear programming can be extended to the infinite dimensional setting of optimal control. The present work complements a recent paper of Weiser and Deuflhard, where convergence rates have not been derived. The choice of free parameters, i.e. the corrector accuracy and the number of corrector steps, is discussed.}, language = {en} } @misc{HinzeSchiela2007, author = {Hinze, Michael and Schiela, Anton}, title = {Discretization of Interior Point Methods for State Constrained Elliptic Optimal Control Problems: Optimal Error Estimates and Parameter Adjustment}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-10414}, number = {07-40}, year = {2007}, abstract = {An adjustment scheme for the relaxation parameter of interior point approaches to the numerical solution of pointwise state constrained elliptic optimal control problems is introduced. The method is based on error estimates of an associated finite element discretization of the relaxed problems and optimally selects the relaxation parameter in dependence on the mesh size of discretization. The finite element analysis for the relaxed problems is carried out and a numerical example is presented which confirms our analytical findings.}, language = {en} } @misc{Schiela2007, author = {Schiela, Anton}, title = {An Interior Point Method in Function Space for the Efficient Solution of State Constrained Optimal Control Problems}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-10471}, number = {07-44}, year = {2007}, abstract = {We propose and analyse an interior point path-following method in function space for state constrained optimal control. Our emphasis is on proving convergence in function space and on constructing a practical path-following algorithm. In particular, the introduction of a pointwise damping step leads to a very efficient method, as verified by numerical experiments.}, language = {en} } @misc{Weiser2007, author = {Weiser, Martin}, title = {Pointwise Nonlinear Scaling for Reaction-Diffusion-Equations}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-10493}, number = {07-45}, year = {2007}, abstract = {Parabolic reaction-diffusion systems may develop sharp moving reaction fronts which pose a challenge even for adaptive finite element methods. We propose a method to transform the equation into an equivalent form that usually exhibits solutions which are easier to discretize, giving higher accuracy for a given number of degrees of freedom. The transformation is realized as an efficiently computable pointwise nonlinear scaling that is optimized for prototypical planar travelling wave solutions of the underlying reaction-diffusion equation. The gain in either performance or accuracy is demonstrated on different numerical examples.}, language = {en} } @misc{FarshbafShaker2003, type = {Master Thesis}, author = {Farshbaf-Shaker, Mohammad-Hassan}, title = {Ein neues Verfahren zur L{\"o}sung des Streuproblems der Maxwell-Gleichungen}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-9914}, school = {Zuse Institute Berlin (ZIB)}, year = {2003}, language = {de} } @misc{Gerber2007, type = {Master Thesis}, author = {Gerber, Susanne}, title = {Perfusionsmodellierung in menschlichen Tumoren}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-9923}, school = {Zuse Institute Berlin (ZIB)}, year = {2007}, abstract = {Im Rahmen dieser Arbeit wurde ein individuell anpassungsf{\"a}higes Modell entwickelt und implementiert, das die Perfusion in menschlichen soliden Tumoren beschreibt und f{\"u}r verschiedene Zeitpunkte w¨ahrend regionaler Hyperthermie ein lokal abh{\"a}ngiges Temperaturprofil berechnet. Da vor jeder Simulation alle wichtigen Parameter anhand von Ultraschall-, MRT- oder Angiogrammbildern individuell bestimmt werden k{\"o}nnen, wird eine patientenspezifische Aussage ¨uber das intratumorale Antwortverhalten bereits vor der eigentlichen Behandlung m{\"o}glich. In Abh¨angigkeit von der Qualit{\"a}t der zur Verf{\"u}gung stehenden anatomischen Daten {\"u}ber das zu simulierende Gebiet kann das Modell beliebig verfeinert oder bei Mangel an detaillierten Informationen auch mit Minimaldaten und reduzierter r{\"a}umlicher Genauigkeit benutzt werden. Die f{\"u}r eine Simulation ben{\"o}tigten 2- oder 3- dimensionalen Geometrien k{\"o}nnen leicht mit der am ZIB entwickelten Software Amira erstellt und zur Berechnung in KARDOS, einem ebenfalls am ZIB implementierten L{\"o}ser f{\"u}r nichtlineare partielle Differentialgleichungen, eingelesen werden. Mit Hilfe dieses Modells wird eine einfache, aber realistische und aussagekr{\"a}ftige Simulation f{\"u}r die Therapieplanung einer klinischen Hyperthermieanwendung erm{\"o}glicht, die innerhalb kurzer Zeit vorbereitet und durchgef{\"u}hrt werden kann.}, language = {de} } @misc{Weber2007, author = {Weber, Marcus}, title = {Conformation-based transition state theory}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-9612}, number = {07-18}, year = {2007}, abstract = {For the treatment of equilibrated molecular systems in a heat bath we propose a transition state theory that is based on conformation dynamics. In general, a set-based discretization of a Markov operator \${\cal P}^\tau\$ does not preserve the Markov property. In this article, we propose a discretization method which is based on a Galerkin approach. This discretization method preserves the Markov property of the operator and can be interpreted as a decomposition of the state space into (fuzzy) sets. The conformation-based transition state theory presented here can be seen as a first step in conformation dynamics towards the computation of essential dynamical properties of molecular systems without time-consuming molecular dynamics simulations.}, language = {en} } @misc{Riemer2006, type = {Master Thesis}, author = {Riemer, Alexander}, title = {Accuracy, Stability, Convergence of Rigorous Thermodynamic Sampling Methods}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-10052}, school = {Zuse Institute Berlin (ZIB)}, year = {2006}, language = {en} } @misc{SchenkWaechterWeiser2007, author = {Schenk, Olaf and W{\"a}chter, Andreas and Weiser, Martin}, title = {Inertia Revealing Preconditioning For Large-Scale Nonconvex Constrained Optimization}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-10314}, number = {07-32}, year = {2007}, abstract = {Fast nonlinear programming methods following the all-at-once approach usually employ Newton's method for solving linearized Karush-Kuhn-Tucker (KKT) systems. In nonconvex problems, the Newton direction is only guaranteed to be a descent direction if the Hessian of the Lagrange function is positive definite on the nullspace of the active constraints, otherwise some modifications to Newton's method are necessary. This condition can be verified using the signs of the KKT's eigenvalues (inertia), which are usually available from direct solvers for the arising linear saddle point problems. Iterative solvers are mandatory for very large-scale problems, but in general do not provide the inertia. Here we present a preconditioner based on a multilevel incomplete \$LBL^T\$ factorization, from which an approximation of the inertia can be obtained. The suitability of the heuristics for application in optimization methods is verified on an interior point method applied to the CUTE and COPS test problems, on large-scale 3D PDE-constrained optimal control problems, as well as 3D PDE-constrained optimization in biomedical cancer hyperthermia treatment planning. The efficiency of the preconditioner is demonstrated on convex and nonconvex problems with \$150^3\$ state variables and \$150^2\$ control variables, both subject to bound constraints.}, language = {en} } @misc{AntoineArnoldBesseetal.2007, author = {Antoine, Xavier and Arnold, Anton and Besse, Christophe and Ehrhardt, Matthias and Sch{\"a}dle, Achim}, title = {A Review of Transparent and Artificial Boundary Conditions Techniques for Linear and Nonlinear Schr{\"o}dinger Equations}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-10332}, number = {07-34}, year = {2007}, abstract = {In this review article we discuss different techniques to solve numerically the time-dependent Schr{\"o}dinger equation on unbounded domains. We present in detail the most recent approaches and describe briefly alternative ideas pointing out the relations between these works. We conclude with several numerical examples from different application areas to compare the presented techniques. We mainly focus on the one-dimensional problem but also touch upon the situation in two space dimensions and the cubic nonlinear case.}, language = {en} } @misc{Schiela2007, author = {Schiela, Anton}, title = {Optimality Conditions for Convex State Constrained Optimal Control Problems with Discontinuous States}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-10342}, number = {07-35}, year = {2007}, abstract = {We discuss first order optimality conditions for state constrained optimal control problems. Our concern is the treatment of problems, where the solution of the state equation is not known to be continuous, as in the case of boundary control in three space dimensions or optimal control with parabolic partial differential equations. We show existence of measure valued Lagrangian multipliers, which have just enough additional regularity to be applicable to all possibly discontinuous solutions of the state equation.}, language = {en} } @misc{SchmidtOevermannBastiaansetal.2008, author = {Schmidt, Heiko and Oevermann, Michael and Bastiaans, Rob J.M. and Kerstein, Alan R.}, title = {A priori Tabulation of Turbulent Flame Speeds via a Combination of a Stochastic Mixing Model and Flamelet Generated Manifolds}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-10532}, number = {08-02}, year = {2008}, abstract = {In this paper we propose a technique for a priori turbulent flame speed tabulation (TFST) for a given parameter space in standard combustion-regime diagrams. It can be used as a subgrid-scale (SGS) model in Large Eddy Simulation (LES). In a first step, stationary laminar flamelets are computed and stored over the progress variable following the ideas of flamelet generated manifolds (FGM). In a second step, the incompressible one-dimensional Navier-Stokes equations supplemented by the equation for the progress variable are solved on a grid that resolves all turbulent scales. Additionally, turbulent transport is implemented via the linear eddy model (LEM). The turbulent flame structures are solved until a statistically stationary mean value of the turbulent flame speed has been reached. The results are stored in a table that could be used by large scale premixed combustion models, e.g. front tracking schemes. Results are compared to an algebraic model and to direct numerical simulations (DNS).