TY - JOUR A1 - Bestuzheva, Ksenia A1 - Gleixner, Ambros A1 - Achterberg, Tobias T1 - Efficient separation of RLT cuts for implicit and explicit bilinear terms JF - Mathematical Programming Y1 - 2025 U6 - https://doi.org/10.1007/s10107-024-02104-0 VL - 210 SP - 47 EP - 74 ER - TY - JOUR A1 - Stengl, Steven-Marian A1 - Gelß, Patrick A1 - Klus, Stefan A1 - Pokutta, Sebastian T1 - Existence and uniqueness of solutions of the Koopman--von Neumann equation on bounded domains JF - Journal of Physics A: Mathematical and Theoretical Y1 - 2024 U6 - https://doi.org/10.1088/1751-8121/ad6f7d VL - 57 IS - 39 ER - TY - JOUR A1 - Böttcher, Julia A1 - Parczyk, Olaf A1 - Sgueglia, Amedeo A1 - Skokan, Jozef T1 - The square of a Hamilton cycle in randomly perturbed graphs JF - Random Structures & Algorithms Y1 - 2024 U6 - https://doi.org/10.1002/rsa.21215 VL - 65 IS - 2 SP - 342 EP - 386 ER - TY - JOUR A1 - Deza, Antoine A1 - Onn, Shmuel A1 - Pokutta, Sebastian A1 - Pournin, Lionel T1 - Kissing polytopes JF - SIAM Journal on Discrete Mathematics N2 - We investigate the following question: How close can two disjoint lattice polytopes contained in a fixed hypercube be? This question stems from various contexts where the minimal distance between such polytopes appears in complexity bounds of optimization algorithms. We provide nearly matching bounds on this distance and discuss its exact computation. We also give similar bounds for disjoint rational polytopes whose binary encoding length is prescribed. Y1 - 2024 U6 - https://doi.org/10.1137/24M1640859 VL - 38 IS - 4 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 - TY - JOUR A1 - Weimann, Kuba A1 - Conrad, Tim T1 - FELRec: Efficient Handling of Item Cold-Start With Dynamic Representation Learning in Recommender Systems JF - International Journal of Data Science and Analytics Y1 - 2024 U6 - https://doi.org/10.1007/s41060-024-00635-5 IS - 2024 PB - Springer Nature ER - TY - JOUR A1 - Binkowski, Felix A1 - Burger, Sven A1 - Kewes, Günter T1 - A tiny Drude scatterer can accurately model a coherent emitter in nanophotonics JF - Nanophotonics Y1 - 2024 U6 - https://doi.org/10.1515/nanoph-2024-0170 VL - 13 SP - 4537 ER - TY - JOUR A1 - Roche, Léo J. A1 - Betz, Fridtjof A1 - Yang, Yuhui A1 - Limame, Imad A1 - Shih, Ching-Wen A1 - Burger, Sven A1 - Reitzenstein, Stephan T1 - Numerical Investigation of a Coupled Micropillar - Waveguide System for Integrated Quantum Photonic Circuits JF - Adv. Quantum Technol. Y1 - 2024 U6 - https://doi.org/10.1002/qute.202400195 VL - 7 SP - 2400195 ER - TY - JOUR A1 - Asadova, Nigar A1 - Achouri, Karim A1 - Arjas, Kristian A1 - Ajuguié, Baptiste A1 - Aydin, Roland A1 - Baron, Alexandre A1 - Beutel, Dominik A1 - Bodermann, Bernd A1 - Boussaoud, Kaoutar A1 - Burger, Sven A1 - Choi, Minseok A1 - Czajkowski, Krzysztof A1 - Evlyukhin, Andrey B. A1 - Fazel-Najafabadi, Atefeh A1 - Fernandez-Corbaton, Ivan A1 - Garg, Puneet A1 - Globosits, David A1 - Hohenester, Ulrich A1 - Kim, Hongyoon A1 - Kim, Seokwoo A1 - Lalanne, Philippe A1 - Le Ru, Eric C. A1 - Meyer, Jörg A1 - Mun, Jungho A1 - Patelli, Lorenzo A1 - Pflug, Lukas A1 - Rockstuhl, Carsten A1 - Rho, Junsuk A1 - Rotter, Stefan A1 - Stout, Brian A1 - Törmä, Päivi A1 - Trigo, Jorge Olmos A1 - Tristram, Frank A1 - Tsitsas, Nikolaos L. A1 - Vallée, Renaud A1 - Vynck, Kevin A1 - Weiss, Thomas A1 - Wiecha, Peter A1 - Wriedt, Thomas A1 - Yannopapas, Vassilios A1 - Yurkin, Maxim A. A1 - Zouros, Grigorios P. T1 - T-matrix representation of optical scattering response: Suggestion for a data format JF - J. Quant. Spectrosc. Radiat. Transf. Y1 - 2025 U6 - https://doi.org/10.1016/j.jqsrt.2024.109310 VL - 333 SP - 109310 ER - TY - JOUR A1 - Kameda, Takeru A1 - Saha, Daniel K. A1 - Ray, Sourav A1 - Togashi, Yuichi A1 - Asano, Katsura T1 - Protocol for calculating binding free energy of RNA:RNA interactions through molecular dynamics simulations using adaptive