arXiv subjects

Andrew W. Eckford

Publications and source records attributed to Andrew W. Eckford.

At least 55 records · Page 3Linked to original sources

arXiv2019

Communication in Plants: Comparison of Multiple Action Potential and Mechanosensitive Signals with Experiments

Both action potentials and mechanosensitive signalling are an important communication mechanisms in plants. Considering an information theoretic framework, this paper explores the effective range of multiple action potentials for a long chain of cells (i.e., up to 100) in different configurations, and introduces the study of multiple mechanosensitive activation signals (generated due to a mechanical stimulus) in plants. For both these signals, we find that the mutual information per cell and information propagation speed tends to increase up to a certain number of receiver cells. However, as the number of cells increase beyond 10 to 12, the mutual information per cell starts to decrease. To validate our model and results, we include an experimental verification of the theoretical model, using a PhytlSigns biosignal amplifier, allowing us to measure the magnitude of the voltage associated with the multiple AP and mechanosensitive activation signals induced by different stimulus in plants. Experimental data is used to calculate the mutual information and information propagation speed, which is compared with corresponding numerical results. Since these signals are used for a variety of important tasks within the plant, understanding them may lead to new bioengineering methods for plants.

q-bio.MN↗

arXiv2019

Expected Density of Cooperative Bacteria in a 2D Quorum Sensing Based Molecular Communication System

The exchange of small molecular signals within microbial populations is generally referred to as quorum sensing (QS). QS is ubiquitous in nature and enables microorganisms to respond to fluctuations in living environments by working together. In this study, a QS-based molecular communication system within a microbial population in a two-dimensional (2D) environment is analytically modeled. Microorganisms are randomly distributed on a 2D circle where each one releases molecules at random times. The number of molecules observed at each randomly-distributed bacterium is first derived by characterizing the diffusion and degradation of signaling molecules within the population. Using the derived result and some approximation, the expected density of cooperative bacteria is derived. Our model captures the basic features of QS. The analytical results for noisy signal propagation agree with simulation results where the Brownian motion of molecules is simulated by a particle-based method. Therefore, we anticipate that our model can be used to predict the density of cooperative bacteria in a variety of QS-coordinated activities, e.g., biofilm formation and antibiotic resistance.

q-bio.CB↗

arXiv2019

Total Power Minimization: Joint Antenna Selection and Beamforming Design

In this paper, we consider the total power minimization problem when we have signal-to-interference-plus-noise ratio (SINR) constraints. The consumed power in the circuits depends on the number of active antennas, which can be modeled using zero-norm. Due to the difficulty of dealing with the non-convex zero-norm, we used the standard alternate weighted one-norm approach. We addressed the total power minimization for a narrowband system with and without per-antenna power constraints (PAPCs). We derived iterative closed-form expressions in both cases. Then we analysed the case when we have multiple bands operating at the same time. Analogous closed-form expressions are provided. Our simulation results show that significant gains can be obtained in terms of the total power required compared to standard methods that do not take into account the circuit power.

eess.SP↗

arXiv2019

Linear Noise Approximation of Intensity-Driven Signal Transduction Channels

Biochemical signal transduction, a form of molecular communication, can be modeled using graphical Markov channels with input-modulated transition rates. Such channel models are strongly non-Gaussian. In this paper we use a linear noise approximation to construct a novel class of Gaussian additive white noise channels that capture essential features of fully- and partially-observed intensity-driven signal transduction. When channel state transitions that are sensitive to the input signal are directly observable, high-frequency information is transduced more efficiently than low-frequency information, and the mutual information rate per bandwidth (spectral efficiency) is significantly greater than when sensitive transitions and observable transitions are disjoint. When both observable and hidden transitions are input-sensitive, we observe a superadditive increase in spectral efficiency.

