Topology Protects Chiral Edge Currents in Stochastic Systems
Physical Review X, 2021 Constructing systems that exhibit timescales much longer than those of the underlying components, as well as emergent dynamical and collective behavior, is a key goal in fields such as synthetic biology and materials self-assembly.
Evelyn Tang +2 more
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A trajectory-based loss function to learn missing terms in bifurcating dynamical systems
Scientific Reports, 2021 Missing terms in dynamical systems are a challenging problem for modeling. Recent developments in the combination of machine learning and dynamical system theory open possibilities for a solution.
Rahel Vortmeyer-Kley +2 more
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An Algorithmic Information Calculus for Causal Discovery and Reprogramming Systems
iScience, 2019 Summary: We introduce and develop a method that demonstrates that the algorithmic information content of a system can be used as a steering handle in the dynamical phase space, thus affording an avenue for controlling and reprogramming systems.
Hector Zenil +7 more
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Tellurium notebooks-An environment for reproducible dynamical modeling in systems biology.
PLoS Computational Biology, 2018 The considerable difficulty encountered in reproducing the results of published dynamical models limits validation, exploration and reuse of this increasingly large biomedical research resource.
J Kyle Medley +7 more
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Tractable nonlinear memory functions as a tool to capture and explain dynamical behaviors
Physical Review Research, 2020 Mathematical approaches from dynamical systems theory are used in a range of fields. This includes biology where they are used to describe processes such as protein-protein interaction and gene regulatory networks.
Edgar Herrera-Delgado +2 more
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DOTcvpSB, a software toolbox for dynamic optimization in systems biology [PDF]
BMC Bioinformatics, 2009 Abstract Background Mathematical optimization aims to make a system or design as effective or functional as possible, computing the quality of the different alternatives using a mathematical model. Most models in systems biology have a dynamic nature, usually described by sets of differential equations.
Tomás Hirmajer +2 more
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Amplification without instability: applying fluid dynamical insights in chemistry and biology
New Journal of Physics, 2013 While amplification of small perturbations often arises from instability, transient amplification is possible locally even in asymptotically stable systems.
Jonathan H McCoy
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An Invitation to Quantum Channels
Quanta, 2018 Open quantum systems have become an active area of research, owing to its potential applications in many different fields ranging from computation to biology.
Vinayak Jagadish, Francesco Petruccione
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Parameter inference in dynamical systems with co-dimension 1 bifurcations [PDF]
Royal Society Open Science, 2019 Dynamical systems with intricate behaviour are all-pervasive in biology. Many of the most interesting biological processes indicate the presence of bifurcations, i.e.
Elisabeth Roesch, Michael P. H. Stumpf
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Foraging Dynamics and Entropy Production in a Simulated Proto-Cell
Entropy, 2022 All organisms depend on a supply of energetic resources to power behavior and the irreversible entropy-producing processes that sustain them. Dissipative structure theory has often been a source of inspiration for better understanding the thermodynamics ...
Benjamin De Bari +2 more
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