TY - GEN A1 - Lie, Han Cheng A1 - Sullivan, T. J. A1 - Teckentrup, Aretha T1 - Random forward models and log-likelihoods in Bayesian inverse problems T2 - SIAM/ASA Journal on Uncertainty Quantification N2 - 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. T3 - ZIB-Report - 18-03 KW - Bayesian inverse problem KW - random likelihood KW - surrogate model KW - posterior consistency KW - probabilistic numerics KW - uncertainty quantification KW - randomised misfit Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-66324 SN - 1438-0064 VL - 6 IS - 4 SP - 1600 EP - 1629 ER - TY - CHAP A1 - Abebe, Muluneh G. A1 - Gomard, Guillaume A1 - Zschiedrich, Lin A1 - Rockstuhl, Carsten A1 - Paetzold, Ulrich W. A1 - Abass, Aimi T1 - Thermodynamics of Photon Recycling in Four Terminal Perovskite/si Tandem Solar Cells T2 - Optical Nanostructures and Advanced Materials for Photovoltaics Y1 - 2017 U6 - https://doi.org/10.1364/PV.2017.PM4A.2 SP - PM4A.2 ER - TY - THES A1 - Djurdjevac Conrad, Natasa T1 - Methods for analyzing complex networks using random walker Y1 - 2012 ER - TY - JOUR A1 - Banisch, Ralf A1 - Djurdjevac Conrad, Natasa T1 - Cycle-flow-based module detection in directed recurrence networks JF - EPL (Europhysics Letters) Y1 - 2014 U6 - https://doi.org/10.1209/0295-5075/108/68008 VL - 108 IS - 6 ER - TY - JOUR A1 - Lorenz, Philipp A1 - Wolf, Frederik A1 - Braun, Jonas A1 - Djurdjevac Conrad, Natasa A1 - Hövel, Philipp T1 - Capturing the Dynamics of Hashtag-Communities JF - International Workshop on Complex Networks and their Applications Y1 - 2017 U6 - https://doi.org/10.1007/978-3-319-72150-7_33 SP - 401 EP - 413 ER - TY - JOUR A1 - Villatoro, Jose A1 - Zühlke, Martin A1 - Riebe, Daniel A1 - Riedel, Jens A1 - Beitz, Toralf A1 - Löhmannsröben, Hans-Gerd T1 - IR-MALDI ion mobility spectrometry JF - Analytical and Bioanalytical Chemistry Y1 - 2016 U6 - https://doi.org/10.1007/s00216-016-9739-x VL - 408 IS - 23 SP - 6259 EP - 6268 ER - TY - JOUR A1 - Igde, Sinaida A1 - Röblitz, Susanna A1 - Müller, Anne A1 - Kolbe, Katharina A1 - Boden, Sophia A1 - Fessele, Claudia A1 - Lindhorst, Thisbe A1 - Weber, Marcus A1 - Hartmann, Laura T1 - Linear Precision Glycomacromolecules with Varying Interligand Spacing and Linker Functionalities Binding to Concanavalin A and the Bacterial Lectin FimH JF - Marcomolecular Bioscience Y1 - 2017 U6 - https://doi.org/10.1002/mabi.201700198 VL - 17 IS - 12 SP - 1700198 ER - TY - GEN A1 - Volkwein, Stefan A1 - Weiser, Martin T1 - Affine Invariant Convergence Analysis for Inexact Augmented Lagrangian-SQP Methods N2 - 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. T3 - ZIB-Report - 00-56 KW - nonlinear programming KW - multiplier methods KW - affine invariant norms KW - Burgers' equation Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6243 ER - TY - GEN A1 - Erdmann, Bodo A1 - Kober, Cornelia A1 - Lang, Jens A1 - Sader, Robert A1 - Zeilhofer, Hans-Florian A1 - Deuflhard, Peter T1 - Efficient and Reliable Finite Element Methods for Simulation of the Human Mandible N2 - 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. T3 - ZIB-Report - 01-14 KW - mandible KW - sensitivity analysis KW - finite element method KW - adaptive grid refinement Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6403 ER - TY - GEN A1 - Weiser, Martin T1 - Linear convergence of an interior point method for linear control constrained optimal control problems N2 - 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. T3 - ZIB-Report - 02-13 KW - linear optimal control KW - infinite dimensional KW - interior point methods KW - inexact Newton methods Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6809 ER - TY - GEN A1 - Hinze, Michael A1 - Schiela, Anton T1 - Discretization of Interior Point Methods for State Constrained Elliptic Optimal Control Problems: Optimal Error Estimates and Parameter Adjustment N2 - 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. T3 - ZIB-Report - 07-40 KW - Elliptic optimal control problem KW - error estimates KW - interior point method KW - pointwise state constraints Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10414 SN - 1438-0064 ER - TY - GEN A1 - Schiela, Anton T1 - An Interior Point Method in Function Space for the Efficient Solution of State Constrained Optimal Control Problems N2 - 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. T3 - ZIB-Report - 07-44 KW - interior point methods in function space KW - optimal control KW - state constraints Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10471 SN - 1438-0064 ER - TY - GEN A1 - Weiser, Martin T1 - Pointwise Nonlinear Scaling for Reaction-Diffusion-Equations N2 - 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. T3 - ZIB-Report - 07-45 KW - reaction-diffusion equations KW - travelling waves KW - nonlinear scaling KW - discretization error Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10493 SN - 1438-0064 ER - TY - THES A1 - Farshbaf-Shaker, Mohammad-Hassan T1 - Ein neues Verfahren zur Lösung des Streuproblems der Maxwell-Gleichungen Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9914 ER - TY - THES A1 - Gerber, Susanne T1 - Perfusionsmodellierung in menschlichen Tumoren N2 - Im Rahmen dieser Arbeit wurde ein individuell anpassungsfähiges Modell entwickelt und implementiert, das die Perfusion in menschlichen soliden Tumoren beschreibt