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      Capacity of electron-based communication over bacterial cables: the full-CSI case

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          Abstract

          Motivated by recent discoveries of microbial communities that transfer electrons across centimeter-length scales, this paper studies the information capacity of bacterial cables via electron transfer, which coexists with molecular communications, under the assumption of full causal channel state information (CSI). The bacterial cable is modeled as an electron queue that transfers electrons from the encoder at the electron donor source, which controls the desired input electron intensity, to the decoder at the electron acceptor sink. Clogging due to local ATP saturation along the cable is modeled. A discrete-time scheme is investigated, enabling the computation of an achievable rate. The regime of asymptotically small time-slot duration is analyzed, and the optimality of binary input distributions is proved, i.e., the encoder transmits at either maximum or minimum intensity, as dictated by the physical constraints of the cable. A dynamic programming formulation of the capacity is proposed, and the optimal binary signaling is determined via policy iteration. It is proved that the optimal signaling has smaller intensity than that given by the myopic policy, which greedily maximizes the instantaneous information rate but neglects its effect on the steady-state cable distribution. In contrast, the optimal scheme balances the tension between achieving high instantaneous information rate, and inducing a favorable steady-state distribution, such that those states characterized by high information rates are visited more frequently, thus revealing the importance of CSI. This work represents a first contribution towards the design of electron signaling schemes in complex microbial structures, e.g., bacterial cables and biofilms, where the tension between maximizing the transfer of information and guaranteeing the well-being of the overall bacterial community arises.

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          Filamentous bacteria transport electrons over centimetre distances.

          Oxygen consumption in marine sediments is often coupled to the oxidation of sulphide generated by degradation of organic matter in deeper, oxygen-free layers. Geochemical observations have shown that this coupling can be mediated by electric currents carried by unidentified electron transporters across centimetre-wide zones. Here we present evidence that the native conductors are long, filamentous bacteria. They abounded in sediment zones with electric currents and along their length they contained strings with distinct properties in accordance with a function as electron transporters. Living, electrical cables add a new dimension to the understanding of interactions in nature and may find use in technology development.
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            Capacity, mutual information, and coding for finite-state Markov channels

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              Molecular communication: modeling noise effects on information rate.

              Molecular communication is a new paradigm for communication between biological nanomachines over a nano- and microscale range. As biological nanomachines (or nanomachines in short) are too small and simple to communicate through traditional communication mechanisms (e.g., through sending and receiving of radio or infrared signals), molecular communication provides a mechanism for a nanomachine (i.e., a sender) to communicate information by propagating molecules (i.e., information molecules) that represent the information to a nanomachine (i.e., a receiver). This paper describes the design of an in vitro molecular communication system and evaluates various approaches to maximize the probability of information molecules reaching a receiver(s) and the rate of information reaching the receiver(s). The approaches considered in this paper include propagating information molecules (diffusion or directional transport along protein filaments), removing excessive information molecules (natural decay or receiver removal of excessive information molecules), and encoding and decoding approaches (redundant information molecules to represent information and to decode information). Two types of molecular communication systems are considered: a unicast system in which a sender communicates with a single receiver and a broadcast system in which a sender communicates with multiple receivers. Through exploring tradeoffs among the various approaches on the two types of molecular communication systems, this paper identifies promising approaches and shows the feasibility of an in vitro molecular communication system.
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                Author and article information

                Journal
                1501.03996

                Numerical methods,Information systems & theory
                Numerical methods, Information systems & theory

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