TY - THES A1 - Tillmann, Peter T1 - Optimizing bifacial tandem solar cells for realistic operation conditions Y1 - 2023 U6 - https://doi.org/10.17169/refubium-39571 ER - TY - CHAP A1 - Mukherjee, Deshabrato A1 - Kalas, Benjámin A1 - Burger, Sven A1 - Sáfrán, György A1 - Serényi, Miklós A1 - Fried, Miklós A1 - Petrik, Péter T1 - Nanostructures for in-situ surface-enhanced Kretschmann-Raether ellipsometry T2 - Proc. SPIE Y1 - 2023 U6 - https://doi.org/10.1117/12.2649080 VL - 12428 SP - 124280S ER - TY - GEN A1 - Betz, Fridtjof A1 - Binkowski, Felix A1 - Hammerschmidt, Martin A1 - Zschiedrich, Lin A1 - Burger, Sven T1 - Source code and simulation results for computing resonance expansions of quadratic quantities with regularized quasinormal modes T2 - Zenodo Y1 - 2022 U6 - https://doi.org/10.5281/zenodo.7376556 ER - TY - CHAP A1 - Chegini, Fatemeh A1 - Steinke, Thomas A1 - Weiser, Martin T1 - Efficient adaptivity for simulating cardiac electrophysiology with spectral deferred correction methods N2 - The locality of solution features in cardiac electrophysiology simulations calls for adaptive methods. Due to the overhead incurred by established mesh refinement and coarsening, however, such approaches failed in accelerating the computations. Here we investigate a different route to spatial adaptivity that is based on nested subset selection for algebraic degrees of freedom in spectral deferred correction methods. This combination of algebraic adaptivity and iterative solvers for higher order collocation time stepping realizes a multirate integration with minimal overhead. This leads to moderate but significant speedups in both monodomain and cell-by-cell models of cardiac excitation, as demonstrated at four numerical examples. Y1 - 2022 ER - TY - JOUR A1 - Straube, Arthur A1 - Winkelmann, Stefanie A1 - Höfling, Felix T1 - Accurate reduced models for the pH oscillations in the urea-urease reaction confined to giant lipid vesicles JF - The Journal of Physical Chemistry B N2 - This theoretical study concerns a pH oscillator based on the urea-urease reaction confined to giant lipid vesicles. Under suitable conditions, differential transport of urea and hydrogen ion across the unilamellar vesicle membrane periodically resets the pH clock that switches the system from acid to basic, resulting in self-sustained oscillations. We analyse the structure of the phase flow and of the limit cycle, which controls the dynamics for giant vesicles and dominates the pronouncedly stochastic oscillations in small vesicles of submicrometer size. To this end, we derive reduced models, which are amenable to analytic treatments that are complemented by numerical solutions, and obtain the period and amplitude of the oscillations as well as the parameter domain, where oscillatory behavior persists. We show that the accuracy of these predictions is highly sensitive to the employed reduction scheme. In particular, we suggest an accurate two-variable model and show its equivalence to a three-variable model that admits an interpretation in terms of a chemical reaction network. The faithful modeling of a single pH oscillator appears crucial for rationalizing experiments and understanding communication of vesicles and synchronization of rhythms. Y1 - 2023 U6 - https://doi.org/10.1021/acs.jpcb.2c09092 VL - 127 IS - 13 SP - 2955 EP - 2967 ER - TY - JOUR A1 - Boltz, Horst-Holger A1 - Kurchan, Jorge A1 - Liu, Andrea J. T1 - Fluctuation distributions of energy minima in complex landscapes JF - Physical Review Research N2 - We discuss the properties of the distributions of energies of minima obtained by gradient descent in complex energy landscapes. We find strikingly similar phenomenology across several prototypical models. We particularly focus on the distribution of energies of minima in the analytically well-understood p-spin-interaction spin-glass model. We numerically find non-Gaussian distributions that resemble the Tracy-Widom distributions often found in problems of random correlated variables, and nontrivial finite-size scaling. Based on this, we propose a picture of gradient-descent dynamics that highlights the importance of a first-passage process in the eigenvalues of the Hessian. This picture provides a concrete link to problems in which the Tracy-Widom distribution is established. Aspects of this first-passage view of gradient-descent dynamics are generic for nonconvex complex landscapes, rationalizing the commonality that we find across models. Y1 - 2020 U6 - https://doi.org/10.1103/PhysRevResearch.3.013061 VL - 3 IS - 1 SP - 013061 ER - TY - JOUR A1 - Carderera, Alejandro A1 - Pokutta, Sebastian A1 - Schütte, Christof A1 - Weiser, Martin T1 - An