TY - JOUR A1 - von Kleist, Max A1 - Schütte, Christof A1 - Zhang, Wei T1 - Statistical analysis of the first passage path ensemble of jump processes JF - Journal of Statistical Physics N2 - The transition mechanism of jump processes between two different subsets in state space reveals important dynamical information of the processes and therefore has attracted considerable attention in the past years. In this paper, we study the first passage path ensemble of both discrete-time and continuous-time jump processes on a finite state space. The main approach is to divide each first passage path into nonreactive and reactive segments and to study them separately. The analysis can be applied to jump processes which are non-ergodic, as well as continuous-time jump processes where the waiting time distributions are non-exponential. In the particular case that the jump processes are both Markovian and ergodic, our analysis elucidates the relations between the study of the first passage paths and the study of the transition paths in transition path theory. We provide algorithms to numerically compute statistics of the first passage path ensemble. The computational complexity of these algorithms scales with the complexity of solving a linear system, for which efficient methods are available. Several examples demonstrate the wide applicability of the derived results across research areas. Y1 - 2018 U6 - https://doi.org/10.1007/s10955-017-1949-x VL - 170 SP - 809 EP - 843 ER - TY - JOUR A1 - Zhang, Wei A1 - Schütte, Christof T1 - Understanding recent deep-learning techniques for identifying collective variables of molecular dynamics BT - Special Issue: 93rd Annual Meeting of the International Association of Applied Mathematics and Mechanics (GAMM) JF - Proceedings in Applied Mathematics and Mechanics N2 - High-dimensional metastable molecular dynamics (MD) can often be characterised by a few features of the system, that is, collective variables (CVs). Thanks to the rapid advance in the area of machine learning and deep learning, various deep learning-based CV identification techniques have been developed in recent years, allowing accurate modelling and efficient simulation of complex molecular systems. In this paper, we look at two different categories of deep learning-based approaches for finding CVs, either by computing leading eigenfunctions of transfer operator associated to the underlying dynamics, or by learning an autoencoder via minimisation of reconstruction error. We present a concise overview of the mathematics behind these two approaches and conduct a comparative numerical study of these two approaches on illustrative examples. Y1 - 2023 U6 - https://doi.org/10.1002/pamm.202300189 VL - 23 IS - 4 ER - TY - CHAP A1 - Koch, Thorsten A1 - Kempke, Nils-Christian A1 - Lindner, Niels A1 - Mehl, Lukas A1 - Wetzel, Manuel A1 - Zittel, Janina T1 - High-Performance Robust Energy System Planning with Storage: A Single-LP Approach T2 - Proceedings of URBSENSE 2026 - 1st International Workshop on URBan SENSEmaking and Intelligence for Safer Cities Y1 - 2026 ER - TY - CHAP A1 - Kunt, Tim T1 - Solving the n-Queens Problem in Higher Dimensions T2 - Operations Research Proceedings 2024. OR 2024 N2 - How many mutually non-attacking queens can be placed on a d-dimensional chessboard of size n? The n-queens problem in higher dimensions is a generalization of the well-known n-queens problem. We present an integer programming formulation of the n-queens problem in higher dimensions and several strengthenings through additional valid inequalities. Compared to recent benchmarks, we achieve a speedup in computational time between 15–70x over all instances of the integer programs. Our computational results prove optimality of certificates for several large instances. Breaking additional, previously unsolved instances with the proposed methods is likely possible. On the primal side, we further discuss heuristic approaches to constructing solutions that turn out to be optimal when compared to the IP. KW - Integer Programming KW - Maximum Independent Set KW - n-Queens Y1 - 2025 U6 - https://doi.org/10.1007/978-3-031-92575-7_29 SP - 205 EP - 211 ER - TY - JOUR A1 - Turner, Mark A1 - Berthold, Timo A1 - Besançon, Mathieu A1 - Koch, Thorsten T1 - Branching via Cutting Plane Selection: Improving Hybrid Branching N2 - Cutting planes and branching are two of the most important algorithms for solving mixed-integer linear programs. For both algorithms, disjunctions play an important role, being used both as branching candidates and as the foundation for some cutting planes. We relate branching decisions and cutting planes to each other through the underlying disjunctions that they are based on, with a focus on Gomory mixed-integer cuts and their corresponding split disjunctions. We show that selecting branching decisions based on quality measures of Gomory mixed-integer cuts leads to relatively small branch-and-bound trees, and that the result improves when