Efficient Reconstruction of Metabolic Pathways by Bidirectional Chemical Search

One of the main challenges in systems biology is the establishment of the metabolome: a catalogue of the metabolites and biochemical reactions present in a specific organism. Current knowledge of biochemical pathways as stored in public databases such as KEGG, is based on carefully curated genomic evidence for the presence of specific metabolites and enzymes that activate particular biochemical reactions. In this paper, we present an efficient method to build a substantial portion of the artificial chemistry defined by the metabolites and biochemical reactions in a given metabolic pathway, which is based on bidirectional chemical search. Computational results on the pathways stored in KEGG reveal novel biochemical pathways

Generic properties of chemical networks: Artificial chemistry based on graph rewriting

We use a Toy Model of chemistry that represents molecules in terms of usual structural formulae to generate large chemical reaction networks. An extremely simplified quantum mechanical energy calculation and a straightforward implementation of reactions as graph rewritings ensure both transparency and closeness to chemical reality, both conditions that are necessary for the analysis of generic properties of large reaction networks. We show that some chemical networks graphs, e.g., repetitive Diels-Alder reactions, have the small-world property and exhibit a scale-free degree distribution. On the other hand, the Formose reaction does not fit well to this paradigm

Returnability as a criterion of disequilibrium in atmospheric reactions network

The concept of network returnability is reformulated as an equilibrium constant for a reaction network. Using this concept we study the atmospheric reaction networks of Earth, Mars, Venus and Titan. We found that the reaction network in the Earth’s atmosphere has the largest disequilibrium, followed by that of Titan which is still far from the most returnable atmospheres of Mars and Venus. We find that the chemical species with null or very low returnability are those in the highest disequilibrium in their respective atmospheres mainly due to physical, biogenic and/or anthropogenic mechanisms

Growing Biochemical Networks: Identifying the Intrinsic Properties

SCOPUS: cp.kinfo:eu-repo/semantics/publishe