biasing force technique JF - STAR Protocols Y1 - 2024 U6 - https://doi.org/10.1016/j.xpro.2024.103223 VL - 5 IS - 3 PB - Elsevier BV ER - TY - JOUR A1 - Sun, Jingtong A1 - Berner, Julius A1 - Richter, Lorenz A1 - Zeinhofer, Marius A1 - Müller, Johannes A1 - Azizzadenesheli, Kamyar A1 - Anandkumar, Anima T1 - Dynamical Measure Transport and Neural PDE Solvers for Sampling N2 - The task of sampling from a probability density can be approached as transporting a tractable density function to the target, known as dynamical measure transport. In this work, we tackle it through a principled unified framework using deterministic or stochastic evolutions described by partial differential equations (PDEs). This framework incorporates prior trajectory-based sampling methods, such as diffusion models or Schrödinger bridges, without relying on the concept of time-reversals. Moreover, it allows us to propose novel numerical methods for solving the transport task and thus sampling from complicated targets without the need for the normalization constant or data samples. We employ physics-informed neural networks (PINNs) to approximate the respective PDE solutions, implying both conceptional and computational advantages. In particular, PINNs allow for simulation- and discretization-free optimization and can be trained very efficiently, leading to significantly better mode coverage in the sampling task compared to alternative methods. Moreover, they can readily be fine-tuned with Gauss-Newton methods to achieve high accuracy in sampling. Y1 - 2024 ER - TY - JOUR A1 - Richter, Lorenz A1 - Sallandt, Leon A1 - Nüsken, Nikolas T1 - From continuous-time formulations to discretization schemes: tensor trains and robust regression for BSDEs and parabolic PDEs JF - Journal of Machine Learning Research N2 - The numerical approximation of partial differential equations (PDEs) poses formidable challenges in high dimensions since classical grid-based methods suffer from the so-called curse of dimensionality. Recent attempts rely on a combination of Monte Carlo methods and variational formulations, using neural networks for function approximation. Extending previous work (Richter et al., 2021), we argue that tensor trains provide an appealing framework for parabolic PDEs: The combination of reformulations in terms of backward stochastic differential equations and regression-type methods holds the romise of leveraging latent low-rank structures, enabling both compression and efficient computation. Emphasizing a continuous-time viewpoint, we develop iterative schemes, which differ in terms of computational efficiency and robustness. We demonstrate both theoretically and numerically that our methods can achieve a favorable trade-off between accuracy and computational efficiency. While previous methods have been either accurate or fast, we have identified a novel numerical strategy that can often combine both of these aspects. Y1 - 2024 UR - https://www.jmlr.org/papers/volume25/23-0982/23-0982.pdf VL - 25 SP - 248 ER - TY - JOUR A1 - Schmitt, Kira A1 - Titschack, Jürgen A1 - Baum, Daniel T1 - CoDA: Interactive Segmentation and Morphological Analysis of Dendroid Structures Exemplified on Stony Cold-Water Corals N2 - Dendroid stony corals build highly complex colonies that develop from a single coral polyp sitting in a cup-like skeleton, called corallite, by asexual reproduction, resulting in a tree-like branching pattern of its skeleton. Despite their beauty and ecological importance as reef builders in tropical shallow-water reefs as well as in cold-water coral mounds in the deep ocean, systematic studies investigating the ontogenetic morphological development of such coral colonies are largely missing. One reason for this is the sheer number of corallites – up to several thousands in a single coral colony. Another limiting factor, especially for the analysis of dendroid cold-water corals, is