}, language = {en} } @misc{CarqueOwinohKleinetal.2008, author = {Carqu{\´e}, Gunter and Owinoh, Antony Z. and Klein, Rupert and Majda, Andrew J.}, title = {Asymptotic Scale Analysis of Precipitating Clouds}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-10548}, number = {08-03}, year = {2008}, abstract = {Asymptotic analyses of the three dimensional compressible flow equations coupled with transport equations for the mixing ratios of water vapour, cloud water and rain water are described. We obtain reduced systems of equations for two particular regimes of length and time scales: Models for the long time evolution of deep convective columns and for the short time evolution of shallow convective layers. The asymptotic deep convective column model is anelastic, yet the vertical motion is pressure free, i.e., it evolves freely in interaction with buoyancy while the horizontal divergence adjusts to fullfil the anelastic constraint. The perturbation pressure guaranteeing compliance with the horizontal divergence constraint obeys a Poisson-type equation. Surprisingly, the vertical velocity plays an important role in the horizontal dynamics through the Coriolis term. The vertical acceleration in a saturated column is directly determined by the buoyancy induced by potential temperature differences relative to the background stratification. This potential temperature deviation is a conserved quantity. Evaporation is the only important microphysical process in the undersaturated regime. The evaporation rate depends on the saturation deficit and the amount of rain water present and determines the (downward) vertical velocity and the distribution of water vapour. To connect the deep convective column solutions to top and bottom boundary conditions, a different flow regime needs to be accounted for. Within shallow layers whose depth is comparable to the column diameters, adjustment to physical boundary conditions can take place. This is the second regime considered in this report. The shallow convective layer regime is shown to be asymptotically described by Boussinesq-type equations. These equations are closed by evolution equations which show that, in the saturated regime, the distributions of potential temperature and cloud water are determined by a condensation rate that is directly proportional to the vertical velocity. In the undersaturated regime, the potential temperature distribution is determined by the amount of rain present, since the water vapour in this case is shown to be a conserved quantity. In both regimes the distribution of rain water depends on the rain water flux.}, language = {en} } @misc{OevermannSchmidtKerstein2008, author = {Oevermann, Michael and Schmidt, Heiko and Kerstein, Alan R.}, title = {Linear-Eddy Modeling of Autoignition under Thermal Stratification}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-10562}, number = {08-05}, year = {2008}, abstract = {The influence of thermal stratification on autoignition at constant volume and high pressure is investigated under turbulent conditions using the one-dimensional Linear-Eddy Model (LEM) and detailed hydrogen/air chemistry. Results are presented for the influence of initial temperature inhomogeneities on the heat release rate and the relative importance of diffusion and chemical reactions. The predicted heat release rates are compared with heat release rates of Chen et al. and Hawkes et al. obtained by two-dimensional Direct Numerical Simulations (DNS). Using the definition of Chen et al. for the displacement speed of the H2 mass fraction tracked at the location of maximum heat release, and a comparison of budget terms, different combustion modes including ignition front propagation and deflagration waves are identified and the results are compared to the DNS data. The LEM approach shows qualitatively and quantitatively reasonable agreement with the DNS data over the whole range of investigated temperature fluctuations. The results presented in this work suggest that LEM is a potential candidate as a sub-model for CFD calculations of HCCI engines.}, language = {en} } @misc{Schiela2008, author = {Schiela, Anton}, title = {An Extended Mathematical Framework for Barrier Methods in Function Space}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-10593}, number = {08-07}, year = {2008}, abstract = {An extended mathematical framework for barrier methods for state constrained optimal control compared to [Schiela, ZIB-Report 07-07] is considered. This allows to apply the results derived there to more general classes of optimal control problems, in particular to boundary control and finite dimensional control.}, language = {en} } @misc{RuprechtSchaedleSchmidtetal.2007, author = {Ruprecht, Daniel and Sch{\"a}dle, Achim and Schmidt, Frank and Zschiedrich, Lin}, title = {Transparent boundary conditons for time-dependent problems}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-9558}, number = {07-12}, year = {2007}, abstract = {A new approach to derive transparent boundary conditions (TBCs) for wave, Schr{\"o}dinger, heat and drift-diffusion equations is presented. It relies on the pole condition and distinguishes between physical reasonable and unreasonable solutions by the location of the singularities of the spatial Laplace transform of the exterior solution. To obtain a numerical algorithm, a M{\"o}bius transform is applied to map the Laplace transform onto the unit disc. In the transformed coordinate the solution is expanded into a power series. Finally, equations for the coefficients of the power series are derived. These are coupled to the equation in the interior, and yield transparent boundary conditions. Numerical results are presented in the last section, showing that the error introduced by the new approximate TBCs decays exponentially in the number of coefficients.}, language = {en} } @misc{KubeLasserWeber2007, author = {Kube, Susanna and Lasser, Caroline and Weber, Marcus}, title = {Monte Carlo sampling of Wigner functions and surface hopping quantum dynamics}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-9604}, number = {07-17}, year = {2007}, abstract = {Wigner transformation provides a one-to-one correspondence between functions on position space (wave functions) and functions on phase space (Wigner functions). Weighted integrals of Wigner functions yield quadratic quantities of wave functions like position and momentum densities or expectation values. For molecular quantum systems, suitably modified classical transport of Wigner functions provides an asymptotic approximation of the dynamics in the high energy regime. The article addresses the computation of Wigner functions by Monte Carlo quadrature. An ad aption of the Metropolis algorithm for the approximation of signed measures with disconnected support is systematically tested in combination with a surface hopping algorithm for non-adiabatic quantum dynamics. The numerical experiments give expectation values and level populations with an error of two to three percent, which agrees with the theoretically expected accuracy.}, language = {en} } @article{GarciaSantiagoHammerschmidtSachsetal.2022, author = {Garcia Santiago, Xavier and Hammerschmidt, Martin and Sachs, Johannes and Burger, Sven and Kwon, Hyunah and Kn{\"o}ller, Marvin and Arens, Tilo and Fischer, Peer and Fernandez-Corbaton, Ivan and Rockstuhl, Carsten}, title = {Toward maximally electromagnetically chiral scatterers at optical frequencies}, volume = {9}, journal = {ACS Photonics}, arxiv = {http://arxiv.org/abs/2112.04422}, doi = {10.1021/acsphotonics.1c01887}, pages = {1954}, year = {2022}, language = {en} } @misc{ErnstSchuetteSigristetal.2021, author = {Ernst, Ariane and Sch{\"u}tte, Christof and Sigrist, Stephan and Winkelmann, Stefanie}, title = {Variance of filtered signals: Characterization for linear reaction networks and application to neurotransmission dynamics}, issn = {1438-0064}, doi = {10.1016/j.mbs.2021.108760}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-82674}, year = {2021}, abstract = {Neurotransmission at chemical synapses relies on the calcium-induced fusion of synaptic vesicles with the presynaptic membrane. The distance to the calcium channels determines the release probability and thereby the postsynaptic signal. Suitable models of the process need to capture both the mean and the variance observed in electrophysiological measurements of the postsynaptic current. In this work, we propose a method to directly compute the exact first- and second-order moments for signals generated by a linear reaction network under convolution with an impulse response function, rendering computationally expensive numerical simulations of the underlying stochastic counting process obsolete. We show that the autocorrelation of the process is central for the calculation of the filtered signal's second-order moments, and derive a system of PDEs for the cross-correlation functions (including the autocorrelations) of linear reaction networks with time-dependent rates. Finally, we employ our method to efficiently compare different spatial coarse graining approaches for a specific model of synaptic vesicle fusion. Beyond the application to neurotransmission processes, the developed theory can be applied to any linear reaction system that produces a filtered stochastic signal.}, language = {en} } @article{ThiesSunkaraRayetal.2023, author = {Thies, Arne and Sunkara, Vikram and Ray, Sourav and Wulkow, Hanna and Celik, M. {\"O}zg{\"u}r and Yerg{\"o}z, Fatih and Sch{\"u}tte, Christof and Stein, Christoph and Weber, Marcus and Winkelmann, Stefanie}, title = {Modelling altered signalling of G-protein coupled receptors in inflamed environment to advance drug design}, volume = {13}, journal = {Scientific Reports}, number = {607}, doi = {10.1038/s41598-023-27699-w}, year = {2023}, abstract = {We previously reported the successful design, synthesis and testing of the prototype opioid painkiller NFEPP that does not elicit adverse side effects. The design process of NFEPP was based on mathematical modelling of extracellular interactions between G-protein coupled receptors (GPCRs) and ligands, recognizing that GPCRs function differently under pathological versus healthy conditions. We now present an additional and novel stochastic model of GPCR function that includes intracellular dissociation of G-protein subunits and modulation of plasma membrane calcium channels and their dependence on parameters of inflamed and healthy tissue (pH, radicals). The model is validated against in vitro experimental data for the ligands NFEPP and fentanyl at different pH values and radical concentrations. We observe markedly reduced binding affinity and calcium channel inhibition for NFEPP at normal pH compared to lower pH, in contrast to the effect of fentanyl. For increasing radical concentrations, we find enhanced constitutive G-protein activation but reduced ligand binding affinity. Assessing the different effects, the results suggest that, compared to radicals, low pH is a more important determinant of overall GPCR function in an inflamed environment. Future drug design efforts should take this into account.