using cuts that more accurately represent the branching decisions. Finally, we show how the history of previously computed Gomory mixed-integer cuts can be used to improve the performance of the state-of-the-art hybrid branching rule of SCIP. Our results show a $4\%$ decrease in solve time, and an $8\%$ decrease in number of nodes over affected instances of MIPLIB 2017. Y1 - 2023 PB - Springer 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 JF - IEEE Transactions on Visualization and Computer Graphics Y1 - 2026 U6 - https://doi.org/10.1109/TVCG.2026.3656066 ER - TY - JOUR A1 - Hadjidimitriou, Natalia Selini A1 - Koch, Thorsten A1 - Lippi, Marco A1 - Petkovic, Milena A1 - Mamei, Marco T1 - Spatial analysis of COVID-19 and the Russia–Ukraine war impacts on natural gas flows using statistical and machine learning models JF - World Wide Web Y1 - 2026 U6 - https://doi.org/https://doi.org/10.1007/s11280-025-01402-7 SN - 1386-145X VL - 29 IS - 2 PB - Springer Science and Business Media LLC ER - TY - GEN A1 - Kempke, Nils-Christian A1 - Maher, Stephen John A1 - Rehfeldt, Daniel A1 - Gleixner, Ambros A1 - Koch, Thorsten A1 - Uslu, Svenja T1 - Distributed Parallel Structure-Aware Presolving for Arrowhead Linear Programs N2 - We present a structure-aware parallel presolve framework specialized to arrowhead linear programs (AHLPs) and designed for high-performance computing (HPC) environments, integrated into the parallel interior point solver PIPS-IPM++. Large-scale LPs arising from automated model generation frequently contain redundancies and numerical pathologies that necessitate effective presolve, yet existing presolve techniques are primarily serial or structure-agnostic and can become time-consuming in parallel solution workflows. Within PIPS-IPM++, AHLPs are stored in distributed memory, and our presolve builds on this to apply a highly parallel, distributed presolve across compute nodes while keeping communication overhead low and preserving the underlying arrowhead structure. We demonstrate the scalability and effectiveness of our approach on a diverse set of AHLPs and compare it against state-of-the-art presolve implementations, including PaPILO and the presolve implemented within Gurobi. Even on a single machine, our presolve significantly outperforms PaPILO by a factor of 18 and Gurobi’s presolve by a factor of 6 in terms of shifted geometric mean runtime, while reducing the problems by a similar amount to PaPILO. Using a distributed compute environment, we outperform Gurobi's presolve by a factor of 13. T3 - ZIB-Report - 26-01 KW - Linear Programming KW - Presolving KW - Large-Scale Optimization KW - Distributed Parallel Computing KW - Arrowhead Y1 - 2026 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-103034 SN - 1438-0064 ER - TY - JOUR A1 - Sato, Mako A1 - Koch, Thorsten A1 - Le, Thi Thai T1 - Influence of frictional drag on Kelvin-Helmholtz instability in viscous fluids JF - Physics of Fluids N2 - The Kelvin-Helmholtz instability arises at the interface between two fluid layers with a tangential velocity discontinuity, significantly impacting the safety of systems in industrial applications. Despite extensive studies, many theoretical analyses neglect viscosity and frictional drag due to the complexity of solving the dispersion equation. However, including these effects is crucial, as viscosity alters the growth rate of the instability, while frictional drag influences energy dissipation and momentum transfer. In this study, these effects are incorporated into both finite and infinite flows. The assumption of a potential flow combined with a dissipation method is employed to derive the dispersion equation, providing a more tractable approach than direct calculation methods. The results indicate that, in the case of infinite flows, the frictional drag suppresses the growth of the instability for long waves (small wavenumber k) but enhances it for short waves (large k). In contrast, the surface tension dominates, while the frictional drag only slightly affects the growth rate in the case of finite flows bounded by solid walls. Y1 - 2026 U6 - https://doi.org/10.1063/5.0306177 VL - 38 IS - 1 PB - AIP Publishing CY - Physics of Fluids ER - TY - GEN A1 - Hartmann, Carsten A1 - Richter, Lorenz A1 - Schütte, Christof A1 - Zhang, Wei T1 - Variational characterization of free energy: Theory and algorithms N2 - The article surveys and extends variational formulations of the thermodynamic free energy and discusses their information-theoretic content from the perspective of mathematical statistics. We revisit the well-known Jarzynski equality for nonequilibrium free energy sampling within the framework of importance sampling and Girsanov change-of-measure transformations. The implications of the different variational formulations for designing efficient stochastic optimization and nonequilibrium simulation algorithms for computing free energies are discussed and illustrated. T3 - ZIB-Report - 17-52 KW - Importance