efficient first-order conditional gradient algorithm in data-driven sparse identification of nonlinear dynamics to solve sparse recovery problems under noise JF - Journal of Computational and Applied Mathematics N2 - Governing equations are essential to the study of nonlinear dynamics, often enabling the prediction of previously unseen behaviors as well as the inclusion into control strategies. The discovery of governing equations from data thus has the potential to transform data-rich fields where well-established dynamical models remain unknown. This work contributes to the recent trend in data-driven sparse identification of nonlinear dynamics of finding the best sparse fit to observational data in a large library of potential nonlinear models. We propose an efficient first-order Conditional Gradient algorithm for solving the underlying optimization problem. In comparison to the most prominent alternative algorithms, the new algorithm shows significantly improved performance on several essential issues like sparsity-induction, structure-preservation, noise robustness, and sample efficiency. We demonstrate these advantages on several dynamics from the field of synchronization, particle dynamics, and enzyme chemistry. Y1 - 2021 ER - TY - JOUR A1 - Jäger, Klaus A1 - Sutter, Johannes A1 - Hammerschmidt, Martin A1 - Schneider, Philipp-Immanuel A1 - Becker, Christiane T1 - Prospects of light management in perovskite/silicon tandem solar cells JF - Nanophotonics Y1 - 2021 U6 - https://doi.org/10.1515/nanoph-2020-0674 VL - 10 SP - 1991 ER - TY - JOUR A1 - Liu, Yongtao A1 - Zhou, Zhiguang A1 - Wang, Fan A1 - Kewes, Günter A1 - Wen, Shihui A1 - Burger, Sven A1 - Wakiani, Majid Ebrahimi A1 - Xi, Peng A1 - Yang, Jiong A1 - Yang, Xusan A1 - Benson, Oliver A1 - Jin, Dayong T1 - Axial localization and tracking of self-interference nanoparticles by lateral point spread functions JF - Nat. Commun. Y1 - 2021 U6 - https://doi.org/10.1038/s41467-021-22283-0 VL - 12 SP - 2019 ER - TY - JOUR A1 - Lücke, Marvin A1 - Lu, Jingyi A1 - Quevedo, Daniel E. T1 - Coding for secrecy in remote state estimation with an adversary JF - IEEE Transactions on Automatic Control N2 - We study the problem of remote state estimation in the presence of an eavesdropper. A sensor transmits state information over a packet-dropping link to a legitimate user. This information is randomly overheard by an eavesdropper. To reduce information leakage to the eavesdropper, previous studies have shown that by encoding the estimate with the acknowledgments (Acks), perfect secrecy can be achieved. However, this strategy greatly relies on the accuracy of the Acks and may easily fail if the Acks are compromised by cyberattacks. In this article, we tackle this issue by proposing to switch between sending an encoded state and sending the plain state to stay resilient against fake Acks. Specifically, we assume the Acks to be randomly attacked and derive recursive expressions for the minimum-mean-squared error estimates and error covariance matrices at the legitimate user and at the eavesdropper. Based upon this, we propose a transmission policy that depends on the probability of synchronization. We formulate a partially observable Markov decision process to model the evolution of the synchronization status and derive associated optimal transmission policies. Numerical examples are provided to verify the theoretical results. Y1 - 2022 U6 - https://doi.org/10.1109/TAC.2022.3169839 VL - 67 IS - 9 SP - 4955 EP - 4962 ER - TY - JOUR A1 - Chegini, Fatemeh A1 - Kopanicakova, Alena A1 - Krause, Rolf A1 - Weiser, Martin T1 - Efficient Identification of Scars using Heterogeneous Model Hierarchies JF - EP Europace N2 - Aims. Detection and quantification of myocardial scars are helpful both for diagnosis of heart diseases and for building personalized simulation models. Scar tissue is generally charac­terized by a different conduction of electrical excitation. We aim at estimating conductivity-related parameters from endocardial mapping data, in particular the conductivity tensor. Solving this inverse problem requires computationally expensive monodomain simulations on fine discretizations. Therefore, we aim at accelerating the estimation using a multilevel method combining electrophysiology models of different complexity, namely the mono­domain and the eikonal model. Methods. Distributed parameter estimation is performed by minimizing the misfit between simulated and measured electrical activity on the endocardial surface, subject to the mono­domain model and regularization, leading to a constrained optimization problem. We formulate this optimization problem, including the modeling of