}, language = {en} } @misc{RayThiesSunkaraetal.2021, author = {Ray, Sourav and Thies, Arne and Sunkara, Vikram and Wulkow, Hanna and Celik, {\"O}zg{\"u}r and Yerg{\"o}z, Fatih and Sch{\"u}tte, Christof and Stein, Christoph and Weber, Marcus and Winkelmann, Stefanie}, title = {Modelling altered signalling of G-protein coupled receptors in inflamed environment to advance drug design}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-82797}, year = {2021}, abstract = {Initiated by mathematical modelling of extracellular interactions between G-protein coupled receptors (GPCRs) and ligands in normal versus diseased (inflamed) environments, we previously reported the successful design, synthesis and testing of the prototype opioid painkiller NFEPP that does not elicit adverse side effects. Uniquely, this design recognised that GPCRs function differently under pathological versus healthy conditions. We now present a novel stochastic model of GPCR function that includes intracellular dissociation of G-protein subunits and modulation of plasma membrane calcium channels associated with parameters of inflamed tissue (pH, radicals). By means of molecular dynamics simulations, we also assessed qualitative changes of the reaction rates due to additional disulfide bridges inside the GPCR binding pocket and used these rates for stochastic simulations of the corresponding reaction jump process. The modelling results were validated with in vitro experiments measuring calcium currents and G-protein activation. We found markedly reduced G-protein dissociation and calcium channel inhibition induced by NFEPP at normal pH, and enhanced constitutive G-protein activation but lower probability of ligand binding with increasing radical concentrations. These results suggest that, compared to radicals, low pH is a more important determinant of overall GPCR function in an inflamed environment. Future drug design efforts should take this into account.}, language = {en} } @phdthesis{Pakhomov2021, author = {Pakhomov, Anton}, title = {Efficient modeling and optimization of surface second-harmonic generation from nanophotonic components}, doi = {10.22032/dbt.49369}, year = {2021}, language = {en} } @article{Djurdjevac2021, author = {Djurdjevac, Ana}, title = {Linear Parabolic Problems in Random Moving Domains}, volume = {9}, number = {2}, doi = {https://doi.org/10.1137/19M1284889}, pages = {848 -- 879}, year = {2021}, abstract = {We consider linear parabolic equations on a random non-cylindrical domain. Utilizing the domain mapping method, we write the problem as a partial differential equation with random coefficients on a cylindrical deterministic domain. Exploiting the deterministic results concerning equations on non-cylindrical domains, we state the necessary assumptions about the velocity filed and in addition, about the flow transformation that this field generates. In this paper we consider both cases, the uniformly bounded with respect to the sample and log-normal type transformation. In addition, we give an explicit example of a log-normal type transformation and prove that it does not satisfy the uniformly bounded condition. We define a general framework for considering linear parabolic problems on random non-cylindrical domains. As the first example, we consider the heat equation on a random tube domain and prove its well-posedness. Moreover, as the other example we consider the parabolic Stokes equation which illustrates the case when it is not enough just to study the plain-back transformation of the function, but instead to consider for example the Piola type transformation, in order to keep the divergence free property.}, language = {en} } @article{DjurdjevacGraeserHerbert2021, author = {Djurdjevac, Ana and Gr{\"a}ser, Carsten and Herbert, Philip J.}, title = {Non-stationary incompressible linear fluid equations in a moving domain}, journal = {arXiv}, arxiv = {http://arxiv.org/abs/2106.08312}, year = {2021}, abstract = {This article considers non-stationary incompressible linear fluid equations in a moving domain. We demonstrate the existence and uniqueness of an appropriate weak formulation of the problem by making use of the theory of time-dependent Bochner spaces. It is not possible to directly apply established evolving Hilbert space theory due to the incompressibility constraint. After we have established the well-posedness, we derive and analyse a time discretisation of the system.}, language = {en} } @article{ColomMikheevaAchourietal.2023, author = {Colom, Remi and Mikheeva, Elena and Achouri, Karim and Zuniga-Perez, Jesus and Bonod, Nicolas and Martin, Olivier J. F. and Burger, Sven and Genevet, Patrice}, title = {Crossing of the branch cut: the topological origin of a universal 2π-phase retardation in non-Hermitian metasurfaces}, volume = {17}, journal = {Laser Photonics Rev.}, arxiv = {http://arxiv.org/abs/2202.05632}, doi = {10.1002/lpor.202200976}, pages = {2200976}, year = {2023}, language = {en} } @article{MontefuscoSchuetteWinkelmann2023, author = {Montefusco, Alberto and Sch{\"u}tte, Christof and Winkelmann, Stefanie}, title = {A route to the hydrodynamic limit of a reaction-diffusion master equation using gradient structures}, volume = {83}, journal = {SIAM Journal on Applied Mathematics}, number = {2}, arxiv = {http://arxiv.org/abs/2201.02613}, doi = {10.1137/22M1488831}, pages = {837 -- 861}, year = {2023}, abstract = {The reaction-diffusion master equation (RDME) is a lattice-based stochastic model for spatially resolved cellular processes. It is often interpreted as an approximation to spatially continuous reaction-diffusion models, which, in the limit of an infinitely large population, may be described by means of reaction-diffusion partial differential equations. Analyzing and understanding the relation between different mathematical models for reaction-diffusion dynamics is a research topic of steady interest. In this work, we explore a route to the hydrodynamic limit of the RDME which uses gradient structures. Specifically, we elaborate on a method introduced in [J. Maas and A. Mielke, J. Stat. Phys., 181 (2020), pp. 2257-2303] in the context of well-mixed reaction networks by showing that, once it is complemented with an appropriate limit procedure, it can be applied to spatially extended systems with diffusion. Under the assumption of detailed balance, we write down a gradient structure for the RDME and use the method in order to produce a gradient structure for its hydrodynamic limit, namely, for the corresponding RDPDE.}, language = {en} } @article{DellnitzHuellermeierLueckeetal.2023, author = {Dellnitz, Michael and H{\"u}llermeier, Eyke and L{\"u}cke, Marvin and Ober-Bl{\"o}baum, Sina and Offen, Christian and Peitz, Sebastian and Pfannschmidt, Karlson}, title = {Efficient Time-Stepping for Numerical Integration Using Reinforcement Learning}, volume = {45}, journal = {SIAM Journal on Scientific Computing}, number = {2}, doi = {10.1137/21M1412682}, pages = {A579 -- A595}, year = {2023}, language = {en} } @misc{PfluegerKlineFernandezHerreroetal.2020, author = {Pfl{\"u}ger, Mika and Kline, R Joseph and Fern{\´a}ndez Herrero, Anal{\´i}a and Hammerschmidt, Martin and Soltwisch, Victor and Krumrey, Michael}, title = {Extracting dimensional parameters of gratings produced with self-aligned multiple patterning using grazing-incidence small-angle x-ray scattering [Source Code]}, doi = {10.24433/CO.0953516.v2}, year = {2020}, language = {en} } @article{GaoRickertUrbanetal.2022, author = {Gao, Timm and Rickert, Lucas and Urban, Felix and Große, Jan and Srocka, Nicole and Rodt, Sven and Musial, Anna and Zolnacz, Kinga and Mergo, Pawel and Dybka, Kamil and Urbanczyk, Waclaw and Sek, Grzegorz and Burger, Sven and Reitzenstein, Stephan and Heindel, Tobias}, title = {A quantum key distribution testbed using a plug\&play telecom-wavelength single-photon source}, volume = {9}, journal = {Appl. Phys. Rev.}, arxiv = {http://arxiv.org/abs/2105.03473}, doi = {10.1063/5.0070966}, pages = {011412}, year = {2022}, language = {en} } @article{TorunSchneiderHammerschmidtetal.2021, author = {Torun, Cem G{\"u}ney and Schneider, Philipp-Immanuel and Hammerschmidt, Martin and Burger, Sven and Munns, Joseph H.D. and Schr{\"o}der, Tim}, title = {Optimized diamond inverted nanocones for enhanced color center to fiber coupling}, volume = {118}, journal = {Appl. Phys. Lett.}, arxiv = {http://arxiv.org/abs/2105.13333}, doi = {10.1063/5.0050338}, pages = {234002}, year = {2021}, language = {en} } @article{AhibozAndresenManleyetal.2021, author = {Ahiboz, Doguscan and Andresen, Elina and Manley, Phillip and Resch-Genger, Ute and W{\"u}rth, Christian and Becker, Christiane}, title = {Metasurface-Enhanced Photon Upconversion upon 1550 nm Excitation}, volume = {9}, journal = {Adv. Opt. Mater.