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    <title>https://opus4.kobv.de/opus4-zib</title>
    <description>OPUS documents</description>
    <link>https://opus4.kobv.de/opus4-zib/index/index/</link>
    <pubDate>Fri, 06 Mar 2026 09:53:53 +0100</pubDate>
    <lastBuildDate>Fri, 06 Mar 2026 09:53:53 +0100</lastBuildDate>
    <item>
      <title>A Flexible Open-Source Framework for FPGA-based Network-Attached Accelerators using SpinalHDL</title>
      <link>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10305</link>
      <description>Domain-specific accelerators are increasingly vital in heterogeneous computing systems, driven by the demand for higher computational capacity and especially energy efficiency. Network-attached FPGAs promise a scalable and flexible alternative to closely coupled FPGAs for integrating accelerators into computing environments. While the advantages of specialized hardware implementations are apparent, traditional hardware development and integration remain time-consuming and complex.&#13;
&#13;
We present an open-source framework which combines a hardware shell with supporting software libraries, which enables fast development and deployment of FPGA-based network-attached accelerators. In contrast to traditional approaches using VHDL or Verilog, we leverage generative programming with SpinalHDL, providing a flexible hardware description with multi-level abstractions. This work eases the integration of accelerators into existing network infrastructures and simplifies adaptation to different FPGAs, eliminating complex and lengthy top-level hardware descriptions.</description>
      <author>Niklas Schelten; Steffen Christgau; Anton Schulte; Bettina Schnor; Hannes Signer; Benno Stabernack</author>
      <category>conferenceobject</category>
      <guid>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10305</guid>
      <pubDate>Fri, 06 Mar 2026 09:53:53 +0100</pubDate>
    </item>
    <item>
      <title>Minimizing and Maximizing the Shannon Entropy for Fixed Marginals</title>
      <link>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10304</link>
      <description>The mutual information (MI) between two random variables is an important&#13;
correlation measure in data analysis. The Shannon entropy of a joint probability distri-&#13;
bution is the variable part under fixed marginals. We aim to minimize and maximize it&#13;
to obtain the largest and smallest MI possible in this case, leading to a scaled MI ratio&#13;
for better comparability. We present algorithmic approaches and optimal solutions for&#13;
a set of problem instances based on data from molecular evolution. We show that this&#13;
allows us to construct a sensible, systematic correction to raw MI values.</description>
      <author>Paula Franke; Kay Hamacher; Paul Manns</author>
      <category>conferenceobject</category>
      <guid>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10304</guid>
      <pubDate>Thu, 05 Mar 2026 13:35:56 +0100</pubDate>
    </item>
    <item>
      <title>Globally Optimal Pose from Orthographic Silhouettes</title>
      <link>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10301</link>
      <description>We solve the problem of determining the pose of known shapes in R^3 from their unoccluded silhouettes. The pose is determined up to global optimality using a simple yet under-explored property of the area-of-silhouette: its continuity w.r.t trajectories in the rotation space. The proposed method utilises pre-computed silhouette-signatures, modelled as a response surface of the area-of-silhouettes. Querying this silhouette-signature response surface for pose estimation leads to a strong branching of the rotation search space, making resolution-guided candidate search feasible. Additionally, we utilise the aspect ratio of 2D ellipses fitted to projected silhouettes as an auxiliary global shape signature to accelerate the pose search. This combined strategy forms the first method to efficiently estimate globally optimal pose from just the silhouettes, without being guided by correspondences, for any shape, irrespective of its convexity and genus. We validate our method on synthetic and real examples, demonstrating significantly improved accuracy against comparable approaches.</description>
      <author>Agniva Sengupta; Dilara Kuş; Jianning Li; Stefan Zachow</author>
      <category>conferenceobject</category>
      <guid>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10301</guid>
      <pubDate>Wed, 04 Mar 2026 09:37:26 +0100</pubDate>
    </item>
    <item>
