2023

Alberto Montefusco, Christof Schütte, Stefanie Winkelmann 
A route to the hydrodynamic limit of a reactiondiffusion master equation using gradient structures

SIAM Journal on Applied Mathematics, 83(2), pp. 837861, 2023 
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arXiv
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Arthur Straube, Stefanie Winkelmann, Felix Höfling 
Accurate reduced models for the pH oscillations in the ureaurease reaction confined to giant lipid vesicles

The Journal of Physical Chemistry B, 127(13), pp. 29552967, 2023 (preprint available as ZIBReport 2221) 
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arXiv
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Mauricio del Razo, Stefanie Winkelmann, Rupert Klein, Felix Höfling 
Chemical diffusion master equation: formulations of reactiondiffusion processes on the molecular level

Journal of Mathematical Physics, 64(1), 2023 
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arXiv

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 Gprotein coupled receptors in inflamed environment to advance drug design

Scientific Reports, 13(607), 2023 
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Christopher Secker, Konstantin Fackeldey, Marcus Weber, Sourav Ray, Christoph Gorgulla, Christof Schütte 
Novel multiobjective affinity approach allows to identify pHspecific μopioid receptor agonists

2023 (under review) 
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2022

Mauricio del Razo, Daniela Frömberg, Arthur Straube, Christof Schütte, Felix Höfling, Stefanie Winkelmann 
A probabilistic framework for particlebased reaction–diffusion dynamics using classical Fock space representations

Letters in Mathematical Physics, 112(49), 2022 
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arXiv
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Alberto Montefusco, Upanshu Sharma, Oliver Tse 
FourierCattaneo equation: stochastic origin, variational formulation, and asymptotic limits

2022 (under review) 
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Maximilian Engel, Guillermo OlicónMéndez, Nathalie Unger, Stefanie Winkelmann 
Synchronization and random attractors for reaction jump processes

2022 (under review) 
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arXiv
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HorstHolger 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

Hans Christian Öttinger, Alberto Montefusco, Mark A. Peletier 
A Framework of Nonequilibrium Statistical Mechanics. I. Role and Types of Fluctuations

Journal of NonEquilibrium Thermodynamics, 46(1), pp. 113, 2021 
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Alberto Montefusco, Mark A. Peletier, Hans Christian Öttinger 
A Framework of Nonequilibrium Statistical Mechanics. II. CoarseGraining

Journal of NonEquilibrium Thermodynamics, 46(1), pp. 1533, 2021 
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JanHendrik Niemann, Stefanie Winkelmann, Sarah Wolf, Christof Schütte 
Agentbased modeling: Population limits and large timescales

Chaos: An Interdisciplinary Journal of Nonlinear Science, 31(3), 2021 
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Alexander Mielke, Alberto Montefusco, Mark A. Peletier 
Exploring families of energydissipation landscapes via tilting: three types of EDP convergence

Continuum Mechanics and Thermodynamics, Vol.33, pp. 611637, 2021 
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Amal Alphonse, Diogo Caetano, Ana Djurdjevac, Charles M. Elliott 
Function spaces, time derivatives and compactness for evolving families of Banach spaces with applications to PDEs

arXiv, 2021 (under review) 
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arXiv

Daniela Frömberg, Felix Höfling 
Generalized master equation for firstpassage problems in partitioned spaces

Journal of Physics A: Mathematical and Theoretical, Vol.54, p. 215601, 2021 
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Ana Djurdjevac

Linear Parabolic Problems in Random Moving Domains

9(2), pp. 848879, 2021 
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Stefanie Winkelmann, Johannes Zonker, Christof Schütte, Natasa Djurdjevac Conrad 
Mathematical modeling of spatiotemporal population dynamics and application to epidemic spreading

Mathematical Biosciences, Vol.336, 2021 
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arXiv

Ana Djurdjevac, Carsten Gräser, Philip J. Herbert 
Nonstationary incompressible linear fluid equations in a moving domain

arXiv, 2021 
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arXiv

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. 98889893, 2021 
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Pietro Tierno, Tom H. Johansen, Arthur Straube 
Thermally active nanoparticle clusters enslaved by engineered domain wall traps

Nature Commun., Vol.12, p. 5813, 2021 
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2020

Stefanie Winkelmann,
Christof Schütte

Stochastic Dynamics in Computational Biology

Springer International Publishing, 2020, ISBN: 9783030623869 
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2019

Margarita Kostré

Hybrid Models and Simulations of ReactionDiffusion Processes

Master's thesis, Freie Universität Berlin, Frank Noe (Advisor), 2019 
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2018

Manuel Dibak, Mauricio J. del Razo, David de Sancho, Christof Schütte, Frank Noé 
MSM/RD: Coupling Markov state models of molecular kinetics with reactiondiffusion simulations

Journal of Chemical Physics, 148(21), 2018 
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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. 114115111411518, 2017 (preprint available as ZIBReport 1729) 
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Stefanie Winkelmann

Markov Control with Rare State Observation: Average Optimality

Markov Processes and Related Fields, Vol.23, pp. 134, 2017 (preprint available as ZIBReport 1659) 
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Andreas Bittracher, Péter Koltai, Stefan Klus, Ralf Banisch, Michael Dellnitz, Christof Schütte 
Transition manifolds of complex metastable systems: Theory and datadriven computation of effective dynamics

ZIBReport 1722 (accepted for publication on 20170923) 
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S. Rüdrich, Marco Sarich, Christof Schütte 
Utilizing hitting times for ﬁnding metastable sets in nonreversible Markov chains

Journal of Comp. Dynamics, 2017 (under review, preprint available as ) 
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2016

Stefanie Winkelmann, Christof Schütte 
The Spatiotemporal Master Equation: Approximation of ReactionDiffusion Dynamics via Markov State Modeling

Journal of Chemical Physics, 145(21), 2016 (preprint available as ZIBReport 1660) 
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Stefan Klus, Christof Schütte 
Towards tensorbased methods for the numerical approximation of the PerronFrobenius and Koopman operator

Journal of Computational Dynamics, 3(2), pp. 139161, 2016 
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2015

Ivan Kryven, Susanna Röblitz, Christof Schütte 
Solution of the chemical master equation by radial basis functions approximation with interface tracking

BMC Systems Biology, 9(67), pp. 112, 2015 
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Patrick Gelß, Sebastian Matera, Christof Schütte 
Solving the master equation without kinetic Monte Carlo: tensor train approximations for a CO oxidation model

ZIBReport 1541 
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2014

Alexander Bockmayr, Heike Siebert, Susanna Röblitz, Christof Schütte, Peter Deuflhard 
Advanced mathematical modeling in systems biology

MATHEONMathematics for Key Technologies, Vol.1, pp. 2944, Peter Deuflhard, Martin Grötschel, Dietmar Hömberg, Jürg Kramer, Volker Mehrmann, Konrad Polthier, Frank Schmidt, Christof Schütte, Martin Skutela, Jürgen Sprekels (Eds.), European Mathematical Society, 2014 
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