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Improving Efficiency of Metabolic Flux Sampling via Monte-Carlo Algorithm From Network Prep.pdf

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Improving Efficiency of Metabolic Flux Sampling via Monte-Carlo Algorithm From Network Prep

Improving Efficiency of Metabolic Flux Sampling via Monte-Carlo Algorithm: From Network Preprocessing to the Emergence of Bypass Pathways Lu Xie*#, Yi Zhang*# *School of Life Science, University of Science and Technology of China, Hefei, Anhui, P. R. China. #These people contribute equally to this work. Abstract Constraint-based modeling is a widely used approach to analyze metabolic networks which were reconstructed from variety of biological data. The linear constraints, such as mass conservation constraint, reversibility constraint, biological capacity constraint, can be imposed hands down in the linear programming or uniform random sampling. But recently, a non-linear constraint, known as “loop law”, is challenging the existing algorithms. Here a more simple and efficient sampling method was presented and contains three steps: (1) Network preprocessing: pick up the non-zero flux excluding the zero flux to decrease the rows of the stoichiometric matrix, and discover the latent loops of the network by linear programming; (2) Sampling the flux space: sample the null space of the stoichiometric matrix using Simulated Annealing Monte-Carlo method with a potential energy function which was defined to enforce additional constraints mentioned above, including the virtual chemical potential constraint (VCPC for short) to apply the loop-law; (3) Checking results: inspect that whether the samples have loop flux or not by solving an inequality. In addition, a new type of pathway has emerged: the bypass pathway, which has exchange flux with environment but is independent to the biomass synthesis. A linear programming based method was presented for eliminating the bypass fluxes (EBF for short), and the result shows an improved correlation among some cascading reactions. These methods were employed to analyze the genome-scale metabolic network of Helicobacter pylori. Keywords: constraint-based, loop law, Simulated Annealing Monte-Carlo. 1. Int