Estimation of Small-Scale Kinetic Parameters of Escherichia coli (E. coli) Model by Enhanced Segment Particle Swarm Optimization Algorithm ESe-PSO

• Published in: Processes
• Main Author: Azrag M.A.K.; Zain J.M.; Kadir T.A.A.; Yusoff M.; Jaber A.S.; Abdlrhman H.S.M.; Ahmed Y.H.Z.; Husain M.S.B.
• Format: Article
• Language: English
• Published: Multidisciplinary Digital Publishing Institute (MDPI) 2023
• Online Access: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85146715808&doi=10.3390%2fpr11010126&partnerID=40&md5=0bae85d30bee22e5bfb3b8c09a167aa8

The ability to create “structured models” of biological simulations is becoming more and more commonplace. Although computer simulations can be used to estimate the model, they are restricted by the lack of experimentally available parameter values, which must be approximated. In this study, an Enhanced Segment Particle Swarm Optimization (ESe-PSO) algorithm that can estimate the values of small-scale kinetic parameters is described and applied to E. coli’s main metabolic network as a model system. The glycolysis, phosphotransferase system, pentose phosphate, the TCA cycle, gluconeogenesis, glyoxylate pathways, and acetate formation pathways of Escherichia coli are represented by the Differential Algebraic Equations (DAE) system for the metabolic network. However, this algorithm uses segments to organize particle movements and the dynamic inertia weight ((Formula presented.)) to increase the algorithm’s exploration and exploitation potential. As an alternative to the state-of-the-art algorithm, this adjustment improves estimation accuracy. The numerical findings indicate a good agreement between the observed and predicted data. In this regard, the result of the ESe-PSO algorithm achieved superior accuracy compared with the Segment Particle Swarm Optimization (Se-PSO), Particle Swarm Optimization (PSO), Genetic Algorithm (GA), and Differential Evolution (DE) algorithms. As a result of this innovative approach, it was concluded that small-scale and even entire cell kinetic model parameters can be developed. © 2023 by the authors.