Optimizing Molecular Communication Protocols through Simulated Emission and Detection

Abstract

Abstract Molecular communication offers a promising alternative to traditional electromagnetic systems, particularly in biological and constrained environments where conventional signals fail. This research presents the design, simulation, and evaluation of a molecular communication protocol using an open source simulator tailored for reaction diffusion systems. The study aimed to optimize modulation, encoding, and error-handling strategies to ensure reliable data transmission over various distances and time scales. The simulation environment was first validated against real-world experimental results, confirming that molecule arrival trends in simulation closely reflected physical diffusion behavior. Three modulation schemes direct bit mapping on-off keying, manchester encoded on-off keying, and molecule shift keying were evaluated across different set of communication ranges. Molecule shift keying consistently demonstrated the lowest bit error rates due to its use of distinct molecule types, while Manchester encoding improved bit detection in moderately noisy settings at the cost of reduced data rate.A global fixed-threshold decoding mechanism was implemented to detect bit sequences from molecule count data. For error correction, Hamming and Reed-Solomon codes were integrated and tested. Hamming performed well for single-bit errors under low noise, while Reed-Solomon codes showed potential for more complex scenarios, although it required longer bit sequences for optimal performance. The study also demonstrated the feasibility of multi-receiver communication, where distinct bit streams were decoded using molecule type differentiation. Overall, the findings contribute a practical framework for developing adaptable and optimized molecular communication systems, with clear directions for future advancement. Its novelty lies in showing how simulation driven techniques can effectively model real world behavior for optimizing molecular communication protocols under varying conditions.