Translated Chemical Reaction Networks [PDF]
Bulletin of Mathematical Biology, 2014 Many biochemical and industrial applications involve complicated networks of simultaneously occurring chemical reactions. Under the assumption of mass action kinetics, the dynamics of these chemical reaction networks are governed by systems of polynomial ordinary differential equations.
Johnston MD.
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Grip on complexity in chemical reaction networks [PDF]
Beilstein Journal of Organic Chemistry, 2017 A new discipline of “systems chemistry” is emerging, which aims to capture the complexity observed in natural systems within a synthetic chemical framework.
Albert S. Y. Wong, Wilhelm T. S. Huck
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Splitting Reactions Preserves Nondegenerate Behaviors in Chemical Reaction Networks
SIAM Journal on Applied Mathematics, 2023 some minor calculational errors fixed in the ...
M. Banaji
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A human-machine interface for automatic exploration of chemical reaction networks [PDF]
Nature CommunicationsAutonomous reaction network exploration algorithms offer a systematic approach to explore mechanisms of complex chemical processes. However, the resulting reaction networks are so vast that an exploration of all potentially accessible intermediates is ...
Miguel Steiner, Markus Reiher
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Thermodynamic Uncertainty Relation and Thermodynamic Speed Limit in Deterministic Chemical Reaction Networks [PDF]
Physical Review Letters, 2021 We generalize the thermodynamic uncertainty relation (TUR) and thermodynamic speed limit (TSL) for deterministic chemical reaction networks (CRNs). The scaled diffusion coefficient derived by considering the connection between macro- and mesoscopic CRNs ...
Kohei Yoshimura, Sosuke Ito
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Diffusive network connected chemical reaction networks
Systems Science & Control EngineeringA novel type of networked Chemical Reaction Network (CRN) model is proposed in this paper where the CRN subsystem nodes are connected in a bi-directional state-difference-driven way, forming a diffusive network. The diffusive connecting elements can also
Katalin M. Hangos +2 more
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Chemical reaction networks for computing logarithm [PDF]
Synthetic Biology, 2017 Abstract Living cells constantly process information from their living environment. It has recently been shown that a number of cell signaling mechanisms (e.g. G protein-coupled receptor and epidermal growth factor) can be interpreted as computing the logarithm of the ligand concentration.
Chou CT.
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Nonequilibrium Thermodynamics of Chemical Reaction Networks: Wisdom from Stochastic Thermodynamics [PDF]
Physical Review X, 2016 We build a rigorous nonequilibrium thermodynamic description for open chemical reaction networks of elementary reactions. Their dynamics is described by deterministic rate equations with mass action kinetics.
Riccardo Rao, Massimiliano Esposito
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Chemical Reaction Networks Explain Gas Evolution Mechanisms in Mg-Ion Batteries. [PDF]
J Am Chem Soc, 2023 Out-of-equilibrium electrochemical reaction mechanisms are notoriously difficult to characterize. However, such reactions are critical for a range of technological applications.
Spotte-Smith EWC +8 more
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Chemoton 2.0: Autonomous Exploration of Chemical Reaction Networks. [PDF]
J Chem Theory Comput, 2022 Fueled by advances in hardware and algorithm design, large-scale automated explorations of chemical reaction space have become possible. Here, we present our approach to an open-source, extensible framework for explorations of chemical reaction ...
Unsleber JP, Grimmel SA, Reiher M.
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