Oscillation of molecular machines with enzymes

Advances in nanotechnology have made it possible to engineer nanomachines. Single nanomachine has limited abilities to accomplish target goals, so a nanonetwork, which is composed of interconnected nanomachines, is expected. To perform cooperative operations, the synchronization of the nanomachines is essential. However, one of the main challenges in synchronizing the nanomachines is the study and analysis of the noise. This paper proposes an oscillation model with the presence of enzymes in the transmission environment, where the enzymes can react with the released molecules. Oscillation occurs as the periodic increase and decrease of the molecules concentration. Simulations and analysis are performed to determine how the enzymes, the system parameters and the noise impact the oscillation. The presented enzymes in the environment function as accelerating the molecular diffusion, making the system reaches stability faster. The molecule counting noise, which is taken as the most relevant diffusion-based noise, may affect the molecules concentration passing the threshold earlier or later than expected. Compared with the scenario that the enzymes are not presented in the transmission environment, the molecule counting noise has a relatively small influence on the oscillation where enzymes are presented in the transmission environment.