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Andrew W. Eckford

Publications and source records attributed to Andrew W. Eckford.

At least 73 records · Page 4Linked to original sources
arXiv2017

Effect of Local Population Uncertainty on Cooperation in Bacteria

Bacteria populations rely on mechanisms such as quorum sensing to coordinate complex tasks that cannot be achieved by a single bacterium. Quorum sensing is used to measure the local bacteria population density, and it controls cooperation by ensuring that a bacterium only commits the resources for cooperation when it expects its neighbors to reciprocate. This paper proposes a simple model for sharing a resource in a bacterial environment, where knowledge of the population influences each bacterium's behavior. Game theory is used to model the behavioral dynamics, where the net payoff (i.e., utility) for each bacterium is a function of its current behavior and that of the other bacteria. The game is first evaluated with perfect knowledge of the population. Then, the unreliability of diffusion introduces uncertainty in the local population estimate and changes the perceived payoffs. The results demonstrate the sensitivity to the system parameters and how population uncertainty can overcome a lack of explicit coordination.

q-bio.CB↗
arXiv2017

Asynchronous Peak Detection for Demodulation in Molecular Communication

Molecular communication requires low-complexity symbol detection algorithms to deal with the many sources of uncertainty that are inherent in these channels. This paper proposes two variants of a high-performance asynchronous peak detection algorithm for a receiver that makes independent observations. The first variant has low complexity and measures the largest observation within a sampling interval. The second variant adds decision feedback to mitigate inter-symbol interference. Although the algorithm does not require synchronization between the transmitter and receiver, results demonstrate that the bit error performance of symbol-by-symbol detection using the first variant is better than using a single sample whose sampling time is chosen a priori. The second variant is shown to have performance comparable to that of an energy detector. Both variants of the algorithm demonstrate better resilience to timing offsets than that of existing detectors.

cs.IT↗
arXiv2016

RNA as a Nanoscale Data Transmission Medium: Error Analysis

RNA can be used as a high-density medium for data storage and transmission; however, an important RNA process -- replication -- is noisy. This paper presents an error analysis for RNA as a data transmission medium, analyzing how deletion errors increase in a collection of replicated DNA strands over time.

cs.ET↗
arXiv2016

Analyzing Dependent Placements of Small Cells in a Two-Layer Heterogeneous Network with a Rate Coverage Constraint

We consider the downlink of a two-layer heterogeneous network, comprising macro cells (MCs) and small cells (SCs). The existing literature generally assumes independent placements of the access points (APs) in different layers; in contrast, we analyze a dependent placement where SC APs are placed at locations with poor service from the MC layer. Our goal is to obtain an estimate of the number of SCs required to maintain a target outage rate. Such an analysis is trivial if the MCs are located according to a Poisson point process (PPP), which provides a lower bound on performance. Here, we consider MCs placed on a hexagonal grid, which complements the PPP model by providing an upper bound on performance. We first provide accurate bounds for the average interference within a MC when SCs are not used. Then, by obtaining the outage areas, we estimate the number of SCs required within an MC to overcome outage. If resource allocation amongst SCs is not used, we show that the problem of outage is not solved completely, and the residual outage area depends on whether co-channel or orthogonal SCs are used. Simulations show that a much smaller residual outage area is obtained with orthogonal SCs.

cs.IT↗
arXiv2016

Finite-State Channel Models for Signal Transduction in Neural Systems

Information theory provides powerful tools for understanding communication systems. This analysis can be applied to intercellular signal transduction, which is a means of chemical communication among cells and microbes. We discuss how to apply information-theoretic analysis to ligand-receptor systems, which form the signal carrier and receiver in intercellular signal transduction channels. We also discuss the applications of these results to neuroscience.

q-bio.QM↗
arXiv2016

Capacity of a Simple Intercellular Signal Transduction Channel

We model biochemical signal transduction, based on a ligand-receptor binding mechanism, as a discrete-time finite-state Markov channel, which we call the BIND channel. We show how to obtain the capacity of this channel, for the case of binary output, binary channel state, and arbitrary finite input alphabets. We show that the capacity-achieving input distribution is IID. Further, we show that feedback does not increase the capacity of this channel. We show how the capacity of the discrete-time channel approaches the capacity of Kabanov's Poisson channel, in the limit of short time steps and rapid ligand release.