und für verschiedene Zeitpunkte w¨ahrend regionaler Hyperthermie ein lokal abhängiges Temperaturprofil berechnet. Da vor jeder Simulation alle wichtigen Parameter anhand von Ultraschall-, MRT- oder Angiogrammbildern individuell bestimmt werden können, wird eine patientenspezifische Aussage ¨uber das intratumorale Antwortverhalten bereits vor der eigentlichen Behandlung möglich. In Abh¨angigkeit von der Qualität der zur Verfügung stehenden anatomischen Daten über das zu simulierende Gebiet kann das Modell beliebig verfeinert oder bei Mangel an detaillierten Informationen auch mit Minimaldaten und reduzierter räumlicher Genauigkeit benutzt werden. Die für eine Simulation benötigten 2- oder 3- dimensionalen Geometrien können leicht mit der am ZIB entwickelten Software Amira erstellt und zur Berechnung in KARDOS, einem ebenfalls am ZIB implementierten Löser für nichtlineare partielle Differentialgleichungen, eingelesen werden. Mit Hilfe dieses Modells wird eine einfache, aber realistische und aussagekräftige Simulation für die Therapieplanung einer klinischen Hyperthermieanwendung ermöglicht, die innerhalb kurzer Zeit vorbereitet und durchgeführt werden kann. Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9923 ER - TY - GEN A1 - Weber, Marcus T1 - Conformation-based transition state theory N2 - 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. T3 - ZIB-Report - 07-18 KW - dynamical systems KW - transition state theory KW - rare events Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9612 ER - TY - THES A1 - Riemer, Alexander T1 - Accuracy, Stability, Convergence of Rigorous Thermodynamic Sampling Methods Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10052 ER - TY - GEN A1 - Schenk, Olaf A1 - Wächter, Andreas A1 - Weiser, Martin T1 - Inertia Revealing Preconditioning For Large-Scale Nonconvex Constrained Optimization N2 - 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. T3 - ZIB-Report - 07-32 KW - nonconvex constrained optimization KW - interior-point method KW - inertia KW - multilevel incomplete factorization Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10314 SN - 1438-0064 ER - TY - GEN A1 - Antoine, Xavier A1 - Arnold, Anton A1 - Besse, Christophe A1 - Ehrhardt, Matthias A1 - Schädle, Achim T1 - A Review of Transparent and Artificial Boundary Conditions Techniques for Linear and Nonlinear Schrödinger Equations N2 - In this review article we discuss different techniques to solve numerically the time-dependent Schrödinger 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. T3 - ZIB-Report - 07-34 KW - Schrödinger equation KW - transparent boundary condition KW - discrete convolution KW - unbounded domain Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10332 SN - 1438-0064 ER - TY - GEN A1 - Schiela, Anton T1 - Optimality Conditions for Convex State Constrained Optimal Control Problems with Discontinuous States N2 - 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. T3 - ZIB-Report - 07-35 KW - optimal control KW - state constraints KW - optimality conditions Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10342 SN - 1438-0064 ER - TY - GEN A1 - Schmidt, Heiko A1 - Oevermann, Michael A1 - Bastiaans, Rob J.M. A1 - Kerstein, Alan R. T1 - A priori Tabulation of Turbulent Flame Speeds via a Combination of a Stochastic Mixing Model and Flamelet Generated Manifolds N2 - 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). T3 - ZIB-Report - 08-02 KW - Verbrennung KW - Flammenstrukturen KW - stochastisches Turbulenzmodell KW - FGM KW - turbulente Brenngeschwindigkeiten KW - turbulent premixed combustion KW - flame structures KW - linear eddy model KW - flamelet generated manifolds KW - turbulent flame speeds Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10532 SN - 1438-0064 ER - TY - GEN A1 - Carqué, Gunter A1 - Owinoh, Antony Z. A1 - Klein, Rupert A1 - Majda, Andrew J. T1 - Asymptotic Scale Analysis of Precipitating Clouds N2 - 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. T3 - ZIB-Report - 08-03 KW - atmospheric moist convection KW - deep convection KW - shallow convection KW - precipitating clouds KW - asymptotic analysis Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10548 SN - 1438-0064 ER - TY - GEN A1 - Oevermann, Michael A1 - Schmidt, Heiko A1 - Kerstein, Alan R. T1 - Linear-Eddy Modeling of Autoignition under Thermal Stratification N2 - 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. T3 - ZIB-Report - 08-05 KW - HCCI KW - Selbstzündung KW - Turbulenz KW - Linear-Eddy Modell KW - HCCI KW - autoignition KW - thermal explosion KW - turbulence KW - Linear-Eddy Model Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10562 SN - 1438-0064 ER - TY - GEN A1 - Schiela, Anton T1 - An Extended Mathematical Framework for Barrier Methods in Function Space N2 - 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. T3 - ZIB-Report - 08-07 Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10593 SN - 1438-0064 ER - TY - GEN A1 - Ruprecht, Daniel A1 - Schädle, Achim A1 - Schmidt, Frank A1 - Zschiedrich, Lin T1 - Transparent boundary conditons for time-dependent problems N2 - A new approach to derive transparent boundary conditions (TBCs) for wave, Schrödinger, 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 Möbius 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. T3 - ZIB-Report - 07-12 KW - transparent boundary condition KW - non-reflecting boundary condition KW - pole condition KW - wave equation KW - Schrödinger equation KW - drift diffusion equation Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9558 ER - TY - GEN A1 - Kube, Susanna A1 - Lasser, Caroline A1 - Weber, Marcus T1 - Monte Carlo sampling of Wigner functions and surface hopping quantum dynamics N2 - 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. T3 - ZIB-Report - 07-17 KW - Metropolis Monte Carlo KW - approximation KW - quadrature KW - oscillating functions Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9604 ER - TY - JOUR A1 - Garcia Santiago, Xavier A1 - Hammerschmidt, Martin A1 - Sachs, Johannes A1 - Burger, Sven A1 - Kwon, Hyunah A1 - Knöller, Marvin A1 - Arens, Tilo A1 - Fischer, Peer A1 - Fernandez-Corbaton, Ivan A1 - Rockstuhl, Carsten T1 - Toward maximally electromagnetically chiral scatterers at optical frequencies JF - ACS Photonics Y1 - 2022 U6 - https://doi.org/10.1021/acsphotonics.1c01887 VL - 9 SP - 1954 ER - TY - GEN A1 - Ernst, Ariane A1 - Schütte, Christof A1 - Sigrist, Stephan A1 - Winkelmann, Stefanie T1 - Variance of filtered signals: Characterization for linear reaction networks and application to neurotransmission dynamics N2 - 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. T3 - ZIB-Report - 21-15 KW - linear reaction networks KW - cross-correlation KW - neurotransmission Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-82674 SN - 1438-0064 ER - TY - JOUR A1 - Thies, Arne A1 - Sunkara, Vikram A1 - Ray, Sourav A1 - Wulkow, Hanna A1 - Celik, M. Özgür A1 - Yergöz, Fatih A1 - Schütte, Christof A1 - Stein, Christoph A1 - Weber, Marcus A1 - Winkelmann, Stefanie T1 - Modelling altered signalling of G-protein coupled receptors in inflamed environment to advance drug design JF - Scientific Reports N2 - 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. Y1 - 2023 U6 - https://doi.org/10.1038/s41598-023-27699-w VL - 13 IS - 607 ER - TY - GEN A1 - Ray, Sourav A1 - Thies, Arne A1 - Sunkara, Vikram A1 - Wulkow, Hanna A1 - Celik, Özgür A1 - Yergöz, Fatih A1 - Schütte, Christof A1 - Stein, Christoph A1 - Weber, Marcus A1 - Winkelmann, Stefanie T1 - Modelling altered signalling of G-protein coupled receptors in inflamed environment to advance drug design N2 - 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. T3 - ZIB-Report - 21-19 Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-82797 SN - 1438-0064 ER - TY - THES A1 - Pakhomov, Anton T1 - Efficient modeling and optimization of surface second-harmonic generation from nanophotonic components Y1 - 2021 U6 - https://doi.org/10.22032/dbt.49369 ER - TY - JOUR A1 - Djurdjevac, Ana T1 - Linear Parabolic Problems in Random Moving Domains N2 - 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. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.1137/19M1284889 VL - 9 IS - 2 SP - 848 EP - 879 ER - TY - JOUR A1 - Djurdjevac, Ana A1 - Gräser, Carsten A1 - Herbert, Philip J. T1 - Non-stationary incompressible linear fluid equations in a moving domain JF - arXiv N2 - 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. Y1 - 2021 ER - TY - JOUR A1 - Colom, Remi A1 - Mikheeva, Elena A1 - Achouri, Karim A1 - Zuniga-Perez, Jesus A1 - Bonod, Nicolas A1 - Martin, Olivier J. F. A1 - Burger, Sven A1 - Genevet, Patrice T1 - Crossing of the branch cut: the topological origin of a universal 2π-phase retardation in non-Hermitian metasurfaces JF - Laser Photonics Rev. Y1 - 2023 U6 - https://doi.org/10.1002/lpor.202200976 VL - 17 SP - 2200976 ER - TY - JOUR A1 - Montefusco, Alberto A1 - Schütte, Christof A1 - Winkelmann, Stefanie T1 - A route to the hydrodynamic limit of a reaction-diffusion master equation using gradient structures JF - SIAM Journal on Applied Mathematics N2 - 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. Y1 - 2023 U6 - https://doi.org/10.1137/22M1488831 VL - 83 IS - 2 SP - 837 EP - 861 ER - TY - JOUR A1 - Dellnitz, Michael A1 - Hüllermeier, Eyke A1 - Lücke, Marvin A1 - Ober-Blöbaum, Sina A1 - Offen, Christian A1 - Peitz, Sebastian A1 - Pfannschmidt, Karlson T1 - Efficient Time-Stepping for Numerical Integration Using Reinforcement Learning JF - SIAM Journal on Scientific Computing Y1 - 2023 U6 - https://doi.org/10.1137/21M1412682 VL - 45 IS - 2 SP - A579 EP - A595 ER - TY - GEN A1 - Pflüger, Mika A1 - Kline, R Joseph A1 - Fernández Herrero, Analía A1 - Hammerschmidt, Martin A1 - Soltwisch, Victor A1 - Krumrey, Michael T1 - Extracting dimensional parameters of gratings produced with self-aligned multiple patterning using grazing-incidence small-angle x-ray scattering [Source Code] Y1 - 2020 U6 - https://doi.org/10.24433/CO.0953516.v2 ER - TY - JOUR A1 - Gao, Timm A1 - Rickert, Lucas A1 - Urban, Felix A1 - Große, Jan A1 - Srocka, Nicole A1 - Rodt, Sven A1 - Musial, Anna A1 - Zolnacz, Kinga A1 - Mergo, Pawel A1 - Dybka, Kamil A1 - Urbanczyk, Waclaw A1 - Sek, Grzegorz A1 - Burger, Sven A1 - Reitzenstein, Stephan A1 - Heindel, Tobias T1 - A quantum key distribution testbed using a plug&play telecom-wavelength single-photon source JF - Appl. Phys. Rev. Y1 - 2022 U6 - https://doi.org/10.1063/5.0070966 VL - 9 SP - 011412 ER - TY - JOUR A1 - Torun, Cem Güney A1 - Schneider, Philipp-Immanuel A1 - Hammerschmidt, Martin A1 - Burger, Sven A1 - Munns, Joseph H.D. A1 - Schröder, Tim T1 - Optimized