q-bio.QM↗

arXiv2019

The Effect of Channel Uncertainty on Max-Min Goodput

In this paper, we consider the effect of channel uncertainty on the rates reliably delivered to the users; i.e., the goodput. After the base station (BS) designs a set of beamformers for a specific objective, the BS must select the operating or transmission data rate for each user. However, under channel uncertainty, higher transmission rates cause higher outage probability, and the delivered rate drops. Since lower rates are not desirable, one must balance between the transmission rate and outage. In this paper, we first explain how approximating the PDF of a quadratic form with a positive definite matrix can be used to obtain the outage probability for any set of beamfomers and transmission rate. Then we focus on the specific case of maximizing the minimum delivered rate, where we modify a robust beamforming approach to maximize the resulting goodput. We then derive iterative closed-form expressions for this case. The simulation results illustrate the efficacy of our analysis and the significant gains that can be obtained by optimizing the goodput metric.

eess.SP↗

arXiv2019

Using Game Theory for Real-Time Behavioural Dynamics in Microscopic Populations with Noisy Signalling

This paper introduces the application of game theory to understand noisy real-time signalling and the resulting behavioural dynamics in microscopic populations such as bacteria and other cells. It presents a bridge between the fields of molecular communication and microscopic game theory. Molecular communication uses conventional communication engineering theory and techniques to study and design systems that use chemical molecules as information carriers. Microscopic game theory models interactions within and between populations of cells and microorganisms. Integrating these two fields provides unique opportunities to understand and control microscopic populations that have imperfect signal propagation. Two examples, namely bacteria quorum sensing and tumour cell signalling, are presented with potential games to demonstrate the application of this approach. Finally, a case study of bacteria resource sharing demonstrates how noisy signalling can alter the distribution of behaviour.

q-bio.CB↗

arXiv2019

The Channel Capacity of Channelrhodopsin and Other Intensity-Driven Signal Transduction Receptors

Biological systems transduce signals from their surroundings through a myriad of pathways. In this paper, we describe signal transduction as a communication system: the signal transduction receptor acts as the receiver in this system, and can be modeled as a finite-state Markov chain with transition rates governed by the input signal. Using this general model, we give the mutual information under IID inputs in discrete time, and obtain the mutual information in the continuous-time limit. We show that the mutual information has a concise closed-form expression with clear physical significance. We also give a sufficient condition under which the Shannon capacity is achieved with IID inputs. We illustrate our results with three examples: the light-gated Channelrhodopsin-2 (ChR2) receptor; the ligand-gated nicotinic acetylcholine (ACh) receptor; and the ligand-gated Calmodulin (CaM) receptor. In particular, we show that the IID capacity of the ChR2 receptor is equal to its Shannon capacity. We finally discuss how the results change if only certain properties of each state can be observed, such as whether an ion channel is open or closed.

cs.IT↗

arXiv2019

Scheduling for VoLTE: Resource Allocation Optimization and Low-Complexity Algorithms

We consider scheduling and resource allocation in long-term evolution (LTE) networks across voice over LTE (VoLTE) and best-effort data users. The difference between these two is that VoLTE users get scheduling priority to receive their required quality of service. As we show, strict priority causes data services to suffer. We propose new scheduling and resource allocation algorithms to maximize the sum- or proportional fair (PF) throughout amongst data users while meeting VoLTE demands. Essentially, we use VoLTE as an example application with both a guaranteed bit-rate and strict application-specific requirements. We first formulate and solve the frame-level optimization problem for throughput maximization; however, this leads to an integer problem coupled across the LTE transmission time intervals (TTIs). We then propose a TTI-level problem to decouple scheduling across TTIs. Finally, we propose a heuristic, with extremely low complexity. The formulations illustrate the detail required to realize resource allocation in an implemented standard. Numerical results show that the performance of the TTI-level scheme is very close to that of the frame-level upper bound. Similarly, the heuristic scheme works well compared to TTI-level optimization and a baseline scheduling algorithm. Finally, we show that our PF optimization retains the high fairness index characterizing PF-scheduling.

cs.NI↗

arXiv2018

Symbol-by-Symbol Maximum Likelihood Detection for Cooperative Molecular Communication