q-bio.MN↗
arXiv2016

Distributed Cooperative Detection for Multi-Receiver Molecular Communication

In this paper, a cooperative diffusion-based molecular communication system is considered where distributed receivers collaboratively determine a transmitter's signal. In this system, the receivers first make local hard decisions about the current transmitted bit and then report these decisions to a fusion center (FC). The FC combines the local hard decisions to make a global decision using an N-out-of-K fusion rule. Asymmetric and symmetric topologies are considered and for each topology, two reporting scenarios, namely, perfect reporting and noisy reporting, are addressed. Closed-form analytical expressions for the expected global error probability are derived for all considered topologies and scenarios. Numerical and simulation results show that system reliability can be greatly improved by combining the detection information of distributed receivers.

cs.IT↗
arXiv2016

Shannon Capacity of Signal Transduction for Multiple Independent Receptors

Cyclic adenosine monophosphate (cAMP) is considered a model system for signal transduction, the mechanism by which cells exchange chemical messages. Our previous work calculated the Shannon capacity of a single cAMP receptor; however, a typical cell may have thousands of receptors operating in parallel. In this paper, we calculate the capacity of a cAMP signal transduction system with an arbitrary number of independent, indistinguishable receptors. By leveraging prior results on feedback capacity for a single receptor, we show (somewhat unexpectedly) that the capacity is achieved by an IID input distribution, and that the capacity for n receptors is n times the capacity for a single receptor.

cs.IT↗
arXiv2015

Analyzing the Impact of Access Point Density on the Performance of Finite-Area Networks

Assuming a network of infinite extent, several researchers have analyzed small-cell networks using a Poisson point process (PPP) location model, leading to simple analytic expressions. The general assumption has been that these results apply to finite-area networks as well. However, do the results of infinite-area networks apply to finite-area networks? In this paper, we answer this question by obtaining an accurate approximation for the achievable signal-to-interference-plus-noise ratio (SINR) and user capacity in the downlink of a \textit{finite-area} network with \textit{a fixed number of} access points (APs). The APs are uniformly distributed within the area of interest. Our analysis shows that, crucially, the results of infinite-area networks are very different from those for finite-area networks of low-to-medium AP density. Comprehensive simulations are used to illustrate the accuracy of our analysis. For practical values of signal transmit powers and AP densities, the analytic expressions capture the behavior of the system well. As an added benefit, the formulations developed here can be used in parametric studies for network design. Here, the analysis is used to obtain the required number of APs to guarantee a desired target capacity in a finite-area network.

cs.IT↗
arXiv2015

Design and Optimizing of On-Chip Kinesin Substrates for Molecular Communication

Lab-on-chip devices and point-of-care diagnostic chip devices are composed of many different components such as nanosensors that must be able to communicate with other components within the device. Molecular communication is a promising solution for on-chip communication. In particular, kinesin driven microtubule (MT) motility is an effective means of transferring information particles from one component to another. However, finding an optimal shape for these channels can be challenging. In this paper we derive a mathematical optimization model that can be used to find the optimal channel shape and dimensions for any transmission period. We derive three specific models for the rectangular channels, regular polygonal channels, and regular polygonal ring channels. We show that the optimal channel shapes are the square-shaped channel for the rectangular channel, and circular-shaped channel for the other classes of shapes. Finally, we show that among all 2 dimensional shapes the optimal design choice that maximizes information rate is the circular-shaped channel.

cs.IT↗
arXiv2015

A Universal Channel Model for Molecular Communication Systems with Metal-Oxide Detectors

