Results 11 to 20 of about 254,055 (254)
What makes a reaction network “chemical”?
Journal of Cheminformatics, 2022 Background Reaction networks (RNs) comprise a set X of species and a set $$\mathscr {R}$$ R of reactions $$Y\rightarrow Y'$$ Y → Y ′ , each converting a multiset of educts $$Y\subseteq X$$ Y ⊆ X into a multiset $$Y'\subseteq X$$ Y ′ ⊆ X of products.
Stefan Müller +2 more
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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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Modular verification of chemical reaction network encodings via serializability analysis. [PDF]
Theor Comput Sci, 2016 Lakin MR, Stefanovic D, Phillips A.
europepmc +2 more sources
Autonomous learning of generative models with chemical reaction network ensembles. [PDF]
J R Soc InterfacePoole W, Ouldridge TE, Gopalkrishnan M.
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Independent Decompositions of Chemical Reaction Networks [PDF]
Bulletin of Mathematical Biology, 2021 A chemical reaction network (CRN) is composed of reactions that can be seen as interactions among entities called species, which exist within the system. Endowed with kinetics, CRN has a corresponding set of ordinary differential equations (ODEs). In Chemical Reaction Network Theory, we are interested with connections between the structure of the CRN ...
Bryan S. Hernandez +1 more
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The Exploration of Chemical Reaction Networks [PDF]
Annual Review of Physical Chemistry, 2020 Modern computational chemistry has reached a stage at which massive exploration into chemical reaction space with unprecedented resolution with respect to the number of potentially relevant molecular structures has become possible. Various algorithmic advances have shown that such structural screenings must and can be automated and routinely carried ...
Unsleber, Jan P., Reiher, Markus
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Concordant chemical reaction networks [PDF]
Mathematical Biosciences, 2012 We describe a large class of chemical reaction networks, those endowed with a subtle structural property called concordance. We show that the class of concordant networks coincides precisely with the class of networks which, when taken with any weakly monotonic kinetics, invariably give rise to kinetic systems that are injective --- a quality that ...
Shinar, Guy, Feinberg, Martin
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Nonequilibrium Thermodynamics in Biochemical Systems and Its Application
Entropy, 2021 Living systems are open systems, where the laws of nonequilibrium thermodynamics play the important role. Therefore, studying living systems from a nonequilibrium thermodynamic aspect is interesting and useful.
Dongliang Zhang, Qi Ouyang
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On Quantitative Comparison of Chemical Reaction Network Models [PDF]
Electronic Proceedings in Theoretical Computer Science, 2019 Chemical reaction networks (CRNs) provide a convenient language for modelling a broad variety of biological systems. These models are commonly studied with respect to the time series they generate in deterministic or stochastic simulations. Their dynamic
Ozan Kahramanoğulları
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Siphons in Chemical Reaction Networks [PDF]
Bulletin of Mathematical Biology, 2010 Siphons in a chemical reaction system are subsets of the species that have the potential of being absent in a steady state. We present a characterization of minimal siphons in terms of primary decomposition of binomial ideals, we explore the underlying geometry, and we demonstrate the effective computation of siphons using computer algebra software ...
Shiu, Anne, Sturmfels, Bernd
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