scar tissue and different regularizations, and design an efficient iterative solver. We consider monodomain grid hierarchies and monodomain-eikonal model hierarchies in a recursive multilevel trust-region method. Results. From several numerical examples, both the efficiency of the method and the estimation quality, depending on the data, are investigated. The multilevel solver is significantly faster than a comparable single level solver. Endocardial mapping data of realistic density appears to be just sufficient to provide quantitatively reasonable estimates of location, size, and shape of scars close to the endocardial surface. Conclusion. In several situations, scar reconstruction based on eikonal and monodomain models differ significantly, suggesting the use of the more accurate but more expensive monodomain model for this purpose. Still, eikonal models can be utilized to accelerate the computations considerably, enabling the use of complex electrophysiology models for estimating myocardial scars from endocardial mapping data. Y1 - 2021 U6 - https://doi.org/10.1093/europace/euaa402 VL - 23 SP - i113 EP - i122 ER - TY - CHAP A1 - Jäger, Klaus A1 - Tillmann, Peter A1 - Katz, Eugene A. A1 - Becker, Christiane T1 - Simulating bifacial perovskite/silicon tandem solar cells in large PV fields T2 - OSA Advanced Photonics Congress Y1 - 2020 U6 - https://doi.org/10.1364/PVLED.2020.PvTh1G.3 SP - PvTh1G.3 ER - TY - JOUR A1 - Jäger, Klaus A1 - Tillmann, Peter A1 - Katz, Eugene A. A1 - Becker, Christiane T1 - Perovskite/silicon tandem solar cells: Effect of luminescent coupling and bifaciality JF - Sol. RRL Y1 - 2021 U6 - https://doi.org/10.1002/solr.202000628 VL - 5 SP - 2000628 ER - TY - JOUR A1 - Manley, Phillip A1 - Segantini, Michele A1 - Ahiboz, Doguscan A1 - Hammerschmidt, Martin A1 - Arnaoutakis, Georgios A1 - MacQueen, Rowan W. A1 - Burger, Sven A1 - Becker, Christiane T1 - Double-layer metasurface for enhanced photon up-conversion JF - APL Photon. Y1 - 2021 U6 - https://doi.org/10.1063/5.0040839 VL - 6 SP - 036103 ER - TY - JOUR A1 - Pakhomov, Anton V. A1 - Hammerschmidt, Martin A1 - Burger, Sven A1 - Pertsch, Thomas A1 - Setzpfand, Frank T1 - Modeling of surface-induced second-harmonic generation from multilayer structures by the transfer matrix method JF - Opt. Express Y1 - 2021 U6 - https://doi.org/10.1364/OE.417066 VL - 29 SP - 9098 ER - TY - JOUR A1 - Binkowski, Felix A1 - Wu, Tong A1 - Lalanne, Philippe A1 - Burger, Sven A1 - Govorov, Alexander O. T1 - Hot Electron Generation through Near-Field Excitation of Plasmonic Nanoresonators JF - ACS Photonics Y1 - 2021 U6 - https://doi.org/10.1021/acsphotonics.1c00231 VL - 8 SP - 1243 ER - TY - JOUR A1 - Cvetkovic, Nada A1 - Conrad, Tim A1 - Lie, Han Cheng T1 - A Convergent Discretisation Method for Transition Path Theory for Diffusion Processes JF - Multiscale Modeling & Simulation Y1 - 2021 U6 - https://doi.org/10.1137/20M1329354 VL - 19 IS - 1 SP - 242 EP - 266 PB - Society for Industrial and Applied Mathematics ER - TY - BOOK A1 - Deuflhard, Peter A1 - Weiser, Martin T1 - Numerische Mathematik 3. Adaptive Lösung partieller Differentialgleichungen Y1 - 2020 SN - 978-3-11-069168-9 U6 - https://doi.org/10.1515/9783110689655 PB - de Gruyter ET - 2 ER - TY - JOUR A1 - Sikorski, Alexander A1 - Weber, Marcus A1 - Schütte, Christof T1 - The Augmented Jump Chain JF - Advanced Theory and Simulations N2 - Modern methods of simulating molecular systems are based on the mathematical theory of Markov operators with a focus on autonomous equilibrated systems. However, non-autonomous physical systems or non-autonomous simulation processes are becoming more and more important. A representation of non-autonomous Markov jump processes is presented as autonomous Markov chains on space-time. Augmenting the spatial information of the embedded Markov chain by the temporal information of the associated jump times, the so-called augmented jump chain is derived. The augmented jump chain inherits the sparseness of the infinitesimal generator of the original process and therefore provides a useful tool for studying time-dependent dynamics even in high dimensions. Furthermore, possible generalizations and applications to the computation of committor functions and coherent sets in the non-autonomous setting are discussed. After deriving the theoretical foundations, the concepts with a proof-of-concept Galerkin discretization of the transfer operator of the augmented jump chain applied to simple examples are illustrated. Y1 - 2021 U6 - https://doi.org/10.1002/adts.202000274 VL - 4 IS - 4 PB - Wiley-VCH ER - TY - JOUR A1 - Sechi, Renata A1 - Sikorski, Alexander A1 - Weber, Marcus T1 - Estimation