      <title>Distributed Parallel Structure-Aware Presolving for Arrowhead Linear Programs</title>
      <link>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10303</link>
      <description>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.&#13;
&#13;
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.</description>
      <author>Nils-Christian Kempke; Stephen John Maher; Daniel Rehfeldt; Ambros Gleixner; Thorsten Koch; Svenja Uslu</author>
      <category>reportzib</category>
      <guid>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10303</guid>
      <pubDate>Tue, 03 Mar 2026 23:15:01 +0100</pubDate>
    </item>
    <item>
      <title>Sammlungsdaten als Forschungsdaten in den Digital Humanities</title>
      <link>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10299</link>
      <description/>
      <author>Patrick Dinger; Anja Gerber; Anna Gnyp; Frank von Hagel; Georg Hohmann; Celia Krause; Sarah Wagner; Alexander Winkler</author>
      <category>conferenceobject</category>
      <guid>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10299</guid>
      <pubDate>Mon, 02 Mar 2026 22:04:18 +0100</pubDate>
    </item>
    <item>
      <title>Nano IR spectroscopy on Silicon-Supported Organic–Inorganic Hybrid Materials</title>
      <link>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10298</link>
      <description/>
      <author>Carolin Mehrmann; Jacob Johny; Petra Ebbinghaus; Martin Hammerschmidt; Ankita Das; Xin Wei; Marc F. Tesch; Martin Rabe</author>
      <category>article</category>
      <guid>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10298</guid>
      <pubDate>Thu, 26 Feb 2026 10:32:31 +0100</pubDate>
    </item>
    <item>
      <title>Comparing Branching Rules for the Quota Steiner Tree Problem with Interference</title>
      <link>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10297</link>
      <description>Branching decisions play a crucial role in branch-and-bound algorithms for solving combinatorial optimization problems. In this paper, we investigate several branching rules applied to the Quota Steiner Tree Problem with Interference (QSTPI). The Quota Steiner Tree Problem (QSTP) generalizes the classical Steiner Tree Problem (STP) in graphs by seeking a minimum-cost tree that connects a subset of profit-associated vertices whose cumulative profit meets or exceeds a given quota. The QSTPI introduces interference among vertices: Selecting certain vertices simultaneously reduces their individual contributions to the overall profit. This problem arises, for example, in positioning and connecting wind turbines, where turbines possibly shadow other turbines, reducing their energy yield. Unlike classical STP variants, large QSTPI instances require significantly more branching to compute provably optimal solutions. In contrast to branching on variables, we utilize the combinatorial structure of the QSTPI by branching on the graph's vertices. We adapt classical and problem-specific branching rules and present a comprehensive computational study comparing the effectiveness of these branching strategies.</description>
      <author>Jaap Pedersen; Niels Lindner; Daniel Rehfeldt; Thorsten Koch</author>
      <category>conferenceobject</category>
      <guid>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10297</guid>
      <pubDate>Wed, 25 Feb 2026 12:14:10 +0100</pubDate>
    </item>
    <item>
      <title>Improving Perovskite/CIGS Tandem Solar Cells for Higher Power Conversion Efficiency through Light Management and Bandgap Engineering</title>
      <link>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10296</link>
      <description/>
      <author>Guillermo Farias-Basulto; Thede Mehlhop; Nicolas J. Otto; Tobias Bertram; Klaus Jäger; Stefan Gall; Nikolaus Weinberger; Rutger Schlatmann; Iver Lauermann; Reiner Klenk; Emil List-Kratochvil; Christian A. Kaufmann</author>
      <category>article</category>
      <guid>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10296</guid>
      <pubDate>Tue, 24 Feb 2026 18:02:42 +0100</pubDate>
    </item>
    <item>
      <title>Semi-automatic geometrical reconstruction and analysis of filopodia dynamics in 4D two-photon microscopy images</title>
      <link>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10295</link>
      <description>Background: Filopodia are thin and dynamic membrane protrusions that play a crucial role in cell migration, axon guidance, and other processes where cells explore and interact with their surroundings. Historically, filopodial dynamics have been studied in great detail in 2D in cultured cells, and more recently in 3D culture as well as living brains. However, there is a lack of efficient tools to trace and track filopodia in 4D images of complex brain cells.&#13;
