Publications - Working papers
Please find below working papers of our group. Currently, we list 58 working papers.
In the list are only not published papers present. If you look for a preprint of an already published paper you must look in the "Published papers" section.
If you have problems accessing electronic information, please let us know:
©NOTICE: All working papers are copyrighted by the authors; If you would like to use all or a portion of any paper, please contact the author.
Defining Autocatalysis in Chemical Reaction Networks
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
Download
[ PDF ]
Abstract
Autocatalysis is a deceptively simple concept, referring to the situation
that a chemical species X catalyzes its own formation. From the
perspective of chemical kinetics, autocatalysts show a regime of
super-linear growth. Given a chemical reaction network, however, it is
not at all straightforward to identify species that are autocatalytic in
the sense that there is a sub-network that takes X as input and
produces more than one copy of X as output. The difficulty arises from
the need to distinguish autocatalysis e.g. from the superposition of
a cycle that consumes and produces equal amounts of X and a pathway that
produces X. To deal with this issue, a number of competing notions,
such as exclusive autocatalysis and autocatalytic cycles, have been
introduced. A closer inspection of concepts and their usage by different
authors shows, however, that subtle differences in the definitions often
makes conceptually matching ideas difficult to bring together formally.
In this contribution we make some of the available approaches comparable
by translating them into a common formal framework that uses integer
hyperflows as a basis to study autocatalysis in large chemical reaction
networks. As an application we investigate the prevalence of
autocatalysis in metabolic networks.
Keywords
stoichiometry, directed hypergraph, hyperflow, chemical organization, metabolic networks, origins of life