In this paper, we propose an end-to-end channel model for molecular communication systems with metal-oxide sensors. In particular, we focus on the recently developed table top molecular communication platform. The system is separated into two parts: the propagation and the sensor detection. There is derived, based on this, a more realistic end-to-end channel model. However, since some of the coefficients in the derived models are unknown, we collect a great deal of experimental data to estimate these coefficients and evaluate how they change with respect to the different system parameters. Finally, a noise model is derived for the system to complete an end-to-end system model for the tabletop platform.

cs.ET↗
arXiv2014

Symbol interval optimization for molecular communication with drift

In this paper, we propose a symbol interval optimization algorithm in molecular communication with drift. Proper symbol intervals are important in practical communication systems since information needs to be sent as fast as possible with low error rates. There is a trade-off, however, between symbol intervals and inter-symbol interference (ISI) from Brownian motion. Thus, we find proper symbol interval values considering the ISI inside two kinds of blood vessels, and also suggest no ISI system for strong drift models. Finally, an isomer-based molecule shift keying (IMoSK) is applied to calculate achievable data transmission rates (achievable rates, hereafter). Normalized achievable rates are also obtained and compared in one-symbol ISI and no ISI systems.

cs.IT↗
arXiv2014

Scaling laws for molecular communication

In this paper, we investigate information-theoretic scaling laws, independent from communication strategies, for point-to-point molecular communication, where it sends/receives information-encoded molecules between nanomachines. Since the Shannon capacity for this is still an open problem, we first derive an asymptotic order in a single coordinate, i.e., i) scaling time with constant number of molecules $m$ and ii) scaling molecules with constant time $t$. For a single coordinate case, we show that the asymptotic scaling is logarithmic in either coordinate, i.e., $Θ(\log t)$ and $Θ(\log m)$, respectively. We also study asymptotic behavior of scaling in both time and molecules and show that, if molecules and time are proportional to each other, then the asymptotic scaling is linear, i.e., $Θ(t)=Θ(m)$.

cs.IT↗
arXiv2013

Channel and Noise Models for Nonlinear Molecular Communication Systems

Recently, a tabletop molecular communication platform has been developed for transmitting short text messages across a room. The end-to-end system impulse response for this platform does not follow previously published theoretical works because of imperfect receiver, transmitter, and turbulent flows. Moreover, it is observed that this platform resembles a nonlinear system, which makes the rich body of theoretical work that has been developed by communication engineers not applicable to this platform. In this work, we first introduce corrections to the previous theoretical models of the end-to-end system impulse response based on the observed data from experimentation. Using the corrected impulse response models, we then formulate the nonlinearity of the system as noise and show that through simplifying assumptions it can be represented as Gaussian noise. Through formulating the system's nonlinearity as the output a linear system corrupted by noise, the rich toolbox of mathematical models of communication systems, most of which are based on linearity assumption, can be applied to this platform.

cs.ET↗
arXiv2013

Table-Top Molecular Communication: Text Messages Through Chemical Signals

In this work, we describe the first modular, and programmable platform capable of transmitting a text message using chemical signalling -- a method also known as molecular communication. This form of communication is attractive for applications where conventional wireless systems perform poorly, from nanotechnology to urban health monitoring. Using examples, we demonstrate the use of our platform as a testbed for molecular communication, and illustrate the features of these communication systems using experiments. By providing a simple and inexpensive means of performing experiments, our system fills an important gap in the molecular communication literature, where much current work is done in simulation with simplified system models. A key finding in this paper is that these systems are often nonlinear in practice, whereas current simulations and analysis often assume that the system is linear. However, as we show in this work, despite the nonlinearity, reliable communication is still possible. Furthermore, this work motivates future studies on more realistic modelling, analysis, and design of theoretical models and algorithms for these systems.

cs.ET↗
arXiv2013

Capacity of a Simple Intercellular Signal Transduction Channel

We model the ligand-receptor molecular communication channel with a discrete-time Markov model, and show how to obtain the capacity of this channel. We show that the capacity-achieving input distribution is iid; further, unusually for a channel with memory, we show that feedback does not increase the capacity of this channel.

cs.IT↗
arXiv2011

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.

physics.bio-ph↗