&#13;
Results: To address this issue, we have developed a semi-automatic workflow for tracing filopodia in 3D images and tracking the traced filopodia over time. The workflow was developed based on high-resolution data of photoreceptor axon terminals in the in vivo context of normal Drosophila brain development, but devised to be applicable to filopodia in any system, including at different temporal and spatial scales. In contrast to the pre-existing methods, our workflow relies solely on the original intensity images without the requirement for segmentation or complex preprocessing. The workflow was realized in C++ within the Amira software system and consists of two main parts, dataset pre-processing, and geometrical filopodia reconstruction, where each of the two parts comprises multiple steps. In this paper, we provide an extensive workflow description and demonstrate its versatility for two different axo-dendritic morphologies, R7 and Dm8 cells. Finally, we provide an analysis of the time requirements for user input and data processing.&#13;
&#13;
Conclusion: To facilitate simple application within Amira or other frameworks, we share the source code, which is available at https://github.com/zibamira/filopodia-tool.</description>
      <author>Blaž Brence; Josephine Brummer; Vincent J. Dercksen; Mehmet Neset Özel; Abhishek Kulkarni; Neele Wolterhoff; Steffen Prohaska; Peter Robin Hiesinger; Daniel Baum</author>
      <category>article</category>
      <guid>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10295</guid>
      <pubDate>Tue, 24 Feb 2026 10:15:24 +0100</pubDate>
    </item>
    <item>
      <title>Pole-Expansion of the T-Matrix Based on a Matrix-Valued AAA-Algorithm</title>
      <link>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10294</link>
      <description/>
      <author>Jan David Fischbach; Fridtjof Betz; Lukas Rebholz; Puneet Garg; Kristina Frizyuk; Felix Binkowski; Sven Burger; Martin Hammerschmidt; Carsten Rockstuhl</author>
      <category>article</category>
      <guid>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10294</guid>
      <pubDate>Mon, 23 Feb 2026 14:00:15 +0100</pubDate>
    </item>
    <item>
      <title>New Version of the COR Simulation Engine</title>
      <link>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10292</link>
      <description>The COR simulation engine is a tool devoted to evaluating cosmic ray trajectories in Earth's magnetosphere. It is part of the COR System, available at https://cor.crmodels.org, and it also functions as a standalone command line tool. The former tool was published in 2022. We report the new version of the tool status with improved performance, precision, new functions/features, and refactored code.</description>
      <author>Ján Villim; Martin Nguyen; Pavol Bobik; Jan Genci; Daniel Gecášek</author>
      <category>conferenceobject</category>
      <guid>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10292</guid>
      <pubDate>Wed, 18 Feb 2026 15:37:42 +0100</pubDate>
    </item>
    <item>
      <title>Photomask linewidth measurement comparison including an improved model-based through-focus measurement approach</title>
      <link>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10291</link>
      <description/>
      <author>Jan Krüger; Sven Dopslaff; Phillip Manley; Detlef Bergmann; Rainer Köning; Gaoliang Dai; Kai Hahm; Philipp-Immanuel Schneider; Martin Hammerschmidt; Lin Zschiedrich; Harald Bosse; Bernd Bodermann</author>
      <category>article</category>
      <guid>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10291</guid>
      <pubDate>Wed, 18 Feb 2026 10:08:39 +0100</pubDate>
    </item>
    <item>
      <title>Künstliche Intelligenz in Bibliotheken</title>
      <link>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10288</link>
      <description>Der Bibliotheksverbund Bayern und der Kooperative Bibliotheksverbund Berlin-Brandenburg haben in einem gemeinsamen Ideenworkshop im Mai 2025 Potenziale, Herausforderungen, Projekteansätze und Handlungsbedarfe bei Anwendung Künstlicher Intelligenz in Bibliotheken analysiert und diskutiert. Für die Handlungsfelder Interne Geschäftsgänge, Bibliotheksdienste, Forschungsnahe Dienste, Informationskompetenz und Analyse von Nutzungsdaten wurden Bedarfe identifiziert, Projektideen entwickelt und Handlungsempfehlungen formuliert.</description>
      <author>Fabian Franke; Frank Seeliger; Tomasz Stompor; Steffen Wawra</author>
