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Circuit Theory for Chemical Reaction Networks [PDF]
Physical Review X, 2023 We lay the foundation of a circuit theory for chemical reaction networks. Chemical reactions are grouped into chemical modules solely characterized by their current-concentration characteristic—as electrical devices by their current-voltage (I-V) curve ...
Francesco Avanzini +2 more
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Exploring the programmability of autocatalytic chemical reaction networks [PDF]
Nature CommunicationsNetworks of chemical reactions exhibit emergent properties under out-of-equilibrium conditions. Recent advances in systems chemistry demonstrate that networks with sufficient chemical complexity can be harnessed to emulate properties important for ...
Dmitrii V. Kriukov +2 more
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Chemical Reaction Networks’ Programming for Solving Equations [PDF]
Current Issues in Molecular Biology, 2022 The computational ability of the chemical reaction networks (CRNs) using DNA as the substrate has been verified previously. To solve more complex computational problems and perform the computational steps as expected, the practical design of the basic ...
Ziwei Shang, Changjun Zhou, Qiang Zhang
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Structural reduction of chemical reaction networks based on topology [PDF]
Physical Review Research, 2021 We develop a model-independent reduction method of chemical reaction systems based on the stoichiometry, which determines their network topology. A subnetwork can be eliminated systematically to give a reduced system with fewer degrees of freedom.
Yuji Hirono +3 more
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Operant conditioning of stochastic chemical reaction networks. [PDF]
PLoS Computational Biology, 2022 Adapting one's behavior to environmental conditions and past experience is a key trait of living systems. In the biological world, there is evidence for adaptive behaviors such as learning even in naturally occurring, non-neural, single-celled organisms.
David Arredondo, Matthew R Lakin
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Molecular codes in biological and chemical reaction networks. [PDF]
PLoS ONE, 2013 Shannon's theory of communication has been very successfully applied for the analysis of biological information. However, the theory neglects semantic and pragmatic aspects and thus cannot directly be applied to distinguish between (bio-) chemical ...
Dennis Görlich, Peter Dittrich
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Robust finite automata in stochastic chemical reaction networks [PDF]
Royal Society Open Science, 2021 Finite-state automata (FSA) are simple computational devices that can nevertheless illustrate interesting behaviours. We propose that FSA can be employed as control circuits for engineered stochastic biological and biomolecular systems.
David Arredondo, Matthew R. Lakin
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Integration of biowaste into chemical reaction networks [PDF]
, 2021 As the chemical sector looks to decarbonize, one promising solution is the utilization of bio-feedstocks and biowaste to produce functional molecules. There is, therefore, great interest in understanding how and where to integrate these resources within ...
Adarsh Arun +3 more
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Chemical Reaction Networks Possess Intrinsic, Temperature-Dependent Functionality [PDF]
Entropy, 2020 Temperature influences the life of many organisms in various ways. A great number of organisms live under conditions where their ability to adapt to changes in temperature can be vital and largely determines their fitness.
Stephan O. Adler, Edda Klipp
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Autonomous DNA nanostructures instructed by hierarchically concatenated chemical reaction networks [PDF]
Nature Communications, 2021 Integration and communication of distinct chemical reaction networks is a biological strategy for controlling dynamics of hierarchical structures. Here, the authors report ATP-fuelled autonomous DNA nanotube assembly regulated by DNA strand displacement ...
Jie Deng, Andreas Walther
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