arXiv subjects

Andrew W. Eckford

Publications and source records attributed to Andrew W. Eckford.

At least 37 records · Page 2Linked to original sources

arXiv2023

Lightweight Channel Codes for ISI Mitigation in Molecular Communication between Bionanosensors

Channel memory and inter-symbol interference (ISI) are harmful factors in diffusion-based molecular communication (DBMC) between bionanosensors. To tackle these problems, this paper proposes a lightweight ISI-mitigating coding scheme to improve the system performance by shaping the signal using a constrained code. To characterize the proposed coding scheme theoretically, we derive analytical expressions for the bit error rate (BER) and the achievable rate based on Central Limit Theorem. Computer simulations are conducted to verify the accuracy of the theoretical results and demonstrate the superiority of the proposed coding scheme compared with the existing coding schemes.

cs.IT↗

arXiv2023

A Computational Approach for the Characterization of Airborne Pathogen Transmission in Turbulent Molecular Communication Channels

Airborne pathogen transmission mechanisms play a key role in the spread of infectious diseases such as COVID-19. In this work, we propose a computational fluid dynamics (CFD) approach to model and statistically characterize airborne pathogen transmission via pathogen-laden particles in turbulent channels from a molecular communication viewpoint. To this end, turbulent flows induced by coughing and the turbulent dispersion of droplets and aerosols are modeled by using the Reynolds-averaged Navier-Stokes equations coupled with the realizable $k-ε$ model and the discrete random walk model, respectively. Via simulations realized by a CFD simulator, statistical data for the number of received particles are obtained. These data are post-processed to obtain the statistical characterization of the turbulent effect in the reception and to derive the probability of infection. Our results reveal that the turbulence has an irregular effect on the probability of infection, which shows itself by the multi-modal distribution as a weighted sum of normal and Weibull distributions. Furthermore, it is shown that the turbulent MC channel is characterized via multi-modal, i.e., sum of weighted normal distributions, or stable distributions, depending on the air velocity.

physics.flu-dyn↗

arXiv2023

Molecular Communication for Quorum Sensing Inspired Cooperative Drug Delivery

A cooperative drug delivery system is proposed, where quorum sensing (QS), a density-dependent bacterial behavior coordination mechanism, is employed by synthetic bacterium-based nanomachines (B-NMs) for controllable drug delivery. In our proposed system, drug delivery is only triggered when there are enough QS molecules, which in turn only happens when there are enough B-NMs. This makes the proposed system can be used to achieve a high release rate of drug molecules from a high number of B-NMs when the population density of B-NMs may not be known. Analytical expressions for i) the expected activation probability of the B-NM due to randomly-distributed B-NMs and ii) the expected aggregate absorption rate of drug molecules due to randomly-distributed QS activated B-NMs are derived. Analytical results are verified by particle-based simulations. The derived results can help to predict and control the impact of environmental factors (e.g. diffusion coefficient and degradation rate) on the absorption rate of drug molecules since rigorous diffusion-based molecular channels are considered. Our results show that the activation probability at the B-NM increases as this B-NM is located closer to the center of the B-NM population and the aggregate absorption rate of the drug molecules non-linearly increases as the population density increases.

q-bio.QM↗

arXiv2023

Explicitly Solvable Continuous-time Inference for Partially Observed Markov Processes

Many natural and engineered systems can be modeled as discrete state Markov processes. Often, only a subset of states are directly observable. Inferring the conditional probability that a system occupies a particular hidden state, given the partial observation, is a problem with broad application. In this paper, we introduce a continuous-time formulation of the sum-product algorithm, which is a well-known discrete-time method for finding the hidden states' conditional probabilities, given a set of finite, discrete-time observations. From our new formulation, we can explicitly solve for the conditional probability of occupying any state, given the transition rates and observations within a finite time window. We apply our algorithm to a realistic model of the cystic fibrosis transmembrane conductance regulator (CFTR) protein for exact inference of the conditional occupancy probability, given a finite time series of partial observations.