of the Koopman Generator by Newton's Extrapolation JF - Multiscale Modeling and Simulation N2 - This article addresses the problem of estimating the Koopman generator of a Markov process. The direct computation of the infinitesimal generator is not easy because of the discretization of the state space, in particular because of the trade-off inherent in the choice of the best lag time to study the process. Short lag times implies a strong discretization of the state space and a consequent loss of Markovianity. Large lag times bypass events on fast timescales. We propose a method to approximate the generator with the computation of the Newton polynomial extrapolation. This technique is a multistep approach which uses as its input Koopman transfer operators evaluated for a series of lag times. Thus, the estimated infinitesimal generator combines information from different time resolutions and does not bias only fast- or slow-decaying dynamics. We show that the multi-scale Newton method can improve the estimation of the generator in comparison to the computation using finite difference or matrix logarithm methods. Y1 - 2020 U6 - https://doi.org/10.1137/20M1333006 VL - 19 IS - 2 SP - 758 EP - 774 PB - SIAM ER - TY - THES A1 - Venkatareddy, Narendra Lagumaddepalli T1 - Revealing secrets of mussel-glue mimetic peptides - From advanced NMR to computational process modelling Y1 - 2020 ER - TY - THES A1 - Eshtewy, Neveen Ali Salem T1 - Mathematical Modeling of Metabolic-Genetic Networks Y1 - 2020 ER - TY - JOUR A1 - Öttinger, Hans Christian A1 - Montefusco, Alberto A1 - Peletier, Mark A. T1 - A Framework of Nonequilibrium Statistical Mechanics. I. Role and Types of Fluctuations JF - Journal of Non-Equilibrium Thermodynamics N2 - Understanding the fluctuations by which phenomenological evolution equations with thermodynamic structure can be enhanced is the key to a general framework of nonequilibrium statistical mechanics. These fluctuations provide an idealized representation of microscopic details. We consider fluctuation-enhanced equations associated with Markov processes and elaborate the general recipes for evaluating dynamic material properties, which characterize force-flux constitutive laws, by statistical mechanics. Markov processes with continuous trajectories are conveniently characterized by stochastic differential equations and lead to Green–Kubo-type formulas for dynamic material properties. Markov processes with discontinuous jumps include transitions over energy barriers with the rates calculated by Kramers. We describe a unified approach to Markovian fluctuations and demonstrate how the appropriate type of fluctuations (continuous versus discontinuous) is reflected in the mathematical structure of the phenomenological equations. Y1 - 2021 U6 - https://doi.org/10.1515/jnet-2020-0068 VL - 46 IS - 1 SP - 1 EP - 13 PB - De Gruyter ER - TY - JOUR A1 - Montefusco, Alberto A1 - Peletier, Mark A. A1 - Öttinger, Hans Christian T1 - A Framework of Nonequilibrium Statistical Mechanics. II. Coarse-Graining JF - Journal of Non-Equilibrium Thermodynamics N2 - For a given thermodynamic system, and a given choice of coarse-grained state variables, the knowledge of a force-flux constitutive law is the basis for any nonequilibrium modeling. In the first paper of this series we established how, by a generalization of the classical fluctuation-dissipation theorem (FDT), the structure of a constitutive law is directly related to the distribution of the fluctuations of the state variables. When these fluctuations can be expressed in terms of diffusion processes, one may use Green–Kubo-type coarse-graining schemes to find the constitutive laws. In this paper we propose a coarse-graining method that is valid when the fluctuations are described by means of general Markov processes, which include diffusions as a special case. We prove the success of the method by numerically computing the constitutive law for a simple chemical reaction A⇄B. Furthermore, we show that, for such a system, one cannot find a consistent constitutive law by any Green–Kubo-like scheme. Y1 - 2021 U6 - https://doi.org/10.1515/jnet-2020-0069 VL - 46 IS - 1 SP - 15 EP - 33 PB - De Gruyter ER - TY - JOUR A1 - Sunkara, Vikram A1 - Heinz, Gitta A. A1 - Heinrich, Frederik F. A1 - Durek, Pawel A1 - Mobasheri, Ali A1 - Mashreghi, Mir-Farzin A1 - Lang, Annemarie T1 - Combining segmental bulk- and single-cell RNA-sequencing to define the chondrocyte gene expression signature in the murine knee joint JF - bioarxiv (Accepted in Osteoarthr. Cartil.) Y1 - 2020 U6 - https://doi.org/10.1101/2020.06.13.148056 ER - TY - JOUR A1 - Lang, Annemarie A1 - Helfmeier, Sarah A1 - Stefanowski, Jonathan