The spatio-temporal modelling of mechanisms underlying pain relief via the µ-opioid receptor
We model all different aspects of μ-opioid receptor activation. This starts with the binding of an opioid to the receptor, followed by conformnational changes, spatio-temporal resolved signaling processes in the cell, the signaling effects, and the internalization and recovering of the μ-opioid receptor via the arrestin route. For this goal we need to model non-reversible molecular and signaling processes. The scientific goal is to estimate missing parameters, characteristic time-scales of the elementary steps, and coherent structures of non-reversible processes from (also experimental) data.
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2023
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Sourav Ray, Konstantin Fackeldey, Christoph Stein, Marcus Weber | Coarse Grained MD Simulations of Opioid interactions with the µ-opioid receptor and the surrounding lipid membrane | Biophysica, 3(2), pp. 263-275, 2023 |
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Thomas Ternes, Karl-Heinz Bauer, Frank Brauer, Jörg Drewes, Adriano Joss, Georg Hiller, Kevin Jewell, Jörg Oehlmann, Michael Radke, Ulrike Schulte-Oehlmann, Thomas Schwartz, Peter Seel, Jeanette Völker, Lilo Weber, Marcus Weber | Handlungsempfehlung zur integrativen Bewertung der weitergehenden Abwasserbehandlung von kommunalen Kläranlagen | Christian Wilhelm (Ed.), DWA / GDCh, 2023, ISBN: 978-3-96862-563-8 |
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Arne Thies, Vikram Sunkara, Sourav Ray, Hanna Wulkow, M. Özgür Celik, Fatih Yergöz, Christof Schütte, Christoph Stein, Marcus Weber, Stefanie Winkelmann | Modelling altered signalling of G-protein coupled receptors in inflamed environment to advance drug design | Scientific Reports, 13(607), 2023 |
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2022 |
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Rita Fernandes, Suvrat Chaowdhary, Noureldin Saleh, Natalia Mikula, Katerina Kanevche, Hans Berlepsch, Naoki Hosogi, Joachim Heberle, Marcus Weber, Christoph Böttcher, Beate Koksch | Cyanine Dye Coupling Mediates Self-assembly of a pH Sensitive Peptide into Novel 3D Architectures | Angewandte Chemie, 61(48), p. e202208647, 2022 |
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Renata Sechi, Konstantin Fackeldey, Surahit Chewle, Marcus Weber | SepFree NMF: A Toolbox for Analyzing the Kinetics of Sequential Spectroscopic Data | Algorithms, 15(9), p. 297, 2022 |
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Horst-Holger Boltz, Alexei Sirbu, Nina Stelzer, Primal de Lanerolle, Stefanie Winkelmann, Paolo Annibale | The Impact of Membrane Protein Diffusion on GPCR Signaling | Cells, 11(10), p. 1660, 2022 |
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2021 |
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Andreas Bittracher, Christof Schütte | A probabilistic algorithm for aggregating vastly undersampled large Markov chains | Physica D: Nonlinear Phenomena, Vol.416, 2021 (preprint available as ZIB-Report 20-21) |
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Susanne Röhl, Marcus Weber, Konstantin Fackeldey | Computing the minimal rebinding effect for non-reversible processes | Multiscale Modeling and Simulation, 19(1), pp. 460-477, 2021 |
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Andreas Bittracher, Stefan Klus, Boumediene Hamzi, Christof Schütte | Dimensionality Reduction of Complex Metastable Systems via Kernel Embeddings of Transition Manifolds | Journal of Nonlinear Science, Vol.31, 2021 |
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Andreas Bittracher, Johann Moschner, Beate Koksch, Roland Netz, Christof Schütte | Exploring the locking stage of NFGAILS amyloid fibrillation via transition manifold analysis | The European Physical Journal B, Vol.94, 2021 |
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Sourav Ray, Arne Thies, Vikram Sunkara, Hanna Wulkow, Özgür Celik, Fatih Yergöz, Christof Schütte, Christoph Stein, Marcus Weber, Stefanie Winkelmann | Modelling altered signalling of G-protein coupled receptors in inflamed environment to advance drug design | ZIB-Report 21-19 |
