Molecular Communication Using Brownian Motion with Drift

Inspired by biological communication systems, molecular communication has been proposed as a viable scheme to communicate between nano-sized devices separated by a very short distance. Here, molecules are released by the transmitter into the medium, which are then sensed by the receiver. This paper develops a preliminary version of such a communication system focusing on the release of either one or two molecules into a fluid medium with drift. We analyze the mutual information between transmitter and the receiver when information is encoded in the time of release of the molecule. Simplifying assumptions are required in order to calculate the mutual information, and theoretical results are provided to show that these calculations are upper bounds on the true mutual information. Furthermore, optimized degree distributions are provided, which suggest transmission strategies for a variety of drift velocities.Comment: 20 pages, 7 figures, Accepted for publication in IEEE Trans. on NanoBioscienc

Molecular communication in fluid media: The additive inverse Gaussian noise channel

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.Comment: 28 pages, 8 figures. Submitted to IEEE Transactions on Information Theory. Corrects minor typos in the first versio

A method for molecular dynamics on curved surfaces

Dynamics simulations of constrained particles can greatly aid in understanding the temporal and spatial evolution of biological processes such as lateral transport along membranes and self-assembly of viruses. Most theoretical efforts in the field of diffusive transport have focussed on solving the diffusion equation on curved surfaces, for which it is not tractable to incorporate particle interactions even though these play a crucial role in crowded systems. We show here that it is possible to combine standard constraint algorithms with the classical velocity Verlet scheme to perform molecular dynamics simulations of particles constrained to an arbitrarily curved surface, in which such interactions can be taken into account. Furthermore, unlike Brownian dynamics schemes in local coordinates, our method is based on Cartesian coordinates allowing for the reuse of many other standard tools without modifications, including parallelisation through domain decomposition. We show that by applying the schemes to the Langevin equation for various surfaces, confined Brownian motion is obtained, which has direct applications to many biological and physical problems. Finally we present two practical examples that highlight the applicability of the method: (i) the influence of crowding and shape on the lateral diffusion of proteins in curved membranes and (ii) the self-assembly of a coarse-grained virus capsid protein model.Comment: 30 pages, 5 figure

Detection Algorithms for Molecular MIMO

In this paper, we propose a novel design for molecular communication in which both the transmitter and the receiver have, in a 3-dimensional environment, multiple bulges (in RF communication this corresponds to antenna). The proposed system consists of a fluid medium, information molecules, a transmitter, and a receiver. We simulate the system with a one-shot signal to obtain the channel's finite impulse response. We then incorporate this result within our mathematical analysis to determine interference. Molecular communication has a great need for low complexity, hence, the receiver may have incomplete information regarding the system and the channel state. Thus, for the cases of limited information set at the receiver, we propose three detection algorithms, namely adaptive thresholding, practical zero forcing, and Genie-aided zero forcing.Comment: 6 pages, 6 figures, 2015 IEEE ICC accepte

Information Rates of ASK-Based Molecular Communication in Fluid Media

This paper studies the capacity of molecular communications in fluid media, where the information is encoded in the number of transmitted molecules in a time-slot (amplitude shift keying). The propagation of molecules is governed by random Brownian motion and the communication is in general subject to inter-symbol interference (ISI). We first consider the case where ISI is negligible and analyze the capacity and the capacity per unit cost of the resulting discrete memoryless molecular channel and the effect of possible practical constraints, such as limitations on peak and/or average number of transmitted molecules per transmission. In the case with a constrained peak molecular emission, we show that as the time-slot duration increases, the input distribution achieving the capacity per channel use transitions from binary inputs to a discrete uniform distribution. In this paper, we also analyze the impact of ISI. Crucially, we account for the correlation that ISI induces between channel output symbols. We derive an upper bound and two lower bounds on the capacity in this setting. Using the input distribution obtained by an extended Blahut-Arimoto algorithm, we maximize the lower bounds. Our results show that, over a wide range of parameter values, the bounds are close.Comment: 31 pages, 8 figures, Accepted for publication on IEEE Transactions on Molecular, Biological, and Multi-Scale Communication