A1 - Kuppe, Aditi A1 - Sunkara, Vikram A1 - Pfeiffenberger, Moritz A1 - Wolter, Angelique A1 - Damerau, Alexandra A1 - Hemmati-Sadeghi, Shabnam A1 - Ringe, Jochen A1 - Haag, Rainer A1 - Hauser, Anja E. A1 - Löhning, Max A1 - Perka, Carsten A1 - Duda, Georg A1 - Hoff, Paula A1 - Schmidt-Bleek, Katharina A1 - Gaber, Timo A1 - Buttgereit, Frank T1 - HIF-stabilization prevents delayed fracture healing JF - bioarxiv Y1 - 2020 U6 - https://doi.org/10.1101/2020.07.02.182832 ER - TY - JOUR A1 - Laydon, Daniel J. A1 - Sunkara, Vikram A1 - Boelen, Lies A1 - Bangham, Charles R. M. A1 - Asquith, Becca T1 - The relative contributions of infectious and mitotic spread to HTLV-1 persistence JF - PLOS Computational Biology Y1 - 2020 U6 - https://doi.org/10.1371/journal.pcbi.1007470 ER - TY - JOUR A1 - Schiela, Anton A1 - Stöcklein, Matthias A1 - Weiser, Martin T1 - A primal dual projection algorithm for efficient constraint preconditioning JF - SIAM Journal on Scientific Computing N2 - We consider a linear iterative solver for large scale linearly constrained quadratic minimization problems that arise, for example, in optimization with PDEs. By a primal-dual projection (PDP) iteration, which can be interpreted and analysed as a gradient method on a quotient space, the given problem can be solved by computing sulutions for a sequence of constrained surrogate problems, projections onto the feasible subspaces, and Lagrange multiplier updates. As a major application we consider a class of optimization problems with PDEs, where PDP can be applied together with a projected cg method using a block triangular constraint preconditioner. Numerical experiments show reliable and competitive performance for an optimal control problem in elasticity. Y1 - 2021 U6 - https://doi.org/10.1137/20M1380739 VL - 43 IS - 6 SP - A4095 EP - A4120 ER - TY - JOUR A1 - Mielke, Alexander A1 - Montefusco, Alberto A1 - Peletier, Mark A. T1 - Exploring families of energy-dissipation landscapes via tilting: three types of EDP convergence JF - Continuum Mechanics and Thermodynamics N2 - This paper revolves around a subtle distinction between two concepts: passing to the limit in a family of gradient systems, on one hand, and deriving effective kinetic relations on the other. The two concepts are strongly related, and in many examples they even appear to be the same. Our main contributions are to show that they are different, to show that well-known techniques developed for the former may give incorrect results for the latter, and to introduce new tools to remedy this. The approach is based on the Energy-Dissipation Principle that provides a variational formulation to gradient-flow equations that allows one to apply techniques from Γ-convergence of functional on states and functionals on trajectories. Y1 - 2021 U6 - https://doi.org/10.1007/s00161-020-00932-x VL - 33 SP - 611 EP - 637 PB - Springer ER - TY - THES A1 - Santiago, Xavier Garcia T1 - Numerical methods for shape optimization of photonic nanostructures Y1 - 2021 U6 - https://doi.org/10.5445/IR/1000131006 ER - TY - JOUR A1 - Ramos Leite, Tiago A1 - Zschiedrich, Lin A1 - Kizilkaya, Orhan A1 - McPeak, Kevin M. T1 - Resonant Plasmonic–Biomolecular Chiral Interactions in the Far-Ultraviolet: Enantiomeric Discrimination of sub-10 nm Amino Acid Films JF - Nano Lett. Y1 - 2022 UR - https://digitalcommons.lsu.edu/chem_engineering_pubs/34/ U6 - https://doi.org/10.1021/acs.nanolett.2c01724 VL - 22 SP - 7343 ER - TY - JOUR A1 - Rej, Sourav A1 - Santiago, Eva Yazmin A1 - Baturina, Olga A1 - Zhang, Yu A1 - Burger, Sven A1 - Kment, Stepan A1 - Govorov, Alexander O. A1 - Naldoni, Alberto T1 - Colloidal Titanium Nitride Nanobars for Broadband Inexpensive Plasmonics and Photochemistry from Visible to Mid-IR Wavelengths JF - Nano Energy Y1 - 2022 U6 - https://doi.org/10.1016/j.nanoen.2022.107989 VL - 104 SP - 107989 ER - TY - JOUR A1 - Rickert, Lucas A1 - Betz, Fridtjof A1 - Plock, Matthias A1 - Burger, Sven A1 - Heindel, Tobias T1 - High-performance designs for fiber-pigtailed quantum-light sources based on quantum dots in electrically-controlled circular Bragg gratings JF - Opt. Express Y1 - 2023 U6 - https://doi.org/10.1364/OE.486060 VL - 31 SP - 14750 ER - TY - GEN A1 - Rickert, Lucas A1 - Betz, Fridtjof A1 - Plock, Matthias A1 - Burger, Sven A1 - Heindel, Tobias T1 - Data publication for "High-performance designs for fiber-pigtailed quantum-light sources based on quantum dots in electrically-controlled circular Bragg gratings" T2 - Zenodo Y1 - 2022 U6 - https://doi.org/10.5281/zenodo.7360516 SP - 7360516 ER - TY - JOUR A1 - Gorgulla, Christoph A1 - Jayaraj, Abhilash A1 - Fackeldey, Konstantin A1 - Arthanari, Haribabu