Robust Optimal Design of Oscillatory Genetic Networks Using a Novel VonPSO Algorithm

In order to realize stable cellular functions, engineered genetic circuits need to overcome intrinsic noise and perturbations in cellular environments. Without enough robustness, the performance of synthetic genetic networks easily deteriorate. Designing a robust network structure for synthetic networks become an important task in computational systems biology. The purpose of optimal network design is to obtain networks that meet the requirements using computational approaches under necessary constraints. Robust optimal design of oscillatory genetic networks is converted to a combinational problem that can be solved by optimization methods. This study proposes a novel VonPSO method that applies a local neighborhood in information exchange structure between particles to solve the robust optimal design problem. The discrete VonPSO algorithm applies mutation and crossover operations to generate new candidate solutions, thus searching the robust network structure. Simulation experiments of four oscillatory networks indicate the proposed algorithm is effective in enhancing the average robustness of oscillatory genetic networks under three types of perturbations.