Designing a simulatable environment for genetic circuitbased receivers in molecular communications

Inspired by nature, Molecular Communications (MC) has emerged over the past decade as a field that utilizes molecules as information carriers. This approach offers enhanced biocompatibility compared to traditional electromagnetic methods. The interdisciplinary nature of MC and the extensive research conducted in this area underscore its potential, particularly for medical applications. Yet, challenges such as intersymbol interference (ISI) and lower data rates, stemming from the inherent stochastic nature of MC, persist. While theoretical studies abound, bridging these concepts to practical applications remains a significant challenge, emphasizing the gap between theory and real-world implementation. Adopting an interdisciplinary approach, this thesis explores the integration of synthetic biology and molecular communications to address practical challenges in the field generating a realistic network environment. To combat the challenge of ISI, the pre-equalizer method is employed. This approach uses two interacting molecule types to mitigate the signal's heavy-tail effect. The approach is fine-tuned by a novel framework Parameter Finder to adjust the parameters of the communication scenario and MOL-Eye diagram is also integrated to enhance the precision of the molecular communication system. The findings reveal that integrating the system model with the pre-equalizer approach, alongside the use of the Parameter Finder tool, is highly beneficial for fine-tuning simulation parameters in the biological implementation of the pre-equalizer method. Additionally, the MOL-Eye diagram proves to be an effective tool for enhancing the selection of optimal parameters, providing a robust assessment of the performance of molecular signals.