eess.SP↗

arXiv2022

Stochastic Modeling of Biofilm Formation with Bacterial Quorum Sensing

Bacteria generally live in complicated structures called biofilms, consisting of communicating bacterial colonies and extracellular polymeric substance (EPS). Since biofilms are related to detrimental effects such as infection or antibiotic resistance in different settings, it is essential to model their formation. In this paper, a stochastic model is proposed for biofilm formation, using bacterial quorum sensing (QS). In this model, the biological processes in the biofilm formation are modeled as a chemical reaction network which includes bacterial reproduction, productions of autoinducer and EPS, and their diffusion. The modified explicit tau-leap simulation algorithm is adapted based on the two-state QS mechanism. Our approach is validated by using the experimental results of $\textit{Pseudomonas putida}$ IsoF bacteria for autoinducer and bacteria concentration. It is also shown that the percentage of EPS in the biofilm increases significantly after the state change in QS, while it decreases before QS is activated. The presented work shows how the biofilm growth can be modeled realistically by using the QS mechanism in stochastic simulations of chemical reactions.

q-bio.QM↗

arXiv2022

Low Complexity First: Duration-Centric ISI Mitigation in Molecular Communication via Diffusion

In this paper, we propose a novel inter-symbol interference (ISI) mitigation scheme for molecular communication via diffusion (MCvD) systems with the optimal detection interval. Its rationale is to exploit the discarded duration (i.e., the symbol duration outside this optimal interval) to relieve ISI in the target system. Following this idea, we formulate an objective function to quantify the impact of the discarded time on bit error rate (BER) performance. Besides, an optimally reusable interval within the discarded duration is derived in closed form, which applies to both the absorbing and passive receivers. Finally, numerical results validate our analysis and show that for the considered MCvD system, significant BER improvements can be achieved by using the derived reusable duration.

eess.SP↗

arXiv2022

Selectivity of Protein Interactions Stimulated by Terahertz Signals

It has been established that Terahertz (THz) band signals can interact with biomolecules through resonant modes. Specifically, of interest here, protein activation. Our research goal is to show how directing the mechanical signaling inside protein molecules using THz signals can control changes in their structure and activate associated biochemical and biomechanical events. To establish that, we formulate a selectivity metric that quantifies the system performance and captures the capability of the nanoantenna to induce a conformational change in the desired protein molecule/population. The metric provides a score between -1 and 1 that indicates the degree of control we have over the system to achieve targeted protein interactions. To develop the selectivity measure, we first use the Langevin stochastic equation driven by an external force to model the protein behavior. We then determine the probability of protein folding by computing the steady-state energy of the driven protein and then generalize our model to account for protein populations. Our numerical analysis results indicate that a maximum selectivity score is attained when only the targeted population experiences a folding behavior due to the impinging THz signal. From the achieved selectivity values, we conclude that the system response not only depends on the resonant frequency but also on the system controlling parameters namely, the nanoantenna force, the damping constant, and the abundance of each protein population. The presented work sheds light on the potential associated with the electromagnetic-based control of protein networks, which could lead to a plethora of applications in the medical field ranging from bio-sensing to targeted therapy.

q-bio.MN↗

arXiv2022

An Extended Kalman Filter for Distance Estimation and Power Control in Mobile Molecular Communication

In this paper, we consider a mobile molecular communication (MC) system consisting of two mobile nanomachines, a transmitter and a receiver, propelled by a positive drift velocity and Brownian motion in a realistic blood-vessel-type flow regime. Considering the nonlinear movement of the nanomachines, an extended Kalman filter is employed to estimate the distance from the transmitter. Furthermore, based on the predicted distance, to keep the number of received molecules for bit 1 at a stable level, we employ power control on the number of transmitted molecules based on the distance between the transmitter and the receiver and the residual molecules in the channel from the previous transmission. Finally, the optimal detection threshold is obtained by minimizing the error probability. It is verified that a fixed optimal detection threshold can be effective for the power control scheme in the mobile MC. The bit error rate (BER) performance of our scheme is verified via simulation results.

cs.IT↗

arXiv2022

Detection Interval for Diffusion Molecular Communication: How Long is Enough?

