TY - JOUR A1 - Harth, Philipp A1 - Udvary, Daniel A1 - Boelts, Jan A1 - Baum, Daniel A1 - Macke, Jakob H. A1 - Hege, Hans-Christian A1 - Oberlaender, Marcel T1 - Dissecting origins of wiring specificity in dense cortical connectomes JF - bioRxiv N2 - Wiring specificity in the cortex is observed across scales from the subcellular to the network level. It describes the deviations of connectivity patterns from those expected in randomly connected networks. Understanding the origins of wiring specificity in neural networks remains difficult as a variety of generative mechanisms could have contributed to the observed connectome. To take a step forward, we propose a generative modeling framework that operates directly on dense connectome data as provided by saturated reconstructions of neural tissue. The computational framework allows testing different assumptions of synaptic specificity while accounting for anatomical constraints posed by neuron morphology, which is a known confounding source of wiring specificity. We evaluated the framework on dense reconstructions of the mouse visual and the human temporal cortex. Our template model incorporates assumptions of synaptic specificity based on cell type, single-cell identity, and subcellular compartment. Combinations of these assumptions were sufficient to model various connectivity patterns that are indicative of wiring specificity. Moreover, the identified synaptic specificity parameters showed interesting similarities between both datasets, motivating further analysis of wiring specificity across species. Y1 - 2024 U6 - https://doi.org/10.1101/2024.12.14.628490 ER - TY - CHAP A1 - Klenert, Nicolas A1 - Schwoerer, Finn A1 - Hajarolasvadi, Noushin A1 - Bournez, Siloé A1 - Arlt, Tobias A1 - Mahnke, Heinz-Eberhard A1 - Lepper, Verena A1 - Baum, Daniel T1 - Improving the Identification of Layers in 3D Images of Ancient Papyrus using Artificial Neural Networks T2 - 2025 IEEE/CVF Winter Conference on Applications of Computer Vision Workshops (WACVW), Tucson, AZ, USA N2 - The process of digitally unfolding ancient documents, such as folded papyrus packages, from 3D image data aims to be a non-invasive means to make previously hidden writing visible without risking to damage the precious documents. One of the main tasks necessary to digitally unfold a document is the geometric reconstruction of the writing substrate, which is a prerequisite for its subsequent unfolding. All current reconstruction methods require the existence of an interspace between different layers of the document to ensure a correct topology. Layers that appear merged together in the 3D image often result in wrong connections between layers and thus also in a wrong topology of the reconstructed geometry, which hinders the successful unfolding. Here, we propose to use a neural network to facilitate the discrimination of the layers. Using papyrus documents as an example of a particularly difficult writing material, we show that this significantly reduces the number of wrong connections and improves the overall identification of the layers. This in turn enables fully automatic digital unfolding of large areas of highly complex papyrus packages. Utilizing explainable AI (XAI) further allows us to explore the results of the applied neural network. Y1 - 2025 U6 - https://doi.org/10.1109/WACVW65960.2025.00143 SP - 1204 EP - 1212 ER - TY - GEN A1 - Binkowski, Felix A1 - Betz, Fridtjof A1 - Hammerschmidt, Martin A1 - Zschiedrich, Lin A1 - Burger, Sven T1 - Source code and simulation results: Resonance modes in microstructured photonic waveguides - Efficient and accurate computation based on AAA rational approximation T2 - Zenodo Y1 - 2024 U6 - https://doi.org/10.5281/zenodo.14202408 SP - doi: 10.5281/zenodo.14202408 ER - TY - JOUR A1 - Binkowski, Felix A1 - Betz, Fridtjof A1 - Hammerschmidt, Martin A1 - Zschiedrich, Lin A1 - Burger, Sven T1 - Resonance modes in microstructured photonic waveguides: Efficient and accurate computation based on AAA rational approximation JF - Nanophotonics Y1 - 2025 U6 - https://doi.org/10.1515/nanoph-2024-0755 VL - 14 SP - 1665 ER - TY - JOUR A1 - Clausecker, Robert A1 - Lemire, Daniel A1 - Schintke, Florian T1 - Faster Positional-Population Counts for AVX2, AVX-512, and ASIMD JF - CoRR Y1 - 2024 U6 - https://doi.org/10.48550/arXiv.2412.16370 VL - abs/2412.16370 SP - 1 EP - 23 ER - TY - JOUR A1 - Donati, Luca A1 - Chewle, Surahit A1 - St. Pierre, Dominik A1 - Natarajan, Vijay A1 - Weber, Marcus T1 - Topological analysis reveals multiple pathways in molecular dynamics JF - Journal of Chemical Theory and Computation N2 - Molecular Dynamics simulations are indispensable tools for comprehending the dynamic behavior of biomolecules, yet extracting meaningful molecular pathways from these simulations remains challenging due to the vast amount of high dimensional data. In this work, we present Molecular Kinetics via Topology (MoKiTo), a novel approach that combines the ISOKANN algorithm to determine the membership function of a molecular system with a topological analysis tool inspired by the Mapper algorithm. Our strategy efficiently identifies and characterizes distinct molecular pathways, enabling the detection and visualization of critical conformational transitions and rare events. This method offers deeper insights into molecular mechanisms, facilitating the design of targeted interventions in drug discovery and protein engineering. Y1 - 2025 U6 - https://doi.org/10.1021/acs.jctc.5c00819 VL - 21 IS - 20 SP - 10385 EP - 10397 CY - J. Chem. Theory Comput. ER - TY - JOUR A1 - Trepczynski, Adam A1 - Kneifel, Paul A1 - Heyland, Mark A1 - Leskovar, Marko A1 - Moewis, Philippe A1 - Damm, Philipp A1 - Taylor, William R. A1 - Zachow, Stefan A1 - Duda, Georg T1 - Impact of the External Knee Flexion Moment on Patello-Femoral Loading Derived from in vivo Loads and Kinematics JF - Frontiers in Bioengineering and Biotechnology N2 - Anterior knee pain and other patello-femoral (PF) complications frequently limit the success of total knee arthroplasty as the final treatment of end stage osteoarthritis. However, knowledge about the invivo loading conditions at the PF joint remains limited, as no direct measurements are available. We hypothesised that the external knee flexion moment (EFM) is highly predictive of the PF contact forces during activities with substantial flexion of the loaded knee.Six patients (65-80 years, 67-101 kg) with total knee arthroplasty (TKA) performed two activities of daily living: sit-stand-sit and squat. Tibio-femoral (TF) contact forces were measured in vivo using instrumented tibial components, while synchronously internal TF and PF kinematics were captured with mobile fluoroscopy. The measurements were used to compute PF contact forces using patient specific musculoskeletal models. The relationship between the EFM and the PF contact force was quantified using linear regression.Mean peak TF contact forces of 1.97 to 3.24 times body weight (BW) were found while peak PF forces reached 1.75 to 3.29 times body weight (BW). The peak EFM ranged from 3.2 to 5.9 %BW times body height, and was a good predictor of the PF contact force (R^2 = 0.95 and 0.88 for sit-standsit and squat, respectively).The novel combination of in vivo TF contact forces and internal patellar kinematics enabled a reliable assessment of PF contact forces. The results of the regression analysis suggest that PF forces can be estimated based solely on the EFM from quantitative gait analysis. Our study also demonstrates the relevance of PF contact forces, which reach magnitudes similar to TF forces during activities of daily living. Y1 - 2024 U6 - https://doi.org/10.3389/fbioe.2024.1473951 VL - 12 ER - TY - JOUR A1 - Masing, Berenike A1 - Lindner, Niels A1 - Bortoletto, Enrico T1 - Computing All Shortest Passenger Routes with a Tropical Dijkstra Algorithm JF - EURO Journal on Transportation and Logistics N2 - Given a public transportation network, which and how many passenger routes can potentially be shortest paths, when all possible timetables are taken into account? This question leads to shortest path problems on graphs with interval costs on their arcs and is closely linked to multi-objective optimization. We introduce a Dijkstra algorithm based on polynomials over the tropical semiring that computes complete or minimal sets of efficient paths. We demonstrate that this approach is computationally feasible by employing it on the public transport network of the city of Wuppertal and instances of the benchmarking set TimPassLib, and we evaluate the resulting sets of passenger