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Kinetic derivation of the Hessian geometric structure in chemical reaction networks
Physical Review Research, 2022 The theory of chemical kinetics forms the basis to describe the dynamics of chemical reaction networks. Owing to physical and thermodynamic constraints, the networks possess various structures, which can be utilized to characterize important properties ...
Tetsuya J. Kobayashi +3 more
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Physical Review Research, 2020 In nonequilibrium chemical reaction systems, a fundamental relationship between unbalanced kinetic one-way fluxes and thermodynamic chemical driving forces is believed to exist. However, in fact, the formula for this fundamental relation, in general, and
Yongli Peng +3 more
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On the Complexity of Reconstructing Chemical Reaction Networks [PDF]
Mathematics in Computer Science, 2013 The analysis of the structure of chemical reaction networks is crucial for a better understanding of chemical processes. Such networks are well described as hypergraphs. However, due to the available methods, analyses regarding network properties are typically made on standard graphs derived from the full hypergraph description, e.g.\ on the so-called ...
Rolf Fagerberg +4 more
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Timing in chemical reaction networks [PDF]
Proceedings of the Twenty-Fifth Annual ACM-SIAM Symposium on Discrete Algorithms, 2013 Chemical reaction networks (CRNs) formally model chemistry in a well-mixed solution. CRNs are widely used to describe information processing occurring in natural cellular regulatory networks, and with upcoming advances in synthetic biology, CRNs are a promising programming language for the design of artificial molecular control circuitry.
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PLoS Computational Biology, 2022 Prior work on abiogenesis, the emergence of life from non-life, suggests that it requires chemical reaction networks that contain self-amplifying motifs, namely, autocatalytic cores.
Zhen Peng, Jeff Linderoth, David A Baum
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Synthesizing and tuning stochastic chemical reaction networks with specified behaviours. [PDF]
J R Soc Interface, 2018 Murphy N +4 more
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Chemical master equation and Langevin regimes for a gene transcription model [PDF]
, 2007 Gene transcription models must take account of intrinsic stochasticity. The Chemical Master Equation framework is based on modelling assumptions that are highly appropriate for this context, and the Stochastic Simulation Algorithm (also known as ...
Higham, Desmond J. +4 more
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Robust Mechanism Discovery with Atom Conserving Chemical Reaction Neural Networks
, 2023 Chemical reaction neural networks (CRNNs) established as the state-of-the-art tool for autonomous mechanism discovery. While they encode some fundamental physical laws, mass- and atom conservation are still violated.
Felix, Döppel, Martin, Votsmeier
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Information geometric inequalities of chemical thermodynamics
Physical Review Research, 2021 We study a connection between chemical thermodynamics and information geometry. We clarify a relation between the Gibbs free energy of an ideal dilute solution and an information geometric quantity called an f divergence.
Kohei Yoshimura, Sosuke Ito
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Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry [PDF]
, 2014 While structures and reactivities of many small molecules can be computed efficiently and accurately using quantum chemical methods, heuristic approaches remain essential for modeling complex structures and large-scale chemical systems.
Rappoport, Dmitrij +3 more
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