Motivated by the fact that living cells use molecular circuits (i.e., a set of chemical reactions) for information processing, this paper investigates the problem of designing molecular circuits for demodulation. In our earlier work, we use a Markovian approach to derive a demodulator for diffusion-based molecular communication. The demodulation filters take the form of an ordinary differential equation, which computes the log-posteriori probability of a transmission symbol being sent. This paper considers the realization of these demodulation filters using molecular circuits assuming the transmission symbols are rectangular pulses of the same duration but different amplitudes, i.e., concentration modulation. This paper makes a number of contributions. First, we use time-scale separation and renewal theory to analytically derive an approximation of the demodulation filter from our earlier work. Second, we present a method to turn this approximation into a molecular circuit. By using simulations, we show that the output of the derived molecular circuit is approximately equal to the log-posteriori probability calculated by the exact demodulation filter if the log-posteriori probability is positive. Third, we demonstrate that a biochemical circuit in yeast behaves similarly to the derived molecular demodulation filter and is therefore a candidate for implementing the derived filter.
@cite_9: With much advancement in the field of nanotechnology, bioengineering, and synthetic biology over the past decade, microscales and nanoscales devices are becoming a reality. Yet the problem of engineering a reliable communication system between tiny devices is still an open problem. At the same time, despite the prevalence of radio communication, there are still areas where traditional electromagnetic waves find it difficult or expensive to reach. Points of interest in industry, cities, and medical applications often lie in embedded and entrenched areas, accessible only by ventricles at scales too small for conventional radio waves and microwaves, or they are located in such a way that directional high frequency systems are ineffective. Inspired by nature, one solution to these problems is molecular communication (MC), where chemical signals are used to transfer information. Although biologists have studied MC for decades, it has only been researched for roughly 10 year from a communication engineering lens. Significant number of papers have been published to date, but owing to the need for interdisciplinary work, much of the results are preliminary. In this survey, the recent advancements in the field of MC engineering are highlighted. First, the biological, chemical, and physical processes used by an MC system are discussed. This includes different components of the MC transmitter and receiver, as well as the propagation and transport mechanisms. Then, a comprehensive survey of some of the recent works on MC through a communication engineering lens is provided. The survey ends with a technology readiness analysis of MC and future research directions.
@cite_15: Abstract In this paper, we study a molecular communication system operating over a moving propagation medium. Using the convection–diffusion equation, we present the first separate models for the channel response and the corrupting noise. The flow-based molecular channel is shown to be linear but time-varying and the noise corrupting the signal is additive white Gaussian with a signal dependent magnitude. By modelling the ligand–receptor binding process, it is shown that the molecular communication reception process in this channel has a low-pass characteristic that colours the additive noise. A whitening filter is proposed to compensate for this low-pass characteristic. Simulation results demonstrate the benefit of the whitening filter and the effect of medium motion on bit error rate.
@cite_7: In this paper, we perform receiver design for a diffusive molecular communication environment. Our model includes flow in any direction, sources of information molecules in addition to the transmitter, and enzymes in the propagation environment to mitigate intersymbol interference. We characterize the mutual information between receiver observations to show how often independent observations can be made. We derive the maximum likelihood sequence detector to provide a lower bound on the bit error probability. We propose the family of weighted sum detectors for more practical implementation and derive their expected bit error probability. Under certain conditions, the performance of the optimal weighted sum detector is shown to be equivalent to a matched filter. Receiver simulation results show the tradeoff in detector complexity versus achievable bit error probability, and that a slow flow in any direction can improve the performance of a weighted sum detector.
@cite_39: Abstract In this paper, a strength-based optimum signal detection scheme for binary concentration-encoded molecular communication (CEMC) system has been presented. In CEMC, a single type of information molecule is assumed to carry the information from the transmitting nanomachine (TN), through the propagation medium, to the receiving nanomachine (RN) in the form of received concentration of information molecules at the location of the RN. We consider a pair of nanomachines communicating by means of on–off keying (OOK) transmission protocol in a three-dimensional ideal (i.e. free) diffusion-based unbounded propagation environment. First, based on stochastic chemical kinetics of the reaction events between ligand molecules and receptors, we develop a mathematical receiver model of strength-based detection scheme for OOK CEMC system. Using an analytical approach, we explain the receiver operating characteristic (ROC) curves of the receiver thus developed. Finally, we propose a variable threshold -based detection scheme and explain its communication range and rate dependent characteristics. We show that it provides an improvement in the communication ranges compared to fixed threshold -based detection scheme. (Part of this paper has been peer-reviewed and published in BWCCA-2012 conference in Victoria, BC, 12–14 November, 2012 [20] .)
For a recent survey on molecular communication, see @cite_9 . Although there was much earlier work on demodulation, see e.g. @cite_7 @cite_39 @cite_15 , this paper differs from the earlier work in two key aspects. First, most earlier work assumed that the demodulation is based on one sample point per symbol; however, this work assumes that demodulation is based on the continuous history of the number of active receptors. Second, most earlier work did not consider a demodulator which is made entirely from chemical reactions.