Johannes Falk

Phone: +49 421 200 3535
Mail: jfalk (at) constructor.university
Position: Post-Doctoral Researcher

CV

Johannes has a Master of Science in physics from the Julius-Maximilians-Universität of Würzburg with a focus on the theory of complex systems and an MPhys (Hons) from the Heriot-Watt University, Edinburgh with a focus on optoelectronics and laser physics. He received his PhD in theoretical physics from the Technical University of Darmstadt where he used methods from physics to analyse stochastic models and environmental effects in the context of synthetic biology.

Research

Among his research interests is the development of numerical models that are based on the theory of polycontexturality, as well as the analysis of self-organisation in networks of communicating agents. Hereto, he mainly utilizes methods drawn from nonlinear dynamics, statistical physics, and machine learning.

Recent Publications

Categories of important edges in dynamics on graphs
Dzmitry Rumiantsau , Johannes Falk , Piotr Nyczka , Marc-Thorsten Hütt
Royal Society Open Science, 2025.
Cite

                    @article{rumiantsauCategoriesImportantEdges2025,
 abstract = {How important is a single edge of a graph for a specific dynamical task? This question is of practical relevance to many research fields and is pivotal to understanding the structure–function relationships in complex networks more deeply. Here, we design an analysis strategy to answer it and explore the connection of such importance to network topology. Our approach for evaluating dynamical edge importance is based on the differences in time courses between dynamics on the original graph 𝐺 and on the graph 𝐺− missing an edge. To demonstrate the method’s versatility, we apply it to two drastically different classes of dynamics—a minimal model of excitable dynamics, and totalistic cellular automata on graphs as representatives of pattern formation. Our results suggest that the dynamical usage of a graph relies on markedly different topological attributes for these two classes of processes. Finally, we study dynamical edge importance in the macaque cortical area network, to illustrate possible real-world applications. We find that dynamical importance of edges differ between the network and its switch-randomized counterparts, and these differences can be functionally interpreted. Moreover, they are qualitatively distinct for long-time courses and short transients, highlighting different parts of the network’s intended function.},
 author = {Rumiantsau, Dzmitry and Falk, Johannes and Nyczka, Piotr and Hütt, Marc-Thorsten},
 doi = {10.1098/rsos.241086},
 file = {Full Text PDF:/home/johannes/.mozilla/firefox/5ah0aj87.default/zotero/storage/36SIMII9/Rumiantsau et al. - 2025 - Categories of important edges in dynamics on graph.pdf:application/pdf},
 journal = {Royal Society Open Science},
 keywords = {dynamical edge importance, dynamical task, excitable dynamics, macaque cortical area network, totalistic cellular automata},
 month = {April},
 note = {Publisher: Royal Society},
 number = {4},
 pages = {241086},
 title = {Categories of important edges in dynamics on graphs},
 url = {https://royalsocietypublishing.org/doi/10.1098/rsos.241086},
 urldate = {2025-05-20},
 volume = {12},
 year = {2025}
}

Nucleation transitions in polycontextural networks toward consensus
Johannes Falk , Edwin Eichler , Katja Windt , Marc-Thorsten Hütt
The European Physical Journal B, 2024.
Cite

                    @article{falk2024nucleation,
 author = {Falk, Johannes and Eichler, Edwin and Windt, Katja and Hütt, Marc-Thorsten},
 journal = {The European Physical Journal B},
 number = {11},
 pages = {187},
 publisher = {Springer},
 title = {Nucleation transitions in polycontextural networks toward consensus},
 volume = {97},
 year = {2024}
}

Topological insulators and enhancers in networks under generic problem-solving dynamics
Johannes Falk , Edwin Eichler , Katja Windt , Marc-Thorsten Hütt
arXiv preprint arXiv:2301.10550, 2023.
Cite

                    @article{falk2023topological,
 author = {Falk, Johannes and Eichler, Edwin and Windt, Katja and Hütt, Marc-Thorsten},
 journal = {arXiv preprint arXiv:2301.10550},
 title = {Topological insulators and enhancers in networks under generic problem-solving dynamics},
 year = {2023}
}

Collective patterns and stable misunderstandings in networks striving for consensus without a common value system
Johannes Falk , Edwin Eichler , Katja Windt , Marc-Thorsten Hütt
Scientific Reports, 2022.
Cite