diamond inverted nanocones for enhanced color center to fiber coupling JF - Appl. Phys. Lett. Y1 - 2021 U6 - https://doi.org/10.1063/5.0050338 VL - 118 SP - 234002 ER - TY - JOUR A1 - Ahiboz, Doguscan A1 - Andresen, Elina A1 - Manley, Phillip A1 - Resch-Genger, Ute A1 - Würth, Christian A1 - Becker, Christiane T1 - Metasurface-Enhanced Photon Upconversion upon 1550 nm Excitation JF - Adv. Opt. Mater. Y1 - 2021 U6 - https://doi.org/10.1002/adom.202101285 VL - 9 SP - 2101285 ER - TY - JOUR A1 - Martens, Kevin A1 - Funck, Timon A1 - Santiago, Eva Y. A1 - Govorov, Alexander O. A1 - Burger, Sven A1 - Liedl, Tim T1 - Onset of Chirality in Plasmonic Meta-Molecules and Dielectric Coupling JF - ACS Nano Y1 - 2022 U6 - https://doi.org/10.1021/acsnano.2c04729 VL - 16 SP - 16143 ER - TY - CHAP A1 - Perevoznik, Dmitrii A1 - Bose, Surajit A1 - Burger, Sven A1 - Demircan, Ayhan A1 - Morgner, Uwe T1 - Photonic components in polymers made by femtosecond pulses T2 - Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference (CLEO/Europe-EQEC) Y1 - 2021 U6 - https://doi.org/10.1109/CLEO/Europe-EQEC52157.2021.9541906 SP - 1 ER - TY - CHAP A1 - Ahiboz, Doguscan A1 - Andresen, Elina A1 - Manley, Phillip A1 - Resch Genger, Ute A1 - Würth, Christian A1 - Becker, Christiane T1 - Enhanced Photon Upconversion Using Erbium-Doped Nanoparticles Interacting with Silicon Metasurfaces T2 - IEEE 48th Photovoltaic Specialists Conference (PVSC) Y1 - 2021 U6 - https://doi.org/10.1109/PVSC43889.2021.9518495 SP - 2008 EP - 2010 ER - TY - CHAP A1 - Rickert, Lucas A1 - Gao, Timm A1 - Urban, Felix A1 - Große, Jan A1 - Srocka, Nicole A1 - Rodt, Sven A1 - Musial, Anna A1 - Zolnacz, Kinga A1 - Mergo, Pawel A1 - Dybka, Kamil A1 - Urbanczyk, Waclaw A1 - Sek, Grzegorz A1 - Burger, Sven A1 - Reitzenstein, Stephan A1 - Tobias, Heindel T1 - A Quantum Key Distribution Testbed Using Plug&Play Telecom-Wavelength Single-Photons T2 - Quantum Information and Measurement VI Y1 - 2021 U6 - https://doi.org/10.1364/QIM.2021.M2C.1 SP - M2C.1 ER - TY - CHAP A1 - Schneider, Philipp-Immanuel A1 - Garcia-Santiago, Xavier A1 - Wiegand, Benjamin A1 - Anton, Oliver A1 - Krutzik, Markus A1 - Rockstuhl, Carsten A1 - Burger, Sven T1 - Advances in Bayesian optimization for photonics and quantum atom optics applications T2 - OSA Advanced Photonics Congress Y1 - 2021 U6 - https://doi.org/10.1364/IPRSN.2021.JTh1E.2 SP - JTh1E.2 ER - TY - JOUR A1 - Colom, Remi A1 - Binkowski, Felix A1 - Betz, Fridtjof A1 - Kivshar, Yuri A1 - Burger, Sven T1 - Enhanced Purcell factor for nanoantennas supporting interfering resonances JF - Phys. Rev. Research Y1 - 2022 U6 - https://doi.org/10.1103/PhysRevResearch.4.023189 VL - 4 SP - 023189 ER - TY - CHAP A1 - Musial, Anna A1 - Zolnacz, Kinga A1 - Srocka, Nicole A1 - Kravets, Oleh A1 - Große, Jan A1 - Schneider, Philipp-Immanuel A1 - Olszewski, Jacek A1 - Poturaj, Krzystof A1 - Wojcik, Grzegorz A1 - Mergo, Pawel A1 - Dybka, Kamil A1 - Dyrkacz, Mariusz A1 - Dlubek, Michal A1 - Rodt, Sven A1 - Burger, Sven A1 - Zschiedrich, Lin A1 - Urbanczyk, Waclaw A1 - Sek, Grzegorz A1 - Reitzenstein, Stephan T1 - Stand-alone quantum dot-based single-photon source operating at telecommunication wavelengths T2 - 10th International Conference on Spontaneous Coherence in Excitonic Systems ICSCE10 Y1 - 2020 SP - 39 ER - TY - JOUR A1 - Fackeldey, Konstantin A1 - Gorgulla, Christoph A1 - Weber, Marcus T1 - Neue Medikamente dank Supercomputern JF - Spektrum der Wissenschaft N2 - 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. Y1 - 2021 IS - 11 SP - 40 EP - 46 ER - TY - JOUR A1 - Stout, Brian A1 - Colom, Remi A1 - Bonod, Nicolas A1 - McPhedran, Ross C T1 - Spectral expansions of open and dispersive optical systems: Gaussian regularization and convergence JF - New J. Phys. Y1 - 2021 U6 - https://doi.org/10.1088/1367-2630/ac10a6 VL - 23 SP - 083004 ER - TY - CHAP A1 - Bopp, Julian M. A1 - Plock, Matthias A1 - Turan, Tim A1 - Pieplow, Gregor A1 - Burger, Sven A1 - Schröder, Tim T1 - ‘Sawfish’ Spin-Photon Interface for Near-Unity Emitter-to-Waveguide Coupling T2 - Conference on Lasers and Electro-Optics (CLEO) Y1 - 2023 U6 - https://doi.org/10.1364/CLEO_SI.2023.SF1O.6 SP - SF1O.6 ER - TY - CHAP A1 - Hammerschmidt, Martin A1 - Zschiedrich, Lin A1 - Siaudinyté, Lauryna A1 - Manley, Phillip A1 - Schneider, Philipp-Immanuel A1 - Burger, Sven T1 - Forward simulation of coherent beams on grating structures for coherent scatterometry T2 - Proc. SPIE Y1 - 2023 U6 - https://doi.org/10.1117/12.2673231 VL - PC12619 SP - PC1261907 ER - TY - CHAP A1 - Plock, Matthias A1 - Burger, Sven A1 - Schneider, Philipp-Immanuel T1 - Efficient reconstruction of model parameters using Bayesian target-vector optimization T2 - Proc. SPIE Y1 - 2023 U6 - https://doi.org/10.1117/12.2673590 VL - PC12619 SP - PC1261905 ER - TY - JOUR A1 - Yoo, Danbi A1 - Tillmann, Peter A1 - Krauss, Tobias A1 - Sutter, Johannes A1 - Harter, Angelika A1 - Trofimov, Sergei A1 - Naydenov, Boris A1 - Jäger, Klaus A1 - Hauser, Hubert A1 - Becker, Christiane T1 - Comparative Optical Analysis of Imprinted Nano-, Micro- and Biotextures on Solar Glasses for Increased Energy Yield JF - Solar RRL Y1 - 2023 U6 - https://doi.org/10.1002/solr.202300071 VL - 7 SP - 2300071 ER - TY - JOUR A1 - Cereceda-López, Eric A1 - Ostinato, Mattia A1 - Ortiz-Ambriz, Antonio A1 - Straube, Arthur A1 - Palassini, Matteo A1 - Tierno, Pietro T1 - Excluded volume induces buckling in optically driven colloidal rings JF - Phys. Rev. Research N2 - 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. Y1 - 2024 U6 - https://doi.org/10.1103/PhysRevResearch.6.L012044 VL - 6 SP - L012044 ER - TY - JOUR A1 - Nagel, Soeren A1 - Heitzig, Jobst A1 - Schoell, Eckehard T1 - Macroscopic Stochastic Model for Economic Cycle Dynamics JF - Physical Review Letters N2 - 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. Y1 - 2025 U6 - https://doi.org/https://doi.org/10.1103/PhysRevLett.134.047402 VL - 134 IS - 4 SP - 1 EP - 6 PB - American Physical Society ER - TY - JOUR A1 - Anton, Oliver A1 - Henderson, Victoria A. A1 - Da Ros, Elisa A1 - Sekulic, Ivan A1 - Burger, Sven A1 - Schneider, Philipp-Immanuel A1 - Krutzik, Markus T1 - Review and experimental benchmarking of machine learning algorithms for efficient optimization of cold atom experiments JF - Mach. Learn. Sci. Technol. Y1 - 2024 U6 - https://doi.org/10.1088/2632-2153/ad3cb6 VL - 5 SP - 025022 ER - TY - JOUR A1 - Schimunek, Johannes A1 - Seidl, Philipp A1 - Elez, Katarina A1 - Hempel, Tim A1 - Le, Tuan A1 - Noé, Frank A1 - Olsson, Simon A1 - Raich, Lluís A1 - Winter, Robin A1 - Gokcan, Hatice A1 - Gusev, Filipp A1 - Gutkin, Evgeny M. A1 - Isayev, Olexandr A1 - Kurnikova, Maria G. A1 - Narangoda, Chamali H. A1 - Zubatyuk, Roman A1 - Bosko, Ivan P. A1 - Furs, Konstantin V. A1 - Karpenko, Anna D. A1 - Kornoushenko, Yury V. A1 - Shuldau, Mikita A1 - Yushkevich, Artsemi A1 - Benabderrahmane, Mohammed B. A1 - Bousquet-Melou, Patrick A1 - Bureau, Ronan A1 - Charton, Beatrice A1 - Cirou, Bertrand C. A1 - Gil, Gérard A1 - Allen, William J. A1 - Sirimulla, Suman A1 - Watowich, Stanley A1 - Antonopoulos, Nick A1 - Epitropakis, Nikolaos A1 - Krasoulis, Agamemnon A1 - Itsikalis, Vassilis A1 - Theodorakis, Stavros A1 - Kozlovskii, Igor A1 - Maliutin, Anton A1 - Medvedev, Alexander A1 - Popov, Petr A1 - Zaretckii, Mark A1 - Eghbal-Zadeh, Hamid A1 - Halmich, Christina A1 - Hochreiter, Sepp A1 - Mayr, Andreas A1 - Ruch, Peter A1 - Widrich, Michael A1 - Berenger, Francois A1 - Kumar, Ashutosh A1 - Yamanishi, Yoshihiro A1 - Zhang, Kam Y. J. A1 - Bengio, Emmanuel A1 - Bengio, Yoshua A1 - Jain, Moksh J. A1 - Korablyov, Maksym A1 - Liu, Cheng-Hao A1 - Marcou, Gilles A1 - Glaab, Enrico A1 - Barnsley, Kelly A1 - Iyengar, Suhasini M. A1 - Ondrechen, Mary Jo A1 - Haupt, V. Joachim A1 - Kaiser, Florian A1 - Schroeder, Michael A1 - Pugliese, Luisa A1 - Albani, Simone A1 - Athanasiou, Christina A1 - Beccari, Andrea A1 - Carloni, Paolo A1 - D’Arrigo, Giulia A1 - Gianquinto, Eleonora A1 - Goßen, Jonas A1 - Hanke, Anton A1 - Joseph, Benjamin P. A1 - Kokh, Daria B. A1 - Kovachka, Sandra A1 - Manelfi, Candida A1 - Mukherjee, Goutam A1 - Muñiz-Chicharro, Abraham A1 - Musiani, Francesco A1 - Nunes-Alves, Ariane A1 - Paiardi, Giulia A1 - Rossetti, Giulia A1 - Sadiq, S. Kashif A1 - Spyrakis, Francesca A1 - Talarico, Carmine A1 - Tsengenes, Alexandros A1 - Wade, Rebecca C. A1 - Copeland, Conner A1 - Gaiser, Jeremiah A1 - Olson, Daniel R. A1 - Roy, Amitava A1 - Venkatraman, Vishwesh A1 - Wheeler, Travis J. A1 - Arthanari, Haribabu A1 - Blaschitz, Klara A1 - Cespugli, Marco A1 - Durmaz, Vedat A1 - Fackeldey, Konstantin A1 - Fischer, Patrick D. A1 - Gorgulla, Christoph A1 - Gruber, Christian A1 - Gruber, Karl A1 - Hetmann, Michael A1 - Kinney, Jamie E. A1 - Padmanabha Das, Krishna M. A1 - Pandita, Shreya A1 - Singh, Amit A1 - Steinkellner, Georg A1 - Tesseyre, Guilhem A1 - Wagner, Gerhard A1 - Wang, Zi-Fu A1 - Yust, Ryan J. A1 - Druzhilovskiy, Dmitry S. A1 - Filimonov, Dmitry A. A1 - Pogodin, Pavel V. A1 - Poroikov, Vladimir A1 - Rudik, Anastassia V. A1 - Stolbov, Leonid A. A1 - Veselovsky, Alexander V. A1 - De Rosa, Maria A1 - De Simone, Giada A1 - Gulotta, Maria R. A1 - Lombino, Jessica A1 - Mekni, Nedra A1 - Perricone, Ugo A1 - Casini, Arturo A1 - Embree, Amanda A1 - Gordon, D. Benjamin A1 - Lei, David A1 - Pratt, Katelin A1 - Voigt, Christopher A. A1 - Chen, Kuang-Yu A1 - Jacob, Yves A1 - Krischuns, Tim A1 - Lafaye, Pierre A1 - Zettor, Agnès A1 - Rodríguez, M. Luis A1 - White, Kris M. A1 - Fearon, Daren A1 - Von Delft, Frank A1 - Walsh, Martin A. A1 - Horvath, Dragos A1 - Brooks III, Charles L. A1 - Falsafi, Babak A1 - Ford, Bryan A1 - García-Sastre, Adolfo A1 - Yup Lee, Sang A1 - Naffakh, Nadia A1 - Varnek, Alexandre A1 - Klambauer, Günter A1 - Hermans, Thomas M. T1 - A community effort in SARS-CoV-2 drug discovery JF - Molecular Informatics KW - COVID-19 KW - drug discovery KW - machine learning KW - SARS-CoV-2 Y1 - 2023 U6 - https://doi.org/https://doi.org/10.1002/minf.202300262 VL - 43 IS - 1 SP - e202300262 ER - TY - JOUR A1 - Gorgulla, Christoph A1 - Nigam, AkshatKumar A1 - Koop, Matt A1 - Selim Çınaroğlu, Süleyman A1 - Secker, Christopher A1 - Haddadnia, Mohammad A1 - Kumar, Abhishek A1 - Malets, Yehor A1 - Hasson, Alexander A1 - Li, Minkai A1 - Tang, Ming A1 - Levin-Konigsberg, Roni A1 - Radchenko, Dmitry A1 - Kumar, Aditya A1 - Gehev, Minko A1 - Aquilanti, Pierre-Yves A1 - Gabb, Henry A1 - Alhossary, Amr A1 - Wagner, Gerhard A1 - Aspuru-Guzik, Alán A1 - Moroz, Yurii S. A1 - Fackeldey, Konstantin A1 - Arthanari, Haribabu T1 - VirtualFlow 2.0 - The Next Generation Drug Discovery Platform Enabling Adaptive Screens of 69 Billion Molecules JF - bioRxiv KW - preprint Y1 - 2023 U6 - https://doi.org/10.1101/2023.04.25.537981 ER - TY - CHAP A1 - Sekulic, Ivan A1 - Schneider, Philipp-Immanuel A1 - Anton, Oliver A1 - Da Ros, Elisa A1 - Henderson, Victoria A1 - Krutzik, Markus T1 - Efficient machine-learning approach to optimize trapped cold atom ensembles for quantum memory applications T2 - Proc. SPIE Y1 - 2023 U6 - https://doi.org/10.1117/12.2684406 VL - 12740 SP - 127400F ER - TY - GEN A1 - Zonker, Johannes A1 - Padilla-Iglesias, Cecilia A1 - Djurdjevac Conrad, Natasa T1 - Supplementary code and data for Royal Society Open Science Manuscript rsos.230495 N2 - 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. Y1 - 2023 U6 - https://doi.org/10.12752/9254 ER - TY - GEN A1 - Helfmann, Luzie A1 - Djurdjevac Conrad, Natasa A1 - Lorenz-Spreen, Philipp A1 - Schütte, Christof T1 - Supplementary code for the paper Modelling opinion dynamics under the impact of influencer and media strategies N2 - 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. Y1 - 2023 U6 - https://doi.org/10.12752/9267 ER - TY - THES A1 - Binkowski, Felix T1 - Riesz-projection-based methods for the numerical simulation of resonance phenomena in nanophotonics Y1 - 2023 U6 - https://doi.org/10.17169/refubium-41230 ER - TY - JOUR A1 - Oehme, Stephan A1 - Moewis, Philippe A1 - Boeth, Heide A1 - Bartek, Benjamin A1 - von Tycowicz, Christoph A1 - Ehrig, Rainald A1 - Duda, Georg A1 - Jung, Tobias T1 - Altered knee kinematics after posterior cruciate single-bundle reconstruction - a comprehensive prospective biomechanical in vivo analysis JF - Frontiers in Bioengineering and Biotechnology Y1 - 2024 U6 - https://doi.org/10.3389/fbioe.2024.1322136 VL - 12 ER - TY - JOUR A1 - Ernst, Ariane A1 - Falkenhagen, Undine A1 - Winkelmann, Stefanie T1 - Model reduction for calcium-induced vesicle fusion dynamics JF - Proceedings in Applied Mathematics & Mechanics N2 - 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. Y1 - 2023 U6 - https://doi.org/10.1002/pamm.202300184 VL - 23 IS - 4 ER - TY - GEN A1 - Colom, Rémi A1 - Mikheeva, Elena A1 - Achouri, Karim A1 - Zuniga-Perez, Jesus A1 - Bonod, Nicolas A1 - Martin, Olivier J.F. A1 - Burger, Sven A1 - Genevet, Patrice T1 - Crossing of the Branch Cut: The Topological Origin of a Universal 2π-Phase Retardation in Non-Hermitian Metasurfaces (Laser Photonics Rev. 17(6)/2023) T2 - Laser Photonics Rev. Y1 - 2023 U6 - https://doi.org/10.1002/lpor.202370029 VL - 17 SP - 2370029 ER - TY - GEN A1 - Weiser, Martin A1 - Hubig, Michael A1 - Shanmugam Subramaniam, Jayant T1 - Reconstructing Ambient Temperature Changes in Death Time Estimation with a Bayesian Double-Exponential Approach T2 - Zenodo N2 - 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. Y1 - 2025 U6 - https://doi.org/10.5281/zenodo.17702240 ER - TY - JOUR A1 - Sekulic, Ivan A1 - Schaible, Jonas A1 - Müller, Gabriel A1 - Plock, Matthias A1 - Burger, Sven A1 - Martínez-Lahuerta, Víctor José A1 - Gaaloul, Naceur A1 - Schneider, Philipp-Immanuel T1 - Physics-informed Bayesian optimization of expensive-to-evaluate black-box functions JF - Mach. Learn. Sci. Technol. N2 - 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. Y1 - 2025 U6 - https://doi.org/10.1088/2632-2153/ae1f5f VL - 6 SP - 040503 PB - IOP Publishing ER - TY - CHAP A1 - Zschiedrich, Lin A1 - Betz, Fridtjof A1 - Binkowski, Felix A1 - Kuen, Lilli A1 - Hammerschmidt, Martin A1 - Burger, Sven T1 - Efficient Photonic Component Analysis via AAA Rational Approximation T2 - 2025 International Conference on Numerical Simulation of Optoelectronic Devices (NUSOD) Y1 - 2025 U6 - https://doi.org/10.1109/NUSOD64393.2025.11199710 SP - 115 EP - 116 ER - TY - THES A1 - Plock, Matthias T1 - On Methods for Bayesian Optimization of Least Squares Problems and Optimization of Nanophotonic Devices Y1 - 2025 U6 - https://doi.org/10.17169/refubium-48179 ER - TY - GEN A1 - Sekulic, Ivan A1 - Schaible, Jonas A1 - Müller, Gabriel A1 - Plock, Matthias A1 - Burger, Sven A1 - Martinez-Lahuerta, Victor J. A1 - Gaaloul, Naceur A1 - Schneider, Philipp-Immanuel T1 - Data publication for Physics-informed Bayesian optimization of expensive-to-evaluate black-box functions T2 - Zenodo Y1 - 2025 U6 - https://doi.org/10.5281/zenodo.16751507 ER - TY - GEN A1 - Betz, Fridtjof A1 - Binkowski, Felix A1 - Fischbach, Jan David A1 - Feldman, Nick A1 - Zschiedrich, Lin A1 - Rockstuhl, Carsten A1 - Koenderink, A. Femius A1 - Burger, Sven T1 - Uncovering Hidden Resonances in Non-Hermitian Systems with Scattering Thresholds (Laser Photonics Rev. 19(21)/2025) T2 - Laser Photonics Rev. Y1 - 2025 U6 - https://doi.org/10.1002/lpor.70534 VL - 19 IS - 21 SP - e70534 ER - TY - JOUR A1 - Abou Hamdan, Loubnan A1 - Jana, Aloke A1 - Colom, Rémi A1 - Aboujoussef, Nour A1 - Carlson, Cooper A1 - Overvig, Adam A1 - Binkowski, Felix A1 - Burger, Sven A1 - Genevet, Patrice T1 - A Complex-Frequency Framework for Kerker Unidirectionality in Photonic Resonators Y1 - 2026 U6 - https://doi.org/10.21203/rs.3.rs-8444305/v1 ER - TY - JOUR A1 - Trower, Maia A1 - Djurdjevac Conrad, Natasa A1 - Klus, Stefan T1 - Clustering Time-Evolving Networks Using the Spatiotemporal Graph Laplacian JF - Chaos: An Interdisciplinary Journal of Nonlinear Science N2 - 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. Y1 - 2025 U6 - https://doi.org/10.1063/5.0228419 VL - 35 SP - 013126 ER - TY - JOUR A1 - Straube, Arthur A1 - Höfling, Felix T1 - Memory effects in colloidal motion under confinement and driving JF - J. Phys. A: Math. Theor. N2 - 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. Y1 - 2024 U6 - https://doi.org/10.1088/1751-8121/ad5b2d SN - 1751-8113 VL - 57 SP - 295003 PB - IOP Publishing ER - TY - JOUR A1 - Boniface, Dolachai A1 - Straube, Arthur A1 - Tierno, Pietro T1 - Photocatalytic magnetic microgyroscopes with activity-tunable precessional dynamics JF - Nano Letters N2 - 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. Y1 - 2024 U6 - https://doi.org/10.1021/acs.nanolett.4c03386 VL - 24 IS - 47 SP - 14950 EP - 14956 ER - TY - GEN A1 - Villani, Paolo A1 - Weiser, Martin T1 - Adaptive Gaussian process regression for inverse problems. ALGORITMY 2024 N2 - 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. Y1 - 2024 ER - TY - JOUR A1 - Ernst, Marco A1 - Asselineau, Charles-Alexis A1 - Tillmann, Peter A1 - Jäger, Klaus A1 - Becker, Christiane T1 - Modelling bifacial irradiance – Step-by-step comparison and validation of view factor and ray tracing models JF - Appl. Energy Y1 - 2024 U6 - https://doi.org/10.1016/j.apenergy.2024.123574 SN - 0306-2619 VL - 369 SP - 123574 PB - Elsevier BV ER - TY - GEN A1 - Sekulic, Ivan A1 - Schneider, Philipp-Immanuel A1 - Hammerschmidt, Martin A1 - Burger, Sven T1 - Machine-learning driven design of metasurfaces: learn the physics and not the objective function T2 - Proc. SPIE Y1 - 2024 U6 - https://doi.org/10.1117/12.3022119 VL - PC13017 SP - PC130170X ER - TY - GEN A1 - Bopp, Julian M. A1 - Plock, Matthias A1 - Turan, Tim A1 - Pieplow, Gregor A1 - Burger, Sven A1 - Schröder, Tim T1 - ‘Sawfish’ Photonic Crystal Cavity for Near-Unity Emitter-to-Fiber Interfacing in Quantum Network Applications (Advanced Optical Materials 13/2024) T2 - Adv. Optical Mater. Y1 - 2024 U6 - https://doi.org/10.1002/adom.202470046 VL - 12 SP - 2470046 ER - TY - JOUR A1 - Klus, Stefan A1 - Djurdjevac Conrad, Natasa T1 - Dynamical systems and complex networks: A Koopman operator perspective JF - Journal of Physics: Complexity N2 - 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. Y1 - 2024 U6 - https://doi.org/10.1088/2632-072X/ad9e60 VL - 5 IS - 4 SP - 041001 PB - IOP Publishing ER - TY - JOUR A1 - Krüger, Jan A1 - Manley, Phillip A1 - Bergmann, Detlef A1 - Köning, Rainer A1 - Bodermann, Bernd A1 - Eder, Christian A1 - Heinrich, Andreas A1 - Schneider, Philipp-Immanuel A1 - Hammerschmidt, Martin A1 - Zschiedrich, Lin A1 - Manske, Eberhard T1 - Introduction and application of a new approach for model-based optical bidirectional measurements JF - Meas. Sci. Technol. Y1 - 2024 U6 - https://doi.org/10.1088/1361-6501/ad4b53 VL - 35 SP - 085014 ER - TY - JOUR A1 - Manley, Phillip A1 - Hammerschmidt, Martin A1 - Zschiedrich, Lin A1 - Jäger, Klaus A1 - Becker, Christiane A1 - Burger, Sven T1 - Modelling luminescent coupling in multi-junction solar cells: perovskite silicon tandem case study JF - Proc. SPIE Y1 - 2024 U6 - https://doi.org/10.1117/12.3023941 VL - 13014 SP - 1301404 ER - TY - CHAP A1 - Schaible, Jonas A1 - Yoo, Danbi A1 - Winarto, Hanifa A1 - Miaskiewicz, Alexandra A1 - Albrecht, Steve A1 - Wessels, Andreas A1 - Bläsi, Benedikt A1 - Burger, Sven A1 - Jaeger, Klaus A1 - Becker, Christiane T1 - On aesthetical appearance of colored perovskite solar modules T2 - Proc. SPIE Y1 - 2024 U6 - https://doi.org/10.1117/12.3017427 VL - PC13014 SP - PC1301406 PB - SPIE ER - TY - CHAP A1 - Becker, Christiane A1 - Bläsi, Benedikt A1 - Burger, Sven A1 - Ehrler, Bruno A1 - Gordon, Ivan A1 - Isabella, Olindo A1 - Jäger, Klaus A1 - Jost, Marko A1 - Manley, Phillip A1 - Muñoz, Delfina A1 - Paetzold, Ulrich W. A1 - Sai, Hitoshi A1 - Yablonovitch, Eli T1 - Optical challenges for terawatt-scale photovoltaics T2 - Proc. SPIE Y1 - 2024 U6 - https://doi.org/10.1117/12.3016415 VL - PC13014 SP - PC1301401 PB - SPIE ER - TY - CHAP A1 - Semler, Phillip A1 - Weiser, Martin ED - Fackeldey, Konstantin ED - Kannan, Aswin ED - Pokutta, Sebastian ED - Sharma, Kartikey ED - Walter, Daniel ED - Walther, Andrea ED - Weiser, Martin T1 - Adaptive gradient-enhanced Gaussian process surrogates for inverse problems T2 - Mathematical Optimization for Machine Learning: Proceedings of the MATH+ Thematic Einstein Semester 2023 N2 - 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. Y1 - 2025 U6 - https://doi.org/10.1515/9783111376776-005 SP - 59 EP - 78 PB - De Gruyter ER - TY - JOUR A1 - Djurdjevac Conrad, Natasa A1 - Quang Vu, Nhu A1 - Nagel, Soeren T1 - Co-evolving networks for opinion and social dynamics in agent-based models JF - Chaos: An Interdisciplinary Journal of Nonlinear Science N2 - 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. Y1 - 2024 U6 - https://doi.org/10.1063/5.0226054 SN - 1054-1500 VL - 34 IS - 9 ER - TY - GEN A1 - Kuen, Lilli A1 - Löffler, Lorenz A1 - Tsarapkin, Aleksei A1 - Zschiedrich, Lin A1 - Feichtner, Thorsten A1 - Burger, Sven A1 - Höflich, Katja T1 - Source Code and Simulation Results: Chiral and directional optical emission from a dipole source coupled to a helical plasmonic antenna T2 - Zenodo Y1 - 2024 U6 - https://doi.org/10.5281/zenodo.10598255 SP - doi: 10.5281/zenodo.10598255 ER - TY - JOUR A1 - Müller, Gabriel A1 - Martínez-Lahuerta, Victor J. A1 - Sekulic, Ivan A1 - Burger, Sven A1 - Schneider, Philipp-Immanuel