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Quorum sensing (QS) mimickers can be used as an effective tool to disrupt biofilms which consist of communicating bacteria and extracellular polymeric substances. In this paper, a stochastic biofilm disruption model based on the usage of QS mimickers is proposed. A chemical reaction network (CRN) involving four different states is employed to model the biological processes during the biofilm formation and its disruption via QS mimickers. In addition, a state-based stochastic simulation algorithm is proposed to simulate this CRN. The proposed model is validated by the in vitro experimental results of Pseudomonas aeruginosa biofilm and its disruption by rosmarinic acid as the QS mimicker. Our results show that there is an uncertainty in state transitions due to the effect of the randomness in the CRN. In addition to the QS activation threshold, the presented work demonstrates that there are underlying two more thresholds for the disruption of EPS and bacteria, which provides a realistic modeling for biofilm disruption with QS mimickers., Accepted for publication in IEEE Transactions on Molecular, Biological, and Multi-Scale Communications

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., Submitted to ICC 2023

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.

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., Comment: 6 pages, 6 figures- Submitted for Publication in IEEE Transactions on Molecular, Biological and Multi-scale Sciences

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.

For a gambler with side information, Kelly betting gives the optimal log growth rate of the gambler's fortune, which is closely related to the mutual information between the correct winner and the noisy side information. We show conditions under which optimal Kelly betting can be implemented using single-letter codes. We show that single-letter coding is optimal for a wide variety of systems; for example, all systems with diagonal reward matrices admit optimal single-letter codes. We also show that important classes of systems do not admit optimal single-letter codes for Kelly betting, such as when the side information is passed through a Z channel. Our results are important to situations where the computational complexity of the gambler is constrained, and may lead to new insights into the fitness value of information for biological systems., Comment: Submitted to IEEE Transactions on Information Theory

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.

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., Comment: 10 pages, 10 figures, 1 table. Submitted for publication

In this letter, we give a concise, closed-form expression for the differential entropy of the sum of two independent, non-identically-distributed exponential random variables. The derivation is straightforward, but such a concise entropy has not been previously given in the literature. The usefulness of the expression is demonstrated with examples.

This work introduces capacity limits for molecular timing (MT) channels, where information is modulated in the release timing of small information particles, and decoded from the time of arrivals at the receiver. It is shown that the random time of arrival can be represented as an additive noise channel, and for the diffusion-based MT (DBMT) channel this noise is distributed according to the L\'evy distribution. Lower and upper bounds on the capacity of the DBMT channel are derived for the case where the delay associated with the propagation of the information particles in the channel is finite, namely, when the information particles dissipate after a finite time interval. For the case where a single particle is released per channel use, these bounds are shown to be tight. When the transmitter simultaneously releases a large number of particles, the detector at the receiver may not be able to precisely detect the arrival time of all the particles. Therefore, two alternative models are considered: detection based on the particle that arrives first, or detection based on the average arrival times. Tight lower and upper bounds are derived for these two models. It is shown that by controlling the maximal delay of the information particles, the capacity can increase poly-logarithmically with the number of released particles. As each particle takes a random independent path, this diversity of paths is analogous to receiver diversity and can be used to considerably increase the achievable data rates.

In this demonstration, we will present the world's first molecular multiple-input multiple-output (MIMO) communication link to deliver two data streams in a spatial domain. We show that chemical signals such as concentration gradients could be used in MIMO fashion to transfer sequential data. Until now it was unclear whether MIMO techniques, which are used extensively in modern radio communication, could be applied to molecular communication. In the demonstration, using our devised MIMO apparatus and carefully designed detection algorithm, we will show that we can achieve about 1.7 times higher data rate than single input single output (SISO) molecular communication systems., 2 pages, 3 figures, accepted to present on 2015 INFOCOM conference

It is shown how expectation maximization (EM) may be viewed as a message passing algorithm in factor graphs. In particular, a general EM message computation rule is identified. As a factor graph tool, EM may be used to break cycles in a factor graph, and tractable messages may in some cases be obtained where the sum-product messages are unwieldy. As an exemplary application, the paper considers linear Gaussian state space models. Unknown coefficients in such models give rise to multipliers in the corresponding factor graph. A main attraction of EM in such cases is that it results in purely Gaussian message passing algorithms. These Gaussian EM messages are tabulated for several (scalar, vector, matrix) multipliers that frequently appear in applications.

Molecular communication is a biologically-inspired method of communication with attractive properties for microscale and nanoscale devices. In molecular communication, messages are transmitted by releasing a pattern of molecules at a transmitter, which propagate through a fluid medium towards a receiver. In this paper, molecular communication is formulated as a mathematical communication problem in an information-theoretic context. Physically realistic models are obtained, with sufficient abstraction to allow manipulation by communication and information theorists. Although mutual information in these channels is intractable, we give sequences of upper and lower bounds on the mutual information which trade off complexity and performance, and present results to illustrate the feasibility of these bounds in estimating the true mutual information., Submitted to IEEE Transactions on Information Theory. 28 pages, 8 figures

In this paper, two fixed per-information symbol complexity lossless source coding algorithms are modified for estimation and incremental LT decoding over piecewise stationary memoryless channels (PSMC's) with a bounded number of abrupt changes in channel statistics. In particular, as a class of PSMC's, binary symmetric channels are considered with a crossover probability that changes a bounded number of times with no repetitions in the statistics. Simulation results are given which illustrate the benefits of using our algorithms, both in terms of probability of error and in terms of redundancy.

In this paper, we consider a molecular diffusion based communications link that can reliably transport data over-the-air. We show that the system can also reliably transport data across confined structural environments, especially in cases where conventional electromagnetic (EM) wave based systems may fail. In particular, this paper compares the performance of our proprietary molecular communication test-bed with Zigbee wireless sensors in a metal pipe network that does not act as a radio wave-guide. The paper first shows that a molecular-based communication link's performance is determined primarily by the delay time spread of the pulse response. The paper go on to show that molecular-based systems can transmit more reliably in complex and confined structural environments than conventional EM-based systems. The paper then utilizes empirical data to find relationships between the received radio signal strength, the molecular pulse spread, data rate (0.1 bits/s) and the structural propagation environment., IEEE International Conference on Communications (ICC)