https://johannes-falk.de/publications/ https://johannes-falk.de/publications/index.xml Hugo -- gohugo.io en mail@johannes-falk.de (Dr. Johannes Falk) mail@johannes-falk.de (Dr. Johannes Falk) Tue, 30 Jun 2026 11:13:25 +0200 https://johannes-falk.de/publications/categories-of-important-edges-in-dynamics-on-graphs/ Wed, 01 Jan 2025 00:00:00 +0000 https://johannes-falk.de/publications/categories-of-important-edges-in-dynamics-on-graphs/ Not every connection in a network matters equally. Which ones matter depends on what's running on the network. We introduce a way to measure this, and test it on the macaque brain. https://johannes-falk.de/publications/nucleation-transitions-in-polycontextural-networks-toward-consensus/ Mon, 01 Jan 2024 00:00:00 +0000 https://johannes-falk.de/publications/nucleation-transitions-in-polycontextural-networks-toward-consensus/ Consensus clusters in belief networks grow through a nucleation-like phase transition, with self-similar scaling driven by agents' willingness to change views. https://johannes-falk.de/publications/collective-patterns-and-stable-misunderstandings-in-networks-striving-for-consensus-without-a-common-value-system/ Sat, 01 Jan 2022 00:00:00 +0000 https://johannes-falk.de/publications/collective-patterns-and-stable-misunderstandings-in-networks-striving-for-consensus-without-a-common-value-system/ Agents can reach consensus without any shared notion of right or wrong, forming 'stable misunderstandings' where neighbors hold different but compatible views. https://johannes-falk.de/publications/network-location-and-clustering-of-genetic-mutations-determine-chronicity-in-a-stylized-model-of-genetic-diseases/ Sat, 01 Jan 2022 00:00:00 +0000 https://johannes-falk.de/publications/network-location-and-clustering-of-genetic-mutations-determine-chronicity-in-a-stylized-model-of-genetic-diseases/ Where mutations sit in a gene network, and how clustered they are, decides whether a disease becomes chronic or acute—a percolation-based model of disease. https://johannes-falk.de/publications/physics-is-organized-around-transformations-connecting-contextures-in-a-polycontextural-world/ Sat, 01 Jan 2022 00:00:00 +0000 https://johannes-falk.de/publications/physics-is-organized-around-transformations-connecting-contextures-in-a-polycontextural-world/ Applies Günther's polycontextural logic to physics, showing how observers in locally valid logical systems give rise to the transformations theories rely on. https://johannes-falk.de/publications/pipette-show-an-open-source-web-application-to-support-pipetting-into-microplates/ Sat, 01 Jan 2022 00:00:00 +0000 https://johannes-falk.de/publications/pipette-show-an-open-source-web-application-to-support-pipetting-into-microplates/ A free, open-source web app that plans and guides manual pipetting by lighting up microplate wells on a tablet, cutting errors and improving reproducibility. https://johannes-falk.de/publications/knowledge-objects-of-synthetic-biology-from-phase-transitions-to-the-biological-switch/ Wed, 01 Jan 2020 00:00:00 +0000 https://johannes-falk.de/publications/knowledge-objects-of-synthetic-biology-from-phase-transitions-to-the-biological-switch/ A philosophy-of-science view of synthetic biology's 'biological switch,' showing how the same phase-transition model links living switches and laser light. https://johannes-falk.de/publications/a-tightly-regulated-and-adjustable-crispr-dcas9-based-and-gate-in-yeast/ Tue, 01 Jan 2019 00:00:00 +0000 https://johannes-falk.de/publications/a-tightly-regulated-and-adjustable-crispr-dcas9-based-and-gate-in-yeast/ A CRISPR-dCas9 AND gate in yeast that switches genes on only when two inputs are present—tightly controlled, tunable, and adaptable to any target gene. https://johannes-falk.de/publications/context_in_synthetic_biology_memory_effects_of_environments_with_mono-molecular_reactions/ Tue, 01 Jan 2019 00:00:00 +0000 https://johannes-falk.de/publications/context_in_synthetic_biology_memory_effects_of_environments_with_mono-molecular_reactions/ Exact formulas for the memory effects a cellular environment imprints on an embedded genetic circuit, helping predict how synthetic modules really behave. https://johannes-falk.de/publications/stochastische-modelle-und-umgebungseffekte-im-kontext-der-synthetischen-biologie/ Tue, 01 Jan 2019 00:00:00 +0000 https://johannes-falk.de/publications/stochastische-modelle-und-umgebungseffekte-im-kontext-der-synthetischen-biologie/ Doctoral thesis on how stochastic models and environmental effects shape synthetic genetic circuits—from CRISPR/dCas9 switches to memory effects. https://johannes-falk.de/publications/analysis-of-stochastic-bifurcations-with-phase-portraits/ Mon, 01 Jan 2018 00:00:00 +0000 https://johannes-falk.de/publications/analysis-of-stochastic-bifurcations-with-phase-portraits/ A visual phase-portrait method for noisy systems that reveals where stable states sit and uncovers a new type of noise-driven stochastic bifurcation. https://johannes-falk.de/publications/a_minimal_model_of_burst_noise_induced_bistability/ Thu, 27 Apr 2017 00:00:00 +0000 https://johannes-falk.de/publications/a_minimal_model_of_burst_noise_induced_bistability/ Bursty, noisy production of molecules can create or destroy a system's second stable state—even when its average, deterministic behavior stays unchanged. https://johannes-falk.de/publications/on_the_effect_of_the_drive_on_self-organized_criticality/ Thu, 01 Jan 2015 00:00:00 +0000 https://johannes-falk.de/publications/on_the_effect_of_the_drive_on_self-organized_criticality/ In the sandpile model, a state-dependent drive can preserve self-organized criticality or destroy it—favoring some site heights forces system-wide avalanches. https://johannes-falk.de/publications/structural-insulators-and-promotors-in-networks-under-generic-problem-solving-dynamic/ Mon, 01 Jan 0001 00:00:00 +0000 https://johannes-falk.de/publications/structural-insulators-and-promotors-in-networks-under-generic-problem-solving-dynamic/ In networks solving distributed tasks, small-world shortcuts can speed up a solution as 'promotors' or block it as 'insulators,' depending on the link length.