Molecular communication has a key role to play in future medical applications, including detecting, analyzing, and addressing infectious disease outbreaks. Overcoming inter-symbol interference (ISI) is one of the key challenges in the design of molecular communication systems. In this paper, we propose to optimize the detection interval to minimize the impact of ISI while ensuring the accurate detection of the transmitted information symbol, which is suitable for the absorbing and passive receivers. For tractability, based on the signal-to-interference difference (SID) and signal-to-interference-and-noise amplitude ratio (SINAR), we propose a modified-SINAR (mSINAR) to measure the bit error rate (BER) performance for the molecular communication system with a variable detection interval. Besides, we derive the optimal detection interval in closed form. Using simulation results, we show that the BER performance of our proposed mSINAR scheme is superior to the competing schemes, and achieves similar performance to optimal intervals found by the exhaustive search.

cs.IT↗

arXiv2021

Minimal informational requirements for fitness

The existing concept of the "fitness value of information" provides a theoretical upper bound on the fitness advantage of using information concerning a fluctuating environment. Using concepts from rate-distortion theory, we develop a theoretical framework to answer a different pair of questions: What is the minimal amount of information needed for a population to achieve a certain growth rate? What is the minimal amount of information gain needed for one sub-population to achieve a certain average selection coefficient over another? We introduce a correspondence between fitness and distortion and solve for the rate-distortion functions of several systems using analytical and numerical methods. Because accurate information processing is energetically costly, our approach provides a theoretical basis for understanding evolutionary "design principles" underlying information-cost trade-offs.

q-bio.PE↗

arXiv2021

A factor graph EM algorithm for inference of kinetic microstates from patch clamp measurements

We derive a factor graph EM (FGEM) algorithm, a technique that permits combined parameter estimation and statistical inference, to determine hidden kinetic microstates from patch clamp measurements. Using the cystic fibrosis transmembrane conductance regulator (CFTR) and nicotinic acetylcholine receptor (nAChR) as examples, we perform {\em Monte Carlo} simulations to demonstrate the performance of the algorithm. We show that the performance, measured in terms of the probability of estimation error, approaches the theoretical performance limit of maximum {\em a posteriori} estimation. Moreover, the algorithm provides a reliability score for its estimates, and we demonstrate that the score can be used to further improve the performance of estimation. We use the algorithm to estimate hidden kinetic states in lab-obtained CFTR single channel patch clamp traces.

q-bio.QM↗

arXiv2021

K-Means Clustering-Aided Non-Coherent Detection for Molecular Communications

In this paper, we consider non-coherent detection for molecular communication systems in the presence of inter-symbol-interference. In particular, we study non-coherent detectors based on memory-bits-based thresholds in order to achieve low bit-error-ratio (BER) transmission. The main challenge of realizing detectors based on memory-bits-based thresholds is to obtain the channel state information based only on the received signals. We tackle this issue by reformulating the thresholds through intermediate variables, which can be obtained by clustering multi-dimensional data from the received signals, and by using the K-means clustering algorithm. In addition to estimating the thresholds, we show that the transmitted bits can be retrieved from the clustered data. To reduce clustering errors, we propose iterative clustering methods from one-dimensional to multi-dimensional data, which are shown to reduce the BER. Simulation results are presented to verify the effectiveness of the proposed methods.

cs.IT↗

arXiv2021

Modelling the Role of Inter-cellular Communication in Modulating Photosynthesis in Plants

In this paper we show how inter-cellular molecular communication may change the overall levels of photosynthesis in plants. Individual plant cells respond to external stimuli, such as illumination levels, to regulate their photosynthetic output. Here, we present a mathematical model which shows that by sharing information internally using molecular communication, plants may increase overall photosynthate production. Numerical results show that higher mutual information between cells corresponds to an increase in overall photosynthesis by as much as 25 per cent. This suggests that molecular communication plays a vital role in maximising the photosynthesis in plants and therefore suggests new routes to influence plant development in agriculture and elsewhere.

q-bio.MN↗

arXiv2020

The Fitness Value of Information with Delayed Phenotype Switching: Optimal Performance with Imperfect Sensing

