Synchronous optimal design of genetic oscillator networks using a novel VonPSO algorithm

As a common phenomenon in biological systems, synchronization plays a vital role in construction of genetic oscillator networks with specific cellular functions. Considering the complexity of connections, optimal synchronous design of oscillator networks become feasible with optimization approaches. In order to improve the efficiency of optimal synchronous design, a novel VonPSO algorithm that applies Von-Neumann topology is proposed to solve the combinational optimization problem involved in optimizing directed interactions within coupled oscillator networks. This VonPSO algorithm applies mutation and crossover operations to generate new candidates that represent the network adjacent matrices. Using order parameter to evaluate the degree of synchronization, this paper applies a twostages optimization framework that adjusts network topologies and coupling parameters at two independent stages. Simulation outcomes indicate that the proposed framework is effective to improve the synchronous indexes between coupled genetic oscillators using the VonPSO algorithm. Experimental outcomes indicate that synchronization of coupled oscillator networks can be significantly enhanced by the two-stages optimization using VonPSO algorithm.