In this paper, symbol-by-symbol maximum likelihood (ML) detection is proposed for a cooperative diffusion-based molecular communication (MC) system. In this system, the transmitter (TX) sends a common information symbol to multiple receivers (RXs) and a fusion center (FC) chooses the TX symbol that is more likely, given the likelihood of its observations from all RXs. The transmission of a sequence of binary symbols and the resultant intersymbol interference are considered in the cooperative MC system. Three ML detection variants are proposed according to different RX behaviors and different knowledge at the FC. The system error probabilities for two ML detector variants are derived, one of which is in closed form. The optimal molecule allocation among RXs to minimize the system error probability of one variant is determined by solving a joint optimization problem. Also for this variant, the equal distribution of molecules among two symmetric RXs is analytically shown to achieve the local minimal error probability. Numerical and simulation results show that the ML detection variants provide lower bounds on the error performance of simpler, non-ML cooperative variants and demonstrate that these simpler cooperative variants have error performance comparable to ML detectors.

cs.IT↗

arXiv2018

Communication and Information Theory of Single Action Potential Signals in Plants

Many plants, such as Mimosa pudica (the sensitive plant), employ electrochemical signals known as action potentials (APs) for rapid intercellular communication. In this paper, we consider a reaction diffusion model of individual AP signals to analyze APs from a communication and information theoretic perspective. We use concepts from molecular communication to explain the underlying process of information transfer in a plant for a single AP pulse that is shared with one or more receiver cells. We also use the chemical Langevin equation to accommodate the deterministic as well as stochastic component of the system. Finally we present an information theoretic analysis of single action potentials, obtaining achievable information rates for these signals. We show that, in general, the presence of an AP signal can increase the mutual information and information propagation speed among neighboring cells with receivers in different settings.

q-bio.NC↗

arXiv2018

Thermodynamic Properties of Molecular Communication

In this paper, we consider the energy cost of communicating using molecular communication. In a simplified scenario, we show that the energy bound in Landauer's principle can be achieved, implying that molecular communication can approach fundamental thermodynamic limits.

cs.IT↗

arXiv2018

Characterizing Information Propagation in Plants

This paper considers an electro-chemical based communication model for intercellular communication in plants. Many plants, such as Mimosa pudica (the "sensitive plant"), employ electrochemical signals known as action potentials (APs) for communication purposes. In this paper we present a simple model for action potential generation. We make use of the concepts from molecular communication to explain the underlying process of information transfer in a plant. Using the information-theoretic analysis, we compute the mutual information between the input and output in this work. The key aim is to study the variations in the information propagation speed for varying number of plant cells for one simple case. Furthermore we study the impact of the AP signal on the mutual information and information propagation speed. We aim to explore further that how the growth rate in plants can impact the information transfer rate and vice versa.

q-bio.NC↗

arXiv2018

Distortion Distribution of Neural Spike Train Sequence Matching with Optogenetics

This paper uses a simple optogenetic model to compare the timing distortion between a randomly-generated target spike sequence and an externally-stimulated neuron spike sequence. Optogenetics is an emerging field of neuroscience where neurons are genetically modified to express light-sensitive receptors that enable external control over when the neurons fire. Given the prominence of neuronal signaling within the brain and throughout the body, optogenetics has significant potential to improve the understanding of the nervous system and to develop treatments for neurological diseases. This paper primarily considers two different distortion measures. The first measure is the delay in externally-stimulated spikes. The second measure is the root mean square error between the filtered outputs of the target and stimulated spike sequences. The mean and the distribution of the distortion is derived in closed form when the target sequence generation rate is sufficiently low. All derived results are supported with simulations. This work is a step towards an analytical model to predict whether different spike trains were observed from the same stimulus, and the broader goal of understanding the quantity and reliability of information that can be carried by neurons.

