Browsing by Author "Daoutidis, Prodromos"

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    Network generation and analysis of complex biomass conversion systems
    (2011) Rangarajan, Srinivas; Kaminski, Ted; Van Wyk, Eric; Bhan, Aditya; Daoutidis, Prodromos
    A modular computational tool for automated generation and rule-based post-processing of reaction systems in biomass conversion is presented. Cheminformatics and graph theory algorithms are used to generate chemical transformations pertaining to heterogeneous and homogeneous chemistries in the automated rule-based network generator. A domain-specific language provides a user-friendly English-like chemistry specification interface to the network generator. A rule-based pathway analysis module enables the user to extract and query pathways from the reaction network. A demonstration of the features of this tool is presented using Fructose to 5- Hydroxymethylfurfural as a case study.
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    Rule Input Network Generator
    (2018-05-29) Daoutidis, Prodromos; daout001@umn.edu; Daoutidis, Prodromos
    RING is an automated reaction network generation and analysis tool that outputs reaction networks for complex reactive systems from user-defined inputs of initial reactants and chemical reaction rules. RING also takes user-provided post-processing instructions to analyze the topology of the generated network; possible post-processing instructions include: reaction pathway queries to isolate routes from defined reactants to products, lumping instructions to group functionally equivalent species (e.g. isomers) for network reduction, and mechanism queries to establish sequences of elementary steps describing the overall transformations of reactants to products.