Synthetic biology, through genetic circuit engineering in biological cells, is paving the way towards the realization of programmable man-made living devices, able to naturally operate within normally less accessible domains, i.e., the biological and the nanoscale. The control of the information processing and exchange between these engineered-cell devices, based on molecules and biochemical reactions, i.e., Molecular Communication (MC), will be enabling technologies for the emerging paradigm of the Internet of Bio-Nano Things, with applications ranging from tissue engineering to bioremediation. In this paper, the design of genetic circuits to enable MC links between engineered cells is proposed by stemming from techniques for information coding, and inspired by recent studies favoring the efficiency of analog computation over digital in biological cells. In particular, the design of a joint encoder-modulator for the transmission of binary-modulated molecule concentration is coupled with a decoder that computes the a-posteriori log-likelihood ratio of the information bits from the propagated concentration. These functionalities are implemented entirely in the biochemical domain through activation and repression of genes, and biochemical reactions, rather than classical electrical circuits. Biochemical simulations are used to evaluate the proposed design against a theoretical encoder/decoder implementation taking into account impairments introduced by diffusion noise.

Abstract-Molecular Communication (MC) is an enabling paradigm for the interconnection of future devices and networks in the biological environment, with applications ranging from bio-medicine to environmental monitoring and control. The engineering of biological circuits, which allows to manipulate the molecular information processing abilities of biological cells, is a candidate technology for the realization of MC-enabled devices. In this paper, inspired by recent studies favoring the efficiency of analog computation over digital in biological cells, an analog decoder design is proposed based on biological circuit components. In particular, this decoder computes the a-posteriori log-likelihood ratio of parity-check-encoded bits from a binarymodulated concentration of molecules. The proposed design implements the required L-value and the box-plus operations entirely in the biochemical domain by using activation and repression of gene expression, and reactions of molecular species. Each component of the circuit is designed and tuned in this paper by comparing the resulting functionality with that of the corresponding analytical expression. Despite evident differences with classical electronics, biochemical simulation data of the resulting biological circuit demonstrate very close performance in terms of Mean Squared Error (MSE) and Bit Error Rate (BER), and validate the proposed approach for the future realization of MC components.

The programming of biological cells by genetic circuit engineering is enabling the development of man-made devices and systems in the biochemical environment, with applications in the areas of biomedicine, security, and environmental sensing and control, amongst others. The exchange of information through biochemical reactions and molecule transport, i.e., Molecular Communication (MC), stands as one of the foundational paradigms for the design and characterization of these systems. In a previous work, the same authors developed an analog soft decoder design for MC based on biological circuits inspired by the analog information processing in biochemical reactions. While such a design was optimized for an MC channel affected by Gaussian noise, realistic noise models in molecule transport processes and biochemical reactions tend to deviate from this assumption. In this paper, these models are discussed together with the validity of their Gaussian approximations in light of the performance of the log-likelihood ratio calculation of the aforementioned design, numerically evaluated through biochemical simulation. These models, which are directly derived from the theory of molecular diffusion and stochastic chemical reaction analysis, are formulated with a general validity with respect to any future MC system design based on biological circuits.

Abstract-Regarded as one of the future enabling technologies of the Internet of Things at the biological and nanoscale domains, Molecular Communication (MC) promises to enable applications in healthcare, environmental protection, and bioremediation, amongst others. Since MC is directly inspired by communication processes in biological cells, the engineering of biological circuits through cells' genetic code manipulation, which enables access to the cells' information processing abilities, is a candidate technology for the future realization of MC components. In this paper, inspired by previous research on channel coding schemes for MC and biological circuits for cell communications, a joint encoder and modulator design is proposed for the transmission of cellular information through signaling molecules. In particular, the information encoding and modulation are based on a binary parity check scheme, and they are implemented by interconnecting biological circuit components based on gene expression and mass action reactions. Each component is mathematically modeled and tuned according to the desired output. The implementation of the biological circuit in a simulation environment is then presented along with the corresponding numerical results, which validate the proposed design by showing agreement with an ideal encoding and modulator scheme.