      <category/>
      <guid>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10288</guid>
      <pubDate>Mon, 16 Feb 2026 08:34:31 +0100</pubDate>
    </item>
    <item>
      <title>FACET: Multi-Agent AI Supporting Teachers in Scaling Differentiated Learning for Diverse Students</title>
      <link>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10289</link>
      <description>Classrooms are becoming increasingly heterogeneous, comprising learners with diverse performance and motivation levels, language proficiencies, and learning differences such as dyslexia and ADHD. While teachers recognize the need for differentiated instruction, growing workloads create substantial barriers, making differentiated instruction an ideal that is often unrealized in practice. Current AI educational tools, which promise differentiated materials, are predominantly student-facing and performance-centric, ignoring other aspects that shape learning outcomes. We introduce FACET, a teacher-facing multi-agent framework designed to address these gaps by supporting differentiation that accounts for motivation, performance, and learning differences. Developed with educational stakeholders from the outset, the framework coordinates four specialized agents, including learner simulation, diagnostic assessment, material generation, and evaluation within a teacher-in-the-loop design. School principals (N = 30) shaped system requirements through participatory workshops, while in-service K-12 teachers (N = 70) evaluated material quality. Mixed-methods evaluation demonstrates strong perceived value for inclusive differentiation. Practitioners emphasized both the urgent need arising from classroom heterogeneity and the importance of maintaining pedagogical autonomy as a prerequisite for adoption. We discuss implications for future school deployment and outline partnerships for longitudinal classroom implementation.</description>
      <author>Jana Gonnermann-Müller; Jennifer Haase; Nicolas Leins; Moritz Igel; Konstantin Fackeldey; Sebastian Pokutta</author>
      <category>article</category>
      <guid>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10289</guid>
      <pubDate>Fri, 13 Feb 2026 13:42:38 +0100</pubDate>
    </item>
    <item>
      <title>An exciting approach to theoretical spectroscopy</title>
      <link>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10284</link>
      <description/>
      <author>Martí Raya-Moreno; Noah Alexy Dasch; Nasrin Farahani; Ignacio Gonzalez Oliva; Andris Gulans; Manoar Hossain; Hannah Kleine; Martin Kuban; Sven Lubeck; Benedikt Maurer; Pasquale Pavone; Fabian Peschel; Daria Popova-Gorelova; Lu Qiao; Elias Richter; Santiago Rigamonti; Ronaldo Rodrigues Pelá; Kshitij Sinha; Daniel T. Speckhard; Sebastian Tillack; Dmitry Tumakov; Seokhyun Hong; Janis Uzulis; Mara Voiculescu; Cecilia Vona; Mao Yang; Claudia Draxl</author>
      <category>article</category>
      <guid>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10284</guid>
      <pubDate>Fri, 13 Feb 2026 10:07:26 +0100</pubDate>
    </item>
    <item>
      <title>First-principles approach to ultrafast pump-probe spectroscopy in solids</title>
      <link>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10282</link>
      <description/>
      <author>Lu Qiao; Ronaldo Rodrigues Pelá; Claudia Draxl</author>
      <category>article</category>
      <guid>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10282</guid>
      <pubDate>Fri, 13 Feb 2026 10:05:30 +0100</pubDate>
    </item>
    <item>
      <title>Identification of Stress in Heterogeneous Contact Models</title>
      <link>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10286</link>
      <description>We develop a heterogeneous model of the lower limb system to simulate muscle forces and stresses acting on the knee joint. The modelling of the bone dynamics leads to an index-3 DAE, which we discretize by higher order collocation methods. Furthermore, we present an elastomechanical contact knee joint model of the articular cartilage. For the solution of the contact problem we develop an efficient multigrid solver, based on an Augmented-Lagrangian relaxation of the contact constraints. We formulate the identification of joint forces and resulting stresses with respect to different knee joint models as an inverse problem based on&#13;
medical gait data.</description>
      <author>Felix Baumann; Georg Duda; Anton Schiela; Martin Weiser</author>
      <category>incollection</category>
      <guid>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10286</guid>