sampling KW - Donsker-Varadhan principle KW - thermodynamic free energy KW - nonequilibrium molecular dynamics KW - stochastic approximation KW - cross-entropy method Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-65045 SN - 1438-0064 ER - TY - GEN A1 - Chmiela, Antonia A1 - Muñoz, Gonzalo A1 - Serrano, Felipe T1 - On the implementation and strengthening of intersection cuts for QCQPs N2 - The generation of strong linear inequalities for QCQPs has been recently tackled by a number of authors using the intersection cut paradigm - a highly studied tool in integer programming whose flexibility has triggered these renewed efforts in non-linear settings. In this work, we consider intersection cuts using the recently proposed construction of maximal quadratic-free sets. Using these sets, we derive closed-form formulas to compute intersection cuts which allow for quick cut-computations by simply plugging-in parameters associated to an arbitrary quadratic inequality being violated by a vertex of an LP relaxation. Additionally, we implement a cut-strengthening procedure that dates back to Glover and evaluate these techniques with extensive computational experiments. KW - Intersection cuts KW - QCQPs KW - Quadratic-free sets Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-79994 ER - TY - GEN A1 - Bestuzheva, Ksenia A1 - Chmiela, Antonia A1 - Müller, Benjamin A1 - Serrano, Felipe A1 - Vigerske, Stefan A1 - Wegscheider, Fabian T1 - Global Optimization of Mixed-Integer Nonlinear Programs with SCIP 8.0 N2 - For over ten years, the constraint integer programming framework SCIP has been extended by capabilities for the solution of convex and nonconvex mixed-integer nonlinear programs (MINLPs). With the recently published version~8.0, these capabilities have been largely reworked and extended. This paper discusses the motivations for recent changes and provides an overview of features that are particular to MINLP solving in SCIP. Further, difficulties in benchmarking global MINLP solvers are discussed and a comparison with several state-of-the-art global MINLP solvers is provided. T3 - ZIB-Report - 23-01 Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-89348 SN - 1438-0064 ER - TY - JOUR A1 - Raya-Moreno, Martí A1 - Dasch, Noah Alexy A1 - Farahani, Nasrin A1 - Gonzalez Oliva, Ignacio A1 - Gulans, Andris A1 - Hossain, Manoar A1 - Kleine, Hannah A1 - Kuban, Martin A1 - Lubeck, Sven A1 - Maurer, Benedikt A1 - Pavone, Pasquale A1 - Peschel, Fabian A1 - Popova-Gorelova, Daria A1 - Qiao, Lu A1 - Richter, Elias A1 - Rigamonti, Santiago A1 - Rodrigues Pelá, Ronaldo A1 - Sinha, Kshitij A1 - Speckhard, Daniel T. A1 - Tillack, Sebastian A1 - Tumakov, Dmitry A1 - Hong, Seokhyun A1 - Uzulis, Janis A1 - Voiculescu, Mara A1 - Vona, Cecilia A1 - Yang, Mao A1 - Draxl, Claudia T1 - An exciting approach to theoretical spectroscopy Y1 - 2026 ER - TY - JOUR A1 - Donati, Luca A1 - Schütte, Christof A1 - Weber, Marcus T1 - The Kramers turnover in terms of a macro-state projection on phase space JF - Molecular Physics N2 - We have investigated how Langevin dynamics is affected by the friction coefficient using the novel algorithm ISOKANN, which combines the transfer operator approach with modern machine learning techniques. ISOKANN describes the dynamics in terms of an invariant subspace projection of the Koopman operator defined in the entire state space, avoiding approximations due to dimensionality reduction and discretization. Our results are consistent with the Kramers turnover and show that in the low and moderate friction regimes, metastable macro-states and transition rates are defined in phase space, not only in position space. Y1 - 2025 U6 - https://doi.org/10.1080/00268976.2024.2356748 VL - 123 IS - 7-8: Giovanni Ciccotti: A Renaissance Physicist SP - e2356748 PB - Taylor & Francis ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Jocas, Arturas A1 - Weiser, Martin T1 - An Eikonal Approach for Globally Optimal Free Flight Trajectories N2 - We present an eikonal-based approach that is capable of finding a continuous globally optimal trajectory for an aircraft in a stationary wind field. This minimizes emissions and fuel consumption. If the destination is close to a cut locus of the associated Hamilton-Jacobi-Bellman equation, small numerical discretization errors can lead to selecting a merely locally optimal trajectory and missing the globally optimal one. Based on finite element error estimates, we construct a trust region around the cut loci in order to guarantee uniqueness of trajectories for destinations sufficiently far from cut loci. Y1 - 2026 ER - TY - JOUR A1 - Krüger, Jan A1 - Dopslaff, Sven A1 - Manley, Phillip A1 - Bergmann, Detlef A1 - Köning, Rainer A1 - Dai, Gaoliang A1 - Hahm, Kai A1 - Schneider, Philipp-Immanuel A1 - Hammerschmidt, Martin A1 - Zschiedrich, Lin A1 - Bosse, Harald A1 - Bodermann, Bernd T1 - Photomask linewidth measurement comparison including an improved model-based through-focus measurement approach