q-bio.NC↗

arXiv2018

Updating Beamformers to Respond to Changes in Users

We consider a multi-user multiple-input single-output downlink system that provides each user with a prespecified level of quality-of-service. The base station (BS) designs the beamformers so that each user receives a certain signal-to-interference-and-noise ratio (SINR). In contrast to most of the available literature in the beamforming field, we focus on the required modifications when the system changes. We specifically study three cases: (i) user entering the system, (ii) user leaving the system, and (iii) a change in the SINR target. We do so in order to avoid designing the entire system from scratch for every change in the requirements. In each of the three cases, we describe the modifications required to the beamforming directions and the power loading. We consider maximum ratio transmission (MRT), zero-forcing (ZF) and the optimal beamformers. The proposed modifications provide performance that is either exact or very close to that obtained when we redesign the entire system, while having much lower computational cost.

eess.SP↗

arXiv2018

Convex Optimization of Distributed Cooperative Detection in Multi-Receiver Molecular Communication

In this paper, the error performance achieved by cooperative detection among K distributed receivers in a diffusion-based molecular communication (MC) system is analyzed and optimized. In this system, the receivers first make local hard decisions on the transmitted symbol 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. Two reporting scenarios, namely, perfect reporting and noisy reporting, are considered. Closed-form expressions are derived for the expected global error probability of the system for both reporting scenarios. New approximated expressions are also derived for the expected error probability. Convex constraints are then found to make the approximated expressions jointly convex with respect to the decision thresholds at the receivers and the FC. Based on such constraints, suboptimal convex optimization problems are formulated and solved to determine the optimal decision thresholds which minimize the expected error probability of the system. Numerical and simulation results reveal that the system error performance is greatly improved by combining the detection information of distributed receivers. They also reveal that the solutions to the formulated suboptimal convex optimization problems achieve near-optimal global error performance.

cs.IT↗

arXiv2018

Maximum Likelihood Detection for Cooperative Molecular Communication

In this paper, symbol-by-symbol maximum likelihood (ML) detection is proposed for a cooperative diffusion-based molecular communication (MC) system. In this system, a fusion center (FC) chooses the transmitter's symbol that is more likely, given the likelihood of the observations from multiple receivers (RXs). We propose three different ML detection variants according to different constraints on the information available to the FC, which enables us to demonstrate trade-offs in their performance versus the information available. The system error probability for one variant is derived in closed form. Numerical and simulation results show that the ML detection variants provide lower bounds on the error performance of the simpler cooperative variants and demonstrate that majority rule detection has performance comparable to ML detection when the reporting is noisy.

cs.IT↗

arXiv2018

Timing Control of Single Neuron Spikes with Optogenetic Stimulation

This paper predicts the ability to externally control the firing times of a cortical neuron whose behavior follows the Izhikevich neuron model. The Izhikevich neuron model provides an efficient and biologically plausible method to track a cortical neuron's membrane potential and its firing times. The external control is a simple optogenetic model represented by a constant current source that can be turned on or off. This paper considers a firing frequency that is sufficiently low for the membrane potential to return to its resting potential after it fires. The time required for the neuron to charge and for the neuron to recover to the resting potential are fitted to functions of the Izhikevich neuron model parameters. Results show that linear functions of the model parameters can be used to predict the charging times with some accuracy and are sufficient to estimate the highest firing frequency achievable without interspike interference.

q-bio.NC↗

arXiv2017

Root Mean Square Error of Neural Spike Train Sequence Matching with Optogenetics

Optogenetics is an emerging field of neuroscience where neurons are genetically modified to express light-sensitive receptors that enable external control over when the neurons fire. Given the prominence of neuronal signaling within the brain and throughout the body, optogenetics has significant potential to improve the understanding of the nervous system and to develop treatments for neurological diseases. This paper uses a simple optogenetic model to compare the timing distortion between a randomly-generated target spike sequence and an externally-stimulated neuron spike sequence. The distortion is measured by filtering each sequence and finding the root mean square error between the two filter outputs. The expected distortion is derived in closed form when the target sequence generation rate is sufficiently low. Derivations are verified via simulations.

q-bio.NC↗