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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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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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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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Comparison Theorems for Stochastic Chemical Reaction Networks [PDF]
Bulletin of Mathematical Biology, 2023 AbstractContinuous-time Markov chains are frequently used as stochastic models for chemical reaction networks, especially in the growing field of systems biology. A fundamental problem for these Stochastic Chemical Reaction Networks (SCRNs) is to understand the dependence of the stochastic behavior of these systems on the chemical reaction rate ...
Felipe A. Campos +4 more
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Thermodynamics of non-elementary chemical reaction networks [PDF]
New Journal of Physics, 2020 We develop a thermodynamic framework for closed and open chemical networks applicable to non-elementary reactions that do not need to obey mass action kinetics.
Francesco Avanzini +2 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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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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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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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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Complex chemical reaction networks for future information processing [PDF]
Frontiers in NeuroscienceTackling the increasing energy demand of our society is one of the key challenges today. With the rise of artificial intelligence, information and communication technologies started to substantially contribute to this alarming trend and therefore ...
Katja-Sophia Csizi, Emanuel Lörtscher
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