T1 - Emerging frontiers in virtual drug discovery: From quantum mechanical methods to deep learning approaches JF - Current Opinion in Chemical Biology N2 - Virtual screening-based approaches to discover initial hit and lead compounds have the potential to reduce both the cost and time of early drug discovery stages, as well as to find inhibitors for even challenging target sites such as protein–protein interfaces. Here in this review, we provide an overview of the progress that has been made in virtual screening methodology and technology on multiple fronts in recent years. The advent of ultra-large virtual screens, in which hundreds of millions to billions of compounds are screened, has proven to be a powerful approach to discover highly potent hit compounds. However, these developments are just the tip of the iceberg, with new technologies and methods emerging to propel the field forward. Examples include novel machine-learning approaches, which can reduce the computational costs of virtual screening dramatically, while progress in quantum-mechanical approaches can increase the accuracy of predictions of various small molecule properties. Y1 - 2022 U6 - https://doi.org/10.1016/j.cbpa.2022.102156 VL - 69 SP - 102156 EP - 102156-12 ER - TY - GEN A1 - Straube, Arthur A1 - Winkelmann, Stefanie A1 - Höfling, Felix T1 - Accurate reduced models for the pH oscillations in the urea-urease reaction confined to giant lipid vesicles N2 - Our theoretical study concerns an urea-urease-based pH oscillator confined to giant lipid vesicles. Under suitable conditions, differential transport of urea and hydrogen ion across the unilamellar vesicle membrane periodically resets the pH clock that switches the system from acid to basic, resulting in self-sustained oscillations. We analyse the structure of the limit cycle, which controls the dynamics for giant vesicles and dominates the strongly stochastic oscillations in small vesicles of submicrometer size. To this end, we derive reduced models, amenable to analytic treatments, and show that the accuracy of predictions, including the period of oscillations, is highly sensitive to the choice of the reduction scheme. In particular, we suggest an accurate two-variable model and show its equivalence to a three-variable model that admits an interpretation in terms of a chemical reaction network. The accurate description of a single pH oscillator appears crucial for rationalizing experiments and understanding communication of vesicles and synchronization of rhythms. T3 - ZIB-Report - 22-21 Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-88179 SN - 1438-0064 ER - TY - JOUR A1 - Djurdjevac Conrad, Natasa A1 - Köppl, Jonas A1 - Djurdjevac, Ana T1 - Feedback Loops in Opinion Dynamics of Agent-Based Models with Multiplicative Noise JF - Entropy N2 - We introduce an agent-based model for co-evolving opinions and social dynamics, under the influence of multiplicative noise. In this model, every agent is characterized by a position in a social space and a continuous opinion state variable. Agents’ movements are governed by the positions and opinions of other agents and similarly, the opinion dynamics are influenced by agents’ spatial proximity and their opinion similarity. Using numerical simulations and formal analyses, we study this feedback loop between opinion dynamics and the mobility of agents in a social space. We investigate the behaviour of this ABM in different regimes and explore the influence of various factors on the appearance of emerging phenomena such as group formation and opinion consensus. We study the empirical distribution, and, in the limit of infinite number of agents, we derive a corresponding reduced model given by a partial differential equation (PDE). Finally, using numerical examples, we show that a resulting PDE model is a good approximation of the original ABM. Y1 - 2022 U6 - https://doi.org/10.3390/e24101352 VL - 24(10) ER - TY - JOUR A1 - del Razo, Mauricio A1 - Winkelmann, Stefanie A1 - Klein, Rupert A1 - Höfling, Felix T1 - Chemical diffusion master equation: formulations of reaction-diffusion processes on the molecular level JF - Journal of Mathematical Physics N2 - The chemical diffusion master equation (CDME) describes the probabilistic dynamics of reaction--diffusion systems at the molecular level [del Razo et al., Lett. Math. Phys. 112:49, 2022]; it can be considered the master equation for reaction--diffusion processes. The CDME consists of an infinite ordered family of Fokker--Planck equations, where each level of the ordered family corresponds to a certain number of particles and each particle represents a molecule. The equations at each level describe