The ability of organisms to accurately sense their environment and respond accordingly is critical for evolutionary success. However, exactly how the sensory ability influences fitness is a topic of active research, while the necessity of a time delay between when unreliable environmental cues are sensed and when organisms can mount a response has yet to be explored at any length. Accounting for this delay in phenotype response in models of population growth, we find that a critical error probability can exist under certain environmental conditions: an organism with a sensory system with any error probability less than the critical value can achieve the same long-term growth rate as an organism with a perfect sensing system. We also observe a trade off between the evolutionary value of sensory information and robustness to error, mediated by the rate at which the phenotype distribution relaxes to steady-state. The existence of the critical error probability could have several important evolutionary consequences, primarily that sensory systems operating at the non-zero critical error probability may be evolutionarily optimal.

q-bio.PE↗

arXiv2020

Characterization of Cooperators in Quorum Sensing with 2D Molecular Signal Analysis

In quorum sensing (QS), bacteria exchange molecular signals to work together. An analytically-tractable model is presented for characterizing QS signal propagation within a population of bacteria and the number of responsive cooperative bacteria (i.e., cooperators) in a two-dimensional (2D) environment. Unlike prior works with a deterministic topology and a simplified molecular propagation channel, this work considers continuous emission, diffusion, degradation, and reception among randomly-distributed bacteria. Using stochastic geometry, the 2D channel response and the corresponding probability of cooperation at a bacterium are derived. Based on this probability, new expressions are derived for the moment generating function and different orders of moments of the number of cooperators. The analytical results agree with the simulation results obtained by a particle-based method. In addition, the Poisson and Gaussian distributions are compared to approximate the distribution of the number of cooperators and the Poisson distribution provides the best overall approximation. The derived channel response can be generally applied to any molecular communication model where single or multiple transmitters continuously release molecules into a 2D environment. The derived statistics of the number of cooperators can be used to predict and control the QS process, e.g., predicting and decreasing the likelihood of biofilm formation.

cs.IT↗

arXiv2020

Information Rates of Controlled Protein Interactions Using Terahertz Communication

In this work, we present a paradigm bridging electromagnetic (EM) and molecular communication through a stimuli-responsive intra-body model. It has been established that protein molecules, which play a key role in governing cell behavior, can be selectively stimulated using Terahertz (THz) band frequencies. By triggering protein vibrational modes using THz waves, we induce changes in protein conformation, resulting in the activation of a controlled cascade of biochemical and biomechanical events. To analyze such an interaction, we formulate a communication system composed of a nanoantenna transmitter and a protein receiver. We adopt a Markov chain model to account for protein stochasticity with transition rates governed by the nanoantenna force. Both two-state and multi-state protein models are presented to depict different biological configurations. Closed form expressions for the mutual information of each scenario is derived and maximized to find the capacity between the input nanoantenna force and the protein state. The results we obtain indicate that controlled protein signaling provides a communication platform for information transmission between the nanoantenna and the protein with a clear physical significance. The analysis reported in this work should further research into the EM-based control of protein networks.

q-bio.MN↗

arXiv2020

Power Control for ISI Mitigation in Mobile Molecular Communication

In mobile molecular communication (MC), inter-symbol interference (ISI) can be mitigated by power control, requiring accurate estimates of the distance from transmitter to receiver. We present two power control strategies based on binary concentration shift keying (BCSK), namely BCSK with power control based on distance (BCSK-d), and BCSK with power control jointly considering distance and residual molecules in the channel (BCSK-d-RM). Performance of BCSK-d and BCSK-d-RM are analyzed in terms of the bit error rate (BER), the average energy consumption per bit, and the optimal detection threshold. Simulation results show that BCSK-d-RM and BCSK-d outperform BCSK in BER with the varying distance and the number of transmitted molecules. As BCSK-d-RM has higher performance, while BCSK-d has lower complexity, these schemes present a useful design tradeoff for mobile MC.

cs.IT↗

arXiv2019

Modeling Interference-Free 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 an illumination source that stimulates a saturating or decaying membrane current. This paper considers firing frequencies that are 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 numerically fitted to functions of the Izhikevich neuron model parameters and the peak input current. Results show that simple functions of the model parameters and maximum input current can be used to predict the charging and recovery times, even when there are deviations in the actual parameter values. Furthermore, the predictions lead to lower bounds on the firing frequency that can be achieved without significant distortion.

q-bio.NC↗