routes. Y1 - 2025 U6 - https://doi.org/10.1016/j.ejtl.2025.100163 VL - 14 ER - TY - JOUR A1 - del Razo, Mauricio A1 - Delle Site, Luigi T1 - Dynamics of systems with varying number of particles: from Liouville equations to general master equations for open systems JF - SciPost Physics N2 - A varying number of particles is one of the most relevant characteristics of systems of interest in nature and technology, ranging from the exchange of energy and matter with the surrounding environment to the change of particle number through internal dynamics such as reactions. The physico-mathematical modeling of these systems is extremely challenging, with the major difficulty being the time dependence of the number of degrees of freedom and the additional constraint that the increment or reduction of the number and species of particles must not violate basic physical laws. Theoretical models, in such a case, represent the key tool for the design of computational strategies for numerical studies that deliver trustful results. In this manuscript, we review complementary physico-mathematical approaches of varying number of particles inspired by rather different specific numerical goals. As a result of the analysis on the underlying common structure of these models, we propose a unifying master equation for general dynamical systems with varying number of particles. This equation embeds all the previous models and can potentially model a much larger range of complex systems, ranging from molecular to social agent-based dynamics. Y1 - 2024 U6 - https://doi.org/10.21468/SciPostPhys.18.1.001 VL - 18, 001 ER - TY - THES A1 - Ernst, Ariane T1 - Mathematical modeling and analysis of neurotransmission N2 - Modeling and simulation of neurotransmission plays a central role in the scientific investigation of synaptic functioning and neuronal communication. Understanding the neurotransmission process is crucial due to its fundamental significance in cognitive function, with impairments in this process potentially giving rise to severe pathological conditions. Existing modeling approaches capture the dynamic behavior and the probabilistic properties of the synaptic machinery utilizing results from stochastic chemical kinetics. However, the underlying mathematical theory rarely receives detailed consideration. In this thesis, we explore the neurotransmission process from a mathematical perspective and provide important insights that improve efficiency in its modeling and simulation. We introduce a new method for the direct and exact computation of first- and second-order moments of the postsynaptic current for the case of linear reaction networks, circumventing previously employed stochastic simulations. The approach hinges on the computation of the cross-correlation functions for the associated Markov jump process and their characterization by a partial differential equation. Our method can be applied to efficiently compare coarse-graining strategies for neurotransmission models, which we demonstrate for a significant recent model of synaptic vesicle release. We also numerically analyze the feasibility of reducing this particular model and show that a reduction can preserve the characteristics of the mean output current and its standard deviation to a satisfactory degree under typical stimulation conditions, where the approximation error can even be neglected depending on release site position. As the dependency on the local calcium concentration is preserved in the reduced model, it can be subjected to arbitrary types of signals in future studies. Moreover, we investigate the recovery processes of synaptic vesicles and release sites by introducing a nonlinear model with explicit recovery reactions. A sensitivity analysis provides the novel insight that the widely debated identity of the limiting recovery process during sustained stimulation is time-dependent. For our model, the output current’s first-order moment and its deterministic approximation show an exceptionally high level of agreement. We determine this to be an inherent consequence of the model structure due to the independence of the two recovery processes, supporting future use of the deterministic approximation. Parameter estimations confirm our model’s capability of reproducing experimental data. Y1 - 2024 ER -