Engineering genetic circuits in receiver cells for diffusion-based molecular data communications

Abstract

Developments in bioengineering and nanotechnology have ignited the research on biological and molecular communication systems. Despite potential benefits, engineering communication systems to carry data signals using biological messenger molecules is challenging. Diffusing molecules may fall behind their schedule to arrive at a receiver, interfering with symbols of subsequent time slots and distorting the signal. Theoretical molecular communication models often focus solely on the characteristics of the communication channel and fail to provide an end-to-end system response, since they assume a simple thresholding process for a receiver cell and overlook how the receiver can detect the incoming distorted molecular signal. There is a need to develop viable end-to-end communication models. In this paper, we present a model-based framework for designing diffusion-based molecular communication systems coupled with synthetic genetic circuits. We describe a novel approach to encode information as a sequence of bits, each transmitted from a sender as a burst of specific number of molecules, control cellular behavior, and minimize cellular signal interference by employing equalization techniques from communication theory. This approach allows the encoding and de-coding of data bits efficiently using two different types of molecules that act as the data carrier and the antagonist to cancel out the heavy tail of the former. We also present Period Finder, as a tool to optimize communication parameters, including the number of molecules and symbol duration. This tool facilitates automating the choice of communication parameters and identifying the best communication scenarios that can produce efficient cellular signals.