the spatial diffusion of the corresponding set of particles, and they are coupled to each other via reaction operators --linear operators representing chemical reactions. These operators change the number of particles in the system, and thus transport probability between different levels in the family. In this work, we present three approaches to formulate the CDME and show the relations between them. We further deduce the non-trivial combinatorial factors contained in the reaction operators, and we elucidate the relation to the original formulation of the CDME, which is based on creation and annihilation operators acting on many-particle probability density functions. Finally we discuss applications to multiscale simulations of biochemical systems among other future prospects. Y1 - 2023 U6 - https://doi.org/10.1063/5.0129620 VL - 64 IS - 1 ER - TY - JOUR A1 - Lücke, Marvin A1 - Heitzig, Jobst A1 - Koltai, Péter A1 - Molkethin, Nora A1 - Winkelmann, Stefanie T1 - Large population limits of Markov processes on random networks JF - Stochastic Processes and their Applications N2 - We consider time-continuous Markovian discrete-state dynamics on random networks of interacting agents and study the large population limit. The dynamics are projected onto low-dimensional collective variables given by the shares of each discrete state in the system, or in certain subsystems, and general conditions for the convergence of the collective variable dynamics to a mean-field ordinary differential equation are proved. We discuss the convergence to this mean-field limit for a continuous-time noisy version of the so-called "voter model" on Erdős-Rényi random graphs, on the stochastic block model, as well as on random regular graphs. Moreover, a heterogeneous population of agents is studied. For each of these types of interaction networks, we specify the convergence conditions in dependency on the corresponding model parameters. Y1 - 2023 U6 - https://doi.org/10.1016/j.spa.2023.09.007 VL - 166 ER - TY - CHAP A1 - Schneider, Philipp-Immanuel A1 - Zschiedrich, Lin A1 - Hammerschmidt, Martin A1 - Kuen, Lilli A1 - Sekulic, Ivan A1 - Kluge, Julien A1 - Leykauf, Bastian A1 - Krutzik, Markus A1 - Burger, Sven T1 - Boosting quantum optics experiments with Bayesian optimization T2 - Proc. SPIE Y1 - 2022 U6 - https://doi.org/10.1117/12.2632419 VL - 12227 SP - 122270F ER - TY - CHAP A1 - Krüger, Jan A1 - Manley, Phillip A1 - Zschiedrich, Lin A1 - Hammerschmidt, Martin A1 - Schneider, Philipp-Immanuel A1 - Köning, Rainer A1 - Bodermann, Bernd T1 - Untersuchung des Schwingungseinflusses auf gemessene Punktspreizfunktionen in der optischen Mikroskopie T2 - Proc. DGaO Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0287-2022-P005-6 SP - P5 ER - TY - JOUR 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 JF - Adv. Opt. Mater. Y1 - 2024 U6 - https://doi.org/10.1002/adom.202301286 VL - 12 SP - 2301286 ER - TY - CHAP A1 - Manley, Phillip A1 - Krüger, Jan A1 - Zschiedrich, Lin A1 - Hammerschmidt, Martin A1 - Bodermann, Bernd A1 - Köning, Rainer A1 - Schneider, Philipp-Immanuel T1 - Elementary, my dear Zernike: model order reduction for accelerating optical dimensional microscopy T2 - EPJ Web Conf. Y1 - 2022 U6 - https://doi.org/10.1051/epjconf/202226610010 VL - 266 SP - 10010 ER - TY - JOUR A1 - Betz, Fridtjof A1 - Hammerschmidt, Martin A1 - Zschiedrich, Lin A1 - Burger, Sven A1 - Binkowski, Felix T1 - Efficient rational approximation of optical response functions with the AAA algorithm JF - Laser Photonics Rev. Y1 - 2024 U6 - https://doi.org/10.1002/lpor.202400584 VL - 18 SP - 2400584 ER - TY - GEN A1 - Betz, Fridtjof A1 - Hammerschmidt, Martin A1 - Zschiedrich, Lin A1 - Burger, Sven A1 - Binkowski, Felix T1 - Source code and simulation results: Efficient rational approximation of optical response functions with the AAA algorithm T2 - Zenodo Y1 - 2024 U6 - https://doi.org/10.5281/zenodo.10853692 SP - doi: 10.5281/zenodo.10853692 ER - TY - JOUR A1 - Mukherjee, Deshabrato A1 - Kertész, Krisztián A1 - Zolnai, Zsolt A1 - Kovács, Zoltán A1 - Deák, András A1 - Pálinkás, András A1 - Osváth, Zoltán A1 - Olasz, Dániel A1 - Romanenko, Alekszej A1 - Fried, Miklós A1 - Burger, Sven A1 - Sáfrán, György A1 - Petrik, Peter T1 - Optimized Sensing on Gold Nanoparticles Created by Graded-Layer Magnetron Sputtering and Annealing JF - Sens. Actuators B Chem. Y1 - 2025 U6 - https://doi.org/10.1016/j.snb.2024.136875 VL - 425 SP - 136875 ER - TY - JOUR A1 - Betz, Fridtjof A1 - Binkowski, Felix A1 - Kuen, Lilli A1 - Burger, Sven T1 - Version 2 — RPExpand: Software for Riesz projection expansion of resonance phenomena JF - SoftwareX Y1 - 2024 U6 - https://doi.org/10.1016/j.softx.2024.101694 