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Home Members Winkelmann, Stefanie, Dr.

Winkelmann, Stefanie, Dr.

Winkelmann

Contact

Position
Head of Research Group
Room
4104
Phone
+49 30 84185-156
Email
Email
Website
Personal Homepage
Division
Mathematics of Complex Systems
Department
Modeling and Simulation of Complex Processes
Group
Computational Systems Biology

Projects

Projects as Head

Illustration of vesicle recycling dynamics

Modeling Synaptic Plasticity: A Data-Driven Approach to Neurotransmission Dynamics

This project investigates the role of functional proteins in presynaptic neurotransmission and synaptic plasticity by combining data-driven and theory-driven modeling...

Modeling Synaptic Plasticity: A Data-Driven Approach to Neurotransmission Dynamics
Logo Collective Variable

Collective Variables for Spreading Processes on Complex Networks

Analyzing dynamical systems on networks presents an important area of research that unveils a rich interplay between structure and dynamics, offering profound insights...

Collective Variables for Spreading Processes on Complex Networks
Pareto-ML-Optimization-Cycle

AA1-19 Drug Candidates as Pareto Optima in Chemical Space

The search for novel drug candidates that, at the same time, act with high efficacy, comply with defined chemical properties, and also show low off-target effects can be...

AA1-19 Drug Candidates as Pareto Optima in Chemical Space
Oscillator

Synchronization and Geometric Structures of Stochastic Biochemical Oscillators

We study synchronization due to noise and/or coupling in dynamical systems with multiple time scales. The challenge of taming nonuniformly hyperbolic structures is faced...

