Shahram Shafie

Graph-theoretical identification of pathways for biochemical reactions

A rigorous method for identifying biochemical reaction or metabolic pathways through its systematic synthesis has been established. The current method for synthesizing networks of metabolic pathways follows the general framework of a highly exacting combinatorial method. The method is capable of generating not only all combinatorially independent, feasible reaction networks only once, but also those combinations of independent pathways. A case study involving the conversion of glucose to pyruvate with 14 elementary reactions illustrates the efficiency and efficacy of the method. All the results have been obtained with a PC (Pentium-III 550 MHz, 256 MB RAM) within 1 s.

Graph-theoretic approach for identifying catalytic or metabolic pathways

Abstract Stoichiometrically exact and potentially feasible catalytic or metabolic pathways can be found by synthesizing the networks of plausible elementary or metabolic reactions constituting such pathways, respectively. The current contribution presents a mathematically exact algorithmic approach for carrying out the necessary synthesis, which is profoundly complex combinatorially. The approach is based on the unique graph‐representation in terms of P‐graphs (process graphs), a set of axioms, and a group of combinatorial algorithms. The inclusion or exclusion of a step of each elementary or metabolic reaction in the pathway of interest hinges on the general combinatorial properties of feasible reaction networks. At the outset, a brief overview is given of successful applications to date, followed by an outline of the methodology, on which the approach is based. The approach is illustrated by implementing it to three new examples comprising two catalytic reactions, catalytic combustion of hydrogen and reduction of nitrogen oxide, and one metabolic reaction, involved in the production of ethanol by yeast. The efficacy of the approach is discussed in light of the results obtained from these examples. Finally, a brief discourse is given of our current and future efforts.

Graph-theoretic approach to the catalytic-pathway identification of methanol decomposition

Catalytic partial oxidation of methanol (MD) plays a key role in hydrogen production, which is the desirable fuel for both proton exchange membrane and direct methanol fuel cell systems. Thus, the catalytic mechanisms, or pathways, of MD have lately been the focus of intense research interest. Recently, the feasible independent pathways (IPis) have been reported on the basis of a set of highly plausible elementary reactions. Nevertheless, no feasible acyclic combined pathways (APis) comprising IPis have been reported. Such APis can not be ignored in identifying dominant pathways.