}, doi = {10.1002/adom.202101285}, pages = {2101285}, year = {2021}, language = {en} } @article{MartensFunckSantiagoetal.2022, author = {Martens, Kevin and Funck, Timon and Santiago, Eva Y. and Govorov, Alexander O. and Burger, Sven and Liedl, Tim}, title = {Onset of Chirality in Plasmonic Meta-Molecules and Dielectric Coupling}, volume = {16}, journal = {ACS Nano}, arxiv = {http://arxiv.org/abs/2110.06689}, doi = {10.1021/acsnano.2c04729}, pages = {16143}, year = {2022}, language = {en} } @inproceedings{PerevoznikBoseBurgeretal.2021, author = {Perevoznik, Dmitrii and Bose, Surajit and Burger, Sven and Demircan, Ayhan and Morgner, Uwe}, title = {Photonic components in polymers made by femtosecond pulses}, booktitle = {Conference on Lasers and Electro-Optics Europe \& European Quantum Electronics Conference (CLEO/Europe-EQEC)}, doi = {10.1109/CLEO/Europe-EQEC52157.2021.9541906}, pages = {1}, year = {2021}, language = {en} } @inproceedings{AhibozAndresenManleyetal.2021, author = {Ahiboz, Doguscan and Andresen, Elina and Manley, Phillip and Resch Genger, Ute and W{\"u}rth, Christian and Becker, Christiane}, title = {Enhanced Photon Upconversion Using Erbium-Doped Nanoparticles Interacting with Silicon Metasurfaces}, booktitle = {IEEE 48th Photovoltaic Specialists Conference (PVSC)}, doi = {10.1109/PVSC43889.2021.9518495}, pages = {2008 -- 2010}, year = {2021}, language = {en} } @inproceedings{RickertGaoUrbanetal.2021, author = {Rickert, Lucas and Gao, Timm and Urban, Felix and Große, Jan and Srocka, Nicole and Rodt, Sven and Musial, Anna and Zolnacz, Kinga and Mergo, Pawel and Dybka, Kamil and Urbanczyk, Waclaw and Sek, Grzegorz and Burger, Sven and Reitzenstein, Stephan and Tobias, Heindel}, title = {A Quantum Key Distribution Testbed Using Plug\&Play Telecom-Wavelength Single-Photons}, booktitle = {Quantum Information and Measurement VI}, doi = {10.1364/QIM.2021.M2C.1}, pages = {M2C.1}, year = {2021}, language = {en} } @inproceedings{SchneiderGarciaSantiagoWiegandetal.2021, author = {Schneider, Philipp-Immanuel and Garcia-Santiago, Xavier and Wiegand, Benjamin and Anton, Oliver and Krutzik, Markus and Rockstuhl, Carsten and Burger, Sven}, title = {Advances in Bayesian optimization for photonics and quantum atom optics applications}, booktitle = {OSA Advanced Photonics Congress}, doi = {10.1364/IPRSN.2021.JTh1E.2}, pages = {JTh1E.2}, year = {2021}, language = {en} } @article{ColomBinkowskiBetzetal.2022, author = {Colom, Remi and Binkowski, Felix and Betz, Fridtjof and Kivshar, Yuri and Burger, Sven}, title = {Enhanced Purcell factor for nanoantennas supporting interfering resonances}, volume = {4}, journal = {Phys. Rev. Research}, arxiv = {http://arxiv.org/abs/2111.03339}, doi = {10.1103/PhysRevResearch.4.023189}, pages = {023189}, year = {2022}, language = {en} } @inproceedings{MusialZolnaczSrockaetal.2020, author = {Musial, Anna and Zolnacz, Kinga and Srocka, Nicole and Kravets, Oleh and Große, Jan and Schneider, Philipp-Immanuel and Olszewski, Jacek and Poturaj, Krzystof and Wojcik, Grzegorz and Mergo, Pawel and Dybka, Kamil and Dyrkacz, Mariusz and Dlubek, Michal and Rodt, Sven and Burger, Sven and Zschiedrich, Lin and Urbanczyk, Waclaw and Sek, Grzegorz and Reitzenstein, Stephan}, title = {Stand-alone quantum dot-based single-photon source operating at telecommunication wavelengths}, booktitle = {10th International Conference on Spontaneous Coherence in Excitonic Systems ICSCE10}, pages = {39}, year = {2020}, language = {en} } @article{FackeldeyGorgullaWeber2021, author = {Fackeldey, Konstantin and Gorgulla, Christoph and Weber, Marcus}, title = {Neue Medikamente dank Supercomputern}, journal = {Spektrum der Wissenschaft}, number = {11}, pages = {40 -- 46}, year = {2021}, abstract = {Die aktuelle Pandemie verdeutlicht, wie wichtig es ist, rasch geeignete Arzneimittel zu finden. In Computer­simulationen gelingt das erheblich schneller als im Labor. Gegen das Coronavirus ließen sich auf diese Weise bereits Wirkstoffkandidaten identifizieren.}, language = {de} } @article{StoutColomBonodetal.2021, author = {Stout, Brian and Colom, Remi and Bonod, Nicolas and McPhedran, Ross C}, title = {Spectral expansions of open and dispersive optical systems: Gaussian regularization and convergence}, volume = {23}, journal = {New J. Phys.}, doi = {10.1088/1367-2630/ac10a6}, pages = {083004}, year = {2021}, language = {en} } @inproceedings{BoppPlockTuranetal.2023, author = {Bopp, Julian M. and Plock, Matthias and Turan, Tim and Pieplow, Gregor and Burger, Sven and Schr{\"o}der, Tim}, title = {'Sawfish' Spin-Photon Interface for Near-Unity Emitter-to-Waveguide Coupling}, booktitle = {Conference on Lasers and Electro-Optics (CLEO)}, doi = {10.1364/CLEO_SI.2023.SF1O.6}, pages = {SF1O.6}, year = {2023}, language = {en} } @inproceedings{HammerschmidtZschiedrichSiaudinyteetal.2023, author = {Hammerschmidt, Martin and Zschiedrich, Lin and Siaudinyt{\´e}, Lauryna and Manley, Phillip and Schneider, Philipp-Immanuel and Burger, Sven}, title = {Forward simulation of coherent beams on grating structures for coherent scatterometry}, volume = {PC12619}, booktitle = {Proc. SPIE}, arxiv = {http://arxiv.org/abs/2309.06109}, doi = {10.1117/12.2673231}, pages = {PC1261907}, year = {2023}, language = {en} } @inproceedings{PlockBurgerSchneider2023, author = {Plock, Matthias and Burger, Sven and Schneider, Philipp-Immanuel}, title = {Efficient reconstruction of model parameters using Bayesian target-vector optimization}, volume = {PC12619}, booktitle = {Proc. SPIE}, doi = {10.1117/12.2673590}, pages = {PC1261905}, year = {2023}, language = {en} } @article{YooTillmannKraussetal.2023, author = {Yoo, Danbi and Tillmann, Peter and Krauss, Tobias and Sutter, Johannes and Harter, Angelika and Trofimov, Sergei and Naydenov, Boris and J{\"a}ger, Klaus and Hauser, Hubert and Becker, Christiane}, title = {Comparative Optical Analysis of Imprinted Nano-, Micro- and Biotextures on Solar Glasses for Increased Energy Yield}, volume = {7}, journal = {Solar RRL}, doi = {10.1002/solr.202300071}, pages = {2300071}, year = {2023}, language = {en} } @article{CerecedaLopezOstinatoOrtizAmbrizetal.2024, author = {Cereceda-L{\´o}pez, Eric and Ostinato, Mattia and Ortiz-Ambriz, Antonio and Straube, Arthur and Palassini, Matteo and Tierno, Pietro}, title = {Excluded volume induces buckling in optically driven colloidal rings}, volume = {6}, journal = {Phys. Rev. Research}, arxiv = {http://arxiv.org/abs/2312.14047}, doi = {10.1103/PhysRevResearch.6.L012044}, pages = {L012044}, year = {2024}, abstract = {In our combined experimental, theoretical and numerical work, we study the out of equilibrium deformations in a shrinking ring of optically trapped, interacting colloidal particles. Steerable optical tweezers are used to confine dielectric microparticles along a circle of discrete harmonic potential wells, and to reduce the ring radius at a controlled quench speed. We show that excluded-volume interactions are enough to induce particle sliding from their equilibrium positions and nonequilibrium zigzag roughening of the colloidal structure. Our work unveils the underlying mechanism of interfacial deformation in radially driven microscopic discrete rings.}, language = {en} } @article{NagelHeitzigSchoell2025, author = {Nagel, Soeren and Heitzig, Jobst and Schoell, Eckehard}, title = {Macroscopic Stochastic Model for Economic Cycle Dynamics}, volume = {134}, journal = {Physical Review Letters}, number = {4}, publisher = {American Physical Society}, arxiv = {http://arxiv.org/abs/2312.16708}, doi = {https://doi.org/10.1103/PhysRevLett.134.047402}, pages = {1 -- 6}, year = {2025}, abstract = {We present a stochastic dynamic model which can explain economic cycles. We show that the macroscopic description yields a complex dynamical landscape consisting of multiple stable fixed points, each corresponding to a split of the population into a large low and a small high income group. The stochastic fluctuations induce switching between the resulting metastable states and excitation oscillations just below a deterministic bifurcation. The shocks are caused by the decisions of a few agents who have a disproportionate influence over the macroscopic state of the economy due to the unequal distribution of wealth among the population. The fluctuations have a long-term effect on the growth of economic output and lead to business cycle oscillations exhibiting coherence resonance, where the correlation time is controlled by the population size which is inversely proportional to the noise intensity.}, language = {en} } @article{AntonHendersonDaRosetal.2024, author = {Anton, Oliver and Henderson, Victoria A. and Da Ros, Elisa and Sekulic, Ivan and Burger, Sven and Schneider, Philipp-Immanuel and Krutzik, Markus}, title = {Review and experimental benchmarking of machine learning algorithms for efficient optimization of cold atom experiments}, volume = {5}, journal = {Mach. Learn. Sci. Technol.}, arxiv = {http://arxiv.org/abs/2312.13397}, doi = {10.1088/2632-2153/ad3cb6}, pages = {025022}, year = {2024}, language = {en} } @article{SchimunekSeidlElezetal.2024, author = {Schimunek, Johannes and Seidl, Philipp and Elez, Katarina and Hempel, Tim and Le, Tuan and No{\´e}, Frank and Olsson, Simon and Raich, Llu{\´i}s and Winter, Robin and Gokcan, Hatice and Gusev, Filipp and Gutkin, Evgeny M. and Isayev, Olexandr and Kurnikova, Maria G. and Narangoda, Chamali H. and Zubatyuk, Roman and Bosko, Ivan P. and Furs, Konstantin V. and Karpenko, Anna D. and Kornoushenko, Yury V. and Shuldau, Mikita and Yushkevich, Artsemi and Benabderrahmane, Mohammed B. and Bousquet-Melou, Patrick and Bureau, Ronan and Charton, Beatrice and Cirou, Bertrand C. and Gil, G{\´e}rard and Allen, William J. and Sirimulla, Suman and Watowich, Stanley and Antonopoulos, Nick and Epitropakis, Nikolaos and Krasoulis, Agamemnon and Itsikalis, Vassilis and Theodorakis, Stavros and Kozlovskii, Igor and Maliutin, Anton and Medvedev, Alexander and Popov, Petr and Zaretckii, Mark and Eghbal-Zadeh, Hamid and Halmich, Christina and Hochreiter, Sepp and Mayr, Andreas and Ruch, Peter and Widrich, Michael and Berenger, Francois and Kumar, Ashutosh and Yamanishi, Yoshihiro and Zhang, Kam Y. J. and Bengio, Emmanuel and Bengio, Yoshua and Jain, Moksh J. and Korablyov, Maksym and Liu, Cheng-Hao and Marcou, Gilles and Glaab, Enrico and Barnsley, Kelly and Iyengar, Suhasini M. and Ondrechen, Mary Jo and Haupt, V. Joachim and Kaiser, Florian and Schroeder, Michael and Pugliese, Luisa and Albani, Simone and Athanasiou, Christina and Beccari, Andrea and Carloni, Paolo and D'Arrigo, Giulia and Gianquinto, Eleonora and Goßen, Jonas and Hanke, Anton and Joseph, Benjamin P. and Kokh, Daria B. and Kovachka, Sandra and Manelfi, Candida and Mukherjee, Goutam and Mu{\~n}iz-Chicharro, Abraham and Musiani, Francesco and Nunes-Alves, Ariane and Paiardi, Giulia and Rossetti, Giulia and Sadiq, S. Kashif and Spyrakis, Francesca and Talarico, Carmine and Tsengenes, Alexandros and Wade, Rebecca C. and Copeland, Conner and Gaiser, Jeremiah and Olson, Daniel R. and Roy, Amitava and Venkatraman, Vishwesh and Wheeler, Travis J. and Arthanari, Haribabu and Blaschitz, Klara and Cespugli, Marco and Durmaz, Vedat and Fackeldey, Konstantin and Fischer, Patrick D. and Gorgulla, Christoph and Gruber, Christian and Gruber, Karl and Hetmann, Michael and Kinney, Jamie E. and Padmanabha Das, Krishna M. and Pandita, Shreya and Singh, Amit and Steinkellner, Georg and Tesseyre, Guilhem and Wagner, Gerhard and Wang, Zi-Fu and Yust, Ryan J. and Druzhilovskiy, Dmitry S. and Filimonov, Dmitry A. and Pogodin, Pavel V. and Poroikov, Vladimir and Rudik, Anastassia V. and Stolbov, Leonid A. and Veselovsky, Alexander V. and De Rosa, Maria and De Simone, Giada and Gulotta, Maria R. and Lombino, Jessica and Mekni, Nedra and Perricone, Ugo and Casini, Arturo and Embree, Amanda and Gordon, D. Benjamin and Lei, David and Pratt, Katelin and Voigt, Christopher A. and Chen, Kuang-Yu and Jacob, Yves and Krischuns, Tim and Lafaye, Pierre and Zettor, Agn{\`e}s and Rodr{\´i}guez, M. Luis and White, Kris M. and Fearon, Daren and Von Delft, Frank and Walsh, Martin A. and Horvath, Dragos and Brooks III, Charles L. and Falsafi, Babak and Ford, Bryan and Garc{\´i}a-Sastre, Adolfo and Yup Lee, Sang and Naffakh, Nadia and Varnek, Alexandre and Klambauer, G{\"u}nter and Hermans, Thomas M.