Using existing digital tools for efficient metabolic pathway simulations.
The complexity of full-cell metabolic and regulatory pathways currently hinders high accuracy biological simulations with traditional Ordinary Differential Equation (ODE) solver-based methodologies. In this paper event-driven simulators used to tackle problems of similar complexity in Very Large Scale Integration (VLSI) digital designs are employed to trade-off complexity for accuracy. An event-driven model for typical enzymatically catalyzed reactions is proposed and compared with standard ODE solutions on single reactions and a biologically relevant portion of a metabolic pathway. The system shows good stability and controlled error propagation, and allows reduction of computational effort in systems where few concentrations are actively changing at any given time, as well as integration of other models such as on/off gene activation, stochastic and discrete behavior.
Macchiarulo
Luca
L
Fac. of Electr. Eng., Hawaii Univ., Honolulu, HI 96822, USA. lucam@hawaii.edu
D000465:Algorithms; D001695:Biology / Q000379:methods; D003198:Computer Simulation; D007700:Kinetics; D008433:Mathematics; D053858:Metabolic Networks and Pathways; D008660:Metabolism; D008954:Models, Biological; D008956:Models, Chemical; D015233:Models, Statistical; D012984:Software; D013269:Stochastic Processes