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      Improving Receiver Performance of Diffusive Molecular Communication with Enzymes

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          Abstract

          This paper studies the mitigation of intersymbol interference in a diffusive molecular communication system using enzymes that freely diffuse in the propagation environment. The enzymes form reaction intermediates with information molecules and then degrade them so that they cannot interfere with future transmissions. A lower bound expression on the expected number of molecules measured at the receiver is derived. A simple binary receiver detection scheme is proposed where the number of observed molecules is sampled at the time when the maximum number of molecules is expected. Insight is also provided into the selection of an appropriate bit interval. The expected bit error probability is derived as a function of the current and all previously transmitted bits. Simulation results show the accuracy of the bit error probability expression and the improvement in communication performance by having active enzymes present.

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          Most cited references 13

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          Stochastic simulation of chemical kinetics.

          Stochastic chemical kinetics describes the time evolution of a well-stirred chemically reacting system in a way that takes into account the fact that molecules come in whole numbers and exhibit some degree of randomness in their dynamical behavior. Researchers are increasingly using this approach to chemical kinetics in the analysis of cellular systems in biology, where the small molecular populations of only a few reactant species can lead to deviations from the predictions of the deterministic differential equations of classical chemical kinetics. After reviewing the supporting theory of stochastic chemical kinetics, I discuss some recent advances in methods for using that theory to make numerical simulations. These include improvements to the exact stochastic simulation algorithm (SSA) and the approximate explicit tau-leaping procedure, as well as the development of two approximate strategies for simulating systems that are dynamically stiff: implicit tau-leaping and the slow-scale SSA.
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            Molecular communication and networking: opportunities and challenges.

            The ability of engineered biological nanomachines to communicate with biological systems at the molecular level is anticipated to enable future applications such as monitoring the condition of a human body, regenerating biological tissues and organs, and interfacing artificial devices with neural systems. From the viewpoint of communication theory and engineering, molecular communication is proposed as a new paradigm for engineered biological nanomachines to communicate with the natural biological nanomachines which form a biological system. Distinct from the current telecommunication paradigm, molecular communication uses molecules as the carriers of information; sender biological nanomachines encode information on molecules and release the molecules in the environment, the molecules then propagate in the environment to receiver biological nanomachines, and the receiver biological nanomachines biochemically react with the molecules to decode information. Current molecular communication research is limited to small-scale networks of several biological nanomachines. Key challenges to bridge the gap between current research and practical applications include developing robust and scalable techniques to create a functional network from a large number of biological nanomachines. Developing networking mechanisms and communication protocols is anticipated to introduce new avenues into integrating engineered and natural biological nanomachines into a single networked system. In this paper, we present the state-of-the-art in the area of molecular communication by discussing its architecture, features, applications, design, engineering, and physical modeling. We then discuss challenges and opportunities in developing networking mechanisms and communication protocols to create a network from a large number of bio-nanomachines for future applications.
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              Molecular communication in fluid media: The additive inverse Gaussian noise channel

               ,  ,   (2010)
              We consider molecular communication, with information conveyed in the time of release of molecules. The main contribution of this paper is the development of a theoretical foundation for such a communication system. Specifically, we develop the additive inverse Gaussian (IG) noise channel model: a channel in which the information is corrupted by noise with an inverse Gaussian distribution. We show that such a channel model is appropriate for molecular communication in fluid media - when propagation between transmitter and receiver is governed by Brownian motion and when there is positive drift from transmitter to receiver. Taking advantage of the available literature on the IG distribution, upper and lower bounds on channel capacity are developed, and a maximum likelihood receiver is derived. Theory and simulation results are presented which show that such a channel does not have a single quality measure analogous to signal-to-noise ratio in the AWGN channel. It is also shown that the use of multiple molecules leads to reduced error rate in a manner akin to diversity order in wireless communications. Finally, we discuss some open problems in molecular communications that arise from the IG system model.
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                Author and article information

                Journal
                08 May 2013
                2013-12-16
                Article
                10.1109/TNB.2013.2295546
                1305.1926

                http://arxiv.org/licenses/nonexclusive-distrib/1.0/

                Custom metadata
                13 pages, 8 figures, 1 table. To appear in IEEE Transactions on Nanobioscience (submitted January 22, 2013; minor revision October 16, 2013; accepted December 4, 2013)
                cs.IT cs.ET math.IT

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