Synchronization and Geometric Structures of Stochastic Biochemical Oscillators

Publications

2025
Approximating particle-based clustering dynamics by stochastic PDEs SIAM Journal on Applied Dynamical Systems, 24(2), pp. 1231-1250, 2025 Nathalie Wehlitz, Mohsen Sadeghi, Alberto Montefusco, Christof Schütte, Grigorios A. Pavliotis, Stefanie Winkelmann BibTeX
arXiv
DOI
Independently engaging protein tethers of different length enhance synaptic vesicle trafficking to the plasma membrane The Journal of Physiology, 2025 Manon Berns, Mirza Yildiz, Stefanie Winkelmann, Alexander Walter BibTeX
DOI
Multi-grid reaction-diffusion master equation: applications to morphogen gradient modelling Bulletin of Mathematical Biology, Vol.87, p. 6, 2025 Radek Erban, Stefanie Winkelmann BibTeX
arXiv
DOI
Parameter Optimization for a Neurotransmission Recovery Model Bulletin of Mathematical Biology, Vol.87, 2025 Ariane Ernst, Anastasia Bankowski, Meida Jusyte, Toluwani Okunola, Tino Petrov, Alexander Walter, Stefanie Winkelmann BibTeX
DOI
2024
Learning interpretable collective variables for spreading processes on networks Physical Review E, 109(2), p. L022301, 2024 Marvin Lücke, Stefanie Winkelmann, Jobst Heitzig, Nora Molkenthin, Péter Koltai BibTeX
arXiv
DOI
Partial mean-field model for neurotransmission dynamics Mathematical Biosciences, Vol.369, 2024 Alberto Montefusco, Luzie Helfmann, Toluwani Okunola, Stefanie Winkelmann, Christof Schütte BibTeX
arXiv
DOI
Synchronization and random attractors in reaction jump processes Journal of Dynamics and Differential Equations, 2024 Maximilian Engel, Guillermo Olicón-Méndez, Nathalie Wehlitz, Stefanie Winkelmann BibTeX
arXiv
DOI
Understanding Memory Mechanisms in Socio-Technical Systems: the Case of an Agent-based Mobility Model Advances in Complex Systems, Vol.27, 2024 Gesine Steudle, Stefanie Winkelmann, Steffen Fürst, Sarah Wolf BibTeX
DOI
2023
A route to the hydrodynamic limit of a reaction-diffusion master equation using gradient structures SIAM Journal on Applied Mathematics, 83(2), pp. 837-861, 2023 Alberto Montefusco, Christof Schütte, Stefanie Winkelmann BibTeX
arXiv
DOI
Accurate reduced models for the pH oscillations in the urea-urease reaction confined to giant lipid vesicles The Journal of Physical Chemistry B, 127(13), pp. 2955-2967, 2023 (preprint available as ZIB-Report 22-21) Arthur Straube, Stefanie Winkelmann, Felix Höfling PDF (ZIB-Report)
BibTeX
arXiv
DOI
Chemical diffusion master equation: formulations of reaction-diffusion processes on the molecular level Journal of Mathematical Physics, 64(1), 2023 Mauricio del Razo, Stefanie Winkelmann, Rupert Klein, Felix Höfling BibTeX
DOI
arXiv
Large population limits of Markov processes on random networks Stochastic Processes and their Applications, Vol.166, 2023 Marvin Lücke, Jobst Heitzig, Péter Koltai, Nora Molkethin, Stefanie Winkelmann BibTeX
DOI
arXiv
Model reduction for calcium-induced vesicle fusion dynamics Proceedings in Applied Mathematics & Mechanics, 23(4), 2023 Ariane Ernst, Undine Falkenhagen, Stefanie Winkelmann BibTeX
DOI
Modelling altered signalling of G-protein coupled receptors in inflamed environment to advance drug design Scientific Reports, 13(607), 2023 Arne Thies, Vikram Sunkara, Sourav Ray, Hanna Wulkow, M. Özgür Celik, Fatih Yergöz, Christof Schütte, Christoph Stein, Marcus Weber, Stefanie Winkelmann BibTeX
DOI
Rate-limiting recovery processes in neurotransmission under sustained stimulation Mathematical Biosciences, Vol.362, 2023 Ariane Ernst, Nathalie Unger, Christof Schütte, Alexander Walter, Stefanie Winkelmann BibTeX
arXiv
DOI
2022
A probabilistic framework for particle-based reaction–diffusion dynamics using classical Fock space representations Letters in Mathematical Physics, 112(49), 2022 Mauricio del Razo, Daniela Frömberg, Arthur Straube, Christof Schütte, Felix Höfling, Stefanie Winkelmann BibTeX
arXiv
DOI
Discovering collective variable dynamics of agent-based models 25th International Symposium on Mathematical Theory of Networks and Systems MTNS 2022, 2022 Marvin Lücke, Peter Koltai, Stefanie Winkelmann, Nora Molkethin, Jobst Heitzig BibTeX
DOI
The Impact of Membrane Protein Diffusion on GPCR Signaling Cells, 11(10), p. 1660, 2022 Horst-Holger Boltz, Alexei Sirbu, Nina Stelzer, Primal de Lanerolle, Stefanie Winkelmann, Paolo Annibale BibTeX
DOI
Variance of filtered signals: Characterization for linear reaction networks and application to neurotransmission dynamics Mathematical Biosciences, Vol.343, 2022 (preprint available as ZIB-Report 21-15) Ariane Ernst, Christof Schütte, Stephan Sigrist, Stefanie Winkelmann PDF (ZIB-Report)
BibTeX
DOI
2021
Agent-based modeling: Population limits and large timescales Chaos: An Interdisciplinary Journal of Nonlinear Science, 31(3), 2021 Jan-Hendrik Niemann, Stefanie Winkelmann, Sarah Wolf, Christof Schütte PDF
BibTeX
URN
DOI
From interacting agents to density-based modeling with stochastic PDEs Communications in Applied Mathematics and Computational Science, 16(1), pp. 1-32, 2021 (preprint available as ZIB-Report 19-21) Luzie Helfmann, Natasa Djurdjevac Conrad, Ana Djurdjevac, Stefanie Winkelmann, Christof Schütte PDF (ZIB-Report)
BibTeX
arXiv
DOI
Mathematical modeling of spatio-temporal population dynamics and application to epidemic spreading Mathematical Biosciences, Vol.336, 2021 Stefanie Winkelmann, Johannes Zonker, Christof Schütte, Natasa Djurdjevac Conrad BibTeX
DOI
arXiv
Modelling altered signalling of G-protein coupled receptors in inflamed environment to advance drug design ZIB-Report 21-19 Sourav Ray, Arne Thies, Vikram Sunkara, Hanna Wulkow, Özgür Celik, Fatih Yergöz, Christof Schütte, Christoph Stein, Marcus Weber, Stefanie Winkelmann PDF
BibTeX
URN
Stochastic pH oscillations in a model of the urea–urease reaction confined to lipid vesicles J. Phys. Chem. Lett., Vol.12, pp. 9888-9893, 2021 Arthur Straube, Stefanie Winkelmann, Christof Schütte, Felix Höfling BibTeX
DOI
2020
Stochastic Dynamics in Computational Biology Springer International Publishing, 2020, ISBN: 978-3-030-62386-9 Stefanie Winkelmann, Christof Schütte BibTeX
DOI
2018
Human mobility and innovation spreading in ancient times: a stochastic agent-based simulation approach EPJ Data Science, 7(1), 2018 Natasa Djurdjevac Conrad, Luzie Helfmann, Johannes Zonker, Stefanie Winkelmann, Christof Schütte BibTeX
DOI
2017
Hybrid models for chemical reaction networks: Multiscale theory and application to gene regulatory systems The Journal of Chemical Physics, 147(11), pp. 114115-1-114115-18, 2017 (preprint available as ZIB-Report 17-29) Stefanie Winkelmann, Christof Schütte PDF
PDF (ZIB-Report)
BibTeX
DOI
Markov Control with Rare State Observation: Average Optimality Markov Processes and Related Fields, Vol.23, pp. 1-34, 2017 (preprint available as ZIB-Report 16-59) Stefanie Winkelmann PDF (ZIB-Report)
BibTeX
2016
The Spatiotemporal Master Equation: Approximation of Reaction-Diffusion Dynamics via Markov State Modeling Journal of Chemical Physics, 145(21), 2016 (preprint available as ZIB-Report 16-60) Stefanie Winkelmann, Christof Schütte PDF
PDF (ZIB-Report)
BibTeX
DOI
2015
Optimal Treatment Strategies in the Context of 'Treatment for Prevention' against HIV/1 in Resource-Poor Settings PloS Computational Biology, 11(4), 2015 Sulav Duwal, Stefanie Winkelmann, Christof Schütte, Max von Kleist BibTeX
DOI
2014
Markov Control Processes with Rare State Observation: Theory and Application to Treatment Scheduling in HIV-1 Communications in Mathematical Sciences, 12(5), pp. 859-877, 2014 (preprint available as ZIB-Report 13-34) Stefanie Winkelmann, Christof Schütte, Max von Kleist PDF (ZIB-Report)
BibTeX
DOI
2013
Markov Control Processes with Rare State Observation: Sensitivity Analysis with Respect to Optimal Treatment Strategies against HIV-1 International Journal of Biomathematics and Biostatistics, 2(1), 2013 Stefanie Winkelmann, Christof Schütte, Max von Kleist BibTeX
Markov Decision Processes with Information Costs Doctoral thesis, Freie Universität Berlin, Christof Schütte (Advisor), 2013 Stefanie Winkelmann BibTeX
2012
Optimal control of molecular dynamics using Markov state models Math. Program. (Series B), 134(1), pp. 259-282, 2012 Christof Schütte, Stefanie Winkelmann, Carsten Hartmann BibTeX
DOI