}, title = {A community effort in SARS-CoV-2 drug discovery}, volume = {43}, journal = {Molecular Informatics}, number = {1}, doi = {https://doi.org/10.1002/minf.202300262}, pages = {e202300262}, year = {2024}, language = {en} } @article{GorgullaNigamKoopetal.2023, author = {Gorgulla, Christoph and Nigam, AkshatKumar and Koop, Matt and Selim {\c{C}}{\i}naroğlu, S{\"u}leyman and Secker, Christopher and Haddadnia, Mohammad and Kumar, Abhishek and Malets, Yehor and Hasson, Alexander and Li, Minkai and Tang, Ming and Levin-Konigsberg, Roni and Radchenko, Dmitry and Kumar, Aditya and Gehev, Minko and Aquilanti, Pierre-Yves and Gabb, Henry and Alhossary, Amr and Wagner, Gerhard and Aspuru-Guzik, Al{\´a}n and Moroz, Yurii S. and Fackeldey, Konstantin and Arthanari, Haribabu}, title = {VirtualFlow 2.0 - The Next Generation Drug Discovery Platform Enabling Adaptive Screens of 69 Billion Molecules}, journal = {bioRxiv}, doi = {10.1101/2023.04.25.537981}, year = {2023}, language = {en} } @inproceedings{SekulicSchneiderAntonetal.2023, author = {Sekulic, Ivan and Schneider, Philipp-Immanuel and Anton, Oliver and Da Ros, Elisa and Henderson, Victoria and Krutzik, Markus}, title = {Efficient machine-learning approach to optimize trapped cold atom ensembles for quantum memory applications}, volume = {12740}, booktitle = {Proc. SPIE}, doi = {10.1117/12.2684406}, pages = {127400F}, year = {2023}, language = {en} } @misc{ZonkerPadillaIglesiasDjurdjevacConrad2023, author = {Zonker, Johannes and Padilla-Iglesias, Cecilia and Djurdjevac Conrad, Natasa}, title = {Supplementary code and data for Royal Society Open Science Manuscript rsos.230495}, doi = {10.12752/9254}, year = {2023}, abstract = {In this repository are all files necessary to run the agent-based model of the paper "Insights into drivers of mobility and cultural dynamics of African hunter-gatherers over the past 120 000 years", Royal Society Open Science, 10(11), 2023.}, language = {en} } @misc{HelfmannDjurdjevacConradLorenzSpreenetal.2023, author = {Helfmann, Luzie and Djurdjevac Conrad, Natasa and Lorenz-Spreen, Philipp and Sch{\"u}tte, Christof}, title = {Supplementary code for the paper Modelling opinion dynamics under the impact of influencer and media strategies}, doi = {10.12752/9267}, year = {2023}, abstract = {This repository contains the Julia code accompanying the paper "Modelling opinion dynamics under the impact of influencer and media strategies", Scientific Reports, Vol.13, p. 19375, 2023.}, language = {en} } @phdthesis{Binkowski2023, author = {Binkowski, Felix}, title = {Riesz-projection-based methods for the numerical simulation of resonance phenomena in nanophotonics}, doi = {10.17169/refubium-41230}, year = {2023}, language = {en} } @article{OehmeMoewisBoethetal.2024, author = {Oehme, Stephan and Moewis, Philippe and Boeth, Heide and Bartek, Benjamin and von Tycowicz, Christoph and Ehrig, Rainald and Duda, Georg and Jung, Tobias}, title = {Altered knee kinematics after posterior cruciate single-bundle reconstruction - a comprehensive prospective biomechanical in vivo analysis}, volume = {12}, journal = {Frontiers in Bioengineering and Biotechnology}, doi = {10.3389/fbioe.2024.1322136}, year = {2024}, language = {en} } @article{ErnstFalkenhagenWinkelmann2023, author = {Ernst, Ariane and Falkenhagen, Undine and Winkelmann, Stefanie}, title = {Model reduction for calcium-induced vesicle fusion dynamics}, volume = {23}, journal = {Proceedings in Applied Mathematics \& Mechanics}, number = {4}, doi = {10.1002/pamm.202300184}, year = {2023}, abstract = {In this work, we adapt an established model for the Ca2+-induced fusion dynamics of synaptic vesicles and employ a lumping method to reduce its complexity. In the reduced system, sequential Ca2+-binding steps are merged to a single releasable state, while keeping the important dependence of the reaction rates on the local Ca2+ concentration. We examine the feasibility of this model reduction for a representative stimulus train over the physiologically relevant site-channel distances. Our findings show that the approximation error is generally small and exhibits an interesting nonlinear and non-monotonic behavior where it vanishes for very low distances and is insignificant at intermediary distances. Furthermore, we give expressions for the reduced model's reaction rates and suggest that our approach may be used to directly compute effective fusion rates for assessing the validity of a fusion model, thereby circumventing expensive simulations.}, language = {en} } @misc{ColomMikheevaAchourietal.2023, author = {Colom, R{\´e}mi and Mikheeva, Elena and Achouri, Karim and Zuniga-Perez, Jesus and Bonod, Nicolas and Martin, Olivier J.F. and Burger, Sven and Genevet, Patrice}, title = {Crossing of the Branch Cut: The Topological Origin of a Universal 2π-Phase Retardation in Non-Hermitian Metasurfaces (Laser Photonics Rev. 17(6)/2023)}, volume = {17}, journal = {Laser Photonics Rev.}, doi = {10.1002/lpor.202370029}, pages = {2370029}, year = {2023}, language = {en} } @misc{WeiserHubigShanmugamSubramaniam2025, author = {Weiser, Martin and Hubig, Michael and Shanmugam Subramaniam, Jayant}, title = {Reconstructing Ambient Temperature Changes in Death Time Estimation with a Bayesian Double-Exponential Approach}, journal = {Zenodo}, doi = {10.5281/zenodo.17702240}, year = {2025}, abstract = {Code and data for the reconstruction of ambient temperature drop in time of death estimation We provide Octave code and temperature measurement data for - empirircally estimating thermal sensor likelihood - estimating time and amplitude of a single sudden ambient temperature drop from temperature measurement data in two thermally different compartments.}, language = {en} } @article{SekulicSchaibleMuelleretal.2025, author = {Sekulic, Ivan and Schaible, Jonas and M{\"u}ller, Gabriel and Plock, Matthias and Burger, Sven and Mart{\´i}nez-Lahuerta, V{\´i}ctor Jos{\´e} and Gaaloul, Naceur and Schneider, Philipp-Immanuel}, title = {Physics-informed Bayesian optimization of expensive-to-evaluate black-box functions}, volume = {6}, journal = {Mach. Learn. Sci. Technol.}, publisher = {IOP Publishing}, doi = {10.1088/2632-2153/ae1f5f}, pages = {040503}, year = {2025}, abstract = {Abstract Bayesian optimization with Gaussian process surrogates is a popular approach for optimizing expensive-to-evaluate functions in terms of time, energy, or computational resources. Typically, a Gaussian process models a scalar objective derived from observed data. However, in many real-world applications, the objective is a combination of multiple outputs from physical experiments or simulations. Converting these multidimensional observations into a single scalar can lead to information loss, slowing convergence and yielding suboptimal results. To address this, we propose to use multi-output Gaussian processes to learn the full vector of observations directly, before mapping them to the scalar objective via an inexpensive analytical function. This physics-informed approach retains more information from the underlying physical processes, improving surrogate model accuracy. As a result, the approach accelerates optimization and produces better final designs compared to standard implementations.}, language = {en} } @inproceedings{ZschiedrichBetzBinkowskietal.2025, author = {Zschiedrich, Lin and Betz, Fridtjof and Binkowski, Felix and Kuen, Lilli and Hammerschmidt, Martin and Burger, Sven}, title = {Efficient Photonic Component Analysis via AAA Rational Approximation}, booktitle = {2025 International Conference on Numerical Simulation of Optoelectronic Devices (NUSOD)}, doi = {10.1109/NUSOD64393.2025.11199710}, pages = {115 -- 116}, year = {2025}, language = {en} } @phdthesis{Plock2025, author = {Plock, Matthias}, title = {On Methods for Bayesian Optimization of Least Squares Problems and Optimization of Nanophotonic Devices}, doi = {10.17169/refubium-48179}, year = {2025}, language = {en} } @misc{SekulicSchaibleMuelleretal.2025, author = {Sekulic, Ivan and Schaible, Jonas and M{\"u}ller, Gabriel and Plock, Matthias and Burger, Sven and Martinez-Lahuerta, Victor J. and Gaaloul, Naceur and Schneider, Philipp-Immanuel}, title = {Data publication for Physics-informed Bayesian optimization of expensive-to-evaluate black-box functions}, journal = {Zenodo}, doi = {10.5281/zenodo.16751507}, year = {2025}, language = {en} } @misc{BetzBinkowskiFischbachetal.2025, author = {Betz, Fridtjof and Binkowski, Felix and Fischbach, Jan David and Feldman, Nick and Zschiedrich, Lin and Rockstuhl, Carsten and Koenderink, A. Femius and Burger, Sven}, title = {Uncovering Hidden Resonances in Non-Hermitian Systems with Scattering Thresholds (Laser Photonics Rev. 19(21)/2025)}, volume = {19}, journal = {Laser Photonics Rev.}, number = {21}, doi = {10.1002/lpor.70534}, pages = {e70534}, year = {2025}, language = {en} } @article{AbouHamdanJanaColometal.2026, author = {Abou Hamdan, Loubnan and Jana, Aloke and Colom, R{\´e}mi and Aboujoussef, Nour and Carlson, Cooper and Overvig, Adam and Binkowski, Felix and Burger, Sven and Genevet, Patrice}, title = {A Complex-Frequency Framework for Kerker Unidirectionality in Photonic Resonators}, doi = {10.21203/rs.3.rs-8444305/v1}, year = {2026}, language = {en} } @article{TrowerDjurdjevacConradKlus2025, author = {Trower, Maia and Djurdjevac Conrad, Natasa and Klus, Stefan}, title = {Clustering Time-Evolving Networks Using the Spatiotemporal Graph Laplacian}, volume = {35}, journal = {Chaos: An Interdisciplinary Journal of Nonlinear Science}, arxiv = {http://arxiv.org/abs/2407.12864}, doi = {10.1063/5.0228419}, pages = {013126}, year = {2025}, abstract = {Time-evolving graphs arise frequently when modeling complex dynamical systems such as social networks, traffic flow, and biological processes. Developing techniques to identify and analyze communities in these time-varying graph structures is an important challenge. In this work, we generalize existing spectral clustering algorithms from static to dynamic graphs using canonical correlation analysis (CCA) to capture the temporal evolution of clusters. Based on this extended canonical correlation framework, we define the spatio-temporal graph Laplacian and investigate its spectral properties. We connect these concepts to dynamical systems theory via transfer operators, and illustrate the advantages of our method on benchmark graphs by comparison with existing methods. We show that the spatio-temporal graph Laplacian allows for a clear interpretation of cluster structure evolution over time for directed and undirected graphs.