2023
Alberto Montefusco, Christof Schütte, Stefanie Winkelmann	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	BibTeX arXiv DOI
Arthur Straube, Stefanie Winkelmann, Felix Höfling	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)	PDF (ZIB-Report) BibTeX arXiv DOI
Mauricio del Razo, Stefanie Winkelmann, Rupert Klein, Felix Höfling	Chemical diffusion master equation: formulations of reaction-diffusion processes on the molecular level	Journal of Mathematical Physics, 64(1), 2023	BibTeX DOI arXiv
Marvin Lücke, Jobst Heitzig, Péter Koltai, Nora Molkethin, Stefanie Winkelmann	Large population limits of Markov processes on random networks	Stochastic Processes and their Applications, 2023 (epub ahead of print)	BibTeX DOI arXiv
Marvin Lücke, Stefanie Winkelmann, Jobst Heitzig, Nora Molkenthin, Péter Koltai	Learning Interpretable Collective Variables of the Noisy Voter Model	2023 (under review)	BibTeX DOI
Ariane Ernst, Undine Falkenhagen, Stefanie Winkelmann	Model reduction for Ca2+-induced vesicle fusion dynamics	Proceedings in Applied Mathematics & Mechanics, 2023 (accepted for publication)	BibTeX DOI
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	BibTeX DOI
Alberto Montefusco, Luzie Helfmann, Toluwani Okunola, Stefanie Winkelmann, Christof Schütte	Partial mean-field model for neurotransmission dynamics	2023 (under review)	BibTeX arXiv
Ariane Ernst, Nathalie Unger, Christof Schütte, Alexander Walter, Stefanie Winkelmann	Rate-limiting recovery processes in neurotransmission under sustained stimulation	Mathematical Biosciences, Vol.362, 2023	BibTeX arXiv DOI
2022
Mauricio del Razo, Daniela Frömberg, Arthur Straube, Christof Schütte, Felix Höfling, Stefanie Winkelmann	A probabilistic framework for particle-based reaction–diffusion dynamics using classical Fock space representations	Letters in Mathematical Physics, 112(49), 2022	BibTeX arXiv DOI
Maximilian Engel, Guillermo Olicón-Méndez, Nathalie Unger, Stefanie Winkelmann	Synchronization and random attractors for reaction jump processes	2022 (under review)	BibTeX arXiv DOI
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	BibTeX DOI
Ariane Ernst, Christof Schütte, Stephan Sigrist, Stefanie Winkelmann	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)	PDF (ZIB-Report) BibTeX DOI
2021
Jan-Hendrik Niemann, Stefanie Winkelmann, Sarah Wolf, Christof Schütte	Agent-based modeling: Population limits and large timescales	Chaos: An Interdisciplinary Journal of Nonlinear Science, 31(3), 2021	PDF BibTeX URN DOI
Luzie Helfmann, Natasa Djurdjevac Conrad, Ana Djurdjevac, Stefanie Winkelmann, Christof Schütte	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)	PDF (ZIB-Report) BibTeX arXiv DOI
Stefanie Winkelmann, Johannes Zonker, Christof Schütte, Natasa Djurdjevac Conrad	Mathematical modeling of spatio-temporal population dynamics and application to epidemic spreading	Mathematical Biosciences, Vol.336, 2021	BibTeX DOI arXiv
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	PDF BibTeX URN
Arthur Straube, Stefanie Winkelmann, Christof Schütte, Felix Höfling	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	BibTeX DOI
2020
Stefanie Winkelmann, Christof Schütte	Stochastic Dynamics in Computational Biology	Springer International Publishing, 2020, ISBN: 978-3-030-62386-9	BibTeX DOI
2018
Natasa Djurdjevac Conrad, Luzie Helfmann, Johannes Zonker, Stefanie Winkelmann, Christof Schütte	Human mobility and innovation spreading in ancient times: a stochastic agent-based simulation approach	EPJ Data Science, 7(1), 2018	BibTeX DOI
2017
Stefanie Winkelmann, Christof Schütte	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)	PDF PDF (ZIB-Report) BibTeX DOI
Stefanie Winkelmann	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)	PDF (ZIB-Report) BibTeX
2016
Stefanie Winkelmann, Christof Schütte	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)	PDF PDF (ZIB-Report) BibTeX DOI
2015
Sulav Duwal, Stefanie Winkelmann, Christof Schütte, Max von Kleist	Optimal Treatment Strategies in the Context of 'Treatment for Prevention' against HIV/1 in Resource-Poor Settings	PloS Computational Biology, 11(4), 2015	BibTeX DOI
2014
Stefanie Winkelmann, Christof Schütte, Max von Kleist	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)	PDF (ZIB-Report) BibTeX DOI
2013
Stefanie Winkelmann, Christof Schütte, Max von Kleist	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	BibTeX
Stefanie Winkelmann	Markov Decision Processes with Information Costs	Doctoral thesis, Freie Universität Berlin, Christof Schütte (Advisor), 2013	BibTeX
2012
Christof Schütte, Stefanie Winkelmann, Carsten Hartmann	Optimal control of molecular dynamics using Markov state models	Math. Program. (Series B), 134(1), pp. 259-282, 2012	BibTeX DOI