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Register a new userMolecular Communication Between Two Populations of Bacteria
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Added by
Arash Einolghozati
Publication date
2012
fields
Informatics Engineering
and research's language is
English
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Molecular communication is an expanding body of research. Recent advances in biology have encouraged using genetically engineered bacteria as the main component in the molecular communication. This has stimulated a new line of research that attempts to study molecular communication among bacteria from an information-theoretic point of view. Due to high randomness in the individual behavior of the bacterium, reliable communication between two bacteria is almost impossible. Therefore, we recently proposed that a population of bacteria in a cluster is considered as a node capable of molecular transmission and reception. This proposition enables us to form a reliable node out of many unreliable bacteria. The bacteria inside a node sense the environment and respond accordingly. In this paper, we study the communication between two nodes, one acting as the transmitter and the other as the receiver. We consider the case in which the information is encoded in the concentration of molecules by the transmitter. The molecules produced by the bacteria in the transmitter node propagate in the environment via the diffusion process. Then, their concentration sensed by the bacteria in the receiver node would decode the information. The randomness in the communication is caused by both the error in the molecular production at the transmitter and the reception of molecules at the receiver. We study the theoretical limits of the information transfer rate in such a setup versus the number of bacteria per node. Finally, we consider M-ary modulation schemes and study the achievable rates and their error probabilities.
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The prospect of new biological and industrial applications that require communication in micro-scale, encourages research on the design of bio-compatible communication networks using networking primitives already available in nature. One of the most promising candidates for constructing such networks is to adapt and engineer specific types of bacteria that are capable of sensing, actuation, and above all, communication with each other. In this paper, we describe a new architecture for networks of bacteria to form a data collecting network, as in traditional sensor networks. The key to this architecture is the fact that the node in the network itself is a bacterial colony; as an individual bacterium (biological agent) is a tiny unreliable element with limited capabilities. We describe such a network under two different scenarios. We study the data gathering (sensing and multihop communication) scenario as in sensor networks followed by the consensus problem in a multi-node network. We will explain as to how the bacteria in the colony collectively orchestrate their actions as a node to perform sensing and relaying tasks that would not be possible (at least reliably) by an individual bacterium. Each single bacterium in the colony forms a belief by sensing external parameter (e.g., a molecular signal from another node) from the medium and shares its belief with other bacteria in the colony. Then, after some interactions, all the bacteria in the colony form a common belief and act as a single node. We will model the reception process of each individual bacteria and will study its impact on the overall functionality of a node. We will present results on the reliability of the multihop communication for data gathering scenario as well as the speed of convergence in the consensus scenario.
The design of biological networks using bacteria as the basic elements of the network is initially motivated by a phenomenon called quorum sensing. Through quorum sensing, each bacterium performs sensing the medium and communicating it to others via molecular communication. As a result, bacteria can orchestrate and act collectively and perform tasks impossible otherwise. In this paper, we consider a population of bacteria as a single node in a network. In our version of biological communication networks, such a node would communicate with one another via molecular signals. As a first step toward such networks, this paper focuses on the study of the transfer of information to the population (i.e., the node) by stimulating it with a concentration of special type of a molecules signal. These molecules trigger a chain of processes inside each bacteria that results in a final output in the form of light or fluorescence. Each stage in the process adds noise to the signal carried to the next stage. Our objective is to measure (compute) the maximum amount of information that we can transfer to the node. This can be viewed as the collective sensing capacity of the node. The molecular concentration, which carries the information, is the input to the node, which should be estimated by observing the produced light as the output of the node (i.e., the entire population of bacteria forming the node). We focus on the noise caused by the random process of trapping molecules at the receptors as well as the variation of outputs of different bacteria in the node. The capacity variation with the number of bacteria in the node and the number of receptors per bacteria is obtained. Finally, we investigated the collective sensing capability of the node when a specific form of molecular signaling concentration is used.
The design of biologically-inspired wireless communication systems using bacteria as the basic element of the system is initially motivated by a phenomenon called emph{Quorum Sensing}. Due to high randomness in the individual behavior of a bacterium, reliable communication between two bacteria is almost impossible. Therefore, we have recently proposed that a population of bacteria in a cluster is considered as a bio node in the network capable of molecular transmission and reception. This proposition enables us to form a reliable bio node out of many unreliable bacteria. In this paper, we study the communication between two nodes in such a network where information is encoded in the concentration of molecules by the transmitter. The molecules produced by the bacteria in the transmitter node propagate through the diffusion channel. Then, the concentration of molecules is sensed by the bacteria population in the receiver node which would decode the information and output light or fluorescent as a result. The uncertainty in the communication is caused by all three components of communication, i.e., transmission, propagation and reception. We study the theoretical limits of the information transfer rate in the presence of such uncertainties. Finally, we consider M-ary signaling schemes and study their achievable rates and corresponding error probabilities.
In this paper, we present an analytical model for a diffusive molecular communication (MC) system with a reversible adsorption receiver in a fluid environment. The time-varying spatial distribution of the information molecules under the reversible adsorption and desorption reaction at the surface of a bio-receiver is analytically characterized. Based on the spatial distribution, we derive the number of newly-adsorbed information molecules expected in any time duration. Importantly, we present a simulation framework for the proposed model that accounts for the diffusion and reversible reaction. Simulation results show the accuracy of our derived expressions, and demonstrate the positive effect of the adsorption rate and the negative effect of the desorption rate on the net number of newly-adsorbed information molecules expected. Moreover, our analytical results simplify to the special case of an absorbing receiver.
A diffusion-based molecular communication system has two major components: the diffusion in the medium, and the ligand-reception. Information bits, encoded in the time variations of the concentration of molecules, are conveyed to the receiver front through the molecular diffusion in the medium. The receiver, in turn, measures the concentration of the molecules in its vicinity in order to retrieve the information. This is done via ligand-reception process. In this paper, we develop models to study the constraints imposed by the concentration sensing at the receiver side and derive the maximum rate by which a ligand-receiver can receive information. Therefore, the overall capacity of the diffusion channel with the ligand receptors can be obtained by combining the results presented in this paper with our previous work on the achievable information rate of molecular communication over the diffusion channel.
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