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As a widely used method in metabolic network studies, Monte-Carlo sampling inthe steady state flux space is known for its flexibility and convenience ofcarrying out different purposes, simply by alternating constraints or objectivefunctions, or appending post processes. Recently the concept of a non-linearconstraint based on the second thermodynamic law, known as "Loop Law", ischallenging current sampling algorithms which will inevitably give rise to theinternal loops. A generalized method is proposed here to eradicate theprobability of the appearance of internal loops during sampling process. Basedon Artificial Centered Hit and Run (ACHR) method, each step of the new samplingprocess will avoid entering "loop-forming" subspaces. This method has beenapplied on the metabolic network of Helicobacter pylori with three differentobjective functions: uniform sampling, optimizing biomass synthesis, optimizingbiomass synthesis efficiency over resources ingested. Comparison betweenresults from the new method and conventional ACHR method shows effectiveelimination of loop fluxes without affecting non-loop fluxes.

Avoid Internal Loops in Steady State Flux Space Sampling