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    Area of Science:

    • Biochemistry
    • Systems Biology
    • Theoretical Chemistry

    Background:

    • Living systems construct necessary molecules and catalysts from food sources.
    • Reflexively Autocatalytic and Food-generated (RAF) theory formalizes these self-sustaining biochemical processes.
    • Previous work established efficient algorithms and mathematical analysis for RAF theory.

    Purpose of the Study:

    • To extend RAF theory to models reflecting ligation and cleavage reactions.
    • To compare predictions from complex models with a simple binary polymer model.
    • To investigate the structural properties of RAFs in these extended models.

    Main Methods:

    • Mathematical analysis of RAF theory.
    • Modeling of binary polymer systems.
    • Investigation of ligation and cleavage reaction patterns.

    Main Results:

    • Certain properties of extended models align with and can be predicted by the simple binary polymer model.
    • Other properties yield different quantitative estimates compared to the simple model.
    • New results concerning the structure of RAFs in ligation-cleavage systems were established.

    Conclusions:

    • The extended RAF models provide a more nuanced understanding of biochemical self-organization.
    • The study highlights both the predictive power and limitations of simplified models.
    • New insights into the structural organization of complex autocatalytic systems were gained.