      <pubDate>Mon, 09 Feb 2026 10:32:34 +0100</pubDate>
    </item>
    <item>
      <title>Assessing data quality in citation analysis: A case study of web of science and Crossref</title>
      <link>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10281</link>
      <description/>
      <author>Guoyang Rong; Ying Chen; Thorsten Koch; Keisuke Honda</author>
      <category>article</category>
      <guid>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10281</guid>
      <pubDate>Wed, 04 Feb 2026 12:22:20 +0100</pubDate>
    </item>
    <item>
      <title>Regression Techniques for Surrogate Modelling in Bayesian Inverse Problems</title>
      <link>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10280</link>
      <description>For many real-world applications, a system of interest can be represented via a mathematical model which depends on a set of parameters. In order to identify the parameters, a set of observations is available and an Inverse Problem is formulated. Identifying the parameters from the observations is often a challenging task, especially when the model is expensive to evaluate. This is the case for Partial Differential Equations models, where numerical simulations which are both inexact and computationally expensive are required to obtain the model output. To ease the computational costs, surrogate models can be used to approximate the forward model. In this work, we present two different regression techniques, Gaussian Process Regression and Lipschitz Regression. After reformulating the Inverse Problem to account for the surrogate model, we develope an adaptive training strategy to train the surrogate model. The proposed training strategy aims at optimizing not only the training points’ positions but also their evaluation accuracies. Moreover, interleaved sampling of the posterior distribution of the unknown parameters is performed while the surrogate model is trained, providing a solution for the Inverse Problem. The quality of the surrogating techniques as well as the effectiveness of the adaptive training strategy are tested through different numerical experiments.</description>
      <author>Paolo Villani</author>
      <category>masterthesis</category>
      <guid>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10280</guid>
      <pubDate>Mon, 02 Feb 2026 12:33:55 +0100</pubDate>
    </item>
    <item>
      <title>High-Performance Robust Energy System Planning with Storage: A Single-LP Approach</title>
      <link>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10277</link>
      <description/>
      <author>Thorsten Koch; Nils-Christian Kempke; Niels Lindner; Lukas Mehl; Manuel Wetzel; Janina Zittel</author>
      <category>conferenceobject</category>
      <guid>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10277</guid>
      <pubDate>Thu, 22 Jan 2026 10:01:10 +0100</pubDate>
    </item>
    <item>
      <title>Spatial analysis of COVID-19 and the Russia–Ukraine war impacts on natural gas flows using statistical and machine learning models</title>
      <link>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10276</link>
      <description/>
      <author>Natalia Selini Hadjidimitriou; Thorsten Koch; Marco Lippi; Milena Petkovic; Marco Mamei</author>
      <category>article</category>
      <guid>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10276</guid>
      <pubDate>Thu, 22 Jan 2026 09:52:30 +0100</pubDate>
    </item>
    <item>
      <title>Novel image registration approach for combining 2D Osterix and collagen bundles images with 3D µCT</title>
      <link>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10272</link>
      <description/>
      <author>Mireille Ngokingha Tchouto; Julia Mehl; Saeed Khomeijani Farahani; Daniel Baum; Georg Duda</author>
      <category>article</category>
      <guid>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10272</guid>
      <pubDate>Thu, 15 Jan 2026 09:47:42 +0100</pubDate>
    </item>
    <item>
      <title>Mean-field optimal control with stochastic leaders</title>
      <link>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10268</link>
