A parity check analog decoder for molecular communication based on biological circuits

Abstract

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.

Designing Molecular Circuits for Approximate Maximum a Posteriori Demodulation of Concentration Modulated Signals

“…In this section, we want to explore the possibility of using chemical species found in living cells to implement Eq. (9). In this section, we will show that a gene promotor circuit named DCS2, which is found in Saccharomyces cerevisiae (yeast) and was studied in [11], behaves similarly to the CM demodulation filter Eq.…”

“…The paper [8] presented a biological circuit for molecular communication from a system-theoretic perspective. There was also work on using analog circuits for soft detection [20] and parity check decoder [9]. The key difference between these few pieces of work and ours is that they use one sample point per symbol.…”

“…(8) and Eq. (9). We propose to determine the Hill function parameters h k , H k and n k such that the difference between the following two expressions is small in the least squares sense:…”

“…In this section, we will show that a gene promotor circuit named DCS2, which is found in Saccharomyces cerevisiae (yeast) and was studied in [11], behaves similarly to the CM demodulation filter Eq. (9). Note that in order to implement the modulator in Fig.…”

“…(9) as an nonhomogenous Poisson process whose instantaneous rate is given by the RHS of Eq. (9). We use the method in [40] to perform this simulation.…”