}, language = {en} } @article{StraubeHoefling2024, author = {Straube, Arthur and H{\"o}fling, Felix}, title = {Memory effects in colloidal motion under confinement and driving}, volume = {57}, journal = {J. Phys. A: Math. Theor.}, publisher = {IOP Publishing}, issn = {1751-8113}, doi = {10.1088/1751-8121/ad5b2d}, pages = {295003}, year = {2024}, abstract = {The transport of individual particles in inhomogeneous environments is complex and exhibits non-Markovian responses. The latter may be quantified by a memory function within the framework of the linear generalised Langevin equation (GLE). Here, we exemplify the implications of steady driving on the memory function of a colloidal model system for Brownian motion in a corrugated potential landscape, specifically, for one-dimensional motion in a sinusoidal potential. To this end, we consider the overdamped limit of the GLE, which is facilitated by separating the memory function into a singular (Markovian) and a regular (non-Markovian) part. Relying on exact solutions for the investigated model, we show that the random force entering the GLE must display a bias far from equilibrium, which corroborates a recent general prediction. Based on data for the mean-square displacement (MSD) obtained from Brownian dynamics simulations, we estimate the memory function for different driving strengths and show that already moderate driving accelerates the decay of the memory function by several orders of magnitude in time. We find that the memory may persist on much longer timescales than expected from the convergence of the MSD to its long-time asymptote. Furthermore, the functional form of the memory function changes from a monotonic decay to a non-monotonic, damped oscillatory behaviour, which can be understood from a competition of confined motion and depinning. Our analysis of the simulation data further reveals a pronounced non-Gaussianity, which questions the Gaussian approximation of the random force entering the GLE.}, language = {en} } @article{BonifaceStraubeTierno2024, author = {Boniface, Dolachai and Straube, Arthur and Tierno, Pietro}, title = {Photocatalytic magnetic microgyroscopes with activity-tunable precessional dynamics}, volume = {24}, journal = {Nano Letters}, number = {47}, arxiv = {http://arxiv.org/abs/2407.11640}, doi = {10.1021/acs.nanolett.4c03386}, pages = {14950 -- 14956}, year = {2024}, abstract = {Magnetic nano/microrotors are passive elements that spin around an axis due to an external rotating field while remaining confined to a close plane. They have been used to date in different applications related to fluid mixing, drug delivery or biomedicine. Here we realize an active version of a magnetic microgyroscope which is simultaneously driven by a photo-activated catalytic reaction and a rotating magnetic field. We investigate the uplift dynamics of this colloidal spinner when it stands up and precesses around its long axis while self-propelling due to the light induced decomposition of hydrogen peroxide in water. By combining experiments with theory, we show that activity emerging from the cooperative action of phoretic and osmotic forces effectively increase the gravitational torque which counteracts the magnetic and viscous ones, and carefully measure its contribution.}, language = {en} } @misc{VillaniWeiser2024, author = {Villani, Paolo and Weiser, Martin}, title = {Adaptive Gaussian process regression for inverse problems. ALGORITMY 2024}, year = {2024}, abstract = {This submission contains the code used for the proceedings paper for ALGORITMY 2024, concerning surrogate model-based inverse problems. Version 2 modified plot appearances and fixed some minor typos.}, language = {en} } @article{ErnstAsselineauTillmannetal.2024, author = {Ernst, Marco and Asselineau, Charles-Alexis and Tillmann, Peter and J{\"a}ger, Klaus and Becker, Christiane}, title = {Modelling bifacial irradiance - Step-by-step comparison and validation of view factor and ray tracing models}, volume = {369}, journal = {Appl. Energy}, publisher = {Elsevier BV}, issn = {0306-2619}, doi = {10.1016/j.apenergy.2024.123574}, pages = {123574}, year = {2024}, language = {en} } @misc{SekulicSchneiderHammerschmidtetal.2024, author = {Sekulic, Ivan and Schneider, Philipp-Immanuel and Hammerschmidt, Martin and Burger, Sven}, title = {Machine-learning driven design of metasurfaces: learn the physics and not the objective function}, volume = {PC13017}, journal = {Proc. SPIE}, doi = {10.1117/12.3022119}, pages = {PC130170X}, year = {2024}, language = {en} } @misc{BoppPlockTuranetal.2024, author = {Bopp, Julian M. and Plock, Matthias and Turan, Tim and Pieplow, Gregor and Burger, Sven and Schr{\"o}der, Tim}, title = {'Sawfish' Photonic Crystal Cavity for Near-Unity Emitter-to-Fiber Interfacing in Quantum Network Applications (Advanced Optical Materials 13/2024)}, volume = {12}, journal = {Adv. Optical Mater.}, doi = {10.1002/adom.202470046}, pages = {2470046}, year = {2024}, language = {en} } @article{KlusDjurdjevacConrad2024, author = {Klus, Stefan and Djurdjevac Conrad, Natasa}, title = {Dynamical systems and complex networks: A Koopman operator perspective}, volume = {5}, journal = {Journal of Physics: Complexity}, number = {4}, publisher = {IOP Publishing}, arxiv = {http://arxiv.org/abs/2405.08940}, doi = {10.1088/2632-072X/ad9e60}, pages = {041001}, year = {2024}, abstract = {The Koopman operator has entered and transformed many research areas over the last years. Although the underlying concept-representing highly nonlinear dynamical systems by infinite-dimensional linear operators-has been known for a long time, the availability of large data sets and efficient machine learning algorithms for estimating the Koopman operator from data make this framework extremely powerful and popular. Koopman operator theory allows us to gain insights into the characteristic global properties of a system without requiring detailed mathematical models. We will show how these methods can also be used to analyze complex networks and highlight relationships between Koopman operators and graph Laplacians.}, language = {en} } @article{KruegerManleyBergmannetal.2024, author = {Kr{\"u}ger, Jan and Manley, Phillip and Bergmann, Detlef and K{\"o}ning, Rainer and Bodermann, Bernd and Eder, Christian and Heinrich, Andreas and Schneider, Philipp-Immanuel and Hammerschmidt, Martin and Zschiedrich, Lin and Manske, Eberhard}, title = {Introduction and application of a new approach for model-based optical bidirectional measurements}, volume = {35}, journal = {Meas. Sci. Technol.}, doi = {10.1088/1361-6501/ad4b53}, pages = {085014}, year = {2024}, language = {en} } @article{ManleyHammerschmidtZschiedrichetal.2024, author = {Manley, Phillip and Hammerschmidt, Martin and Zschiedrich, Lin and J{\"a}ger, Klaus and Becker, Christiane and Burger, Sven}, title = {Modelling luminescent coupling in multi-junction solar cells: perovskite silicon tandem case study}, volume = {13014}, journal = {Proc. SPIE}, arxiv = {http://arxiv.org/abs/2409.15987}, doi = {10.1117/12.3023941}, pages = {1301404}, year = {2024}, language = {en} } @inproceedings{SchaibleYooWinartoetal.2024, author = {Schaible, Jonas and Yoo, Danbi and Winarto, Hanifa and Miaskiewicz, Alexandra and Albrecht, Steve and Wessels, Andreas and Bl{\"a}si, Benedikt and Burger, Sven and Jaeger, Klaus and Becker, Christiane}, title = {On aesthetical appearance of colored perovskite solar modules}, volume = {PC13014}, booktitle = {Proc. SPIE}, publisher = {SPIE}, doi = {10.1117/12.3017427}, pages = {PC1301406}, year = {2024}, language = {en} } @inproceedings{BeckerBlaesiBurgeretal.2024, author = {Becker, Christiane and Bl{\"a}si, Benedikt and Burger, Sven and Ehrler, Bruno and Gordon, Ivan and Isabella, Olindo and J{\"a}ger, Klaus and Jost, Marko and Manley, Phillip and Mu{\~n}oz, Delfina and Paetzold, Ulrich W. and Sai, Hitoshi and Yablonovitch, Eli}, title = {Optical challenges for terawatt-scale photovoltaics}, volume = {PC13014}, booktitle = {Proc. SPIE}, publisher = {SPIE}, doi = {10.1117/12.3016415}, pages = {PC1301401}, year = {2024}, language = {en} } @inproceedings{SemlerWeiser2025, author = {Semler, Phillip and Weiser, Martin}, title = {Adaptive gradient-enhanced Gaussian process surrogates for inverse problems}, booktitle = {Mathematical Optimization for Machine Learning: Proceedings of the MATH+ Thematic Einstein Semester 2023}, editor = {Fackeldey, Konstantin and Kannan, Aswin and Pokutta, Sebastian and Sharma, Kartikey and Walter, Daniel and Walther, Andrea and Weiser, Martin}, publisher = {De Gruyter}, arxiv = {http://arxiv.org/abs/2404.01864}, doi = {10.1515/9783111376776-005}, pages = {59 -- 78}, year = {2025}, abstract = {Generating simulated training data needed for constructing sufficiently accurate surrogate models to be used for efficient optimization or parameter identification can incur a huge computational effort in the offline phase. We consider a fully adaptive greedy approach to the computational design of experiments problem using gradient-enhanced Gaussian process regression as surrogates. Designs are incrementally defined by solving an optimization problem for accuracy given a certain computational budget. We address not only the choice of evaluation points but also of required simulation accuracy, both of values and gradients of the forward model. Numerical results show a significant reduction of the computational effort compared to just position-adaptive and static designs as well as a clear benefit of including gradient information into the surrogate training.}, language = {en} } @article{DjurdjevacConradQuangVuNagel2024, author = {Djurdjevac Conrad, Natasa and Quang Vu, Nhu and Nagel, Soeren}, title = {Co-evolving networks for opinion and social dynamics in agent-based models}, volume = {34}, journal = {Chaos: An Interdisciplinary Journal of Nonlinear Science}, number = {9}, issn = {1054-1500}, arxiv = {http://arxiv.org/abs/2407.00145}, doi = {10.1063/5.0226054}, year = {2024}, abstract = {The rise of digital social media has strengthened the coevolution of public opinions and social interactions, that shape social structures and collective outcomes in increasingly complex ways. Existing literature often explores this interplay as a one-directional influence, focusing on how opinions determine social ties within adaptive networks. However, this perspective overlooks the intrinsic dynamics driving social interactions, which can significantly influence how opinions form and evolve. In this work, we address this gap, by introducing the co-evolving opinion and social dynamics using stochastic agent-based models. Agents' mobility in a social space is governed by both their social and opinion similarity with others. Similarly, the dynamics of opinion formation is driven by the opinions of agents in their social vicinity. We analyze the underlying social and opinion interaction networks and explore the mechanisms influencing the appearance of emerging phenomena, like echo chambers and opinion consensus. To illustrate the model's potential for real-world analysis, we apply it to General Social Survey data on political identity and public opinion regarding governmental issues. Our findings highlight the model's strength in capturing the coevolution of social connections and individual opinions over time.