      <description>We consider interacting agent systems with a large number of stochastic agents (or particles) influenced by a fixed number of external stochastic lead agents. Such examples arise, for example in models of opinion dynamics, where a small number of leaders (influencers) can steer the behaviour of a large population of followers. In this context, we study a partial mean-field limit where the number of followers tends to infinity, while the number of leaders stays constant. The partial mean-field limit dynamics is then given by a McKean-Vlasov stochastic differential equation (SDE) for the followers, coupled to a controlled Itô-SDE governing the dynamics of the lead agents. For a given cost functional that the lead agents seek to minimise, we show that the unique optimal control of the finite agent system convergences to the optimal control of the limiting system. This establishes that the low-dimensional control of the partial (mean-field) system provides an effective approximation for controlling the high-dimensional finite agent system. In addition, we propose a stochastic gradient descent algorithm that can efficiently approximate the mean-field control. Our theoretical results are illustrated on opinion dynamics model with lead agents, where the control objective is to drive the followers to reach consensus in finite time.</description>
      <author>Sebastian Zimper; Ana Djurdjevac; Carsten Hartmann; Christof Schütte; Natasa Djurdjevac Conrad</author>
      <category>article</category>
      <guid>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10268</guid>
      <pubDate>Tue, 13 Jan 2026 11:21:22 +0100</pubDate>
    </item>
    <item>
      <title>Revealing the Atomistic Mechanism of Rare Events in Molecular Dynamics</title>
      <link>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10267</link>
      <description>Interpretable reaction coordinates are essential for understanding rare conformational transitions in molecular dynamics. The Atomistic Mechanism Of Rare Events in Molecular Dynamics (AMORE-MD) framework enhances interpretability of deep-learned reaction coordinates by connecting them to atomistic mechanisms, without requiring any a priori knowledge of collective variables, pathways, or endpoints. Here, AMORE-MD employs the ISOKANN algorithm to learn a neural membership function χ representing the dominant slow process, from which transition pathways are reconstructed as minimum-energy paths aligned with the gradient of χ, and atomic contributions are quantified through gradient-based sensitivity analysis. Iterative enhanced sampling further enriches transition regions and improves coverage of rare events enabling recovery of known mechanisms and chemically interpretable structural rearrangements at atomic resolution for the Müller-Brown potential, alanine dipeptide, and the elastin-derived hexapeptide VGVAPG.</description>
      <author>Jakob Kresse; Alexander Sikorski; Surahit Chewle; Vikram Sunkara; Marcus Weber</author>
      <category>article</category>
      <guid>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10267</guid>
      <pubDate>Mon, 12 Jan 2026 16:42:25 +0100</pubDate>
    </item>
    <item>
      <title>Importance sampling of unbounded random stopping times: computing committor functions and exit rates without reweighting</title>
      <link>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10266</link>
      <description>Rare events in molecular dynamics are often related to noise-induced transitions between different macroscopic states (e.g., in protein folding). A common feature of these rare transitions is that they happen on timescales that are on average exponentially long compared to the characteristic timescale of the system, with waiting time distributions that have (sub)exponential tails and infinite support. As a result, sampling such rare events can lead to trajectories that can be become arbitrarily long, with not too low probability, which makes the reweighting of such trajectories a real challenge. Here, we discuss rare event simulation by importance sampling from a variational perspective, with a focus on applications in molecular dynamics, in particular the computation of committor functions. The idea is to design importance sampling schemes that (a) reduce the variance of a rare event estimator while controlling the average length of the trajectories and (b) that do not require the reweighting of possibly very long trajectories. In doing so, we study different stochastic control formulations for committor and mean first exit times, which we compare both from a theoretical and a computational point of view, including numerical studies of some benchmark examples.</description>
      <author>Carsten Hartmann; Annika Jöster; Christof Schütte; Alexander Sikorski; Marcus Weber</author>
      <category>article</category>
      <guid>https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10266</guid>
      <pubDate>Mon, 12 Jan 2026 15:36:10 +0100</pubDate>
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