VL - 26 SP - 101694 ER - TY - CHAP A1 - Steyer, Joshua A1 - Chegini, Fatemeh A1 - Potse, Mark A1 - Loewe, Axel A1 - Weiser, Martin T1 - Continuity of Microscopic Cardiac Conduction in a Computational Cell-by-Cell Model T2 - 2023 Computing in Cardiology Conference (CinC) N2 - Conduction velocity in cardiac tissue is a crucial electrophysiological parameter for arrhythmia vulnerability. Pathologically reduced conduction velocity facilitates arrhythmogenesis because such conduction velocities decrease the wavelength with which re-entry may occur. Computational studies on CV and how it changes regionally in models at spatial scales multiple times larger than actual cardiac cells exist. However, microscopic conduction within cells and between them have been studied less in simulations. In this work, we study the relation of microscopic conduction patterns and clinically observable macroscopic conduction using an extracellular-membrane-intracellular model which represents cardiac tissue with these subdomains at subcellular resolution. By considering cell arrangement and non-uniform gap junction distribution, it yields anisotropic excitation propagation. This novel kind of model can for example be used to understand how discontinuous conduction on the microscopic level affects fractionation of electrograms in healthy and fibrotic tissue. Along the membrane of a cell, we observed a continuously propagating activation wavefront. When transitioning from one cell to the neighbouring one, jumps in local activation times occurred, which led to lower global conduction velocities than locally within each cell. Y1 - 2023 U6 - https://doi.org/10.22489/CinC.2023.385 SN - 2325-887X VL - 50 PB - Computing in Cardiology ER - TY - JOUR A1 - Plock, Matthias A1 - Binkowski, Felix A1 - Zschiedrich, Lin A1 - Schneider, Phillip-Immanuel A1 - Burger, Sven T1 - Fabrication uncertainty guided design optimization of a photonic crystal cavity by using Gaussian processes JF - J. Opt. Soc. Am. B Y1 - 2024 U6 - https://doi.org/10.1364/JOSAB.505767 VL - 41 SP - 850 ER - TY - GEN A1 - Plock, Matthias A1 - Binkowski, Felix A1 - Zschiedrich, Lin A1 - Schneider, Phillip-Immanuel A1 - Burger, Sven T1 - Research data for "Fabrication uncertainty guided design optimization of a photonic crystal cavity by using Gaussian processes" T2 - Zenodo Y1 - 2024 U6 - https://doi.org/10.5281/zenodo.8131611 SP - doi: 10.5281/zenodo.8131611 ER - TY - GEN A1 - Musial, Anna A1 - Sek, Grzegorz A1 - Schneider, Philipp-Immanuel A1 - Reitzenstein, Stephan T1 - Fiber-coupled solid-state-based single-photon sources T2 - Specialty Optical Fibers Y1 - 2024 U6 - https://doi.org/10.1016/B978-0-443-18495-6.00004-4 SP - 345 EP - 384 PB - Woodhead Publishing ER - TY - JOUR A1 - Kuen, Lilli A1 - Löffler, Lorenz A1 - Tsarapkin, Aleksei A1 - Zschiedrich, Lin A1 - Feichtner, Thorsten A1 - Burger, Sven A1 - Höflich, Katja T1 - Chiral and directional optical emission from a dipole source coupled to a helical plasmonic antenna JF - Appl. Phys. Lett. Y1 - 2024 U6 - https://doi.org/10.1063/5.0201748 VL - 124 SP - 231102 ER - TY - GEN A1 - Betz, Fridtjof A1 - Binkowski, Felix A1 - Burger, Sven A1 - Kuen, Lilli T1 - RPExpand (Version 2.0) T2 - Zenodo Y1 - 2023 U6 - https://doi.org/10.5281/zenodo.10371002 SP - doi: 10.5281/zenodo.10371002 ER - TY - CHAP A1 - Chegini, Fatemeh A1 - Froehly, Algiane A1 - Huynh, Ngoc Mai Monica A1 - Pavarino, Luca A1 - Potse, Mark A1 - Scacchi, Simone A1 - Weiser, Martin T1 - Efficient numerical methods for simulating cardiac electrophysiology with cellular resolution T2 - 10th Int. Conf. Computational Methods for Coupled Problems in Science and Engineering 2023 N2 - The cardiac extracellular-membrane-intracellular (EMI) model enables the precise geometrical representation and resolution of aggregates of individual myocytes. As a result, it not only yields more accurate simulations of cardiac excitation compared to homogenized models but also presents the challenge of solving much larger problems. In this paper, we introduce recent advancements in three key areas: (i) the creation of artificial, yet realistic grids, (ii) efficient higher-order time stepping achieved by combining low-overhead spatial adaptivity on the algebraic level with progressive spectral deferred correction methods, and (iii) substructuring domain decomposition preconditioners tailored to address the complexities of heterogeneous problem structures. The efficiency gains of these proposed methods are demonstrated through numerical results on cardiac meshes of different sizes. Y1 - 2023 UR - https://www.scipedia.com/public/2023f U6 - https://doi.org/10.23967/c.coupled.2023.004 ER -