}, language = {en} } @misc{KuenLoefflerTsarapkinetal.2024, author = {Kuen, Lilli and L{\"o}ffler, Lorenz and Tsarapkin, Aleksei and Zschiedrich, Lin and Feichtner, Thorsten and Burger, Sven and H{\"o}flich, Katja}, title = {Source Code and Simulation Results: Chiral and directional optical emission from a dipole source coupled to a helical plasmonic antenna}, journal = {Zenodo}, doi = {10.5281/zenodo.10598255}, pages = {doi: 10.5281/zenodo.10598255}, year = {2024}, language = {en} } @article{MuellerMartinezLahuertaSekulicetal.2025, author = {M{\"u}ller, Gabriel and Mart{\´i}nez-Lahuerta, Victor J. and Sekulic, Ivan and Burger, Sven and Schneider, Philipp-Immanuel and Gaaloul, Naceur}, title = {Bayesian optimization for state engineering of quantum gases}, volume = {10}, journal = {Quantum Sci. Technol.}, arxiv = {http://arxiv.org/abs/2404.18234}, doi = {10.1088/2058-9565/ad9050}, pages = {015033}, year = {2025}, language = {en} } @article{ErbanWinkelmann2025, author = {Erban, Radek and Winkelmann, Stefanie}, title = {Multi-grid reaction-diffusion master equation: applications to morphogen gradient modelling}, volume = {87}, journal = {Bulletin of Mathematical Biology}, arxiv = {http://arxiv.org/abs/arXiv:2405.02117}, doi = {10.1007/s11538-024-01377-y}, pages = {6}, year = {2025}, abstract = {The multi-grid reaction-diffusion master equation (mgRDME) provides a generalization of stochastic compartment-based reaction-diffusion modelling described by the standard reaction-diffusion master equation (RDME). By enabling different resolutions on lattices for biochemical species with different diffusion constants, the mgRDME approach improves both accuracy and efficiency of compartment-based reaction-diffusion simulations. The mgRDME framework is examined through its application to morphogen gradient formation in stochastic reaction-diffusion scenarios, using both an analytically tractable first-order reaction network and a model with a second-order reaction. The results obtained by the mgRDME modelling are compared with the standard RDME model and with the (more detailed) particle-based Brownian dynamics simulations. The dependence of error and numerical cost on the compartment sizes is defined and investigated through a multi-objective optimization problem.}, language = {en} } @inproceedings{VillaniUngerWeiser2024, author = {Villani, Paolo and Unger, J{\"o}rg F. and Weiser, Martin}, title = {Adaptive Gaussian Process Regression for Bayesian inverse problems}, booktitle = {Proceedings of the Conference Algoritmy 2024}, pages = {214 -- 224}, year = {2024}, abstract = {We introduce a novel adaptive Gaussian Process Regression (GPR) methodology for efficient construction of surrogate models for Bayesian inverse problems with expensive forward model evaluations. An adaptive design strategy focuses on optimizing both the positioning and simulation accuracy of training data in order to reduce the computational cost of simulating training data without compromising the fidelity of the posterior distributions of parameters. The method interleaves a goal-oriented active learning algorithm selecting evaluation points and tolerances based on the expected impact on the Kullback-Leibler divergence of surrogated and true posterior with a Markov Chain Monte Carlo sampling of the posterior. The performance benefit of the adaptive approach is demonstrated for two simple test problems.}, language = {en} } @article{AndresArconesWeiserKoutsourelakisetal.2023, author = {Andr{\´e}s Arcones, Daniel and Weiser, Martin and Koutsourelakis, Faidon-Stelios and Unger, J{\"o}rg F.}, title = {A Bayesian Framework for Simulation-based Digital Twins of Bridges}, volume = {6}, journal = {EUROSTRUCT 2023:European Association on Quality Control of Bridges and Structures: Digital Transformation in Sustainability}, number = {5}, doi = {10.1002/cepa.2177}, pages = {734 -- 740}, year = {2023}, abstract = {Simulation-based digital twins have emerged as a powerful tool for evaluating the mechanical response of bridges. As virtual representations of physical systems, digital twins can provide a wealth of information that complements traditional inspection and monitoring data. By incorporating virtual sensors and predictive maintenance strategies, they have the potential to improve our understanding of the behavior and performance of bridges over time. However, as bridges age and undergo regular loading and extreme events, their structural characteristics change, often differing from the predictions of their initial design. Digital twins must be continuously adapted to reflect these changes. In this article, we present a Bayesian framework for updating simulation-based digital twins in the context of bridges. Our approach integrates information from measurements to account for inaccuracies in the simulation model and quantify uncertainties. Through its implementation and assessment, this work demonstrates the potential for digital twins to provide a reliable and up-to-date representation of bridge behavior, helping to inform decision-making for maintenance and management.}, language = {en} } @inproceedings{AndresArconesWeiserKoutsourelakisetal.2023, author = {Andr{\´e}s Arcones, Daniel and Weiser, Martin and Koutsourelakis, Faidon-Stelios and Unger, J{\"o}rg F.}, title = {Evaluation of Model Bias Identification Approaches Based on Bayesian Inference and Applications to Digital Twins}, booktitle = {5th ECCOMAS Thematic Conference on Uncertainty Quantification in Computational Sciences and Engineering}, pages = {1 -- 15}, year = {2023}, abstract = {In recent years, the use of simulation-based digital twins for monitoring and assessment of complex mechanical systems has greatly expanded. Their potential to increase the information obtained from limited data makes them an invaluable tool for a broad range of real-world applications. Nonetheless, there usually exists a discrepancy between the predicted response and the measurements of the system once built. One of the main contributors to this difference in addition to miscalibrated model parameters is the model error. Quantifying this socalled model bias (as well as proper values for the model parameters) is critical for the reliable performance of digital twins. Model bias identification is ultimately an inverse problem where information from measurements is used to update the original model. Bayesian formulations can tackle this task. Including the model bias as a parameter to be inferred enables the use of a Bayesian framework to obtain a probability distribution that represents the uncertainty between the measurements and the model. Simultaneously, this procedure can be combined with a classic parameter updating scheme to account for the trainable parameters in the original model. This study evaluates the effectiveness of different model bias identification approaches based on Bayesian inference methods. This includes more classical approaches such as direct parameter estimation using MCMC in a Bayesian setup, as well as more recent proposals such as stat-FEM or orthogonal Gaussian Processes. Their potential use in digital twins, generalization capabilities, and computational cost is extensively analyzed.}, language = {en} } @article{MaierWeiserConrad2025, author = {Maier, Kristina and Weiser, Martin and Conrad, Tim}, title = {Hybrid PDE-ODE Models for Efficient Simulation of Infection Spread in Epidemiology}, volume = {481}, journal = {Proceedings of the Royal Society A}, number = {2306}, publisher = {Royal Society}, arxiv = {http://arxiv.org/abs/2405.12938}, doi = {10.1098/rspa.2024.0421}, year = {2025}, abstract = {This paper introduces a novel hybrid model combining Partial Differential Equations (PDEs) and Ordinary Differential Equations (ODEs) to simulate infectious disease dynamics across geographic regions. By leveraging the spatial detail of PDEs and the computational efficiency of ODEs, the model enables rapid evaluation of public health interventions. Applied to synthetic environments and real-world scenarios in Lombardy, Italy, and Berlin, Germany, the model highlights how interactions between PDE and ODE regions affect infection dynamics, especially in high-density areas. Key findings reveal that the placement of model boundaries in densely populated regions can lead to inaccuracies in infection spread, suggesting that boundaries should be positioned in areas of lower population density to better reflect transmission dynamics. Additionally, regions with low population density hinder infection flow, indicating a need for incorporating, e.g., jumps in the model to enhance its predictive capabilities. Results indicate that the hybrid model achieves a balance between computational speed and accuracy, making it a valuable tool for policymakers in real-time decision-making and scenario analysis in epidemiology and potentially in other fields requiring similar modeling approaches.}, language = {en} } @article{AndresArconesWeiserKoutsourelakisetal.2024, author = {Andr{\´e}s Arcones, Daniel and Weiser, Martin and Koutsourelakis, Faidon-Stelios and Unger, J{\"o}rg F.}, title = {Model bias identification for Bayesian calibration of stochastic digital twins of bridges}, volume = {41}, journal = {Applied Stochastic Models in Business and Industry}, number = {3}, doi = {10.1002/asmb.2897}, year = {2024}, abstract = {Simulation-based digital twins must provide accurate, robust and reliable digital representations of their physical counterparts. Quantifying the uncertainty in their predictions plays, therefore, a key role in making better-informed decisions that impact the actual system. The update of the simulation model based on data must be then carefully implemented. When applied to complex standing structures such as bridges, discrepancies between the computational model and the real system appear as model bias, which hinders the trustworthiness of the digital twin and increases its uncertainty. Classical Bayesian updating approaches aiming to infer the model parameters often fail at compensating for such model bias, leading to overconfident and unreliable predictions. In this paper, two alternative model bias identification approaches are evaluated in the context of their applicability to digital twins of bridges. A modularized version of Kennedy and O'Hagan's approach and another one based on Orthogonal Gaussian Processes are compared with the classical Bayesian inference framework in a set of representative benchmarks. Additionally, two novel extensions are proposed for such models: the inclusion of noise-aware kernels and the introduction of additional variables not present in the computational model through the bias term. The integration of such approaches in the digital twin corrects the predictions, quantifies their uncertainty, estimates noise from unknown physical sources of error and provides further insight into the system by including additional pre-existing information without modifying the computational model.