                    
@article{falkCollectivePatternsStable2022,
  title = {Collective Patterns and Stable Misunderstandings in Networks Striving for Consensus without a Common Value System},
  author = {Falk, Johannes and Eichler, Edwin and Windt, Katja and H{\"u}tt, Marc-Thorsten},
  year = {2022},
  month = feb,
  journal = {Scientific Reports},
  volume = {12},
  number = {1},
  pages = {3028},
  publisher = {{Nature Publishing Group}},
  issn = {2045-2322},
  doi = {10.1038/s41598-022-06880-7}
}

Pipette Show: An Open Source Web Application to Support Pipetting into Microplates
Johannes Falk , Marc Mendler , Johannes Kabisch
ACS Synthetic Biology, 2022.
Cite

                    @article{falk2022pipette
author = {Falk, Johannes and Mendler, Marc and Kabisch, Johannes},
title = {Pipette Show: An Open Source Web Application to Support Pipetting into Microplates},
journal = {ACS Synthetic Biology},
volume = {11},
number = {2},
pages = {996-999},
year = {2022}
}

Network location and clustering of genetic mutations determine chronicity in a stylized model of genetic diseases
Piotr Nyczka , Johannes Falk , Marc-Thorsten Hütt
Scientific Reports, 2022.
Cite

                    @article{nyczka2022network,
 author = {Nyczka, Piotr and Falk, Johannes and Hütt, Marc-Thorsten},
 journal = {Scientific Reports},
 number = {1},
 pages = {19906},
 publisher = {Nature Publishing Group UK London},
 title = {Network location and clustering of genetic mutations determine chronicity in a stylized model of genetic diseases},
 volume = {12},
 year = {2022}
}

Physics is Organized Around Transformations Connecting Contextures in a Polycontextural World
Johannes Falk , Edwin Eichler , Katja Windt , Marc-Thorsten Hütt
Foundations of Science, 2021.
Cite

                    @article{falk2021physics,
 author = {Falk, Johannes and Eichler, Edwin and Windt, Katja and Hütt, Marc-Thorsten},
 journal = {Foundations of Science},
 pages = {1--23},
 publisher = {Springer Netherlands},
 title = {Physics is Organized Around Transformations Connecting Contextures in a Polycontextural World},
 year = {2021}
}

Knowledge Objects of Synthetic Biology: From Phase Transitions to the Biological Switch
Thorsten Kohl , Johannes Falk
Journal for General Philosophy of Science, 2020.
Cite

                    @article{kohl2020knowledge,
 author = {Kohl, Thorsten and Falk, Johannes},
 journal = {Journal for General Philosophy of Science},
 number = {1},
 pages = {1--17},
 publisher = {Springer Netherlands},
 title = {Knowledge Objects of Synthetic Biology: From Phase Transitions to the Biological Switch},
 volume = {51},
 year = {2020}
}

A tightly regulated and adjustable CRISPR-dCas9 based AND gate in yeast
Anja Hofmann , Johannes Falk , Tim Prangemeier , Dominic Happel , Adrian Köber , Andreas Christmann , Heinz Koeppl , Harald Kolmar
Nucleic acids research, 2019.
Cite

                    @article{hofmann2019tightly,
 author = {Hofmann, Anja and Falk, Johannes and Prangemeier, Tim and Happel, Dominic and Köber, Adrian and Christmann, Andreas and Koeppl, Heinz and Kolmar, Harald},
 journal = {Nucleic acids research},
 number = {1},
 pages = {509--520},
 publisher = {Oxford University Press},
 title = {A tightly regulated and adjustable CRISPR-dCas9 based AND gate in yeast},
 volume = {47},
 year = {2019}
}

Context in synthetic biology: Memory effects of environments with mono-molecular reactions
Johannes Falk , Leo Bronstein , Maleen Hanst , Barbara Drossel , Heinz Koeppl
The Journal of Chemical Physics, 2019.
Cite

                    @article{falk2019context,
 author = {Falk, Johannes and Bronstein, Leo and Hanst, Maleen and Drossel, Barbara and Koeppl, Heinz},
 journal = {The Journal of Chemical Physics},
 number = {2},
 pages = {024106},
 publisher = {AIP Publishing},
 title = {Context in synthetic biology: Memory effects of environments with mono-molecular reactions},
 volume = {150},
 year = {2019}
}