JF - Meas. Sci. Technol. Y1 - 2026 U6 - https://doi.org/10.1088/1361-6501/ae44bb VL - 37 SP - 095004 ER - TY - JOUR A1 - Ngokingha Tchouto, Mireille A1 - Mehl, Julia A1 - Khomeijani Farahani, Saeed A1 - Baum, Daniel A1 - Duda, Georg T1 - Novel image registration approach for combining 2D Osterix and collagen bundles images with 3D µCT JF - Journal of Bone and Mineral Research Y1 - 2026 U6 - https://doi.org/10.1093/jbmrpl/ziag009 VL - 10 IS - 3 ER - TY - JOUR A1 - Qiao, Lu A1 - Rodrigues Pelá, Ronaldo A1 - Draxl, Claudia T1 - First-principles approach to ultrafast pump-probe spectroscopy in solids Y1 - 2026 ER - TY - JOUR A1 - del Razo, Mauricio A1 - Lamma, Tommaso A1 - Merbis, Wout T1 - Field theories and quantum methods for stochastic reaction-diffusion systems JF - Rev. Mod. Phys. N2 - Complex systems are composed of many particles or agents that move and interact with one another. In most real-world applications, these systems involve a varying number of particles/agents that change due to interactions with the environment or their internal dynamics. The underlying mathematical framework to model these systems must incorporate the spatial transport of particles/agents and their interactions, as well as changes to their copy numbers, all of which can be formulated in terms of stochastic reaction-diffusion processes. However, the standard probabilistic representation of these processes can be overly complex because of the combinatorial aspects arising due to the non-linear interactions and varying particle numbers. In this manuscript, we review the main field theory representations of stochastic reaction-diffusion systems, which handle these issues "under–the–hood’’. First, we focus on bringing techniques familiar to theoretical physicists —such as second quantization, Fock space, path integrals and quantum field theory— back into the classical domain of reaction-diffusion systems. We demonstrate how various field theory representations, which have evolved historically, can all be unified under a single basis-independent representation. We then extend existing quantum-based methods and notation to work directly on the level of the unifying representation, and we illustrate how they can be used to consistently obtain previous known results in a more straightforward manner, such as numerical discretizations and relations between model parameters at multiple scales. Throughout the work, we contextualize how these representations mirror well-known models of chemical physics depending on their spatial resolution, as well as the corresponding macroscopic (large copy number) limits. The framework presented here may find applications in a diverse set of scientific fields, including physical chemistry, theoretical ecology, epidemiology, game theory and socio-economical models of complex systems, specifically in the modeling and multi-scale simulation of complex systems with varying numbers of particles/agents. The presentation is done in a self-contained educational and unifying manner such that it can be followed by researchers across several fields. Y1 - 2026 U6 - https://doi.org/10.1103/9qlw-gyd7 VL - 98 ER - TY - JOUR A1 - Subramaniam, Jayant Shanmugam A1 - Hubig, Michael A1 - Schenkl, Sebastian A1 - Muggenthaler, Holger A1 - Springer, Steffen A1 - Weiser, Martin A1 - Sudau, Jakob A1 - Shah, Faisal A1 - Mall, Gita T1 - Reconstructing sudden ambient temperature changes for forensic death time estimation using temperatures in two closed compartments: Proof of concept JF - International Journal of Legal Medicine N2 - Ambient temperature TA has a strong impact on temperature-based time since death estimation (TTDE). Frequently TA is lowered instantaneously at some time t0 from a previous value TA0 to TA1 < TA0 by, e.g., opening a window or a door. We aim at reconstructing TA0 and t0. TTDE literature suggests temperature measurements in closed compartments such as cupboards or neighboring rooms, where TA0 could have been ‘preserved’ after t0. We aim to estimate t0 and TA0 from temperature measurements TZ(t) in closed compartments Z at times t > t0. We obtain promising results assuming Newtonian cooling for boxes filled with air, heaps of clothes, or books in two different experimental scenarios. Two different parameter estimators, (TA0^, t0^) based on four temperature measurements and (TA0*, t0*) for 4N measurements were tested. Our results in a climate chamber were partially appropriate for TTDE input. A decline at time t0 from TA0 = 22.5°C ↓ TA1 = 14°C was reconstructed at t = t0 + 95min with relative deviations ρt0^ = 27% and ρTA0^ = 19% relative to t - t0 and TA0 – TA1 respectively, for N = 1 with span Δt = 50min. For N = 200 in a time interval [t0 + 95min, t0 + 295min] we found ρt0^ = 5% and ρTA0^ = 11% with the same Δt. Further research is necessary to guarantee applicability in routine casework, in particular with respect to more elaborate cooling models, estimation algorithms, and evaluation localization. Y1 - 2026 ER -