}, language = {en} } @article{WehlitzSadeghiMontefuscoetal.2025, author = {Wehlitz, Nathalie and Sadeghi, Mohsen and Montefusco, Alberto and Sch{\"u}tte, Christof and Pavliotis, Grigorios A. and Winkelmann, Stefanie}, title = {Approximating particle-based clustering dynamics by stochastic PDEs}, volume = {24}, journal = {SIAM Journal on Applied Dynamical Systems}, number = {2}, arxiv = {http://arxiv.org/abs/2407.18952}, doi = {10.1137/24M1676661}, pages = {1231 -- 1250}, year = {2025}, abstract = {This work proposes stochastic partial differential equations (SPDEs) as a practical tool to replicate clustering effects of more detailed particle-based dynamics. Inspired by membrane mediated receptor dynamics on cell surfaces, we formulate a stochastic particle-based model for diffusion and pairwise interaction of particles, leading to intriguing clustering phenomena. Employing numerical simulation and cluster detection methods, we explore the approximation of the particle-based clustering dynamics through mean-field approaches. We find that SPDEs successfully reproduce spatiotemporal clustering dynamics, not only in the initial cluster formation period, but also on longer time scales where the successive merging of clusters cannot be tracked by deterministic mean-field models. The computational efficiency of the SPDE approach allows us to generate extensive statistical data for parameter estimation in a simpler model that uses a Markov jump process to capture the temporal evolution of the cluster number.}, language = {en} } @article{HoeflingStraube2025, author = {H{\"o}fling, Felix and Straube, Arthur}, title = {Langevin equations and a geometric integration scheme for the overdamped limit of rotational Brownian motion of axisymmetric particles}, volume = {7}, journal = {Physical Review Research}, arxiv = {http://arxiv.org/abs/2403.04501}, doi = {10.1103/wzdn-29p4}, pages = {043034}, year = {2025}, abstract = {The translational motion of anisotropic or self-propelled colloidal particles is closely linked with the particle's orientation and its rotational Brownian motion. In the overdamped limit, the stochastic evolution of the orientation vector follows a diffusion process on the unit sphere and is characterized by an orientation-dependent ("multiplicative") noise. As a consequence, the corresponding Langevin equation attains different forms depending on whether Itō's or Stratonovich's stochastic calculus is used. We clarify that both forms are equivalent and derive them in a top-down approach from a geometric construction of Brownian motion on the unit sphere, based on infinitesimal random rotations. Our approach suggests further a geometric integration scheme for rotational Brownian motion, which preserves the normalization constraint of the orientation vector exactly. We show that a simple implementation of the scheme, using Gaussian random rotations, converges weakly at order 1 of the integration time step, and we outline an advanced variant of the scheme that is weakly exact for an arbitrarily large time step. Due to a favorable prefactor of the discretization error, already the Gaussian scheme allows for integration time steps that are one order of magnitude larger compared to a commonly used algorithm for rotational Brownian dynamics simulations based on projection on the constraining manifold. For torques originating from constant external fields, we prove by virtue of the Fokker-Planck equation that the constructed diffusion process satisfies detailed balance and converges to the correct equilibrium distribution. The analysis is restricted to time-homogeneous rotational Brownian motion (i.e., a single rotational diffusion constant), which is relevant for axisymmetric particles and also chemically anisotropic spheres, such as self-propelled Janus particles.}, language = {en} } @article{SchaibleWinartoŠkorjancetal.2025, author = {Schaible, Jonas and Winarto, Hanifah and Škorjanc, Viktor and Yoo, Danbi and Zimmermann, Lea and J{\"a}ger, Klaus and Sekulic, Ivan and Schneider, Philipp-Immanuel and Burger, Sven and Wessels, Andreas and Bl{\"a}si, Benedikt and Becker, Christiane}, title = {Optimizing Aesthetic Appearance of Perovskite Solar Cells Using Color Filters}, volume = {9}, journal = {Solar RRL}, publisher = {Wiley}, doi = {10.1002/solr.202400627}, pages = {2400627}, year = {2025}, abstract = {The significance of color aesthetics in photovoltaic (PV) modules gains importance, especially in design-centric applications like building-integrated PVs. Color filters based on distributed Bragg reflectors, consisting of alternating thin-film layers of different refractive indices, can modify the appearance of standard silicon modules. This approach is also extended to optimize the color appearance of emerging PV technologies such as perovskite solar cells, which typically exhibit a less appealing gray-brownish appearance. In this contribution, perovskite solar-cell stacks combined with MorphoColor color filters are presented. Angular-resolved reflectance simulations based on wave optics and ray tracing with experimental data are validated, and the color appearance from various viewing angles is evaluated. Additionally, the impact of individual layers on color appearance and the maximum achievable short-circuit current density in the perovskite solar cell is investigated. By applying Bayesian optimization, the color distance is minimized to the targeted appearance. Tailoring the bridging layers between the color filter and the perovskite solar cell is found to strongly influence the color impression due to the coherently combined color filter and perovskite solar cell. The presented color optimization concept allows to customize the aesthetics of emerging PV thin-film technologies such as perovskite solar cells.}, language = {en} } @misc{RocheBetzYangetal.2024, author = {Roche, L{\´e}o J. and Betz, Fridtjof and Yang, Yuhui and Limame, Imad and Shih, Ching-Wen and Burger, Sven and Reitzenstein, Stephan}, title = {Inside Front Cover: Numerical Investigation of a Coupled Micropillar - Waveguide System for Integrated Quantum Photonic Circuits (Adv. Quantum Technol. 12/2024)}, volume = {7}, journal = {Adv. Quantum Technol.}, doi = {10.1002/qute.202470036}, pages = {2470036}, year = {2024}, language = {en} } @inproceedings{MukherjeeBurgerSiefkeetal.2024, author = {Mukherjee, Deshabrato and Burger, Sven and Siefke, Thomas and Gour, Jeetendra and Bodermann, Bernd and Petrik, Peter}, title = {Modeling of dimensions and sensing properties of gold gratings by spectroscopic ellipsometry and finite element method}, volume = {309}, booktitle = {EPJ Web of Conferences}, doi = {10.1051/epjconf/202430902016}, pages = {02016}, year = {2024}, language = {en} } @article{DjurdjevacConradTonelloZonkeretal.2025, author = {Djurdjevac Conrad, Natasa and Tonello, Elisa and Zonker, Johannes and Siebert, Heike}, title = {Detection of dynamic communities in temporal networks with sparse data}, volume = {10}, journal = {Applied Network Science}, publisher = {Springer International Publishing}, doi = {10.1007/s41109-024-00687-3}, year = {2025}, abstract = {Temporal networks are a powerful tool for studying the dynamic nature of a wide range of real-world complex systems, including social, biological and physical systems. In particular, detection of dynamic communities within these networks can help identify important cohesive structures and fundamental mechanisms driving systems behaviour. However, when working with real-world systems, available data is often limited and sparse, due to missing data on systems entities, their evolution and interactions, as well as uncertainty regarding temporal resolution. This can hinder accurate representation of the system over time and result in incomplete or biased community dynamics. In this paper, we compare established methods for community detection and, using synthetic data experiments and real-world case studies, we evaluate the impact of data sparsity on the quality of identified dynamic communities. Our results give valuable insights on the evolution of systems with sparse data, which are less studied in existing literature, but are frequently encountered in real-world applications.}, language = {en} } @article{ZimperCornalbaDjurdjevacConradetal.2025, author = {Zimper, Sebastian and Cornalba, Federico and Djurdjevac Conrad, Natasa and Djurdjevac, Ana}, title = {On reduced inertial PDE models for Cucker-Smale flocking dynamics}, volume = {481}, journal = {Proceedings of the Royal Society A}, publisher = {Royal Society}, arxiv = {http://arxiv.org/abs/2407.18717}, doi = {https://doi.org/10.1098/rspa.2024.0675}, year = {2025}, abstract = {In particle systems, flocking refers to the phenomenon where particles' individual velocities eventually align. The Cucker-Smale model is a well-known mathematical framework that describes this behaviour. Many continuous descriptions of the Cucker-Smale model use PDEs with both particle position and velocity as independent variables, thus providing a full description of the particles mean-field limit (MFL) dynamics. In this paper, we introduce a novel reduced inertial PDE model consisting of two equations that depend solely on particle position. In contrast to other reduced models, ours is not derived from the MFL, but directly includes the model reduction at the level of the empirical densities, thus allowing for a straightforward connection to the underlying particle dynamics. We present a thorough analytical investigation of our reduced model, showing that: firstly, our reduced PDE satisfies a natural and interpretable continuous definition of flocking; secondly, in specific cases, we can fully quantify the discrepancy between PDE solution and particle system. Our theoretical results are supported by numerical simulations.}, language = {en} }