Chemical master versus chemical langevin for first-order reaction networks [PDF]
, 2008 Markov jump processes are widely used to model interacting species in circumstances where discreteness and stochasticity are relevant. Such models have been particularly successful in computational cell biology, and in this case, the interactions are ...
Higham, Desmond J., Khanin, Raya
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Modeling and simulating chemical reactions [PDF]
, 2008 Many students are familiar with the idea of modeling chemical reactions in terms of ordinary differential equations. However, these deterministic reaction rate equations are really a certain large-scale limit of a sequence of finer-scale probabilistic ...
Higham, Desmond J., Higham, D.J.
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Model discrimination of chemical reaction networks by linearization [PDF]
Proceedings of the 2010 American Control Conference, 2010 Systems biologists are often faced with competing models for a given experimental system. Performing experiments can be time-consuming and expensive. Therefore, a method for designing experiments that, with high probability, discriminate between competing models is desired.
Daniel Georgiev +2 more
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Piecewise Linear and Boolean Models of Chemical Reaction Networks [PDF]
Bulletin of Mathematical Biology, 2014 This is an extension of previous work arXiv:1201 ...
Veliz-Cuba, Alan +2 more
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Reaction Networks for Interstellar Chemical Modelling: Improvements and Challenges [PDF]
Space Science Reviews, 2010 Accepted for publication in Space Science ...
Wakelam, Valentine +12 more
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Statistics and Bias-Free Sampling of Reaction Mechanisms from Reaction Network Models [PDF]
, 2023 Selection bias is inevitable in manually curated computational reaction databases but can have a significant impact on generalizability of quantum chemical methods and machine learning models derived from these data sets.
Dmitrij, Rappoport
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Machine Learning Models Capable of Chemical Deduction for Identifying Reaction Products [PDF]
, 2023 Deductive solution strategies are required in prediction scenarios that are under determined, when contradictory information is available, or more generally wherever one-to-many non-functional mappings occur.
Qiyuan, Zhao +3 more
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Chemical reaction network knowledge graphs: the OntoRXN ontology [PDF]
, 2022 : The organization and management of large amounts of data has become a major point in almost all areas of human knowledge. In this context, semantic approaches propose a structure for the target data, defining ontologies that state the types of entities
Bo, Carles +3 more
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Identification of functional differences in metabolic networks using comparative genomics and constraint-based models. [PDF]
PLoS ONE, 2012 Genome-scale network reconstructions are useful tools for understanding cellular metabolism, and comparisons of such reconstructions can provide insight into metabolic differences between organisms.
Joshua J Hamilton, Jennifer L Reed
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A global optimization method for model selection in chemical reactions networks [PDF]
Computers & Chemical Engineering, 2016 Model inference is a challenging problem in the analysis of chemical reactions networks. In order to empirically test which, out of a catalogue of proposed kinetic models, is governing a network of chemical reactions, the user can compare the empirical data obtained in one experiment against the theoretical values suggested by the models under ...
Rafael Blanquero +3 more
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