the existence of many secondary joints in the ideally tree-like structure that make a reconstruction of the skeleton tree extremely tedious. Herein, we present CoDA, the Coral Dendroid structure Analyzer, a visual analytics suite that allows for the first time to investigate the ontogenetic morphological development of complex dendroid coral colonies, exemplified on three important framework-forming dendroid cold-water corals: Lophelia pertusa (Linnaeus, 1758), Madrepora oculata (Linnaeus, 1758), and Goniocorella dumosa (Alcock, 1902). Input to CoDA is an initial instance segmentation of the coral polyp cavities (calices), from which it estimates the skeleton tree of the colony and extracts classical morphological measurements and advanced shape features of the individual corallites. CoDA also works as a proofreading and error correction tool by helping to identify wrong parts in the skeleton tree and providing tools to quickly correct these errors. The final skeleton tree enables the derivation of additional information about the calices/corallite instances that otherwise could not be obtained, including their ontogenetic generation and branching patterns – the basis of a fully quantitative statistical analysis of the coral colony morphology. Part of CoDA is CoDA.Graph, a feature-rich link-and-brush user interface for visualizing the extracted features and 2D graph layouts of the skeleton tree, enabling the real-time exploration of complex coral colonies and their building blocks, the individual corallites and branches. In the future, we expect CoDA to greatly facilitate the analysis of large stony corals of different species and morphotypes, as well as other dendroid structures, enabling new insights into the influence of genetic and environmental factors on their ontogenetic morphological development. Y1 - 2024 ER - TY - JOUR A1 - Shimada, Naoki A1 - Mako, Sato A1 - Yaegashi, Yuta A1 - Koch, Thorsten A1 - Le, Thi Thai T1 - An Application of Modified S-CLSVOF Method to Kelvin-Helmholtz Instability and Comparison with Theoretical Result JF - Journal of Chemical Engineering of Japan N2 - This study focuses on validating a two-phase flow solver based on the modified Simple Coupled Level Set and Volume of Fluid method (Uchihashi et al. (2023)) through viscous Kelvin-Helmholtz instability simulations. Our numerical simulation results are compared with the ones given by Funada and Joseph (2001) to provide reliable predictions of interface behavior under the influence of viscosity. The primary goal is to accurately assess the solver's ability to replicate theoretical analysis of interface behaviors under various conditions. First, the wave between two fluids of identical density is calculated. In addition, the effect of surface tension is investigated. By comparing growth rates, numerical simulations obtain well-agreements with the analytical results on the effect of the fluid viscosity, the wave number, and the surface tension. Finally, fluid density is changed to an air-water system. When relative velocity U is smaller than the criteria of relative velocity U_c given by analytical solutions, the wave is not broken. However, waves are splashed into droplets in the condition of U>U_c. This result agrees with the analysis by Funada and Joseph (2001). These findings provide a robust framework for applying the solver to more complex two-phase flow problems, supporting advancements in numerical simulations of fluid interfaces. Y1 - 2025 U6 - https://doi.org/10.1080/00219592.2025.2451953 VL - 58 IS - 1 PB - Taylor and Francis 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 - 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 - 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 - 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 - 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 - 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 -