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Wolfgang Bauer, Marcus Weber, Eva Diehl-Wiesenecker, Noa Galtung, Monika Prpic, Rajan Somasundaram, Rudolf Tauber, Jochen Schwenk, Patrick Micke, Kai Kappert | Plasma Proteome Fingerprints Reveal Distinctiveness and Clinical Outcome of SARS-CoV-2 Infection | Viruses, 13(12), p. 2456, 2021 |
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Horst-Holger Boltz, Alexei Sirbu, Nina Stelzer, Martin J. Lohse, Christof Schütte, Paolo Annibale | Quantitative spectroscopy of single molecule interaction times | Optic Letters, 46(7), pp. 1538-1541, 2021 |
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2020 |
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Andreas Bittracher, Christof Schütte | A weak characterization of slow variables in stochastic dynamical systems | Advances in Dynamics, Optimization and Computation. Series: Studies in Systems, Decision and Control. A volume dedicated to Michael Dellnitz on the occasion of his 60th birthday, Vol.304, pp. 132-150, Oliver Junge, O. Schütze, Gary Froyland, S. Ober-Blobaum, E. Padberg-Gehle (Eds.), Springer International, 2020, ISBN: 978-3-030-51264-4 |
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Marcus Weber, Weitere Autoren | DIN SPEC 2343: Übertragung von sprachbasierten Daten zwischen Künstlichen Intelligenzen - Festlegung von Parametern und Formaten | Beuth Verlag, 2020 |
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Stefan Klus, Feliks Nüske, Sebastian Peitz, Jan-Hendrik Niemann, Cecilia Clementi, Christof Schütte | Data-driven approximation of the Koopman generator: Model reduction, system identification, and control | Physica D: Nonlinear Phenomena, Vol.406, 2020 (epub ahead of print) |
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Bernhard Reuter | Generalisierte Markov-Modellierung | Springer Spektrum, Wiesbaden, 2020, ISBN: 978-3-658-29711-4 |
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Sourav Ray, Vikram Sunkara, Christof Schütte, Marcus Weber | How to calculate pH-dependent binding rates for receptor-ligand systems based on thermodynamic simulations with different binding motifs | ZIB-Report 20-18 (Molecular Simulation, 46:18, 1443-1452) |
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Robert Julian Rabben, Sourav Ray, Marcus Weber | ISOKANN: Invariant subspaces of Koopman operators learned by a neural network | The Journal of Chemical Physics, 153(11), p. 114109, 2020 |
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Jan Möller, Ali Isbilir, Titiwat Sungkaworn, Brenda Osberg, Christos Karathanasis, Vikram Sunkara, Eugene O Grushevsky, Andreas Bock, Paolo Annibale, Mike Heilemann, Christof Schütte, Martin J. Lohse | Single molecule mu-opioid receptor membrane-dynamics reveal agonist-specific dimer formation with super-resolved precision | Nature Chemical Biology, Vol.16, pp. 946-954, 2020 |
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Mattes Mollenhauer, Ingmar Schuster, Stefan Klus, Christof Schütte | Singular Value Decomposition of Operators on Reproducing Kernel Hilbert Spaces | Advances om Dynamics, Optimization and Computation. Series: Studies in Systems, Decision and Control. A volume dedicated to Michael Dellnitz on his 60th birthday, Vol.304, pp. 109-131, Oliver Junge, O. Schütze, Gary Froyland, S. Ober-Blobaum, K. Padberg-Gehle (Eds.), Springer International, 2020, ISBN: 978-3-030-51264-4 |
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2019 |
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Péter Koltai, Han Cheng Lie, Martin Plonka | Fréchet differentiable drift dependence of Perron–Frobenius and Koopman operators for non-deterministic dynamics | Nonlinearity, 32(11), pp. 4232-4257, 2019 |
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Margarita Kostré | Hybrid Models and Simulations of Reaction-Diffusion Processes | Master's thesis, Freie Universität Berlin, Frank Noe (Advisor), 2019 |
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Stefan Klus, Brooke E. Husic, Mattes Mollenhauer, Frank Noe | Kernel methods for detecting coherent structures in dynamical data | Chaos: An Interdisciplinary Journal of Nonlinear Science, 29(12), 2019 |
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