A1 - Gaaloul, Naceur T1 - Bayesian optimization for state engineering of quantum gases JF - Quantum Sci. Technol. Y1 - 2025 U6 - https://doi.org/10.1088/2058-9565/ad9050 VL - 10 SP - 015033 ER - TY - JOUR A1 - Erban, Radek A1 - Winkelmann, Stefanie T1 - Multi-grid reaction-diffusion master equation: applications to morphogen gradient modelling JF - Bulletin of Mathematical Biology N2 - 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. Y1 - 2025 U6 - https://doi.org/10.1007/s11538-024-01377-y VL - 87 SP - 6 ER - TY - CHAP A1 - Villani, Paolo A1 - Unger, Jörg F. A1 - Weiser, Martin T1 - Adaptive Gaussian Process Regression for Bayesian inverse problems T2 - Proceedings of the Conference Algoritmy 2024 N2 - 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. Y1 - 2024 SP - 214 EP - 224 ER - TY - JOUR A1 - Andrés Arcones, Daniel A1 - Weiser, Martin A1 - Koutsourelakis, Faidon-Stelios A1 - Unger, Jörg F. T1 - A Bayesian Framework for Simulation-based Digital Twins of Bridges JF - EUROSTRUCT 2023:European Association on Quality Control of Bridges and Structures: Digital Transformation in Sustainability N2 - 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. Y1 - 2023 U6 - https://doi.org/10.1002/cepa.2177 VL - 6 IS - 5 SP - 734 EP - 740 ER - TY - CHAP A1 - Andrés Arcones, Daniel A1 - Weiser, Martin A1 - Koutsourelakis, Faidon-Stelios A1 - Unger, Jörg F. T1 - Evaluation of Model Bias Identification Approaches Based on Bayesian Inference and Applications to Digital Twins T2 - 5th ECCOMAS Thematic Conference on Uncertainty Quantification in Computational Sciences and Engineering N2 - 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. Y1 - 2023 UR - https://2023.uncecomp.org/proceedings/pdf/19795.pdf SP - 1 EP - 15 ER - TY - JOUR A1 - Maier, Kristina A1 - Weiser, Martin A1 - Conrad, Tim T1 - Hybrid PDE-ODE Models for Efficient Simulation of Infection Spread in Epidemiology JF - Proceedings of the Royal Society A N2 - 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. Y1 - 2025 U6 - https://doi.org/10.1098/rspa.2024.0421 VL - 481 IS - 2306 PB - Royal Society ER - TY - JOUR A1 - Andrés Arcones, Daniel A1 - Weiser, Martin A1 - Koutsourelakis, Faidon-Stelios A1 - Unger, Jörg F. T1 - Model bias identification for Bayesian calibration of stochastic digital twins of bridges JF - Applied Stochastic Models in Business and Industry N2 - 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. Y1 - 2024 U6 - https://doi.org/10.1002/asmb.2897 VL - 41 IS - 3 ER - TY - JOUR A1 - Wehlitz, Nathalie A1 - Sadeghi, Mohsen A1 - Montefusco, Alberto A1 - Schütte, Christof A1 - Pavliotis, Grigorios A. A1 - Winkelmann, Stefanie T1 - Approximating particle-based clustering dynamics by stochastic PDEs JF - SIAM Journal on Applied Dynamical Systems N2 - 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. Y1 - 2025 U6 - https://doi.org/10.1137/24M1676661 VL - 24 IS - 2 SP - 1231 EP - 1250 ER - TY - JOUR A1 - Höfling, Felix A1 - Straube, Arthur T1 - Langevin equations and a geometric integration scheme for the overdamped limit of rotational Brownian motion of axisymmetric particles JF - Physical Review Research N2 - 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. Y1 - 2025 U6 - https://doi.org/10.1103/wzdn-29p4 VL - 7 SP - 043034 ER - TY - JOUR A1 - Schaible, Jonas A1 - Winarto, Hanifah A1 - Škorjanc, Viktor A1 - Yoo, Danbi A1 - Zimmermann, Lea A1 - Jäger, Klaus A1 - Sekulic, Ivan A1 - Schneider, Philipp‐Immanuel A1 - Burger, Sven A1 - Wessels, Andreas A1 - Bläsi, Benedikt A1 - Becker, Christiane T1 - Optimizing Aesthetic Appearance of Perovskite Solar Cells Using Color Filters JF - Solar RRL N2 - 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. Y1 - 2025 U6 - https://doi.org/10.1002/solr.202400627 VL - 9 SP - 2400627 PB - Wiley ER - TY - GEN A1 - Roche, Léo J. A1 - Betz, Fridtjof A1 - Yang, Yuhui A1 - Limame, Imad A1 - Shih, Ching-Wen A1 - Burger, Sven A1 - Reitzenstein, Stephan T1 - Inside Front Cover: Numerical Investigation of a Coupled Micropillar - Waveguide System for Integrated Quantum Photonic Circuits (Adv. Quantum Technol. 12/2024) T2 - Adv. Quantum Technol. Y1 - 2024 U6 - https://doi.org/10.1002/qute.202470036 VL - 7 SP - 2470036 ER - TY - CHAP A1 - Mukherjee, Deshabrato A1 - Burger, Sven A1 - Siefke, Thomas A1 - Gour, Jeetendra A1 - Bodermann, Bernd A1 - Petrik, Peter T1 - Modeling of dimensions and sensing properties of gold gratings by spectroscopic ellipsometry and finite element method T2 - EPJ Web of Conferences Y1 - 2024 U6 - https://doi.org/10.1051/epjconf/202430902016 VL - 309 SP - 02016 ER - TY - JOUR A1 - Djurdjevac Conrad, Natasa A1 - Tonello, Elisa A1 - Zonker, Johannes A1 - Siebert, Heike T1 - Detection of dynamic communities in temporal networks with sparse data JF - Applied Network Science N2 - 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. Y1 - 2025 U6 - https://doi.org/10.1007/s41109-024-00687-3 VL - 10 PB - Springer International Publishing ER - TY - JOUR A1 - Zimper, Sebastian A1 - Cornalba, Federico A1 - Djurdjevac Conrad, Natasa A1 - Djurdjevac, Ana T1 - On reduced inertial PDE models for Cucker-Smale flocking dynamics JF - Proceedings of the Royal Society A N2 - 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. Y1 - 2025 U6 - https://doi.org/https://doi.org/10.1098/rspa.2024.0675 VL - 481 PB - Royal Society ER -